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| sciencedirectS0925443912000166 | Potentiation of dietary restriction-induced lifespan extension by polyphenols | Dietary restriction (DR) extends lifespan across multiple species including mouse. Antioxidant plant extracts rich in polyphenols have also been shown to increase lifespan. We hypothesized that polyphenols might potentiate DR-induced lifespan extension. Twenty week old C57BL/6 mice were placed on one of three diets: continuous feeding (control), alternate day chow (Intermittent fed, IF), or IF supplemented with polyphenol antioxidants (PAO) from blueberry, pomegranate, and green tea extracts (IF + PAO). Both IF and IF + PAO groups outlived the control group and the IF + PAO group outlived the IF group (all p < 0.001). In the brain, IF induced the expression of inflammatory genes and p38 MAPK phosphorylation, while the addition of PAO reduced brain inflammatory gene expression and p38 MAPK phosphorylation. Our data indicate that while IF overall promotes longevity, some aspects of IF-induced stress may paradoxically lessen this effect. Polyphenol compounds, in turn, may potentiate IF-induced longevity by minimizing specific components of IF-induced cell stress. | [Daniel J. Airesa, Graham Rockwellb, Ting Wangc, Jennifer Fronteraa, Jo Wickd, WenFang Wanga e, Marija Tonkovic-Capina, Jianghua Luf, Lezi Ef, Hao Zhua g i, Russell H. Swerdlowf h i] | Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease | April 2012 | |
| sciencedirectS0160412011001942 | Differential gene expression and a functional analysis of PCB-exposed children: Understanding disease and disorder development | The goal of the present study is to understand the probable molecular mechanism of toxicities and the associated pathways related to observed pathophysiology in high PCB-exposed populations. We have performed a microarray-based differential gene expression analysis of children (mean age 46.1 months) of Central European descent from Slovak Republic in a well-defined study cohort. The subset of children having high blood PCB concentrations (> 75 percentile) were compared against their low PCB counterparts (< 25 percentile), with mean lipid-adjusted PCB values of 3.02 ± 1.3 and 0.06 ± 0.03 ng/mg of serum lipid, for the two groups, respectively (18.1 ± 4.4 and 0.3 ± 0.1 ng/ml of serum). The microarray was conducted with the total RNA from the peripheral blood mononuclear cells of the children using an Affymetrix platform (GeneChip Human genome U133 Plus 2.0 Array) and was analyzed by Gene Spring (GX 10.0). A highly significant set of 162 differentially expressed genes between high and low PCB groups (p value < 0.00001) were identified and subsequently analyzed using the Ingenuity Pathway Analysis tool. The results indicate that Cell-To-Cell Signaling and Interaction, Cellular Movement, Cell Signaling, Molecular Transport, and Vitamin and Mineral Metabolism were the major molecular and cellular functions associated with the differentially altered gene set in high PCB-exposed children. The differential gene expressions appeared to play a pivotal role in the development of probable diseases and disorders, including cardiovascular disease and cancer, in the PCB-exposed population. The analyses also pointed out possible organ-specific effects, e.g., cardiotoxicity, hepatotoxicity and nephrotoxicity, in high PCB-exposed subjects. A few notable genes, such as BCL2, PON1, and ITGB1, were significantly altered in our study, and the related pathway analysis explained their plausible involvement in the respective disease processes, as mentioned. Our results provided insight into understanding the associated molecular mechanisms of complex gene–environment interactions in a PCB-exposed population. Future endeavors of supervised genotyping of pathway-specific molecular epidemiological studies and population biomarker validations are already underway to reveal individual risk factors in these PCB-exposed populations. | [Sisir K. Duttaa, Partha S. Mitraa 1, Somiranjan Ghosha 1, Shizhu Zanga 1, Dean Sonnebornb, Irva Hertz-Picciottob, Tomas Trnovecc, Lubica Palkovicovac, Eva Sovcikovac, Svetlana Ghimbovschid, Eric P. Hoffmand] | Environment International | | |
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| sciencedirectS0142961211014311 | A 3D microfibrous scaffold for long-term human pluripotent stem cell self-renewal under chemically defined conditions | Realizing the potential of human pluripotent stem cell (hPSC)-based therapy requires the development of defined scalable culture systems with efficient expansion, differentiation and isolation protocols. We report an engineered 3D microfiber system that efficiently supports long-term hPSCs self-renewal under chemically defined conditions. The unique feature of this system lies in the application of a 3D ECM-like environment in which cells are embedded, that affords: (i) uniform high cell loading density in individual cell-laden constructs (∼107 cells/ml); (ii) quick recovery of encapsulated cells (<10 min at 37 °C) with excellent preservation of cell viability and 3D multicellular structure; (iii) direct cryopreservation of the encapsulated cells in situ in the microfibers with >17-fold higher cell viability compared to those cultured on Matrigel surface; (iv) long-term hPSC propagation under chemically defined conditions. Four hPSC lines propagated in the microfibrous scaffold for 10 consecutive passages were capable of maintaining an undifferentiated phenotype as demonstrated by the expression of stem cell markers and stable karyotype in vitro and the ability to form derivatives of the three germ layers both in vitro and in vivo. Our 3D microfibrous system has the potential for large-scale cultivation of transplantable hESCs and derivatives for clinical applications. | [Hong Fang Lu, Karthikeyan Narayanan, Sze-Xian Lim, Shujun Gao, Meng Fatt Leong, Andrew C.A. Wan] | Biomaterials | March 2012 | |
| sciencedirectS1096495911002533 | Transcriptomic analyses of intestinal gene expression of juvenile Atlantic cod (Gadus morhua) fed diets with Camelina oil as replacement for fish oil | For aquaculture of marine species to continue to expand, dietary fish oil (FO) must be replaced with more sustainable vegetable oil (VO) alternatives. Most VO are rich in n-6 polyunsaturated fatty acids (PUFA) and few are rich in n-3 PUFA but Camelina oil (CO) is unique in that, besides high 18:3n-3 and n-3/n-6 PUFA ratio, it also contains substantial long-chain monoenes, commonly found in FO. Cod (initial mass ~ 1.4 g) were fed for 12 weeks diets in which FO was replaced with CO. Growth performance, feed efficiency and biometric indices were not affected but lipid levels in liver and intestine tended to increase and those of flesh, decrease, with increasing dietary CO although only significantly for intestine. Reflecting diet, tissue n-3 long-chain PUFA levels decreased whereas 18:3n-3 and 18:2n-6 increased with inclusion of dietary CO. Dietary replacement of FO by CO did not induce major metabolic changes in intestine, but affected genes with potential to alter cellular proliferation and death as well as change structural properties of intestinal muscle. Although the biological effects of these changes are unclear, given the important role of intestine in nutrient absorption and health, further attention should be given to this organ in future. | [Sofia Moraisa 1, Rolf B. Edvardsenb, Douglas R. Tochera, J. Gordon Bella] | Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology | March 2012 | |
| sciencedirectS1532045611001967 | Expression pattern analysis of DNA repair-related and DNA damage response genes revealed by 55 K oligomicroarray upon UV-B irradiation in the intertidal copepod, Tigriopus japonicus | Ultraviolet-B (UV-B) radiation affects the genome stability of aquatic organisms by absorption of certain wavelength at the molecular level. Recently, extensive gene information has been identified from the intertidal copepod, Tigriopus japonicus. Here, we developed a 55 K (54,254 genes) oligomicroarray and tested its usefulness to identify the effect of single dose of UV-B irradiation (12 kJ/m2) on transcriptomes of the copepod T. japonicus. A total of 35,361 spots were identified to be significantly modulated on the 55 K oligomicroarray by hierarchical clustering after exposure to UV-B irradiation over 48 h (6, 12, 24, and 48 h). Of them, 1300 and 588 genes were observed to be up-regulated and down-regulated at all time points, respectively. Particularly, it was observed that several genes involved in DNA repair mechanism were significantly modulated in the UV-B-exposed T. japonicus by microarray and quantitative real-time RT-PCR analysis. In detail, UV-B irradiation specifically up-regulated some genes in non-homologous end-joining (NHEJ), homologous recombination (HR), base excision repair (BER), and mismatch repair (MMR) pathways. On the other hand, a majority of down-regulated genes were representatives for the nucleotide excision repair (NER) mechanism. These results demonstrated that DNA damage would be induced by UV-B irradiation in this species, resulting in reliable induction or repression of various DNA repair mechanism on UV-B-induced DNA damage. In this report, we suggest that a high density microarray-based approach for risk assessment of UV-B irradiation would be useful to elucidate the mechanistic analysis in a non-model organism. This study could also provide a better understanding of molecular mechanisms of cellular protection against UV-B-induced stress. | [Jae-Sung Rheea, Bo-Mi Kimb, Beom-Soon Choia c, Jae-Seong Leea b] | Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology | March 2012 | |
| sciencedirectS0027510711002703 | Microarray analysis of responsible genes in increased growth rate in the subline of HL60 (HL60RG) cells | HL60RG, a subline of human promyelocytic leukemia HL60 cells, has a increased growth rate than their parental cells. To gain information of the mechanisms involved in the increased growth rate of HL60RG, we performed a multiplex fluorescence in situ hybridization (M-FISH), standard cytogenetics analysis (G-banding) and genome scan using 10K SNP mapping array on both cell types. Characteristic genomic alterations in HL60RG cells were identified including uniparental disomy (UPD) of chromosome 1, and hemizygous deletion in 10p and 11p. However, no such defects were observed in HL60 cells. Changes in gene expression in HL60RG cells were determined using expression arrays (Affymetrix GeneChip, HU133A). Candidate genes associated with the rapid growth of HL60RG cells were identified. Two tumor necrosis factor receptors, TNFRSF1B (type II tumor necrosis factor-? receptor) and TNFRSF8 (also known as a tumor marker CD30), which are adjacently located on chromosome 1 showed opposing changes in gene expression in HL60RG cells—over-expression of TNFRSF8 and repression of TNFRSF1B. Differences in the DNA methylation status in the transcriptional regulatory regions of both genes between HL60 and HL60RG was detected by a methylation-specific PCR assay. In conclusion, alterations in chromosome and gene expression in HL60RG may be associated with increased growth rate. | [Yang Luana b, Mieko Kogia c, Palanisamy Rajagurua d, Jin Renb, Teruhide Yamaguchia, Kazuhiro Suzukia, Takayoshi Suzukia] | Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis | 1 March 2012 | |
| sciencedirectS0304423811006753 | Parthenocarpic genetic resources and gene expression related to parthenocarpy among four species in pear (Pyrus spp.) | Parthenocarpy—the production of seedless fruits without fertilization—is very useful for fruit cultivation, especially in self-incompatible species such as pears. To search for parthenocarpic genetic resources in pear, 31 pear accessions [20 Chinese pears (13 Pyrus bretschneideri, seven Pyrus ussuriensis), five European pears (Pyrus communis), two Japanese pears (Pyrus pyrifolia), and four interspecific hybrids] were subjected to flower emasculation and left unpollinated, and then the fruit-set ratio and fruit enlargement were investigated. All European pears examined had a stable and high degree of fruit set, and ‘La France’ had high fruit enlargement. The possibility of stenospermocarpy was ruled out, because the emasculated flowers were left unpollinated in paper bags and the absence of seed was confirmed in the enlarged fruits. Neither Chinese nor Japanese pears treated with emasculation and no pollination showed consistently stable fruit set and fruit enlargement. An analysis of parthenocarpy in the offspring of ‘La France’ suggested that both high fruit set and fruit enlargement were inherited and that it should be possible to introduce parthenocarpy into Japanese pears. Although parthenocarpic ‘La France’ fruits weighed slightly less than those from cross-pollinated flowers, their cortex enlargement compared favorably with that seen with cross-pollinated ones. By using a customized pear cDNA microarray, we compared the gene expression profiles of highly and weakly parthenocarpic cultivars before flowering. Expression of several phenylpropanoid-related genes and photosystem-related genes differed significantly between the two groups. Some of these genes were putatively encoded in the chloroplast genome. These genes might be candidates of DNA markers for achievement of parthenocarpy in Japanese pear breeding. | [Chikako Nishitania, Ayako Yamaguchi-Nakamuraa, Fumiko Hosakaa, Shingo Terakamia, Tokurou Shimizua, Kanako Yanoa, Akihiro Itaib, Toshihiro Saitoa, Toshiya Yamamotoa] | Scientia Horticulturae | | |
| sciencedirectS0031938411005191 | Conditioned taste aversion dependent regulation of amygdala gene expression | The present experiments investigated gene expression in the amygdala following contingent taste/LiCl treatment that supports development of conditioned taste aversion (CTA). The use of whole genome chips and stringent data set filtering led to the identification of 168 genes regulated by CTA compared to non-contingent LiCl treatment that does not support CTA learning. Seventy-six of these genes were eligible for network analysis. Such analysis identified “behavior” as the top biological function, which was represented by 15 of the 76 genes. These genes included several neuropeptides, G protein-coupled receptors, ion channels, kinases, and phosphatases. Subsequent qRT-PCR analyses confirmed changes in mRNA expression for 5 of 7 selected genes. We were able to demonstrate directionally consistent changes in protein level for 3 of these genes; insulin 1, oxytocin, and major histocompatibility complex class I-C. Behavioral analyses demonstrated that blockade of central insulin receptors produced a weaker CTA that was less resistant to extinction. Together, these results support the notion that we have identified downstream genes in the amygdala that contribute to CTA learning. | [Siva K. Panguluria, Nobuyuki Kuwabaraa, Yi Kangb, Nigel Coopera, Robert F. Lundya] | Physiology & Behavior | 28 February 2012 | |
| sciencedirectS0303720711006484 | Stimulation of inflammatory gene expression in human preadipocytes by macrophage-conditioned medium: Upregulation of IL-6 production by macrophage-derived IL-1? | The aim of this study was to examine the effects of macrophage secretions on global gene expression in human preadipocytes using microarrays. Preadipocytes were cultured with unconditioned or conditioned medium from U937 macrophages, and gene expression examined with Agilent arrays (43,000 probes). 472 transcripts were differentially regulated (>2-fold difference; P < 0.05) between preadipocytes in the conditioned medium compared to the unconditioned; 401 were upregulated and 71 downregulated. The upregulated transcripts were particularly linked to inflammation, including IL-1?, IL-6, and CCL20 (16.8-, 10.0-, and 8.9-fold increases, respectively) together with matrix metalloproteinases (MMP3, MMP9 and MMP12). Major pathways regulated by the conditioned medium were linked to inflammation, macrophage infiltration and lipid accumulation. Network analysis identified NFkB and IL-1? as central nodes in the upregulation of multiple inflammation-related genes. Treatment with an IL-1? neutralising antibody abolished the stimulation of IL-6 secretion by conditioned medium, indicating that IL-1? is a key regulator of preadipocyte IL-6 production. Macrophages evoke extensive changes in preadipocyte gene expression. | [Adrian O’Haraa, Fei-Ling Limb, Dawn J. Mazzattib, Paul Trayhurna] | Molecular and Cellular Endocrinology | 26 February 2012 | |
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| sciencedirectS0012160611013935 | Conditional ablation of the Notch2 receptor in the ocular lens | Notch signaling is essential for proper lens development, however the specific requirements of individual Notch receptors have not been investigated. Here we report the lens phenotypes of Notch2 conditionally mutant mice, which exhibited severe microphthalmia, reduced pupillary openings, disrupted fiber cell morphology, eventual loss of the anterior epithelium, fiber cell dysgenesis, denucleation defects, and cataracts. Notch2 mutants also had persistent lens stalks as early as E11.5, and aberrant DNA synthesis in the fiber cell compartment by E14.5. Gene expression analyses showed that upon loss of Notch2, there were elevated levels of the cell cycle regulators Cdkn1a (p21Cip1), Ccnd2 (CyclinD2), and Trp63 (p63) that negatively regulates Wnt signaling, plus down-regulation of Cdh1 (E-Cadherin). Removal of Notch2 also resulted in an increased proportion of fiber cells, as was found in Rbpj and Jag1 conditional mutant lenses. However, Notch2 is not required for AEL proliferation, suggesting that a different receptor regulates this process. We found that Notch2 normally blocks lens progenitor cell death. Overall, we conclude that Notch2-mediated signaling regulates lens morphogenesis, apoptosis, cell cycle withdrawal, and secondary fiber cell differentiation. | [Senthil S. Saravanamuthua, Tien T. Leb, Chun Y. Gaoa, Radu I. Cojocaruc, Pushpa Pandiyand, Chunqiao Liuc, Jun Zhange, Peggy S. Zelenkaa, Nadean L. Brownb] | Developmental Biology | 15 February 2012 | |
| sciencedirectS0731708511005954 | Therapeutic effect of Yunnan Baiyao on rheumatoid arthritis was partially due to regulating arachidonic acid metabolism in osteoblasts | In order to explore the potential therapeutic effect of Yunnan Baiyao (YNB) on rheumatoid arthritis (RA), rat models were constructed and orally administrated with YNB or methotrexate (MTX) in parallel. Clinical physical, histological and biochemical parameters showed trivial therapeutic difference between YNB and MTX applications. Urine and serum metabonomics results indicated that many endogenous metabolites differentially changed among the rats receiving diverse therapeutic interventions. Among them, the fluctuation of arachidonic acid (AA) was thought to make sense. Thus, its relevant metabolites were subjected to quantitation by using osteoblasts treated by YNB in vitro. It was found that YNB extract of 20 ?g/mL could greatly activate the synthesis of intracellular prostaglandin E2 and thromboxane B2 in osteoblasts. Excretion of prostaglandin D2 could be suppressed but not the thromboxane B2. This study proved the efficacy of YNB on curing RA and its potential mechanism through modulating AA metabolism in osteoblasts to some extent. | [Hongbing Hea b, Xiaobin Renb, Xiyue Wanga, Xianzhe Shia, Xiaolin Wanga, Zhongjuan Dingb, Peng Gaoa, Guowang Xua] | Journal of Pharmaceutical and Biomedical Analysis | | |
| sciencedirectS002191501200069X?v=s5 | Role for MRP8 in in-stent restenosis in diabetes | ObjectiveThe most common cause of death in diabetes mellitus is cardiovascular disease. Patients frequently undergo vascular intervention such as stenting. The occurrence of in stent restenosis (ISR) has been reduced by the use of drug eluting stents in non-diabetic patients but the incidence of restenosis and stent thrombosis remains higher in diabetic patients. We investigated the pathogenesis of in stent restenosis in an animal model of type 2 diabetes mellitus.Methods & Results: Stents were placed in Zucker Fatty Rat (ZFR) and wild type rat carotid arteries, and tissues were harvested 14 days post surgery for morphometric analysis. Unstented carotid arteries from both groups were harvested for microarray analysis. In vitro apoptosis, proliferation and migration assays were performed on Rat and Human Aortic Endothelial Cells (EC).ZFRs developed an exaggerated intimal response to stent placement compared to wild type controls 14 days post stent placement. MRP8 and MRP14 were up-regulated in unstented ZFR carotid arteries in comparison to controls. Expression of MRP8/14 was also elevated in EC exposed to high glucose conditions. EC function was impaired by high glucose concentrations, and this effect could be mimicked by MRP8 over-expression. MRP8 knockdown by shRNA significantly restored EC function after exposure to high glucose concentrations. MRP8 expression in glucose exposed cells was also inhibited using pharmacological blockade of glucose-induced pathways.ConclusionsEC dysfunction caused by elevated glucose levels could be mimicked by MRP8/14 over-expression and reversed/prevented by MRP8 knockdown. Thus, MRP8/14 likely plays a role in exaggerated ISR in diabetes mellitus, and MRP8 inhibition may be useful in improving outcome after stent placement in diabetes mellitus. | [A. Stoccaa, D. O’Tooleb, N. Hynesa, S. Hynesc, K. Mashayekhia, L. McGinleya, C. Colemana, S. Sultanc, A. Duffye, S. Tuneva b c d e, T. O’Briena] | Atherosclerosis | | |
| sciencedirectS0142961211013044 | Inhibition of cancer stem cell-like properties and reduced chemoradioresistance of glioblastoma using microRNA145 with cationic polyurethane-short branch PEI | Glioblastomas (GBMs) are the most common primary brain tumors with poor prognosis. CD133 has been considered a putative marker of cancer stem cells (CSCs) in malignant cancers, including GBMs. MicroRNAs (miRNAs), highly conserved small RNA molecules, may target oncogenes and have potential as a therapeutic strategy against cancer. However, the role of miRNAs in GBM-associated CSCs remains mostly unclear. In this study, our miRNA/mRNA-microarray and RT-PCR analysis showed that the expression of miR145 (a tumor-suppressive miRNA) is inversely correlated with the levels of Oct4 and Sox2 in GBM-CD133+ cells and malignant glioma specimens. We demonstrated that miR145 negatively regulates GBM tumorigenesis by targeting Oct4 and Sox2 in GBM-CD133+. Using polyurethane-short branch polyethylenimine (PU-PEI) as a therapeutic-delivery vehicle, PU-PEI-mediated miR145 delivery to GBM-CD133+ significantly inhibited their tumorigenic and CSC-like abilities and facilitated their differentiation into CD133−-non-CSCs. Furthermore, PU-PEI-miR145-treated GBM-CD133+ effectively suppressed the expression of drug-resistance and anti-apoptotic genes and increased the sensitivity of the cells to radiation and temozolomide. Finally, the in vivo delivery of PU-PEI-miR145 alone significantly suppressed tumorigenesis with stemness, and synergistically improved the survival rate when used in combination with radiotherapy and temozolomide in orthotopic GBM-CD133+-transplanted immunocompromised mice. Therefore, PU-PEI-miR145 is a novel therapeutic approach for malignant brain tumors. | [Yi-Ping Yanga 1, Yueh Chienb f 2, Guang-Yuh Chioub f 1, Jong-Yuh Chernge 2, Mong-Lien Wangc, Wen-Liang Lod f, Yuh-Lih Changb g, Pin-I Huanga h, Yi-Wei Chena h, Yang-Hsin Shihc i, Ming-Teh Chenc i, Shih-Hwa Chioua b c f] | Biomaterials | February 2012 | |
| sciencedirectS0011224011003269 | Gene pathway analysis of the mechanism by which the Rho-associated kinase inhibitor Y-27632 inhibits apoptosis in isolated thawed human embryonic stem cells ? | Cryopreservation is an essential technique in basic research and clinical applications of human embryonic stem (hES) cells. Cryopreserved hES cells are fragile and undergo post-thaw apoptosis. We performed gene pathway analysis on cryopreserved and thawed hES cells to examine the effect of Y-27632, a Rho-associated kinase (ROCK) inhibitor, on apoptosis and associated molecular events. Y-27632 was added to the cryopreservation solution and/or the post-thaw medium of two hES cell lines (KhES-1, KhES-3). Post-thaw apoptosis was recorded as a function of time using Giemsa staining and the terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Apoptosis plateaued 12 h after the untreated hES cells were thawed. Gene pathway analysis showed the activation of IL-1?, TGF-?, and their respective receptors (IL-1R, ACVR1C) in the mitogen-activated protein kinase (MAPK) pathway, which resulted in the upregulation of caspase-8 and -10. Quantitative RT-PCR confirmed the upregulation of IL-1?, TGF-?, their respective receptors, and caspase-10 and -3. As these molecules were suppressed by Y-27632, gene pathways involving these molecules probably depend on ROCK activation. The TGF-? receptor antagonist, SB-431542, and an inhibitor of p38MAPK, SB-203580, did not affect apoptosis. Combining Y-27632 with SB-203580, however, resulted in an increase in the survival rate compared with the control. This suggests that the initiation of apoptosis depends on cytokine interactions and multiple ways exist to reduce post-thaw apoptosis in hES cells. Y-27632 can suppress cytokine interactions and the MAPK pathway, thereby reducing the occurrence of apoptosis, and is an effective cryoprotectant for hES cells. | [Hinako Ichikawaa, Naohiro Nakatab, Youichi Abob, Sakiko Shirasawac, Tadayuki Yokoyamac, Susumu Yoshiea, Fengming Yuea, Daihachiro Tomotsunea, Katsunori Sasakia] | Cryobiology | February 2012 | |
| sciencedirectS1087184512000175?v=s5 | Strain-related differences in antibody-mediated changes in gene expression are associated with differences in capsule and location of binding | We recently established that antibody (Ab)-binding can induce gene expression changes in a serotype A strain (H99) of the pathogenic yeast, Cryptococcus neoformans. That study showed that monoclonal antibodies (mAbs) differing in epitope specificity and protective efficacy elicited differences in gene expression. Because many mAbs bind to serotype A and D strains differently, we now investigate the binding of one mAb to two strains representing these serotypes. Cells of the serotype A strain H99 and the serotype D strain 24067 were incubated with near saturating concentrations of the IgG1 capsule-binding mAb 18B7 or MOPC, an irrelevant mAb matched control. Comparative immunofluorescence analysis of mAb 18B7 binding revealed that it bound closer to the cell wall in H99 than 24067, where it was associated with decreased or increased cell diameter, respectively. A comparison of encapsulated cell compressibility showed that strain 24067 was more compressible than that of strain H99. RNA was extracted and used for gene expression analysis using the C. neoformans JEC21 genomic microarray. After 1 h incubation with mAb 18B7, there were just 2 gene expression changes observed with strain 24067 or strain JEC21, unlike the 43 seen with strain H99. After 4 h incubation with mAb 18B7, there were 14 and 140 gene expression changes observed with strain 24067 and JEC21, respectively. Thus, C. neoformans strains differ both in the response and the time of response to mAb binding and these differences may reflect differences in the location of Ab binding, Ab-mediated changes in cell diameter and compressibility of the capsular polysaccharide. | [Erin E. McClellanda, Arturo Casadevallb] | Fungal Genetics and Biology | | |
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| sciencedirectS1874391912000474 | Quantitative analysis of proteins in the tear fluid of patients with diabetic retinopathy | Diabetic retinopathy is the leading cause of new cases of legal blindness among adults in the developed countries. Approximately 40% of all people with diabetes have diabetic retinopathy and 5% of these have sight-threatening form. As the advanced stage, where there is a high risk for vision loss, can develop without any serious symptoms, sometimes it is hard to detect it. A non invasive method to detect biomarkers characteristic for diabetic retinopathy from the tear fluid was developed. Tear samples from diabetic patients with no retinopathy, non proliferative and proliferative stages of diabetic retinopathy were analyzed and the protein content of each sample was compared to the protein content of tear pool from healthy volunteers. The samples were labeled with iTRAQ fourplex labels and were analyzed with nanoHPLC coupled ESI-MS/MS mass spectrometry. The lipocalin 1, lactotransferrin, lacritin, lysozyme C, lipophilin A and immunoglobulin lambda chain were identified as possible biomarker candidates with significantly higher relative levels in the tear of patients with diabetic retinopathy. | [Éva Cs?sza 1, Péter Borossa 1, Adrienne Csutakb d, András Bertab d, Ferenc Tótha, Szilárd Póliskac, Zsolt Töröke, József T?zséra d] | Journal of Proteomics | | |
| sciencedirectS0169260711003166 | Ensemble transcript interaction networks: A case study on Alzheimer's disease | Systems biology techniques are a topic of recent interest within the neurological field. Computational intelligence (CI) addresses this holistic perspective by means of consensus or ensemble techniques ultimately capable of uncovering new and relevant findings. In this paper, we propose the application of a CI approach based on ensemble Bayesian network classifiers and multivariate feature subset selection to induce probabilistic dependences that could match or unveil biological relationships. The research focuses on the analysis of high-throughput Alzheimer's disease (AD) transcript profiling. The analysis is conducted from two perspectives. First, we compare the expression profiles of hippocampus subregion entorhinal cortex (EC) samples of AD patients and controls. Second, we use the ensemble approach to study four types of samples: EC and dentate gyrus (DG) samples from both patients and controls. Results disclose transcript interaction networks with remarkable structures and genes not directly related to AD by previous studies. The ensemble is able to identify a variety of transcripts that play key roles in other neurological pathologies. Classical statistical assessment by means of non-parametric tests confirms the relevance of the majority of the transcripts. The ensemble approach pinpoints key metabolic mechanisms that could lead to new findings in the pathogenesis and development of AD. | [Rubén Armañanzas, Pedro Larrañaga, Concha Bielza] | Computer Methods and Programs in Biomedicine | | |
| sciencedirectS0888754312000067 | Whole-exome sequencing in a single proband reveals a mutation in the CHST8 gene in autosomal recessive peeling skin syndrome | Generalized peeling skin syndrome (PSS) is an autosomal recessive genodermatosis characterized by lifelong, continuous shedding of the upper epidermis. Using whole-genome homozygozity mapping and whole-exome sequencing, we identified a novel homozygous missense mutation (c.229C>T, R77W) within the CHST8 gene, in a large consanguineous family with non-inflammatory PSS type A. CHST8 encodes a Golgi transmembrane N-acetylgalactosamine-4-O-sulfotransferase (GalNAc4-ST1), which we show by immunofluorescence staining to be expressed throughout normal epidermis. A colorimetric assay for total sulfated glycosaminoglycan (GAG) quantification, comparing human keratinocytes (CCD1106 KERTr) expressing wild type and mutant recombinant GalNAc4-ST1, revealed decreased levels of total sulfated GAGs in cells expressing mutant GalNAc4-ST1, suggesting loss of function. Western blotting revealed lower expression levels of mutant recombinant GalNAc4-ST1 compared to wild type, suggesting that accelerated degradation may result in loss of function, leading to PSS type A. This is the first report describing a mutation as the cause of PSS type A. | [Rita M. Cabrala 1, Mazen Kurbana 1, Muhammad Wajida, Yutaka Shimomuraa, Lynn Petukhovaa b, Angela M. Christianoa c] | Genomics | | |
| sciencedirectS0006291X12001167 | Notch2 regulates the development of marginal zone B cells through Fos | B cells are classified into several subsets depending on their functions, marker expression pattern and localization. Marginal zone B (MZB) cells are a distinct lineage from follicular B cells, and regulate host defenses against blood-borne pathogens. Notch2/RBP-J signaling regulates the development of MZB cells by interacting with delta-like 1 ligand, although the target genes for Notch2 signaling remain unclear. We identified Fos as an upregulated gene in LPS-stimulated B cells that received Notch2 signaling. Fos is expressed in CD21highCD23low MZB cells at a higher level compared to CD21IntCD23high follicular B cells. Deleting the Notch2 gene in CD19+ B cells decreased Fos expression in B cells. Overexpression of Fos in Notch2-deficient B cells or bone marrow cells partially restored MZB development. Fos promoter activity was upregulated by Notch2 signaling, indicating that Notch2 directly controls Fos transcription associated with MZB development. These data identify Fos as one of the target genes for Notch2 signaling that is crucial for MZB development. | [Shuichi Iwahashia b, Yoichi Maekawaa, Jun Nishidaa, Chieko Ishifunea, Akiko Kitamuraa, Hideki Arimochia, Keiko Kataokaa, Shigeru Chibac, Mitsuo Shimadab, Koji Yasutomoa] | Biochemical and Biophysical Research Communications | | |
| sciencedirectS0012160612000309 | A protein kinase A and Wnt-dependent network regulating an intermediate stage in epithelial tubulogenesis during kidney development | Genetic interactions regulating intermediate stages of tubulogenesis in the developing kidney have been difficult to define. A systems biology strategy using microarray was combined with in vitro/ex vivo and genetic approaches to identify pathways regulating specific stages of tubulogenesis. Analysis of the progression of the metanephric mesenchyme (MM) through four stages of tubule induction and differentiation (i.e., epithelialization, tubular organization and elongation and early differentiation) revealed signaling pathways potentially involved at each stage and suggested key roles for a number of signaling molecules. A screen of the signaling pathways on in vitro/ex vivo nephron formation implicated a unique regulatory role for protein kinase A (PKA), through PKA-2, in a specific post-epithelialization morphogenetic step (conversion of the renal vesicle to the S-shaped body). Microarray analysis not only confirmed this stage-specificity, but also highlighted the upregulation of Wnt genes. Addition of PKA agonists to LIF-induced nephrons (previously shown to be a Wnt/beta-catenin dependent pathway) disrupted normal tubulogenesis in a manner similar to PKA-agonist treated MM/spinal-cord assays, suggesting that PKA regulates a Wnt-dependent tubulogenesis step. PKA induction of canonical Wnt signaling during tubulogenesis was confirmed genetically using MM from Batgal-reporter mice. Addition of a Wnt synthesis inhibitor to activated PKA cultures rescued tubulogenesis. By re-analysis of existing microarray data from the FGF8, Lim1 and Wnt4 knockouts, which arrest in early tubulogenesis, a network of genes regulating the transition of nascent epithelial cells to tubular epithelium was derived, helping to reconcile in vivo and in vitro/ex vivo data. | [Thomas F. Gallegosa, Valentina Kouznetsovaa, Krystyna Kudlickab, Derina E. Sweeneyc, Kevin T. Busha, Karl Willertb, Marilyn G. Farquharb, Sanjay K. Nigamb] | Developmental Biology | | |
| sciencedirectS0003267011013109 | Liquid chromatography–mass spectrometry based global metabolite profiling: A review | Untargeted, global metabolite profiling (often described as metabonomics or metabolomics) represents an expanding research topic and is, potentially, a major pillar for systems biology studies. To obtain holistic metabolic profiles from complex samples, such as biological fluids or tissue extracts, requires powerful, high resolution and information-rich analytical methods and for this spectroscopic technologies are generally used. Mass spectrometry, coupled to liquid chromatography (LC–MS), is increasingly being used for such investigations as a result of the significant advances in both technologies over the past decade. Here we try to critically review the topic of LC–MS-based global metabolic profiling and describe and compare the results offered by different analytical strategies and technologies. This review highlights the current challenges, limitations and opportunities of the current methodology. | [Georgios A. Theodoridisa [Author Vitae], Helen G. Gikab [Author Vitae], Elizabeth J. Wantc [Author Vitae], Ian D. Wilsond [Author Vitae]] | Analytica Chimica Acta | | |
| sciencedirectS0048357512000041?v=s5 | Possible connection between imidacloprid-induced changes in rice gene transcription profiles and susceptibility to the brown plant hopper Nilaparvatalugens Stål (Hemiptera: Delphacidae) | The chemical pesticide, imidacloprid (IMI) has long-lasting effectiveness against Hemiptera. IMI is commonly used to control the brown planthopper (BPH), Nilaparvata lugens Stål (Hemiptera: Delphacidae). Some chemical pesticides, however, can induce the susceptibility of rice to BPH, which has indirectly led to the resurgence of BPH. The mechanism of the chemical induction of the susceptibility of rice to BPH was not previously understood. Here, a 44K Agilent Rice Expression Microarray was used to identify changes in gene expression that accompany IMI-induced rice susceptibility to BPH. The results showed that 225 genes were differentially expressed, of which 117 were upregulated, and 108 were downregulated. Gene ontology annotation and pathway analysis revealed that differentially expressed genes were mainly classified into the 8 functional groups: oxidation reduction, regulation of cellular process, response to stress, electron carrier activity, metabolic process, transport, signal transducer, and organismal development. The genes encoding plant lipid transfer protein, lignin peroxidase, and flavonol-3-O-methyltransferenase may be important responses to the IMI-induced susceptibility of rice to BPH. The reliability of the microarray data was verified by performing quantitative real-time PCR and the data provide valuable information for further study of the molecular mechanism of IMI-induced susceptibility of rice. | [Yao Chenga, Zhao-Peng Shia, Li-Ben Jianga, Lin-Quan Gea, Jin-Cai. Wua, Gary C. Jahnb] | Pesticide Biochemistry and Physiology | | |
| sciencedirectS0378517311010611 | Drug delivery by polymeric nanoparticles induces autophagy in macrophages | Drug delivery nanosystems are currently used in human therapy. In preliminary studies we have observed that Eudragit® RS nanoparticles, prepared by nanoprecipitation or double emulsion techniques, are cytotoxic for NR8383 rat macrophages. In this study, we expand our previous analysis and suggest that unloaded Eudragit® RS nanoparticles prepared by nanoprecipitation (NP/ERS) may induce important morphological and biochemical cellular modifications leading to cellular death. In NR8383 rat macrophages cell line exposed to doses varying from 15 to 100 ?g/mL, NP/ERS nanoparticles are internalized inside the cells, reach the mitochondria and alter the structure of these organelles. In addition, the exposure to nanoparticles induces cellular autophagy as demonstrated by electron microscopy analysis, microchip array, qRT-PCR and Western blot assays. Although toxicity of nanoparticles has already been evidenced, it is the first time that results show clearly that the toxicity of polymeric nanovectors may be related to an activation of autophagy. | [H. Eidia, O. Jouberta, C. Némosb e, S. Grandemangec, B. Mograbid, B. Foliguete, J. Tournebizea, P. Maincenta, A. Le Faoua, I. Aboukhamisf, B.H. Rihna] | International Journal of Pharmaceutics | 17 January 2012 | |
| sciencedirectS0144861711009155 | A transcriptomic approach to predict the impact of ?-(1,3)-polyglucuronic acid sodium salt and derivatives in the main biological processes | ?-(1,3)-Polyglucuronic acid sodium salt was produced by the regioselective oxidation of curdlan using 2,2,6,6,-tetramethylpiperidine-1-oxyl radical (TEMPO)/NaBr/NaClO systems. This ?-(1,3)-polyuronic acid sodium salt was depolymerized, O-sulphated and O-acetylated. All these molecules have been biologically screened for transcriptomic analysis using DNA array. The transcriptomical responses were studied after statistical gene ontology in order to evaluate biological responses disturbed by the individual treatments of human fibroblast by all these ?-(1,3)-polyglucuronic acid sodium salt derivatives. | [C. Delattrea, P. Michaudb, L. Chaisemartina, J.Y. Berthona, L. Riosa c] | Carbohydrate Polymers | 15 January 2012 | |
| sciencedirectS0041008X11004170 | Epigallocatechin-3-gallate (EGCG) protects against chromate-induced toxicity in vitro | Hexavalent chromium [Cr(VI)] is a human carcinogen that results in the generation of reactive oxygen species (ROS) and a variety of DNA lesions leading to cell death. Epigallocatechin-3-gallate (EGCG), the major polyphenol present in green tea, possesses potent antioxidative activity capable of protecting normal cells from various stimuli-induced oxidative stress and cell death. Here we demonstrated that co-treatment with EGCG protected human normal bronchial epithelial BEAS-2B cells from Cr(VI)-induced cell death in a dose-dependent manner. Cr(VI) induces apoptosis as the primary mode of cell death. Co-treatment of BEAS-2B cells with EGCG dose-dependently suppressed Cr(VI)-induced apoptosis. Fluorescence microscopic analyses and quantitative measurement revealed that EGCG significantly decreased intracellular levels of ROS induced by Cr(VI) exposure. Using a well-established K+/SDS precipitation assay, we further showed that EGCG was able to dose-dependently reduce DNA–protein cross-links (DPC), lesions that could be partially attributed to Cr(VI)-induced oxidative stress. Finally, analyses of Affymetrix microarray containing 28,869 well-annotated genes revealed that, among the 3412 genes changed more than 1.5-fold by Cr(VI) treatment, changes of 2404 genes (70%) were inhibited by pretreatment of EGCG. Real-time PCR confirmed the induction of 3 genes involved in cell death and apoptosis by Cr(VI), which was eliminated by EGCG. In contrast, Cr(VI) reduced the expression of 3 genes related to cellular defense, and this reduction was inhibited by EGCG. Our results indicate that EGCG protects BEAS-2B cells from Cr(VI)-induced cytotoxicity presumably by scavenging ROS and modulating a subset of genes. EGCG, therefore, might serve as a potential chemopreventive agent against Cr(VI) carcinogenesis. | [Fen Wu, Hong Sun, Thomas Kluz, Hailey A. Clancy, Kathrin Kiok, Max Costa] | Toxicology and Applied Pharmacology | 15 January 2012 | |
| sciencedirectS1574789112000026 | Structural and genic characterization of stable genomic regions in breast cancer: Relevance to chemotherapy | BackgroundCancer genomes accumulate frequent and diverse chromosomal abnormalities as well as gene mutations but must maintain the ability to survive in vivo. We hypothesize that genetic selection acts to maintain tumour survival by preserving copy number of specific genes and genomic regions. Genomic regions and genes that remain unaltered in copy number and expression, respectively, may be essential for maintaining tumour survival.MethodsWe analyzed copy number data of 243 previously reported breast tumours and computationally derived stable copy number regions. To identify genes in stable copy number regions with nominal changes in expression, datasets for tumour and normal samples were compared. Results were replicated by analysis of a series of independent copy number, expression and genomic sequencing studies. A subset of stable regions, including stable paralogous regions, were confirmed by quantitative PCR and fluorescence in situ hybridization (FISH) in 5 breast cancer cell lines. We deduced a comprehensive set of dually stable genes (i.e. maintaining nominal copy number and expression) which were categorized according to pathway and ontology assignments. The stability of genes encoding therapeutic drug targets was also assessed.Results and ConclusionTumour genome analysis revealed 766 unstable (amplified and/or deleted) and 812 stable contiguous genomic regions. Replication analysis of an independent set of 171 breast tumours confirmed copy number stability of 1.3 Gb of the genome. We found that 5804 of these genes were dually stable. The composition of this gene set remained essentially unchanged (<2% reduction) after accounting for commonly mutated breast cancer genes found by sequencing and differential expression. The stable breast cancer genome is enriched for cellular metabolism, regulation of gene expression, DNA packaging (chromatin and nucleosome assembly), and regulation of apoptosis functions. Stable genes participating in multiple essential pathways were consistently found to be targets of chemotherapies. Preservation of stable, essential genes may be related to the effectiveness of certain chemotherapeutic agents that act on multiple gene products in this set. | [Nicole I. Parka, Peter K. Roganb c, Heather E. Tarnowskia, Joan H.M. Knolla d] | Molecular Oncology | | |
| sciencedirectS0006291X12000411 | Identification of blood biomarkers of aging by transcript profiling of whole blood | Immunological changes that inevitably occur with aging are related to the onset of various diseases including autoimmune diseases, immunodeficiency, as well as other age-reflecting (AR) diseases. They are becoming serious problems in the global trend of longevity. To understand the AR changes, we searched for genes whose expression profiles in the whole peripheral blood change dramatically as a function of age using the Agilent whole human genome 44K microarray. After examining two cohorts consisting of 154 healthy people between age 23 and 77, we discovered 16 transcripts strongly and reproducibly correlated with age. Analysis using a publicly available gene expression dataset for a variety of human immune cells revealed that some of these transcripts were highly expressed in specific cell types whose number and function are known to change with age. This analysis shed light on the molecular mechanism of AR immunological system changes. Because of its simplicity, the assay system is expected to be useful for understanding individual health conditions. | [Seiji Nakamuraa, Kozo Kawaib, Yumie Takeshitac, Masao Hondac, Toshinari Takamurac, Shuichi Kanekoc, Ryo Matobaa, Kenichi Matsubaraa] | Biochemical and Biophysical Research Communications | | |
| sciencedirectS0006291X1102078X | Heme oxygenase-1 (HO-1) is constitutively up-regulated in top alpinists | Alpinists who challenge Mt. Everest need adaptation to hypoxia before the attack of Mt. Everest. Although this adaptation is important for the success of climbing Mt. Everest, the molecular mechanism on the adaptation to hypoxia is not well understood. In order to clarify this mechanism, we investigated hypoxia-induced gene expressions specific for top alpinists using microarray analyses. We report here that heme oxygenase-1 (HO-1) is significantly higher in the blood of top alpinist compared with non-alpinists. Although HO-1 expression of non-alpinists is also up-regulated in response to hypoxia, HO-1 level of the top alpinists are constitutively higher than that of non-alpinists. Serial examinations of HO-1 in one top alpinist revealed that the higher expression of HO-1 is maintained in high-level several months after the attack of top mountains. Taken together with the biochemical function of HO-1 that catalyzes heme into CO and bilirubin, HO-1 expression may improve the circulation and compensate with oxidative tissue damages induced by hypoxia. These data also suggest that peripheral blood has the memory on hypoxia independent of antigens by maintaining the high-level of HO-1 expression in top alpinists, which merits the rapid adaptation to hypoxia for 8000 m climbing. | [Gota Miuraa, Kazunori Katob, Takahiko Shimizuc, Daniela Shigaa, Takuji Shirasawaa] | Biochemical and Biophysical Research Communications | 6 January 2012 | |
| sciencedirectS0144861711007405 | Biological effect of ?-(1,3)-polyglucuronic acid sodium salt on lipid storage and adipocytes differentiation | ?-(1,3)-Polyglucuronic acid sodium salt produced by the regioselective oxidation of ?-(1,3)-glucan have been studied for its biological impact as putative slimming agent. This ?-(1,3)-polyglucuronic acid sodium salt was synthesized using the conventional 2,2,6,6,-tetramethylpiperidine-1-oxyl radical (TEMPO)/NaBr/NaClO systems at pH 10 and 4 °C. A transcriptomical study using DNA microarray analysis, demonstrated that this heparan like sodium salt locally induced an over-expression of the gene Angiopoietin-like 4 (ANGPTL4 or fasting induced adipose factor (FIAF)) leading to the increase in Adipokine ANGPTL4 synthesis and the inhibition of Lipoprotein Lipase (LPL). In vitro analysis using 3T3-L1 cells have clearly revealed that ?-(1,3)-polyglucuronic acid sodium salt could act in key steps of lipid metabolism by inhibiting the differentiation of pre-adipocytes to mature adipocytes. | [C. Delattrea, L. Chaisemartina, M. Favre-Mercureta, J.Y. Berthona, L. Riosa b] | Carbohydrate Polymers | 4 January 2012 | |
| sciencedirectS0197458011005458 | S-adenosylmethionine reduces the progress of the Alzheimer-like features induced by B-vitamin deficiency in mice | Methylation reactions linked to homocysteine in the one-carbon metabolism are increasingly elicited in Alzheimer's disease, although the association of hyperhomocysteinemia and of low B vitamin levels with the disease is still debated. We previously demonstrated that hyperhomocysteinemia and DNA hypomethylation induced by B vitamin deficiency are associated with PSEN1 and BACE1 overexpression and amyloid production. The present study is aimed at assessing S-adenosylmethionine effects in mice kept under a condition of B vitamin deficiency. To this end, TgCRND8 mice and wild-type littermates were assigned to control or B vitamin deficient diet, with or without S-adenosylmethionine supplementation. We found that S-adenosylmethionine reduced amyloid production, increased spatial memory in TgCRND8 mice and inhibited the upregulation of B vitamin deficiency-induced PSEN1 and BACE1 expression and Tau phosphorylation in TgCRND8 and wild-type mice. Furthermore, S-adenosylmethionine treatment reduced plaque spreading independently on B vitamin deficiency. These results strengthen our previous observations on the possible role of one-carbon metabolism in Alzheimer's disease, highlighting hyperhomocysteinemia-related mechanisms in dementia onset/progression and encourage further studies aimed at evaluating the use of S-adenosylmethionine as a potential candidate drug for the treatment of the disease. | [Andrea Fusoa b, Vincenzina Nicoliaa, Laura Ricceric, Rosaria A. Cavallaroa, Elisa Isopia d, Franco Mangiab, Maria Teresa Fiorenzab, Sigfrido Scarpaa] | Neurobiology of Aging | | |
| sciencedirectS0306452211014485 | Sex-specific changes in gene expression and behavior induced by chronic Toxoplasma infection in mice | There is growing evidence that Toxoplasma gondii modifies the behavior of its intermediate hosts. We investigated the molecular basis of these infection-induced behavioral changes, followed by five related behavioral tests to assess the extent of biological relevance. Gene expression signatures were generated in the frontal cortex of male and female mice during the latent stage of infection. We found marked sex-dependent expression differences in mice. In female mice, Toxoplasma infection altered the expression of genes involved in the development of the forebrain, neurogenesis, and sensory and motor coordination (i.e. downregulation of fatty acid-binding protein 7 and eyes absent homolog 1, upregulation of semaphorin 7A). In male mice, infection led mainly to modulation of genes associated with olfactory function (i.e. downregulation of a number of olfactory receptors and dopamine receptor D4, upregulation of slit homolog 1). Although infection appears to affect the olfactory function in male mice, it is the female but not male mice that exhibited attraction to cat odor. In contrast, infected male mice showed a deficit in social transmission of food preference. In contrast to males, infected females displayed locomotor hyperactivity in open field. General olfaction and sensorimotor gating were normal in both male and female infection. Our results indicate that the sex of the host plays a major role in determining variable brain and behavior changes following Toxoplasma infection. These observations are consistent with heterogeneity of neuropsychiatric outcomes of the infection in humans. | [J. Xiaoa 1, G. Kannanb 1, L. Jones-Brandoa, C. Brannockc, I.N. Krasnovac, J.L. Cadetc, M. Pletnikovb, R.H. Yolkena] | Neuroscience | | |
| sciencedirectS0093691X11005899 | Exploring the application of high-throughput genomics technologies in the field of maternal-embryo communication | Deciphering the complex molecular dialogue between the maternal tract and embryo is crucial to increasing our understanding of pregnancy failure, infertility problems and in the modulation of embryo development, which has consequences through adulthood. High-throughput genomic technologies have been applied to look for a holistic view of the molecular interactions occurring during this dialogue. Among these technologies, microarrays have been widely used, being one of the most popular tools in maternal-embryo communication. Today, next generation sequencing technologies are dwarfing the capabilities of microarrays. The application of these new technologies has broadened to almost all areas of genomics research, because of their massive sequencing capacity. We review the current status of high-throughput genomic technologies and their application to maternal-embryo communication research. We also survey next generation technologies and their huge potential in many research areas. Given the diversity of unanswered questions in the field of maternal-embryo communication and the wide range of possibilities that these technologies offer, here we discuss future perspectives on the use of these technologies to enhance maternal-embryo research. | [Carmen Almiñana, Alireza Fazeli] | Theriogenology | | |
| sciencedirectS175646461100106X | Garlic extract and its selected organosulphur constituents promote ileal immune responses ex vivo | The effects of garlic extract and three organosulphur compounds of garlic on intestinal immune responses in mice were investigated. Peyer’s patch (PP) cells were isolated from mice orally administered with garlic extracts or one of three organosulphur compounds (alliin, allicin, diallyl disulphide (DADS)). PP cells isolated from mice that had been orally injected with ethanol extract significantly produced interferon (IFN)-? and interleukin (IL)-4. IL-2 production in PP cells was significantly reduced by hot-water and ethanol extracts from garlic. PP cells from mice administered with two organosulphur compounds, alliin or DADS (5 mg/kg/day), could produce IL-2, IFN-? and IL-4, whereas allicin showed moderate activity. The enhancement activity of IL-2 and IFN-? productions in PP cells by DADS was higher than those obtained by administration of alliin or allicin. Comprehensive analyses of genetic profiles in PP tissue from mice administered with ethanolic extracts, allicin or alliin revealed that oral administration of samples increased 68–144 genes and decreased 50–52 genes by ?1.8-fold. Analyses of clustering profiles of microarrays indicated that ethanol extract and alliin upregulated the expression of IFN-?. These data showed that garlic and its organosulphur compounds stimulate de novo IFN-? biosynthesis in PP cells, thereby promoting ileal immune responses. | [Natsuko Otaa, Fumihide Takanoa, Shouta Murogaa, Tetsuro Kawabataa, Yasuhito Ishigakib, Nobuo Yahagia, Tomihisa Ohtaa] | Journal of Functional Foods | | |
| sciencedirectS002839081100582X | Substance P activates ADAM9 mRNA expression and induces ?-secretase-mediated amyloid precursor protein cleavage | Altered levels of Substance P (SP), a neuropeptide endowed with neuroprotective and anti-apoptotic properties, were found in brain areas and spinal fluid of Alzheimer's disease (AD) patients. One of the hallmarks of AD is the abnormal extracellular deposition of neurotoxic beta amyloid (A?) peptides, derived from the proteolytic processing of amyloid precursor protein (APP). In the present study, we confirmed, the neurotrophic action of SP in cultured rat cerebellar granule cells (CGCs) and investigated its effects on APP metabolism. Incubation with low (5 mM) potassium induced apoptotic cell death of CGCs and amyloidogenic processing of APP, whereas treatment with SP (200 nM) reverted these effects via NK1 receptors. The non-amyloidogenic effect of SP consisted of reduction of A?1–42, increase of sAPP? and enhanced ?-secretase activity, without a significant change in steady-state levels of cellular APP. The intracellular mechanisms whereby SP alters APP metabolism were further investigated by measuring mRNA and/or steady-state protein levels of key enzymes involved with ?-, ?- and ?-secretase activity. Among them, Adam9, both at the mRNA and protein level, was the only enzyme to be significantly down-regulated following the induction of apoptosis (K5) and up-regulated after SP treatment. In addition to its neuroprotective properties, this study shows that SP is able to stimulate non-amyloidogenic APP processing, thereby reducing the possibility of generation of toxic A? peptides in brain. | [R. Maroldaa, M.T. Ciottia, C. Matronea, R. Possentia b, P. Calissanoc, S. Cavallarod, C. Severinie] | Neuropharmacology | | |
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| sciencedirectS0734975011000899 | Integrative transcriptional analysis between human and mouse cancer cells provides a common set of transformation associated genes | Mouse functional genomics is largely used to investigate relevant aspects of mammalian physiology and pathology. To which degree mouse models may offer accurate representations of molecular events underlining human diseases such as cancer is not yet fully established. Herein we compare gene expression signatures between a set of human cancer cell lines (NCI-60 cell collection) and a mouse cellular model of oncogenic K-ras dependent transformation in order to identify their closeness at the transcriptional level. The results of our integrative and comparative analysis show that in both species as compared to normal cells or tissues the transformation process involves the activation of a transcriptional response. Furthermore, the cellular mouse model of K-ras dependent transformation has a good degree of similarity with several human cancer cell lines and in particular with cell lines containing oncogenic Ras mutations. Moreover both species have similar genetic signatures that are associated to the same altered cellular pathways (e.g. Spliceosome and Proteasome) or to deregulation of the same genes (e.g. cyclin D1, AHSA1 and HNRNPD) detected in the comparison between cancer cells versus normal cells or tissues. In summary, we report one of the first in-depth analysis of global gene expression profiles of a K-ras dependent mouse cell model of transformation and a large collection of human cancer cells as compared to their normal counterparts. Taken together our findings show a strong correlation in the transcriptional and pathway alteration responses between the two species, therefore validating the use of the mouse model as an appropriate tool to investigate human cancer, and indicating that the comparative analysis, as described here, offers a useful approach to identify cancer-specific gene signatures. | [C. Balestrieria, M. Vanonia, S. Hautaniemib, L. Alberghinaa, F. Chiaradonnaa] | Biotechnology Advances | January–February 2012 | |
| sciencedirectS0734975011001200 | Cell growth and cell cycle in Saccharomyces cerevisiae: Basic regulatory design and protein–protein interaction network | In this review we summarize the major connections between cell growth and cell cycle in the model eukaryote Saccharomyces cerevisiae. In S. cerevisiae regulation of cell cycle progression is achieved predominantly during a narrow interval in the late G1 phase known as START (Pringle and Hartwell, 1981). At START a yeast cell integrates environmental and internal signals (such as nutrient availability, presence of pheromone, attainment of a critical size, status of the metabolic machinery) and decides whether to enter a new cell cycle or to undertake an alternative developmental program. Several signaling pathways, that act to connect the nutritional status to cellular actions, are briefly outlined. A Growth & Cycle interaction network has been manually curated. More than one fifth of the edges within the Growth & Cycle network connect Growth and Cycle proteins, indicating a strong interconnection between the processes of cell growth and cell cycle. The backbone of the Growth & Cycle network is composed of middle-degree nodes suggesting that it shares some properties with HOT networks.The development of multi-scale modeling and simulation analysis will help to elucidate relevant central features of growth and cycle as well as to identify their system-level properties. Confident collaborative efforts involving different expertises will allow to construct consensus, integrated models effectively linking the processes of cell growth and cell cycle, ultimately contributing to shed more light also on diseases in which an altered proliferation ability is observed, such as cancer. | [Lilia Alberghinaa, Gabriella Mavellib, Guido Drovandib, Pasquale Palumbob, Stefania Pessinaa, Farida Tripodia, Paola Coccettia, Marco Vanonia] | Biotechnology Advances | January–February 2012 | |
| sciencedirectS0734975011001601 | Overexpression of Far1, a cyclin-dependent kinase inhibitor, induces a large transcriptional reprogramming in which RNA synthesis senses Far1 in a Sfp1-mediated way | The FAR1 gene encodes an 830 residue bifunctional protein, whose major function is inhibition of cyclin-dependent kinase complexes involved in the G1/S transition. FAR1 transcription is maximal between mitosis and early G1 phase. Enhanced FAR1 transcription is necessary but not sufficient for the pheromone-induced G1 arrest, since FAR1 overexpression itself does not trigger cell cycle arrest.Besides its well established role in the response to pheromone, recent evidences suggest that Far1 may also regulate the mitotic cell cycle progression: in particular, it has been proposed that Far1, together with the G1 cyclin Cln3, may be part of a cell sizer mechanism that controls the entry into S phase. Far1 is an unstable protein throughout the cell cycle except during G1 phase. Far1 levels peak in newborn cells as a consequence of a burst of synthetic activity at the end of the previous cycle, and the amounts per cell remain roughly constant during the G1 phase. Phosphorylation (at serine 87) by Cdk1–Cln complexes primes Far1 for ubiquitin-mediated proteolysis.By coupling a genome-wide transcriptional analysis of FAR1-overexpressing and far1? cells grown in ethanol- or glucose-supplemented minimal media with a range of phenotypic analysis, we show that FAR1 overexpression not only coordinately increases RNA and protein accumulation, but induces strong transcriptional remodeling, metabolism being the most affected cellular property, suggesting that the Far1/Cln3 sizer regulates cell growth either directly or indirectly by affecting metabolism and pathways known to modulate ribosome biogenesis.A crucial role in mediating the effect of Far1 overexpression is played by the Sfp1 protein, a key transcriptional regulator of ribosome biogenesis, whose presence is mandatory to allow a coordinated increase in both RNA and protein levels in ethanol-grown cells. | [Stefano Bustia, Laura Gottia, Chiara Balestrieria, Lorenzo Querina, Guido Drovandib, Giovanni Felicib, Gabriella Mavellib, Paola Bertolazzib, Lilia Alberghinaa, Marco Vanonia] | Biotechnology Advances | January–February 2012 | |
| sciencedirectS0145305X11001790 | Insights into the antibacterial and immunomodulatory functions of tilapia hepcidin (TH)2-3 against Vibrio vulnificus infection in mice | The antimicrobial and immunomodulatory functions of the antimicrobial peptide, tilapia hepcidin (TH)2-3, against a bacterial endotoxin under in vitro conditions was previously reported. In this study, we investigated the antibacterial and immunomodulatory functions of TH2-3 in mice infected with the pathogen, Vibrio vulnificus. A TH2-3 injection in V. vulnificus-infected mice produced an increased survival rate compared to mice injected with V. vulnificus only. In addition, a TH2-3 injection increased the bacteriostatic property against V. vulnificus in mice. Gene expressions examined using a microarray demonstrated that TH2-3 modulated several V. vulnificus-responsive genes in the host. A neutralizing antibody assay of mice serum against inactivated V. vulnificus antigen-coated plates demonstrated the induction of an immune response by TH2-3 against the pathogen. Taken together, TH2-3 enhanced the survival rate of mice against the bacterial pathogen V. vulnificus through both antimicrobial and immunomodulatory functions. These properties make the TH2-3 peptide a good candidate for development as a new antimicrobial drug and suggest that TH2-3 can underpin the design of adjuvants for further development of vaccines. | [Chieh-Yu Pana 1, Shang-Chun Leeb 1, Venugopal Rajanbabub 1, Cheng-Hui Lina, Jyh-Yih Chenb] | Developmental & Comparative Immunology | January 2012 | |
| sciencedirectS0012160611013194 | BMP signaling induces visceral endoderm differentiation of XEN cells and parietal endoderm | The extraembryonic endoderm of mammals is essential for nutritive support of the fetus and patterning of the early embryo. Visceral and parietal endoderm are major subtypes of this lineage with the former exhibiting most, if not all, of the embryonic patterning properties. Extraembryonic endoderm (XEN) cell lines derived from the primitive endoderm of mouse blastocysts represent a cell culture model of this lineage, but are biased towards parietal endoderm in culture and in chimeras. In an effort to promote XEN cells to adopt visceral endoderm character we have mimicked different aspects of the in vivo environment. We found that BMP signaling promoted a mesenchymal-to-epithelial transition of XEN cells with up-regulation of E-cadherin and down-regulation of vimentin. Gene expression analysis showed the differentiated XEN cells most resembled extraembryonic visceral endoderm (exVE), a subtype of VE covering the extraembryonic ectoderm in the early embryo, and during gastrulation it combines with extraembryonic mesoderm to form the definitive yolk sac. We found that laminin, a major component of the extracellular matrix in the early embryo, synergised with BMP to promote highly efficient conversion of XEN cells to exVE. Inhibition of BMP signaling with the chemical inhibitor, Dorsomorphin, prevented this conversion suggesting that Smad1/5/8 activity is critical for exVE induction of XEN cells. Finally, we show that applying our new culture conditions to freshly isolated parietal endoderm (PE) from Reichert's membrane promoted VE differentiation showing that the PE is developmentally plastic and can be reprogrammed to a VE state in response to BMP. Generation of visceral endoderm from XEN cells uncovers the true potential of these blastocyst-derived cells and is a significant step towards modelling early developmental events ex vivo. | [Agnieszka Pacaa, Cheryle A. Séguinb, Melanie Clementsc, Michael Ryczkob, Janet Rossantb, Tristan A. Rodriguezc, Tilo Kunatha] | Developmental Biology | 1 January 2012 | |
| sciencedirectS1382668911001669 | Cerebral gene expression and neurobehavioural responses in mice pups exposed to methylmercury and docosahexaenoic acid through the maternal diet | Methylmercury (MeHg) is an environmental neurotoxicant with adverse effects particularly noted in the developing brain. The main source of MeHg exposure is seafood. However, fish is also an important source of n-3 fatty acids such as docosahexaenoic acid (DHA) which has neuroprotective effects, and which plays an important role during the prenatal development of the central nervous system. The aim of the present study was to examine the effects of DHA and MeHg individually, and in combination, on development using accumulation, behavioural and transcriptomic endpoints in a mammalian model. Analyses were performed on 15 day old mice which had been exposed to varying levels of DHA (8 or 24 mg/kg) and/or MeHg (4 mg/kg) throughout development via the maternal diet. Supplementation of the maternal diet with DHA reduced MeHg accumulation in the brain. An accelerated development of grasping reflex was seen in mice offspring in the ‘MeHg + high DHA’ group when compared to ‘MeHg’ and ‘control’. Exposure to MeHg and DHA had an impact on cerebral gene expression as assessed by microarray and qPCR analysis. The results from the present study show the potential of DHA for alleviating toxicity caused by MeHg. This information may contribute towards refining risk/benefit assessment of seafood consumption and may enhance understanding of discrepancies between epidemiological studies of MeHg neurodevelopmental toxicity. | [S. Jayashankara b, C.N. Gloverc, K.I. Folvena, T. Brattelida b, C. Hogstranda d, A.-K. Lundebyea b] | Environmental Toxicology and Pharmacology | January 2012 | |
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| sciencedirectS0090825811007967 | The interactions between MicroRNA-200c and BRD7 in endometrial carcinoma | ObjectiveIncreased expression of miR-200c was recently reported in endometrial carcinoma compared with normal tissues. In this study, we evaluated the role of miR-200c in cell growth and drug sensitivity in endometrial carcinoma and investigated the underlying mechanisms.MethodsThe expression of miR-200c in human endometrial tissues was detected by quantitative RT-PCR. The transfection with anti-miRNA (anti-miR) or the premature form of miRNA (pre-miR) was performed to regulate the level of expression of miRNA-200c in endometrial carcinoma cells, HEC-1A and Ishikawa. To identify the target genes for miR-200c, we performed mRNA microarray after pre-miR-200c transfection in HEC-1A cells.ResultsWe found that miR-200c expression was increased in endometrial carcinoma compared with normal endometrial tissues. Anti-miR or pre-miR-200c could regulate cell survival, proliferation, and apoptosis and affect cytotoxicity in endometrial cancer cells. Through mRNA microarray analysis, we found that miR-200c inhibits the expression of BRD7, which was recently reported as a potential tumor suppressor gene. MiR-200c regulated the translocation of ?-catenin from the cytoplasm to the nucleus via inhibition of BRD7, resulting in increased expression of its transcriptional target genes, cyclinD1 and c-myc.ConclusionThe interaction between miR-200c and BRD7 might have important roles in controlling growth of endometrial of cancer cells and suggest a novel target pathway for treatment of this cancer. | [Young-Ae Parka 1, Jeong-Won Leea 1, Jung-Joo Choia, Hye-Kyung Jeona, YoungJae Choa, ChelHun Choia, Tae-Joong Kima, Nak Woo Leeb, Byoung-Gie Kima, Duk-Soo Baea] | Gynecologic Oncology | January 2012 | |
| sciencedirectS0198885911005490 | Analysis of microRNA expression profiling identifies miR-155 and miR-155* as potential diagnostic markers for active tuberculosis: a preliminary study | To explore biologic behaviors and disease relevance of microRNAs (miRNAs) in the development of active tuberculosis (ATB), we investigated the expression profile of Mycobacterium tuberculosis (MTB) purified protein derivative (PPD)–induced miRNAs to determine the specific miRNAs involved in the pathogenesis of ATB. The expression profile of miRNA under PPD challenge was first measured using microarray analysis in peripheral blood mononuclear cells isolated from ATB patients and healthy controls (HC). The remarkably reactive miRNAs were then validated in a larger cohort by quantitative real-time polymerase chain reaction (qRT-PCR). The receiver operating characteristic (ROC) curve was plotted to evaluate the diagnostic value of the determined PPD-responsive miRNAs. The potential targets for those miRNAs were also predicted by computational programs. Fourteen of 866 human miRNAs exhibited at least 1.8-fold difference in the ratio of expression level before and after stimulation with PPD between the ATB and HC groups. The qRT-PCR study validated the findings from microarray-based screening, in which miR-155 exhibited a fold change of 1.4 in the HC group and 3.7 in the ATB group upon PPD stimulation (p < 0.0001); miR-155* exhibited a fold change of 1.9 in the HC and 4.6 in the ATB group (p < 0.005). In ROC plots, the area under the curve was 0.8972 for miR-155 and 0.7945 for miR-155*. The background expression of these 2 microRNAs exhibited no differences between the ATB and HC groups. miR-155 and miR-155* exhibited characteristic expression by TB-specific antigen, suggesting that they can be potential diagnostic markers under the challenge of specific MTB antigens. | [Jing Wua b, Chanyi Lua b, Ni Diaob, Shu Zhangb, Sen Wangb, Feifei Wangb, Yan Gaob, Jiazhen Chenb, Lingyun Shaob, Jingning Lua, Xuelian Zhanga, Xinhua Wengb, Honghai Wanga, Wenhong Zhangb c, Yuxian Huangb] | Human Immunology | January 2012 | |
| sciencedirectB9780123847478100017 | 1 – Insect Genomics | SummarySummaryGenomic sequencing has become a routinely used molecular biology tool in many insect science laboratories. In fact, whole-genome sequences for 22 insects have already been completed, and sequencing of genomes of many more insects is in progress. This information explosion on gene sequences has led to the development of bioinformatics and several “omics” disciplines, including proteomics, transcriptomics, metabolomics, and structural genomics. Considerable progress has already been made by utilizing these technologies to address long-standing problems in many areas of molecular entomology. Attempts at integrating these independent approaches into a comprehensive systems biology view or model are just beginning. In this chapter, we provide a brief overview of insect whole-genome sequencing as well as information on 22 insect genomes and recent developments in the fields of insect proteomics, transcriptomics, and structural genomics. | [Subba R. Palli] | Insect Molecular Biology and Biochemistry | | |
| sciencedirectS1876107011001040 | Diffuse large B-cell lymphoma classification using linguistic analysis and ensembled artificial neural networks | The purpose of this study is to apply non-medical methods to classify two types of diffuse large B-cell lymphoma (DLBCL), which are the germinal-center type (GCB) and the activated B-cell type (ABC). The study materials are MicroRNAs (miRNAs) acquired from DLBCL patients. In order to achieve this goal, statistical methods (i.e. linguistic analysis) and engineering method (i.e. ensembled artificial neural networks (EANN)) have been independently used to do qualitative and quantitative analysis. On this basis, a novel noise elimination enhanced algorithm has been proposed to improve the efficiency of linguistic analysis, namely ensembled linguistic analysis. According to the results, the phylogenetic tree can achieve better performance than initial linguistic analysis. On the other hand, EANN model was established to perform the classification quantitatively, and sensitivity analysis (SA) for EANN was carried out to evaluate the significance ranking of the miRNAs and finally select the 5 most important miRNAs. Besides, classical linear and logistic regression models were developed for comparison with EANN classification results. The regression results were evidently worse than EANN model. This study proves that each lymphoma type has a distinctive pattern of miRNAs expression and the miRNAs expression pattern of ABC is more close to white noise than GCB. Both linguistic analysis and EANN model achieved accurate results; however the performance of EANN model for classification is much better. The 5 selected important miRNAs will be helpful for further study. | [Xingran Cuia b, Chung-Wu Linc, Maysam F. Abbodd, Quan Liua, Jiann-Shing Shiehe f] | Journal of the Taiwan Institute of Chemical Engineers | January 2012 | |
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| sciencedirectS0945053X11000928 | Drosophila basement membrane collagen col4a1 mutations cause severe myopathy | Recent data from clinical and mammalian genetic studies indicate that COL4A1 mutations manifest with basement membrane defects that result in muscle weakness, cramps, contractures, dystrophy and atrophy. In-depth studies of mutant COL4A1-associated muscle phenotype, however, are lacking and significant details of the muscle-specific pathomechanisms remain unknown. In this study, we have used a comprehensive set of Drosophila col4a1 and col4a2 mutants and a series of genetic and mutational analyses, gene, protein expression, and immunohistochemistry experiments in order to establish a Drosophila model and address some of these questions. The Drosophila genome contains two type IV collagen genes, col4a1 and col4a2. Mutant heterozygotes of either gene are viable and fertile, whereas homozygotes are lethal. In complementation analysis of all known mutants of the locus and a complementation matrix derived from these data we have identified the dominant lesions within the col4a1, but not within the col4a2 gene. Expression of a col4a1 transgene partially rescued the dominant and recessive mutant col4a1 alleles but not the col4a2 mutations that were all recessive. Partial complementation suggested that col4a1 gene mutations have strong antimorph effect likely due to the incorporation of the mutant protein into the triple helix. In col4a1 mutants, morphological changes of the oviduct muscle included severe myopathy with centronuclear myofibers leading to gradual development of female sterility. In larval body wall muscles ultrastructural changes included disturbance of A and I bands between persisting Z bands. In the most severely affected DTS-L3 mutant, we have identified four missense mutations within the coding region of the col4a1 gene two of which affected the Y within the Gly-X-Y unit and a 3′ UTR point mutation. In conclusion, our Drosophila mutant series may serve as an effective model to uncover the mechanisms by which COL4A1 mutations result in compromised myofiber–basement membrane interactions and aberrant muscle function. | [Ildikó Kelemen-Valkonya, Márton Kissa, Judit Csihaa, András Kissa, Urs Birchera, János Szidonyaa, Péter Maróya, Gábor Juhászc, Orbán Komonyia, Katalin Csiszárb, Mátyás Minka] | Matrix Biology | January 2012 | |
| sciencedirectS0882401011001860 | An evaluation of the effects of Lactobacillus ingluviei on body weight, the intestinal microbiome and metabolism in mice | BackgroundFood can modify the intestinal flora, and Lactobacillus ingluviei has been shown to cause weight gain in chicks and ducks but not in mammals.MethodologyFemale BALB/c mice were divided into a control and two experimental groups and were inoculated either once or twice with L. ingluviei or with PBS. Faecal samples were collected and tested using qPCR in order to detect and quantify Lactobacillus spp., Bacteroidetes spp. and Firmicutes spp. Gene expression was examined in liver and adipose tissue by microarray and qPCR. Metabolic indicators in the plasma were also measured.ResultsMice that were inoculated with 4 × 1010L. ingluviei presented a significant increase in weight gain and liver weight and significant increases in Lactobacillus spp. and Firmicutes DNA copy numbers in their faeces. The mRNA levels of fatty acyl synthase (Fas), sterol regulatory element binding factor 1 (Srebp1c), tumour necrosis factor alpha (Tnf), cytochrome P450 2E1 (Cyp2e1), 3-phosphoinositide-dependent protein kinase-1 (Pdpk1), acyl-Coenzyme A dehydrogenase 11 (Acad11), ATP-binding cassette sub family member G (ABCG2) and DEAD box polypeptide 25 (Ddx25) were significantly elevated in the liver tissues of animals in the experimental group. In gonadal adipose tissue, the expression levels of leptin, peroxisome proliferator-activated receptor ? (Pparg) and Srebp1c were significantly higher in animals from the experimental group, whereas the expression of adiponectin was significantly lower in these animals.ConclusionsThe inoculation of L. ingluviei in mice resulted in alterations in the intestinal flora, increased weight gain and liver enlargement, accelerated metabolism and increased inflammation. | [Emmanouil Angelakisa, Delphine Bastelicab, Amira Ben Amaraa, Adil El Filalia, Anne Dutourb, Jean-Louis Megea, Marie-Christine Alessib, Didier Raoulta] | Microbial Pathogenesis | January 2012 | |
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| sciencedirectS0168170211003212 | Changes in the topology of gene expression networks by human immunodeficiency virus type 1 (HIV-1) integration in macrophages | One key step of human immunodeficiency virus type 1 (HIV-1) infection is the integration of its viral cDNA. This process is mediated through complex networks of host–virus interactions that alter several normal cell functions of the host. To study the complexity of disturbances in cell gene expression networks by HIV-1 integration, we constructed a network of human macrophage genes located close to chromatin regions rich in proviruses. To perform the network analysis, we selected 28 genes previously identified as the target of cDNA integration and their transcriptional profiles were obtained from GEO Profiles (NCBI).A total of 2770 interactions among the 28 genes located around the HIV-1 proviruses in human macrophages formed a highly dense main network connected to five sub-networks. The overall network was significantly enriched by genes associated with signal transduction, cellular communication and regulatory processes. To simulate the effects of HIV-1 integration in infected macrophages, five genes with the most number of interaction in the normal network were turned off by putting in zero the correspondent expression values. The HIV-1 infected network showed changes in its topology and alteration in the macrophage functions reflected in a re-programming of biosynthetic and general metabolic process.Understanding the complex virus-host interactions that occur during HIV-1 integration, may provided valuable genomic information to develop new antiviral treatments focusing on the management of some specific gene expression networks associated with viral integration. This is the first gene network which describes the human macrophages genes interactions related with HIV-1 integration. | [María Juliana Soto-Giróna, Felipe García-Vallejob] | Virus Research | January 2012 | |
| sciencedirectS1383571811003810 | A graphical systems model and tissue-specific functional gene sets to aid transcriptomic analysis of chemical impacts on the female teleost reproductive axis | Oligonucleotide microarrays and other ‘omics’ approaches are powerful tools for unsupervised analysis of chemical impacts on biological systems. However, the lack of well annotated biological pathways for many aquatic organisms, including fish, and the limited power of microarray-based analyses to detect low level differential expression of individual genes can hinder the ability to infer and understand chemical effects based on transcriptomic data. Here we report on the supervised assembly of a series of tissue-specific functional gene sets intended to aid transcriptomic analysis of chemical impacts on the female teleost reproductive axis. Gene sets were defined based on an updated graphical systems model of the teleost brain–pituitary–gonadal-hepatic axis. Features depicted in the model were organized into gene sets and mapped to specific probes on three zebrafish (Danio rerio) and two fathead minnow (Pimephales promelas) microarray platforms. Coverage of target genes on the microarrays ranged from 48% for the fathead minnow arrays to 88% for the most current zebrafish platform. Additionally, extended fathead minnow gene sets, incorporating first degree neighbors identified from a Spearman correlation network derived from a large compendium of fathead minnow microarray data, were constructed. Overall, only 14% of the 78 genes queried were connected in the network. Among those, over half had less than five neighbors, while two genes, cyclin b1 and zona pellucida glycoprotein 3, had over 100 first degree neighbors, and were neighbors to one another. Gene set enrichment analyses were conducted using microarray data from a zebrafish hypoxia experiment and fathead minnow time-course experiments conducted with three different endocrine-active chemicals. Results of these analyses demonstrate the utility of the approach for supporting biological inference from ecotoxicogenomic data and comparisons across multiple toxicogenomic experiments. The graphical model, gene mapping, and gene sets described are now available to the scientific community as tools to support ecotoxicogenomic research. | [Daniel L. Villeneuvea, Natàlia Garcia-Reyerob, Dalma Martinovi?-Weigeltc, Zhenhong Lid, Karen H. Watanabed, Edward F. Orlandoe, Carlie A. LaLonea, Stephen W. Edwardsf, Lyle D. Burgoong, Nancy D. Denslowh, Edward J. Perkinsi, Gerald T. Ankleya] | Mutation Research/Genetic Toxicology and Environmental Mutagenesis | | |
| sciencedirectS0304395911006981 | Contribution of spinal galectin-3 to acute herpetic allodynia in mice | To identify endogenous factors involved in herpetic pain, we performed genome-wide microarray analysis of the spinal cord of mice that suffered from herpetic allodynia induced by inoculation with herpes simplex virus type 1, which revealed marked induction of galectin-3, a ?-galactoside-binding lectin. Therefore, we investigated the role of galectin-3 in herpetic allodynia. The expression levels of galectin-3 mRNA and protein were increased with a temporal pattern similar to that of herpetic allodynia. Galectin-3-expressing cells were mainly localized in the superficial dorsal horn, round in shape, and positive for the macrophage/microglia markers Iba-1 and F4/80. In the deep dorsal horn, there were Iba-1-positive cells with ramified and stout processes, which were negative for galectin-3. In the superficial dorsal horn, there were many CD3-positive T cells, but most of the galectin-3-expressing cells were negative for CD3. Galectin-3-expressing cells were negative for the neuronal marker NeuN and the astrocyte marker glial fibrillary acidic protein antibody. Deficiency in galectin-3 markedly reduced herpetic allodynia, without showing an effect on herpes zoster-like skin lesions. Intrathecal injection of galectin-3 produced mechanical allodynia in naive mice, and intrathecal injections of anti-galectin-3 antibodies significantly reduced herpetic allodynia. The present results suggest that galectin-3 in infiltrating macrophages and/or resident microglia in the spinal dorsal horn contributes to herpetic allodynia. Galectin-3 may be a new therapeutic target for the treatment of herpes zoster-associated pain. | [Ichiro Takasakia, Kana Taniguchib, Fumiaki Komatsub, Atsushi Sasakib, Tsugunobu Andohb, Hiroshi Nojimac, Kimiyasu Shirakid, Daniel K. Hsue, Fu-Tong Liue, Ichiro Katof, Koichi Hiragaf, Yasushi Kuraishib] | PAIN | | |
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| sciencedirectS0300483X11003702 | The effect of four non-genotoxic carcinogens and four non-carcinogens on NRK-52E cells using a transcriptomics approach | | [Kate M. Bloch1, Andrew Evans1, Joost van Delft2, Edward A. Lock1] | Toxicology | 18 December 2011 | |
| sciencedirectS0039128X11003825 | ER?36, a new variant of the ER? is expressed in triple negative breast carcinomas and has a specific transcriptomic signature in breast cancer cell lines | Triple negative breast cancer is deprived of estrogen receptor alpha (ER?), progesterone receptor (PR) and HER-2 protein. It constitutes the most heterogeneous and aggressive group of breast carcinomas, for which identification of novel characteristics and characterization of putative targets becomes very demanding. In the present work we have assayed the expression of ER?36, a recently identified ER? variant of 36 kDa, in a series of triple negative breast cancers, in relation to the clinical behavior and other clinico-pathological features of the tumors. While widely expressed within the cytoplasm in almost all tumors, we found that exclusively the membrane/submembrane expression of the receptor exhibits a correlation with patient’s survival. Moreover, membrane ER?36 correlates in an inverse manner with the expression of miRNA210, a pro-angiogenic miR, with high prognostic relevance in triple negative carcinomas. A thorough transcriptomic, pharmacological-based approach in breast cancer cell lines, revealed an early (direct) transcriptional signature of the receptor activation, related to immune system processes and T-cell differentiation, RNA biosynthesis, regulation of metabolism, VEGF signaling and regulation of the cell cycle, with a down-regulation of CREB, NF?B and STATs transcription factors. Finally, ER?36 expression is not limited within breast cancer epithelial linen, but is equally identified in tumor vasculature, peritumoral fat tissue, lymphocytic infiltrate and stromal fibroblasts. In light of the above, ER?36 could represent a major counterpart in triple negative breast cancer. | [Vassiliki Pelekanoua 1, George Notasb 1, Marilena Kampab, Eleftheria Tsentelieroua, Jelena Radojicica, Guy Leclercqc, Elias Castanasb, Efstathios N. Stathopoulosa] | Steroids | | |
| sciencedirectS0308814611008727 | ?- and ?-Mangostin inhibit the proliferation of colon cancer cells via ?-catenin gene regulation in Wnt/cGMP signalling | Aberrant activation of Wnt/?-catenin signalling via genetic errors within ?-catenin or APC has a crucial role in carcinogenesis. Here, we studied two xanthones, ?- and ?-mangostin, as inhibitors of Wnt/?-catenin signalling. The mangostins inhibited TCF/?-catenin transcriptional activity. The mangostins also inhibited protein expression of ?-catenin in colon cancer cells, but the inhibition was independent of the phosphorylation and degradation of ?-catenin. Instead, the mangostins increased the levels of cGMP and cGMP-dependent kinase, indicating that the inhibition of ?-catenin resulted from ?-catenin gene regulation. Our results indicate that mangostins could be potential candidates for preventing colon cancer through a novel mechanism of inhibiting Wnt/?-catenin signalling. | [Ji-Hye Yooa, Kyungsu Kanga, Eun Hye Jhoa, Young-Won Chinb, Jinwoong Kimc, Chu Won Nhoa] | Food Chemistry | 15 December 2011 | |
| sciencedirectS0304383511007403 | Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers | To identify epigenetic-based biomarkers for diagnosis of ovarian cancer we performed MeDIP-Chip in A2780 and CaOV3 ovarian cancer cell lines. Validation by Sequenom massARRAY methylation analysis confirmed a panel of six gene promoters (ARMCX1, ICAM4, LOC134466, PEG3, PYCARD & SGNE1) where hypermethylation discriminated 27 serous ovarian cancer clinical samples versus 12 normal ovarian surface epithelial cells (OSE) (ROC of 0.98). Notably, CpG sites across the transcription start site of a potential long-intergenic non-coding RNA (lincRNA) gene (LOC134466), was shown to be hypermethylated in 81% of serous EOC and could differentiate tumours from OSE (p < 0.05). We propose that this potential biomarker panel holds great promise as a diagnostic test for high-grade (Type II) serous ovarian cancer. | [Brian S. Glossa, Kate I. Pattersona, Caroline A. Bartona, Maria Gonzaleza, James P. Scurryb, Neville F. Hackerc, Robert L. Sutherlanda d, Philippa M. O’Briena d 1, Susan J. Clarka d 1] | Cancer Letters | | |
| sciencedirectS0006295211006496 | Biochemical disorders associated with antiproliferative effect of dehydroepiandrosterone in hepatoma cells as revealed by LC-based metabolomics | DHEA is known to have chemopreventive and antiproliferative activities, and was initially thought to be mediated by inhibition of G6PD. Our previous study has shown that DHEA may act through interference with energy metabolism. To study the effect of pharmacological dose of DHEA on cellular metabolism, and to further delineate the mechanism underlying its antiproliferative effect, we applied a metabolomic approach to globally profile the changes in metabolites in SK-Hep1 cells underexpressing G6PD (Sk-Gi) and control cells (Sk-Sc) after DHEA treatment. RRLC-TOF-MS was used to identify metabolites, and tandem mass spectrometry was used to confirm their identity. DHEA induced changes in glutathione metabolism, lipid metabolism, s-adenosylmethionine (SAM) metabolism, as well as lysine metabolism. Elevation in level of glutathione disulfide, together with a concomitant decrease in level of reduced glutathione, was indicative of increased oxidative stress. Depletion of carnitine and its acyl derivatives reflected decline in fatty acid catabolism. These changes were associated with mitochondrial malfunction and reduction in cellular ATP content. Cardiolipin (CL) and phosphatidylcholine (PC) levels decreased significantly, suggesting that alterations in lipid composition are causally related to decline in mitochondrial function after DHEA treatment. The decline in cellular SAM content was accompanied by decreased expression of methionine adenosyltransferase genes MAT2A and MAT2B. SAM supplementation partially rescued cells from DHEA-induced growth stagnation. Our findings suggest that DHEA causes perturbation of multiple pathways in cellular metabolism. Decreased SAM production, and cardiolipin depletion and the resulting mitochondrial dysfunction underlie the antiproliferative effect of DHEA. | [Mei-Ling Chenga b, Ming-Shi Shiaoc, Daniel Tsun-Yee Chiua b, Shiue-Fen Wenga, Hsiang-Yu Tanga, Hung-Yao Hoa] | Biochemical Pharmacology | 1 December 2011 | |
| sciencedirectS0006295211006587 | Underexpression of miR-224 in methotrexate resistant human colon cancer cells | MicroRNAs (miRNAs) are small non-coding RNAs involved in RNA silencing that play a role in many biological processes. They are involved in the development of many diseases, including cancer. Extensive experimental data show that they play a role in the pathogenesis of cancer as well as the development of drug resistance during treatments. The aim of this work was to detect differentially expressed miRNAs in MTX-resistant cells. Thus, miRNA microarrays of sensitive and MTX-resistant HT29 colon cancer cells were performed. The results were analyzed using the GeneSpring GX11.5 software. Differentially expressed miRNAs in resistant cells were identified and miR-224, which was one of the most differentially expressed miRNAs and with high raw signal values, was selected for further studies. The underexpression of miR-224 was also observed in CaCo-2 and K562 cells resistant to MTX. Putative targets were predicted using TargetScan 5.1 software and integrated with the data from expression microarrays previously performed. This approach allowed us to identify miR-224 targets that were differentially expressed more than 2-fold in resistant cells. Among them CDS2, DCP2, HSPC159, MYST3 and SLC4A4 were validated at the mRNA level by qRT-PCR. Functional assays using an anti-miR against miR-224 desensitized the cells towards MTX, mimicking the resistant phenotype. On the other hand, siRNA treatment against SLC4A4 or incubation of Poly Purine Reverse Hoogsteen (PPRH) hairpins against CDS2 or HSPC159 increased sensitivity to MTX. These results revealed a role for miR-224 and its targets in MTX resistance in HT29 colon cancer cells. | [Núria Mencia, Elisabet Selga, Véronique Noé, Carlos J. Ciudad] | Biochemical Pharmacology | 1 December 2011 | |
| sciencedirectS1388198111001727 | Apo-10'-lycopenoic acid impacts adipose tissue biology via the retinoic acid receptors | Apo-10'-lycopenoic acid (apo-10-lycac), a metabolite of lycopene, has been shown to possess potent biological activities, notably via the retinoic acid receptors (RAR). In the current study, its impact on adipose tissue and adipocytes was studied. In microarray experiments, the set of genes regulated by apo-10-lycac treatments was compared to the set of genes regulated by all-trans retinoic acid (ATRA), the natural ligand of RAR, in adipocytes. Approximately 27.5% of the genes regulated by apo-10-lycac treatments were also regulated by ATRA, suggesting a common ability in terms of gene expression modulation, possibly via RAR transactivation. The physiological impact of apo-10-lycac on adipose tissue biology was evaluated. If it had no effect on adipogenesis in the 3T3-L1 cell model, this metabolite may have a preventative effect against inflammation, by preventing the increase in the inflammatory markers, interleukin 6 and interleukin 1? in various dedicated models. The ability of apo-10-lycac to transactivate the RAR and to modulate the transcription of RAR target gene was brought in vivo in adipose tissue. While apo-10-lycac was not detected in adipose tissue, a metabolite with a molecular weight with 2 Da larger mass was detected, suggesting that a dihydro-apo-10'-lycopenoic acid, may be present in adipose tissue and that this compound could active or may lead to further active RAR-activating apo-10-lycac metabolites. Since apo-10-lycac treatments induce anti-inflammatory effects in adipose tissue but do not inhibit adipogenesis, we propose that apo-10-lycac treatments and its potential active metabolites in WAT may be considered for prevention strategies relevant for obesity-associated pathologies. | [E. Gourantona b 1, G. Aydemirc 1, E. Reynaudd e, J. Marcotorchinoa b, C. Malezeta b, C. Caris-Veyratd e, R. Blomhofff, J.F. Landriera b 2, R. Rühlc g 2] | Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids | December 2011 | |
| sciencedirectS1744117X11000438 | Shift in chicken intestinal gene association networks after infection with Salmonella | A primary infection of Salmonella enteritidis causes a spatial-temporal dependent change in the gene expression patterns in the intestine of chickens (Gallus gallus). This is the result of a dynamic intestinal response to adapt to the altered environment and to optimize its ‘health’ and functionality under the new circumstances. By inferring gene association networks (GANs), the complexities of and changes in biological networks can be uncovered. Within such GANs highly interacting (hub) genes can be identified, which are supposed to be high-level regulators connected to multiple processes. By exploring the intestinal expression of genes differing between control and Salmonella infected chicken in a time-dependent manner differences in GANs were found. In control chickens more developmental processes were observed, whereas in infected chickens relatively more processes were associated to ‘defense/pathogen response’. Moreover the conserved protein domains of the identified hub genes in controls were nuclear-associated, whereas hub genes in infected chickens were involved in ‘cellular communication’. The shift in topology and functionality of the intestinal GANs in control and Salmonella infected animals and the identification of GAN-specific hubs is a first step to understand the complexity of biological networks and processes regulating intestinal health and functionality under normal and disturbed conditions. | [Dirkjan Schokkera, Dirk-Jan de Koningb, Johanna M.J. Rebelc, Mari A. Smitsa] | Comparative Biochemistry and Physiology Part D: Genomics and Proteomics | December 2011 | |
| sciencedirectS1744117X11000396 | Differentially displayed genes with oxygen depletion stress and transcriptional responses in the marine mussel, Mytilus galloprovincialis | Hypoxic events affecting aquatic environments have been reported worldwide and the hypoxia caused by eutrophication is considered one of the serious threats to coastal marine ecosystems. To investigate the molecular-level responses of marine organisms exposed to oxygen depletion stress and to explore the differentially expressed genes induced or repressed by hypoxia, differential display polymerase chain reaction (DD-PCR) was used with mRNAs from the marine mussel, Mytilus galloprovincialis, under oxygen depletion and normal oxygen conditions. In total, 107 cDNA clones were differentially expressed under hypoxic conditions relative to the control mussel group. The differentially expressed genes were analyzed to determine the effects of hypoxia. They were classified into five functional categories: information storage and processing, cellular processes and signaling, metabolism, predicted general function only, and function unknown. The differentially expressed genes were predominantly associated with cellular processing and signaling, and they were particularly related to the signal transduction mechanism, posttranslational modification, and chaperone functions. The observed differences in the DD-PCR of 10 genes (encoding elongation factor 1 alpha, heat shock protein 90, calcium/calmodulin-dependent protein kinase II, GTPase-activating protein, 18S ribosomal RNA, cytochrome oxidase subunit 1, ATP synthase, chitinase, phosphoglycerate/bisphosphoglycerate mutase family protein, and the nicotinic acetylcholine receptor) were confirmed by quantitative RT-PCR and their transcriptional changes in the mussels exposed to hypoxic conditions for 24–72 h were investigated. These results identify biomarker genes for hypoxic stress and provide molecular-level information about the effects of oxygen depletion on marine bivalves. | [Seonock Woo, Hye-Young Jeon, Seong-Ryul Kim, Seungshic Yum] | Comparative Biochemistry and Physiology Part D: Genomics and Proteomics | December 2011 | |
| sciencedirectS1744117X11000608 | Analysis of stress-induced hepatic gene expression in rainbow trout (Oncorhynchus mykiss) selected for high- and low-responsiveness to stress | The production and welfare of intensively reared fish would be improved by reducing stress responsiveness. One approach to achieving this goal is selective breeding utilising stress-responsive genes as direct genetic markers of the desirable trait. As a first step in this process, microarray analysis has been carried out on liver tissues of rainbow trout selectively bred for high (HR) or low (LR) responsiveness to a stressor. Microarray hybridizations provided gene expression profiles for pooled samples of fish confined for 6 h, 24 h and 168 h and for individual fish (168 h only). 161 genes were shown to be differentially regulated in HR and LR fish during confinement exposure and eight of these gene expression profiles were validated by quantitative PCR. Genes of particular interest included intelectin-2 precursor which showed greater than 100-fold higher expression in HR fish compared to LR fish irrespective of whether the fish were confined or not; interferon inducible transmembrane protein 3 which was differentially stress-induced between the two lines; and hepatic pro-opiomelanocortin B (POMC B) which was upregulated during stress in HR fish but downregulated in LR fish. All these offer potential as direct markers of low stress responsiveness in a marker-assisted selection scheme. | [Jhansi K. Pemmasania, Tom G. Pottingerb, Michael T. Cairnsa] | Comparative Biochemistry and Physiology Part D: Genomics and Proteomics | December 2011 | |
| sciencedirectS0012160611012292 | The maternal genes Ci-p53/p73-a and Ci-p53/p73-b regulate zygotic ZicL expression and notochord differentiation in Ciona intestinalis embryos | I isolated a Ciona intestinalis homolog of p53, Ci-p53/p73-a, in a microarray screen of rapidly degraded maternal mRNA by comparing the transcriptomes of unfertilized eggs and 32-cell stage embryos. Higher expression of the gene in eggs and lower expression in later embryonic stages were confirmed by whole-mount in situ hybridization (WISH) and quantitative reverse transcription-PCR (qRT-PCR); expression was ubiquitous in eggs and early embryos. Knockdown of Ci-p53/p73-a by injection of antisense morpholino oligonucleotides (MOs) severely perturbed gastrulation cell movements and expression of notochord marker genes. A key regulator of notochord differentiation in Ciona embryos is Brachyury (Ci-Bra), which is directly activated by a zic-like gene (Ci-ZicL). The expression of Ci-ZicL and Ci-Bra in A-line notochord precursors was downregulated in Ci-p53/p73-a knockdown embryos. Maternal expression of Ci-p53/p73-b, a homolog of Ci-p53/p73-a, was also detected. In Ci-p53/p73-b knockdown embryos, gastrulation cell movements, expression of Ci-ZicL and Ci-Bra in A-line notochord precursors, and expression of notochord marker gene at later stages were perturbed. The upstream region of Ci-ZicL contains putative p53-binding sites. Cis-regulatory analysis of Ci-ZicL showed that these sites are involved in expression of Ci-ZicL in A-line notochord precursors at the 32-cell and early gastrula stages. These results suggest that p53 genes are maternal factors that play a crucial role in A-line notochord differentiation in C. intestinalis embryos by regulating Ci-ZicL expression. | [Takeshi Noda] | Developmental Biology | 1 December 2011 | |
| sciencedirectS1050464811003305 | Insights into the antibacterial and immunomodulatory functions of the antimicrobial peptide, epinecidin-1, against Vibrio vulnificus infection in zebrafish | In the present study, we used Vibrio vulnificus and a zebrafish model system to investigate the inhibitory effect of epinecidin-1 on acute bacterial infection and studied the impacts of pretreatment, co-treatment, and post-treatment with epinecidin-1 on its protective efficacy. In vivo experiments showed that co-treatment with epinecidin-1 and V. vulnificus achieved 78%–97% survival rates after 30 days. When epinecidin-1 and V. vulnificus were co-injected into zebrafish and zebrafish were re-challenged with V. vulnificus after 30 days, zebrafish had survival rates of 22%–47%. Pretreatment and post-treatment with epinecidin-1 obtained respective survival rates of 57% and 60%. In addition, epinecidin-1 modulated the expressions of immune-responsive genes like interleukin (IL)-10, IL-1b, tumor necrosis factor-?, and interferon-? as analyzed by a microarray and qPCR approach. This study demonstrates the use of epinecidin-1 to develop inactivated material for fish bacterial infections which can provide guidelines for the future design of epinecidin-1-bacterial formulations for various in vivo applications. | [Chieh-Yu Pana, Jen-Leih Wub, Cho-Fat Huib, Cheng-Hui Lina, Jyh-Yih Chenc] | Fish & Shellfish Immunology | December 2011 | |
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| sciencedirectS0027510710003283 | Dose-responsiveness and persistence of microRNA expression alterations induced by cigarette smoke in mouse lung | Our previous studies demonstrated that exposure to cigarette smoke (CS), either mainstream or environmental, results in a remarkable downregulation of microRNA expression in the lung of both mice and rats. The goals of the present study were to evaluate the dose responsiveness to CS and the persistence of microRNA alterations after smoking cessation. ICR (CD-1) neonatal mice were exposed whole-body to mainstream CS, at the doses of 119, 292, 438, and 631 mg/m3 of total particulate matter. Exposure started within 12 h after birth and continued daily for 4 weeks. The levels of bulky DNA adducts and 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) were measured by 32P postlabeling procedures, and the expression of 697 mouse microRNAs was analyzed by microarray. The highest CS dose was lethal. Exposure to CS caused a dose-dependent increase of DNA alterations. DNA adducts and, even more sharply, 8-oxodGuo were reverted 1 and 4 weeks after smoking cessation. Exposure to CS resulted in an evident dysregulation of microRNA expression profiles, mainly in the sense of downregulation. The two lowest doses were not particularly effective, while the highest nonlethal dose produced extensive microRNA alterations. The expression of most downregulated microRNAs, including among others 7 members of the let-7 family, was restored one week after smoking cessation. However, the recovery was incomplete for a limited array of microRNAs, including mir-34b, mir-345, mir-421, mir-450b, mir-466, and mir-469. Thus, it appears that microRNAs mainly behave as biomarkers of effect and that exposure to high-dose, lasting for an adequate period of time, is needed to trigger the CS-related carcinogenesis process in the experimental animal model used. | [Alberto Izzottia, Patrizia Largheroa, Mariagrazia Longobardia, Cristina Cartigliaa, Anna Camoiranoa, Vernon E. Steeleb, Silvio De Floraa] | Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis | 1 December 2011 | |
| sciencedirectS0027510710002770 | Interplay between histopathological alterations, cigarette smoke and chemopreventive agents in defining microRNA profiles in mouse lung | We have investigated alterations of microRNA expression profiles in the apparently healthy lung of mice and rats as an early response to exposure to cigarette smoke, either mainstream (MCS) or environmental, and/or to treatment with chemopreventive agents. Further on, we evaluated microRNA alterations at a later stage, when lung tumors were detectable in MCS-exposed mice. Lung samples were available from previous studies, in which strain H mice had been exposed to MCS for 4 months, starting immediately after birth, and then kept in filtered air for an additional 3 months. Some samples were from MCS-exposed mice treated either with N-acetyl-l-cysteine during pregnancy or with phenethyl isothiocyanate after weaning. The analysis of 576 mouse microRNAs showed that MCS strongly dysregulated microRNA expression and that both chemopreventive agents efficiently attenuated this trend, especially in noncancer tissue. MicroRNA expression was affected by histopathology, with specific signatures related to occurrence of pneumonia, adenoma, or bronchoalveolar carcinoma. Within pairs of samples from individual mice, microRNA analysis discriminated adenomatous tissue and especially carcinomatous tissue from the surrounding normal appearing tissue. A series of microRNA alterations characterized the sequential stages of pulmonary carcinogenesis. The involved functions included oncogene activation, inhibition of oncosuppressor genes, recruitment of undifferentiated stem cells, inflammation, inhibition of gap-junctional intercellular communications, angiogenesis, invasiveness, and metastatization. Thus, microRNA expression profiles in lung are dysregulated by MCS along all steps of the carcinogenesis process and depend on the interplay among exposure to noxious agents, treatment with dietary and pharmacological agents, and occurrence of pulmonary diseases. | [Alberto Izzottia, Patrizia Largheroa, Roumen Balanskyb, Ulrich Pfefferc, Vernon E. Steeled, Silvio De Floraa] | Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis | 1 December 2011 | |
| sciencedirectS0027510711000844 | The Aicardi–Goutières syndrome. Molecular and clinical features of RNAse deficiency and microRNA overload | Intracellular RNAses are involved in various functions, including microRNA maturation and turnover. Mutations occurring in genes encoding RNAses cause Aicardi–Goutiéres syndrome (AGS). AGS mutations silence RNAse activity, thus inducing accumulation of endogenous RNAs, mainly consisting of short RNAs and microRNAs. Overload of intracellular RNA triggers Toll like receptor-dependent interferon-alpha production in the brain, which in turn activates neurotoxic lymphocytes and inhibits angiogenesis thus inducing the typical clinical phenotype of AGS. However, these pathogenic mechanisms are attenuated after three years of age by the endogenous production of DNAJP58IPK and Cystatin F, which arrest AGS progression. Because RNAses are involved in microRNA turnover, we evaluated the expression of 957 microRNAs in lymphocytes from AGS patients and control patients. Our results indicate that microRNA overload occurs in AGS patients. This upregulation inhibits microRNA turnover impeding the synthesis of the novel microRNAs required for the differentiation and myelination of the brain during the initial period of postnatal life. These pathogenic mechanisms result in AGS, a neurological syndrome characterized by irritability, mild hyperpyrexia, pyramidal and extrapyramidal signs, and spastic-dystonic tetraplegia. Typical cerebrospinal fluid alterations include lymphocytosis and elevated interferon-alpha levels. Brain imaging demonstrates cerebral calcifications, white matter abnormalities, and progressive cerebral atrophy.Thus, evidence exists that mutations silencing intracellular RNases affect microRNA turnover resulting in the severe clinical consequences in the brain characterizing the clinical feature of AGS. | [A. Pullieroa, E. Fazzib, C. Cartigliaa, S. Orcesic, U. Balottinc, C. Uggettid, R. La Pianae, I. Olivieric, J. Gallib, A. Izzottia] | Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis | 1 December 2011 | |
| sciencedirectS0300483X11003179 | Differential programming of p53-deficient embryonic cells during rotenone block ? | Mitochondrial dysfunction has been implicated in chemical toxicities. The present study used an in vitro model to investigate the differential expression of metabolic pathways during cellular stress in p53-efficient embryonic fibroblasts compared to p53-deficient cells. These cell lines differed with respect to NADH/NAD+ balance. This ratio constitutes a driving force for NAD- and NADH-dependent reactions and is inversed upon exposure to Rotenone (complex I inhibitor). Rotenone perturbed the structure of the elongated fibrillar tubulin network and decreased mRNA expression of tubulin genes both suggesting reprogramming and reorganization of the cytoskeleton in both cell lines. These changes were reflected in the abundance of specific mRNA and microRNA (miRNA) species as determined from genome-based analysis. Changes in mRNA and miRNA expression profiles reflected differences in energy utilizing pathways, consistent with the notion that the p53 pathway influences the cellular response to mitochondrial dysfunction and that at least some control may be embedded within specific mRNA/miRNA networks in embryonic cells. | [M.L. Greena d, A.V. Singha b, L.B. Ruestc, M.M. Pisanoa, R.A. Proughd, T.B. Knudsena e] | Toxicology | 28 November 2011 | |
| sciencedirectS0300483X11003192 | Inter- and intra-laboratory study to determine the reproducibility of toxicogenomics datasets | The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, it predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we assessed whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories.All test centres (TCs) adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen benzo[a]pyrene (B[a]P) and the human hepatoma cell line HepG2 were used to generate three comparable toxicogenomic data sets. High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform. While differences at the global transcriptome level were observed between the TCs, a common subset of B[a]P responsive genes (n = 400 gene probes) was identified at all TCs which included many genes previously reported in the literature as B[a]P responsive. These data show promise that the current generation of microarray technology, in combination with a standard in vitro experimental design, can produce robust data that can be generated reproducibly in independent laboratories. Future work will need to determine whether such reproducible in vitro model(s) can be predictive for a range of toxic chemicals with different mechanisms of action and thus be considered as part of future testing regimes for regulatory risk assessment. | [D.J. Scotta, A.S. Devonshirea, Y.A. Adeleyeb, M.E. Schuttea, M.R. Rodriguesc, T.M. Wilkesa, M.G. Saccoc, L. Gribaldoc, M. Fabbric, S. Coeckec, M. Whelanc, N. Skinnerd, A. Bennette, A. Whiteb, C.A. Foya] | Toxicology | 28 November 2011 | |
| sciencedirectS0300483X11003210 | Oxazolone (OXA) is a respiratory allergen in Brown Norway rats | Oxazolone (OXA) is a potent contact allergen in man, and it is used as a model Th1-allergen to test (Q)SAR's and screening assays for allergenic potential of chemicals. However, it elevates serum IgE levels and Thelper2 cytokines at relatively low doses in test animals, suggesting that it has also respiratory allergenic potential. The lack of human data on respiratory allergenic potential of OXA may be due to lack of significant inhalation exposure. Here, female Brown Norway rats (BN) were sensitized by two or five dermal applications of OXA at the same total dose of 3.75 mg. Controls received vehicle. All animals were challenged by inhalation to 45 mg/m3 OXA on day 21 and necropsy was performed on day 22. All sensitized animals had increased serum IgE. OXA challenge decreased breathing frequency, and induced apnoeic breathing in the sensitized animals – a hallmark of respiratory allergy in our model. An exudative, granulocytic inflammation was observed primarily in the larynx of the sensitized and challenged rats. Microarray analysis of lung tissue, sampled 24 h after challenge, revealed upregulation of several genes and activation of Gene Ontology (GO) pathways, which resembled more closely those found previously in lung tissue of rats sensitized and challenged by the respiratory allergen trimellitic anhydride than by the contact allergen dinitrochlorobenzene. The results indicate that the contact allergen OXA can also be a respiratory allergen, provided that it is inhaled. Its use as a model contact sensitizer must be reconsidered. | [C. Frieke Kupera, Marijana Radonjica, Jos van Trielb, Rob Stieruma, Rianne J. de Groota 1, Josje H.E. Artsc] | Toxicology | 28 November 2011 | |
| sciencedirectS0300483X11003234 | Vanin-1; a potential biomarker for nephrotoxicant-induced renal injury | Because traditional markers for detecting renal injury are generally insensitive and nonspecific, we tried to identify some useful biomarkers. Microarray analyses and quantitative real-time PCR using human renal tubular cells showed that the mRNA expression of VNN-1 which encodes vanin-1, increased after the exposure of these cells to organic solvents (allyl alcohol, ethylene glycol, formaldehyde, chloroform, and phenol) for 24 h. The mRNA levels of other inflammation-related molecules such as monocyte chemoattractant protein 1 (MCP-1) and kidney injury molecule-1 (KIM-1) also increased after the exposure to organic solvents, although their elevations were slower than that of vanin-1. In rats treated with ethylene glycol for 3 weeks, tubular injury was detected by histological examination, but not by traditional biomarkers including serum creatinine and urinary N-acetyl-?-glucosaminidase. The mRNA levels of vanin-1 and Kim-1, but not MCP-1, significantly elevated in the renal cortices of ethylene glycol-exposed rats. On immunofluorescence analyses, vanin-1 signal was detected specifically in the renal tubules with a remarkable expression in the ethylene glycol-treated rats. As a result, compared with control group, higher urinary and serum concentrations of vanin-1 were observed in the ethylene glycol-treated group. These results suggest that vanin-1 is a useful and rapid biomarker for renal tubular injury induced by organic solvents. | [Keiko Hosohataa, Hitoshi Andoa, Yoko Fujiwarab, Akio Fujimuraa b] | Toxicology | 28 November 2011 | |
| sciencedirectS128645791100284X | Gene expression following low dose inhalational Francisella tularensis (SchuS4) exposure in Balb/c mice and the potential role of the epithelium and cell adhesion | Interactions between Francisella tularensis and the host are slowly being elucidated. Microarray technology was used to further characterise the response of Balb/c mice after inhalation of the virulent F. tularensis, SchuS4. The validated array data revealed changes in expression of 476 genes across a 96 h time course following infection (p ≤ 0.05). These data confirm down-regulation of the toll-like receptor pathway (TLR3, 4, 5, 7 and 8), and the induction of IFN-? inducible genes (T-cell specific GTPase, ?2 microglobulin and interleukin 21). The overall response appears to be two staged with an initial up-regulation of genes involved in apoptosis, TNF? production and antigen presentation. This is followed by a large alteration of expression at 96 h as the host succumbs to infection. A key regulatory time-point has been identified at 24 h post challenge, where several transcriptional events may predicate the progression of infection; these include transcriptional regulators of inflammation and proteolytic pathways. Pathway analysis indicates a novel role for cell–cell adhesion and extracellular matrix modulation in infection. Transcripts representing cellular junctions, focal adhesion and adherens junctions changed following infection. Additionally, aspects of extracellular matrix remodelling have been confirmed at the protein level, suggesting an important role of the respiratory epithelium in host response to F. tularensis warranting further study. | [Jonathan David, Amanda J. Gates, Gareth D. Griffiths, Roman A. Lukaszewski] | Microbes and Infection | | |
| sciencedirectS0039128X11003357 | Interplay of estrogen receptors and GPR30 for the regulation of early membrane initiated transcriptional effects: A pharmacological approach | Estrogens exert their effect through ER? and ER? intracellular transcription factors and rapid, usually membrane-initiated receptors, influencing cytosolic signaling and transcription. The nature of extranuclear estrogen elements has not been elucidated so far; classical or alternatively transcribed ER isoforms (ER?36, ER?46) anchored to the plasma membrane and GPR30 (GPER1) have been reported to exert early estrogen actions. Here, we used E2–BSA, an impermeable estradiol analog for a transcriptome analysis in four GREP1 positive breast cancer cell lines with different estrogen receptor profiles (T47D, MCF-7, MDA-MB-231 and SKBR3) in order to evaluate GPER1 transcriptional effects. Early effects of E2–BSA were assayed after 3 h of incubation, in the absence/presence of ICI182,780 (ER-inhibitor) or G15 (GREP1-specific inhibitor). E2–BSA specifically modified 277–549 transcripts in the different cell lines. Two different clusters of transcripts could be identified: (1) the majority of transcripts were inhibited by both ICI182,780 and G15, suggesting an interaction of E2–BSA with a common ER-related element, or a direct ER–GPER1 interaction; (2) a small number of G15-only modified transcripts, in two cell lines (T47D and SKBR3 cells), indicative of specific GPER1-related effects. The latter transcripts were significantly related to pathways including FOXA2/FOXA3 transcription factor networks, RNA-Polymerases Transcription Regulation and lipid metabolism, while ICI/G15 inhibited transcripts affected pathways related to apoptosis, erythropoietin signaling, metabolic effects through the citric acid cycle, IL-4 and IL-5 mediated events and homologous DNA recombination. Finally, we review the current literature of GPER1 actions, in view of our results of ER-dependent and independent GPER1-modified pathways. | [George Notasa, Marilena Kampaa, Vassiliki Pelekanoua b, Elias Castanasa] | Steroids | | |
| sciencedirectS1549963411005302 | Nanoresonator chip-based RNA sensor strategy for detection of circulating tumor cells: response using PCA3 as a prostate cancer marker | There is widespread interest in circulating tumor cells (CTCs) in blood. Direct detection of CTCs (often < 1/mL) is complicated by a number of factors, but the presence of ∼103 to 104 copies of target RNA per CTC, coupled with simple enrichments, can greatly increase detection capability. In this study we used resonance frequency shifts induced by mass-amplifying gold nanoparticles to detect a hybridization sandwich bound to functionalized nanowires. We selected PCA3 RNA as a marker for prostate cancer, optimized antisense binding sites, and defined conditions allowing single nucleotide mismatch discrimination, and used a hybrid resonator integration scheme, which combines elements of top-down fabrication with strengths of bottom-up fabrication, with a view to enable multiplexed sensing. Bound mass calculated from frequency shifts matched mass estimated by counting gold nanoparticles. This represents the first demonstration of use of such nanoresonators, which show promise of both excellent specificity and quantitative sensitivity. | [James A. Sioss PhDa, Rustom Bhiladvala PhDb c 1, Weihua Pan MSd, Mingwei Li PhDb c 2, Susan Patrick BSd, Ping Xin BSd, Stacey L. Dean PhDa, Christine D. Keating PhDa, Theresa S. Mayer PhDb c, Gary A. Clawson PhD MDc d] | Nanomedicine: Nanotechnology, Biology and Medicine | | |
| sciencedirectS0378113511004093 | Adaptation to the chicken intestine in Salmonella Enteritidis PT4 studied by transcriptional analysis | The transcriptional changes that occurred in Salmonella enterica serovar Enteritidis during colonization of the alimentary tract of newly hatched chickens were studied. A whole genome oligonucleotide microarray was used to compare the expression pattern with that from bacteria cultured in nutrient broth in vitro. Amongst other changes Salmonella Pathogenicity Island (SPI)-1, SPI-2 and SPI-5 genes were up-regulated in vivo suggesting a close association with the mucosa during colonization. Particular attention was paid to genes associated with metabolism of dicarboxylic acids and to responses to high osmolarity. Association between the colonization phenotype and gene mutations indicated that the latter was more important as a contribution to the colonization phenotype. | [A.A. Dhawi1, A. Elazomi, M.A. Jones, M.A. Lovell, H. Li, R.D. Emes, P.A. Barrow] | Veterinary Microbiology | 21 November 2011 | |
| sciencedirectS0006295211006563 | Targeting microRNAs involved in human diseases: A novel approach for modification of gene expression and drug development | The identification of all epigenetic modifications (i.e. DNA methylation, histone modifications and expression of noncoding RNAs such as microRNAs) involved in gene regulation is one of the major steps forward for understanding human biology in both normal and pathological conditions and for development of novel drugs. In this context, microRNAs play a pivotal role. This review article focuses on the involvement of microRNAs in the regulation of gene expression, on the possible role of microRNAs in the onset and development of human pathologies, and on the pharmacological alteration of the biological activity of microRNAs. RNA and DNA analogs, which can selectively target microRNAs using Watson–Crick base pairing schemes, provide a rational and efficient way to modulate gene expression. These compounds, termed antago-miR or anti-miR have been described in many examples in the recent literature and have proved to be able to perform regulatory as well as therapeutic functions. Among these, a still not fully exploited class is that of peptide nucleic acids (PNAs), promising tools for the inhibition of miRNA activity, with important applications in gene therapy and in drug development. PNAs targeting miR-122, miR-155 and miR-210 have already been developed and their biological effects studied both in vitro and in vivo. | [Roberto Gambaria b, Enrica Fabbria, Monica Borgattia, Ilaria Lamprontia, Alessia Finottia, Eleonora Brognaraa, Nicoletta Bianchia, Alex Manicardic, Rosangela Marchellic, Roberto Corradinic] | Biochemical Pharmacology | 15 November 2011 | |
| sciencedirectS0012160611012024 | Gene expression profiling at early organogenesis reveals both common and diverse mechanisms in foregut patterning | The thyroid and lungs originate as neighboring bud shaped outgrowths from the midline of the embryonic foregut. When and how organ specific programs regulate development into structures of distinct shapes, positions and functions is incompletely understood. To characterize, at least in part, the genetic basis of these events, we have employed laser capture microdissection and microarray analysis to define gene expression in the mouse thyroid and lung primordia at E10.5. By comparing the transcriptome of each bud to that of the whole embryo as well as to each other, we broadly describe the genes that are preferentially expressed in each developing organ as well as those with an enriched expression common to both. The results thus obtained provide a valuable resource for further analysis of genes previously unrecognized to participate in thyroid and lung morphogenesis and to discover organ specific as well as common developmental mechanisms. As an initial step in this direction we describe a regulatory pathway involving the anti-apoptotic gene Bcl2 that controls cell survival in early thyroid development. | [Henrik Fagmana 1 2, Elena Amendolaa b 1 3, Luca Parrilloa, Pietro Zoppolia, Pina Marottaa, Marzia Scarfòa, Pasquale De Lucab, Denise Pires de Carvalhoc 4, Michele Ceccarellia d, Mario De Felicea c, Roberto Di Lauroa c] | Developmental Biology | 15 November 2011 | |
| sciencedirectS0012160611011973 | Genesis of muscle fiber-type diversity during mouse embryogenesis relies on Six1 and Six4 gene expression | Adult skeletal muscles in vertebrates are composed of different types of myofibers endowed with distinct metabolic and contraction speed properties. Genesis of this fiber-type heterogeneity during development remains poorly known, at least in mammals. Six1 and Six4 homeoproteins of the Six/sine oculis family are expressed throughout muscle development in mice, and Six1 protein is enriched in the nuclei of adult fast-twitch myofibers. Furthermore, Six1/Six4 proteins are known to control the early activation of fast-type muscle genes in myocytes present in the mouse somitic myotome. Using double Six1:Six4 mutants (SixdKO) to dissect in vivo the genesis of muscle fiber-type heterogeneity, we analyzed here the phenotype of the dorsal/epaxial muscles remaining in SixdKO. We show by electron microscopy analysis that the absence of these homeoproteins precludes normal sarcomeric organization of the myofiber leading to a dystrophic aspect, and by immunohistochemistry experiments a deficiency in synaptogenesis. Affymetrix transcriptome analysis of the muscles remaining in E18.5 SixdKO identifies a major role for these homeoproteins in the control of genes that are specifically activated in the adult fast/glycolytic myofibers, particularly those controlling Ca2+ homeostasis. Absence of Six1 and Six4 leads to the development of dorsal myofibers lacking expression of fast-type muscle genes, and mainly expressing a slow-type muscle program. The absence of restriction of the slow-type program during the fetal period in SixdKO back muscles is associated with a decreased HDAC4 protein level, and subcellular relocalization of the transcription repressor Sox6. Six genes thus behave as essential global regulators of muscle gene expression, as well as a central switch to drive the skeletal muscle fast phenotype during fetal development. | [Anne-Françoise Richarda b, Josiane Demignona b, Iori Sakakibaraa b, Julien Pujola b, Maryline Faviera b, Laure Strochlicc, Fabien Le Granda b, Nicolas Sgariotoa b, Anthony Guerneca b, Alain Schmitta b, Nicolas Cagnardd, Ruijin Huange, Claire Legayc, Isabelle Guillet-Deniaua b, Pascal Mairea b] | Developmental Biology | 15 November 2011 | |
| sciencedirectS0264410X11017580 | Pneumococcal sequence type replacement among American Indian children: A comparison of pre- and routine-PCV7 eras | BackgroundMulti-locus sequence typing (MLST) of pneumococcal isolates collected during an efficacy trial of the 7-valent pneumococcal conjugate vaccine (PCV7) among Navajo and White Mountain Apache children from 1998 to 2000 showed a non-differential expansion of pre-existing sequence types (STs) and only one capsule-switching event in the PCV7-randomized communities. PCV7 was introduced as a routine infant vaccine in October 2000. We assessed variability in PCV7 effectiveness and mechanisms of ST replacement after prolonged routine PCV7 use.MethodsWe applied MLST to 267 non-vaccine type pneumococcal carriage and invasive disease isolates from Navajo and White Mountain Apache children from 2006 to 2008, and compared them to those from 1998 to 2000. Microarray was used to confirm capsule switching events.ResultsThe primary mechanism of ST replacement among Navajo and White Mountain Apache children was expansion of existing STs, although introduction of new STs was an important secondary mechanism. ST199, a majority being serotype 19A, was the most common ST in both eras. Only ST193 (serotype 21) was preferentially expanding in the PCV7 era. Three examples of capsule switching were identified. No variability in vaccine effectiveness by ST was observed.ConclusionWe did not observe an influence of ST on PCV7 serotype-specific effectiveness, although some STs may be favored in replacement. | [Jennifer R. Scotta, William P. Hanageb, Marc Lipsitchc, Eugene V. Millard, Lawrence H. Moultone, Jason Hindsf, Raymond Reida, Mathuram Santoshama, Katherine L. O’Briena] | Vaccine | | |
| sciencedirectS1878875011010321 | Low-Level Amplification of Oncogenes Correlates Inversely with Age for Patients with Nontypical Meningiomas | BackgroundThis study sought to identify genes in nontypical meningiomas with gains in copy number (CN) that correlate with earlier age of onset, an indicator of aggressiveness.MethodsAmong 94 adult patients, 91 had 105 meningiomas that were histologically confirmed. World Health Organization grades I (typical), II (atypical), and III (anaplastic) were assigned to tumors in 76, 14, and 1 patient, respectively. Brain invasion indicated that two World Health Organization grade I meningiomas were biologically atypical. DNA from 15 invasive/atypical/anaplastic meningiomas and commercial normal DNA were analyzed with multiplex ligation dependent probe amplification. The CN ratios (fold differences from normal) for 78 genes were determined. The CN ratio was defined as [tumor CN]/[normal CN] for each gene to normalize results.ResultsCharacteristic gene losses (CN ratio < 0.75) occurred in >50% of the invasive/atypical/anaplastic meningiomas at 22q11, 1p34.2, and 1p22.1 loci. Gains (CN ratio ≥ 2.0) occurred in each tumor for 2 or more of 19 genes. Each of the 19 genes' CN ratio was ≥2.0 in multiple tumors, and their collective sums (up to 49.1) correlated inversely with age (r = −0.72), minus an outlier. In patients ≤55 versus >55 years, 5 genes (BIRC2, BRAF, MET, NRAS, and PIK3CA) individually exhibited significantly higher CN ratios (P < 0.05) or a trend for them (P < 0.09), with corrections for multiple comparisons, and their sums correlated inversely with age (r = −0.74).ConclusionsLow levels of amplification for selected oncogenes in invasive/atypical/anaplastic meningiomas were higher in younger adults, with the CN gains potentially underlying biological aggressiveness associated with early tumor development. | [Marie E. Beckner1, Raghuram Sampath2, Ashley B. Flowers5, Kristopher Katira5, Dwain D'Souza3, Shashikant Patil2, Raj B. Patel5, Mary L. Nordberg4 6 7, Anil Nanda2] | World Neurosurgery | | |
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| sciencedirectS0888754311001583 | Differential global gene expression in cystic fibrosis nasal and bronchial epithelium | Respiratory epithelium is the target of therapies, such as gene therapy, for cystic fibrosis (CF) lung disease. To determine the usefulness of the nasal epithelium as a pre-screen for lung-directed therapies, we profiled gene expression in CF and non-CF nasal and bronchial epithelium samples using Illumina HumanRef-8 Expression BeadChips. 863 genes were differentially expressed between CF and non-CF bronchial epithelium but only 15 were differentially expressed between CF and non-CF nasal epithelium ( ≥ 1.5-fold, P ≤ 0.05). The most enriched pathway in CF bronchial epithelium was inflammatory response, whereas in CF nasal epithelium it was amino acid metabolism. We also compared nasal and bronchial epithelium in each group and identified differential expression of cellular movement genes in CF patients and cellular growth genes in non-CF subjects. We conclude that CF and non-CF nasal and bronchial epithelium are transcriptionally distinct and CF nasal epithelium is not a good surrogate for the lung respiratory epithelium. | [Varrie Ogilviea e, Margaret Passmorea e, Laura Hyndmana e, Lisa Jonesa e, Barbara Stevensona e, Abigail Wilsona e, Heather Davidsona e, Robert R. Kitchend, Robert D. Graya e, Pallav Shahb c, Eric W. Altonb e, Jane C. Daviesb c e, David J. Porteousa e, A. Christopher Boyda e] | Genomics | November 2011 | |
| sciencedirectS0090825811006305 | Analysis of differential diagnostic gene expression profiles in uterine leiomyoma and leiomyosarcoma | | [I.K. Dimitrova, P. Ramanathan, M.C. Neville, A.P. Bradford] | Gynecologic Oncology | November 2011 | |
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| sciencedirectS0162013411001279 | Up-regulation of NF-kB-sensitive miRNA-125b and miRNA-146a in metal sulfate-stressed human astroglial (HAG) primary cell cultures | Micro RNAs (miRNAs) constitute a unique class of small, non-coding ribonucleic acids (RNAs) that regulate gene expression at the post-transcriptional level. The presence of two inducible miRNAs, miRNA-125b and miRNA-146a, involved in respectively, astroglial cell proliferation and in the innate immune and inflammatory response, is significantly up-regulated in human neurological disorders including Alzheimer's disease (AD). In this study we analyzed abundances miRNA-125b and miRNA-146a in magnesium-, iron-, gallium, and aluminum-sulfate-stressed human-astroglial (HAG) cells, a structural and immune-responsive brain cell type. The combination of iron- plus aluminum-sulfate was found to be significantly synergistic in up-regulating reactive oxygen species (ROS) abundance, NF-?B-DNA binding and miRNA-125b and miRNA-146a expression. Treatment of metal-sulfate stressed HAG cells with the antioxidant phenyl butyl nitrone (PBN) or the NF-?B inhibitors curcumin, the metal chelator-anti-oxidant pyrollidine dithiocarbamate (PDTC), or the resveratrol analog CAY10512, abrogated both NF-?B signaling and induction of these miRNAs. Our observations further illustrate the potential of physiologically relevant amounts of aluminum and iron sulfates to synergistically up-regulate specific miRNAs known to contribute to AD-relevant pathogenetic mechanisms, and suggest that antioxidants or NF-?B inhibitors may be useful to quench metal-sulfate triggered genotoxicity. | [Aileen I. Poguea b 1, Maire E. Percyc d e, Jian-Guo Cuia b, Yuan Yuan Lia b, S. Bhattacharjeeb, James M. Hilla b, Theodore P.A. Kruckc d e, Yuhai Zhaof, Walter J. Lukiwa b c] | Journal of Inorganic Biochemistry | November 2011 | |
| sciencedirectS0162013411002078 | Aluminium and human breast diseases | The human breast is exposed to aluminium from many sources including diet and personal care products, but dermal application of aluminium-based antiperspirant salts provides a local long-term source of exposure. Recent measurements have shown that aluminium is present in both tissue and fat of the human breast but at levels which vary both between breasts and between tissue samples from the same breast. We have recently found increased levels of aluminium in noninvasively collected nipple aspirate fluids taken from breast cancer patients (mean 268 ± 28 ?g/l) compared with control healthy subjects (mean 131 ± 10 ?g/l) providing evidence of raised aluminium levels in the breast microenvironment when cancer is present. The measurement of higher levels of aluminium in type I human breast cyst fluids (median 150 ?g/l) compared with human serum (median 6 ?g/l) or human milk (median 25 ?g/l) warrants further investigation into any possible role of aluminium in development of this benign breast disease. Emerging evidence for aluminium in several breast structures now requires biomarkers of aluminium action in order to ascertain whether the presence of aluminium has any biological impact. To this end, we report raised levels of proteins that modulate iron homeostasis (ferritin, transferrin) in parallel with raised aluminium in nipple aspirate fluids in vivo, and we report overexpression of mRNA for several S100 calcium binding proteins following long-term exposure of MCF-7 human breast cancer cells in vitro to aluminium chlorhydrate. | [P.D. Darbrea, D. Pugazhendhia, F. Mannellob] | Journal of Inorganic Biochemistry | November 2011 | |
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| sciencedirectS0892036211001905 | Trimethyltin chloride (TMT) neurobehavioral toxicity in embryonic zebrafish | Trimethyltin chloride (TMT) is a neurotoxicant that is widely present in the aquatic environment, primarily from the manufacture of PVC plastic, but few studies have evaluated aquatic neurotoxicity. We have examined TMT dose-dependent malformation and neurobehavioral toxicity in the embryonic zebrafish model. Exposure of embryos to TMT (0–10 ?M) from 48 to 72 hours post fertilization (hpf) elicited a concentration-related increase (0–100%) in malformation incidence with an EC25 of 5.55 ?M. TMT also significantly modulated the frequency of tail flexion, the earliest motor behavior observed in developing zebrafish, and the ability to respond to a mechanical tail touch. Exposure to 5 ?M TMT from 48 to 72 hpf modulated the photomotor response at 4 and 5 days post fertilization and significantly promoted apoptosis in the tail. Our study demonstrates the morphological and behavioral sensitivity of the developing zebrafish to TMT and establishes a platform for future identification of the affected pathways and chemical modulators of TMT toxicity. | [Jiangfei Chena, Changjiang Huanga, Lidan Zhenga, Michael Simonichb, Chenglian Baia, Robert Tanguaya b, Qiaoxiang Donga] | Neurotoxicology and Teratology | November–December 2011 | |
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| sciencedirectS0003269711003939 | Reference genes for the relative quantification of microRNAs in renal cell carcinomas and their metastases | To obtain accurate results in miRNA expression changes between different sample sets using real-time quantitative polymerase chain reaction (RT-qPCR) analyses, normalization to reference genes that are stably expressed across the sample sets is generally used. A literature search of miRNA expression studies in renal cell carcinoma (RCC) proved that non-miRNAs such as small RNAs or mRNAs have most frequently been used without preceding validation of their suitability. In this study, the most stably expressed miRNAs were ascertained from microarray-based data of miRNA expression in nonmalignant and malignant samples from clear cell RCC and from corresponding distant RCC metastases using the geNorm and NormFinder algorithms. Validation experiments with RT-qPCR were performed for the four best-ranked miRNAs (miR-28, miR-103, miR-106a, miR-151) together with the small RNU6B, RNU44, and RNU48 mostly described in literature. miR-28, miR-103, miR-106a, and RNU48 were proved as the most stably expressed genes. miR-28 is recommended as normalizer if only a single reference gene can be used, while the combinations of miR-28 and miR-103 or of miR-28, miR-103, and miR-106a, respectively, are preferred. RNU6B most frequently used as normalizer in miRNA expression studies should be abandoned in order to avoid misleading results. | [Zofia Wotschofskya b c, Helmuth-Alexander Meyerb d, Monika Jungb, Annika Fendlera b c, Ina Wagnere, Carsten Stephanb, Jonas Buschb, Andreas Erbersdoblerf g, Alexander C. Dischh, Hans-Joachim Mollenkopfe, Klaus Jungb c] | Analytical Biochemistry | 15 October 2011 | |
| sciencedirectS0006291X11015439 | NHR-23 dependent collagen and hedgehog-related genes required for molting | NHR-23, a conserved member of the nuclear receptor family of transcription factors, is required for normal development in Caenorhabditis elegans where it plays a critical role in growth and molting. In a search for NHR-23 dependent genes, we performed whole genome comparative expression microarrays on both control and nhr-23 inhibited synchronized larvae. Genes that decreased in response to nhr-23 RNAi included several collagen genes. Unexpectedly, several hedgehog-related genes were also down-regulated after nhr-23 RNAi. A homozygous nhr-23 deletion allele was used to confirm the RNAi knockdown phenotypes and the changes in gene expression. Our results indicate that NHR-23 is a critical co-regulator of functionally linked genes involved in growth and molting and reveal evolutionary parallels among the ecdysozoa. | [Nathaniel A. Kounsa, Johana Nakielnaa, Frantisek Behenskya, Michael W. Krauseb, Zdenek Kostroucha, Marta Kostrouchovaa] | Biochemical and Biophysical Research Communications | 7 October 2011 | |
| sciencedirectS187493991100174X | Prerequisites, performance and profits of transcriptional profiling the abiotic stress response ? | During the last decade, microarrays became a routine tool for the analysis of transcripts in the model plant Arabidopsis thaliana and the crop plant species rice, poplar or barley. The overwhelming amount of data generated by gene expression studies is a valuable resource for every scientist. Here, we summarize the most important findings about the abiotic stress responses in plants. Interestingly, conserved patterns of gene expression responses have been found that are common between different abiotic stresses or that are conserved between different plant species. However, the individual histories of each plant affect the inter-comparability between experiments already before the onset of the actual stress treatment. This review outlines multiple aspects of microarray technology and highlights some of the benefits, limitations and also pitfalls of the technique. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress. | [Joachim Kilian, Florian Peschke, Kenneth W. Berendzen, Klaus Harter, Dierk Wanke] | Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms | | |
| sciencedirectS0142961211005989 | Modulation of the immune-related gene responses to protect mice against Japanese encephalitis virus using the antimicrobial peptide, tilapia hepcidin 1-5 | Japanese encephalitis virus (JEV), a neurotropic flavivirus, is one of the major causes of acute encephalitis in humans. After infection, it is commonly associated with inflammatory reactions and neurological disease. There is still no effective antiviral drug available against Japanese encephalitis virus infection. Recently, a number of investigators found that antimicrobial peptide (AMPs) present a broad range of biological activities including antimicrobial and immunomodulatory activities. In this study, we found that an AMP, tilapia hepcidin (TH)1-5, caused no harm to either cells or test animals during the test course and could control JEV viral infection in BHK-21 cells. Mice co-injected with TH1-5/JEV and subsequently subjected to JEV re-challenge survived and behaved normally. The neuroprotective effects were associated with marked decreases in: (i) the viral load and viral replication within the brain, (ii) neuronal death, and (iii) secondary inflammation resulting from microglial activation. TH1-5 was also determined to enhance adaptive immunity by elevating levels of anti-JEV-neutralizing antibodies in the serum. The microarray data also showed that TH1-5 modulated Socs-6, interleukin (IL)-6, Toll-like receptor (TLR)-1, TLR-7, caspase-4, interferon (IFN)-?1, ATF-3, and several immune-responsive genes to protect mice against JEV infection. In addition, TH1-5 was confirmed to modulate the expressions of several proinflammatory and immune-responsive genes, such as IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, tumor necrosis factor (TNF)-?, IFN-? and monocyte chemoattractant protein (MCP)-1 at both the transcriptional and translational levels in JEV-infected mice. In conclusion, our findings provide mechanistic insights into the actions of TH1-5 against JEV. Results from our in vivo and in vitro experiments clearly indicate that TH1-5 has antiviral, neuroprotective, anti-inflammatory, and immunomodulatory activities. Furthermore, TH1-5 successfully reduced the severity of disease induced by JEV. Our results point out that TH1-5 is a promising candidate for further development as an antiviral agent against JEV infection. | [Han-Ning Huanga, Venugopal Rajanbabub, Chieh-Yu Panb, Yi-Lin Chanc, Cho-Fat Huid, Jyh-Yih Chenb, Chang-Jer Wua] | Biomaterials | October 2011 | |
| sciencedirectS0142961211007034 | The induction of epigenetic regulation of PROS1 gene in lung fibroblasts by gold nanoparticles and implications for potential lung injury | Advances in nanotechnology have given rise to the rapid development of novel applications in biomedicine. However, our understanding in the risks and health safety of nanomaterials is still not complete and various investigations are ongoing. Here, we show that gold nanoparticles (AuNPs) significantly altered the expression of 19 genes in human fetal lung fibroblasts (using the Affymetrix Human Gene 1.0 ST Array). Among the differentially expressed genes, up-regulation of microRNA-155 (miR-155) was observed concomitant with down-regulation of the PROS1 gene. Silencing of miR-155 established PROS1 as its possible target gene. DNA methylation profiling analysis of the PROS1 gene revealed no changes in the methylation status of this gene in AuNP-treated fibroblasts. At the ultrastructural level, chromatin condensation and reorganization was observed in the nucleus of fibroblasts exposed to AuNPs. The findings provide further insights into the molecular mechanisms underlying toxicity of AuNPs and their impact on epigenetic processes. | [Cheng-Teng Nga b, S. Thameem Dheena, Wai-Cheong G. Yipa, Choon-Nam Ongc, Boon-Huat Baya, Lin-Yue Lanry Yungb] | Biomaterials | October 2011 | |
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| sciencedirectS0012160611011377 | Kruppel-like factor 5 is required for formation and differentiation of the bladder urothelium | Kruppel-like transcription factor 5 (Klf5) was detected in the developing and mature murine bladder urothelium. Herein we report a critical role of KLF5 in the formation and terminal differentiation of the urothelium. The ShhGfpCre transgene was used to delete the Klf5floxed alleles from bladder epithelial cells causing prenatal hydronephrosis, hydroureter, and vesicoureteric reflux. The bladder urothelium failed to stratify and did not express terminal differentiation markers characteristic of basal, intermediate, and umbrella cells including keratins 20, 14, and 5, and the uroplakins. The effects of Klf5 deletion were unique to the developing bladder epithelium since maturation of the epithelium comprising the bladder neck and urethra was unaffected by the lack of KLF5. mRNA analysis identified reductions in Ppar?, Grhl3, Elf3, and Ovol1expression in Klf5 deficient fetal bladders supporting their participation in a transcriptional network regulating bladder urothelial differentiation. KLF5 regulated expression of the mGrhl3 promoter in transient transfection assays. The absence of urothelial Klf5 altered epithelial–mesenchymal signaling leading to the formation of an ectopic alpha smooth muscle actin positive layer of cells subjacent to the epithelium and a thinner detrusor muscle that was not attributable to disruption of SHH signaling, a known mediator of detrusor morphogenesis. Deletion of Klf5 from the developing bladder urothelium blocked epithelial cell differentiation, impaired bladder morphogenesis and function causing hydroureter and hydronephrosis at birth. | [Sheila M. Bella, Liqian Zhanga, Angela Mendellb, Yan Xua, Hans Michael Haitchia 1, James L. Lessardb, Jeffrey A. Whitsetta] | Developmental Biology | 1 October 2011 | |
| sciencedirectS0269749111002193 | Global gene expression profile induced by the UV-filter 2-ethyl-hexyl-4-trimethoxycinnamate (EHMC) in zebrafish (Danio rerio) | Residues of the UV-filter 2-ethyl-hexyl-4-trimethoxycinnamate (EHMC) are ubiquitously found in aquatic biota but potential adverse effects in fish are fairly unknown. To identify molecular effects and modes of action of EHMC we applied a gene expression profiling in zebrafish using whole genome microarrays. Transcriptome analysis and validation of targeted genes were performed after 14 days of exposure of male zebrafish. Concentrations of 2.2 ?g/L and 890 ?g/L EHMC lead to alteration of 1096 and 1137 transcripts, respectively, belonging to many pathways. Genes involved in lipid metabolism and estrogenic pathway (vtg1), lipid biosynthesis (ptgds), vitamin A metabolic process (rbp2a), DNA damage and apoptosis (gadd45b), and regulation of cell growth (igfbp1a) were investigated by qRT-PCR analysis in whole body, liver, brain and testis. The analysis showed tissue-specific gene profiles and revealed that EHMC slightly affects the transcription of genes involved in hormonal pathways including vtg1, esr1, esr2b, ar, cyp19b and hsd17?3. | [Sara Zucchia, Daniela M. Oggiera b, Karl Fenta c] | Environmental Pollution | October 2011 | |
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| sciencedirectS1567576911002323 | The regulation of CD4+ T cell immune responses toward Th2 cell development by prostaglandin E2 | As an important immune mediator, PGE2 plays an important role in the immune tolerance, autoimmune diseases, immune regulation and tumor immunotolerance. PGE2 is considered to be a promising candidate for the control of the immune diseases. To further understand the immuno-modulating effects of PGE2 on CD4+ T cells, in vitro investigation was conducted in the present study. The results showed that PGE2 inhibited the proliferation of T cells in vitro in a dose-dependent manner. Gene expression profiling showed that 1716 genes were down regulated and 73 genes were up regulated with a change of 1.5 fold. Several signal transduction pathways were involved, such as TNF-? and NF-kB signaling pathway, T cell receptor signaling pathway, IL-2 signaling pathway, and MAPK pathway. The results showed that PGE2 inhibited IFN-?, TNF-? and IL-4 production by CD4+ T cells 24 h after cell culture. A comparison between IFN-? and IL-4 production showed that PGE2 enhanced the relative ratio of IL-4 to IFN-? in CD4+ T cells culture, and regulated CD4+ T cells toward Th2 cell development. The results of the present study indicated that PGE2 has the potential to treat Th1-mediated inflammatory diseases by regulating CD4+ T cells toward Th2 cell immune response. | [Yu-Shi Baoa 1, Ping Zhangb 1, Ru-Juan Xiea, Mei Wangc, Zhi-Yong Wangd, Zheng Zhouc, Wen-Jing Zhaic, Si-Zhou Fengc, Ming-Zhe Hanc] | International Immunopharmacology | October 2011 | |
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| sciencedirectS0161589011007292 | Migrating Schistosoma japonicum schistosomula induce an innate immune response and wound healing in the murine lung | The migrating schistosomulum is an important stage of the schistosome lifecycle and represents a key target for elimination of infection by natural and vaccine-induced host immune responses. To gain a better understanding of how schistosomes initiate a primary host immune response we have characterised the host lung response to migrating Schistosoma japonicum schistosomula using a combination of histopathology, microarray analysis and real-time PCR. Our findings indicate that the early pulmonary response to these migrating larvae is characteristic of innate inflammation and wound healing. This response is associated with significant up-regulation of several genes with immunoregulatory function including Ch25h, Hmox1 and Retnla which may act to control the nature or magnitude of the inflammatory response to the migrating schistosomula, promoting both parasite and host survival. These findings contribute to our understanding of host–parasite interactions associated with schistosome and, especially, S. japonicum infection, and may aid the future design of novel vaccines that target the lung stage schistosomulum. | [Melissa L. Burkea, Laken McGarveya, Henry J. McSorleya 1, Helle Bielefeldt-Ohmannb, Donald P. McManusa, Geoffrey N. Goberta] | Molecular Immunology | October–November 2011 | |
| sciencedirectS0197458009003571 | Transcriptional profile of Parkinson blood mononuclear cells with LRRK2 mutation | To gain insight into systemic molecular events associated with an age-related neurodegenerative disorder, we compared gene expression patterns in peripheral blood mononuclear cells (PBMCs) sampled from elderly, healthy controls and from Parkinson's disease (PD) patients carrying the most frequently found mutation of the LRRK2 gene (G2019S). A transcriptomic approach enabled us to detect differentially expressed genes and revealed perturbations of pathways known to be involved in PD-related neurodegeneration: the ubiquitin–proteasome system, the mitochondrial oxidation system, inflammation, axonal guidance, calcium signalling and apoptosis. Moreover, alterations of the MAP kinase pathway, the actin cytoskeleton, the ephrin receptor system and vesicular transport – all recently associated with the LRRK2 G2019S mutation pathogenesis – were noted. Furthermore, we acquired new evidences of dysregulation in leukocyte extravasation signalling and immune system pathways in PD. These data show that the G2019S mutation affects the entire body and highlight some of the molecular events observed in the brain. This PBMC transcriptomic approach could be used to better understand neurodegeneration in PD and decipher new pathogenetic mechanisms, even at early stages of the disease. | [Eugénie Muteza b c, Lydie Larvora b, Frédéric Leprêtrea b d, Vincent Mourouxa b, Dorota Hamaleke, Jean-Pierre Kerckaerta d, Jordi Pérez-Turf, Nawal Waucquierc, Christel Vanbesien-Mailliota b g, Aurélie Duflota b, David Devosa b c, Luc Defebvrea b c, Alexandre Kreislera b c, Bernard Frigarde, Alain Destéea b c, Marie-Christine Chartier-Harlina b] | Neurobiology of Aging | October 2011 | |
| sciencedirectS1357272511001725 | Suppression of lung cancer cell invasion and metastasis by connexin43 involves the secretion of follistatin-like 1 mediated via histone acetylation | Although connexin has been recognized as a tumor suppressor in many types of cancer, the underlying mechanisms are poorly understood. We have previously shown that transfection of connexin43 (Cx43) cDNA retarded the growth of a highly metastatic human pulmonary giant cell carcinoma cell line, PG, both in vitro and in vivo. Here, we further demonstrate that the metastasis and invasion, but not the migration, of PG cells are also inhibited following Cx43 transfection. The diminishment of metastasis and invasion is associated with down-regulation of genes including MMP-2, S100A, LAMA4, and HDAC10, as well as up-regulation of genes such as MTSS1 and FSTL1 as revealed by gene chip analysis. Interestingly, the suppression effects of Cx43 are related to secreted factor(s), which are blocked by FSTL1 antibody treatment in a dose-dependent manner. Furthermore, the FSTL1 promoter was shown to be associated with acetylated histones H3 and H4 upon Cx43 transfection. These data suggest that Cx43 inhibits the invasion and metastasis of PG cells by modulating the secretion of FSTL1, which is regulated by histone acetylation. Cx43 may act as a “histone deacetylase inhibitor” to modulate gene expression and subsequent cellular functions in PG cells. | [Wei Zhao, Hai-Bo Han, Zhi-Qian Zhang] | The International Journal of Biochemistry & Cell Biology | October 2011 | |
| sciencedirectS0014299911006297 | Fusion of core pathways reveals a horizontal synergistic mechanism underlying combination therapy | Combination therapies have recently been shown to be more effective than monotherapies that may provide synergistic effects in the treatment of stroke, but its selective mechanism still remains unclear. Based on the median-effect method, the combination therapy of jasminoidin and ursodeoxycholic acid had a synergic effect on reducing the infarct volume. The numbers of up- or down-regulated genes by at least 1.5-fold in the vehicle, jasminoidin, ursodeoxycholic acid, and the combination of jasminoidin and ursodeoxycholic acid treatment groups were 228, 95, 136, and 101, respectively. According to clustering and principal component analysis, the pattern of gene expression in the combination group was similar to that of jasminoidin group rather than ursodeoxycholic acid group. Based on these nine top sequences in the combination group excluding four overlapping pathways (MAPK-ERK, Kitlg, Icam1-Ap1, and prolactin), the jasminoidin group had four (PRLR-STAT1, AcvR2-AcvR1B, ACVR1/2A-SMAD1, GHR-NF-?B) contributing pathways, and the ursodeoxycholic acid group had one (IL-6) contributing pathway. Based on the multiple-pathway-dependent comparison analysis (MPDCA), it may lead to the conclusion that jasminoidin possibly contributes more important pharmacological effect in the combined treatment as jasminoidin regulated 80% of the pathways that the combination group mediated. The study reveals a horizontal synergistic effect by optimizing the fusion of more pathways from the compounds with more contribution to the combination therapy. Rather than selecting compounds only based on experience in the past, this study would give a new insight into the systematic strategies for designing synergistic combination therapies. | [Zhong Wanga, Zhi-Wei Jinga, Cai-Xiu Zhoua, Liang Zhangb, Jing Chengb, Zhan-Jun Zhangc, Jun Liua, Cun-Shuan Xud, Peng-Tao Lie, Yong-Yan Wanga] | European Journal of Pharmacology | 30 September 2011 | |
| sciencedirectS0306452211008049 | Vascular endothelial growth factor C acts as a neurotrophic factor for dopamine neurons in vitro and in vivo | Neurotrophic factors regulate the development and maintenance of the nervous system and protect and repair dopaminergic neurons in animal models of Parkinson's disease (PD). Vascular endothelial growth factors A (VEGF-A) and B have also neurotrophic effects on various types of neurons, including dopaminergic neurons. We examined the ability of the key lymphangiogenic factor VEGF-C to protect dopaminergic cells in vitro and in vivo. The study was initiated by a finding from microarray profiling of Neuro2A-20 cells which revealed up-regulation of VEGF-C by glial cell-line–derived neurotrophic factor (GDNF). Next, we observed that VEGF-C can rescue embryonic dopaminergic neurons and activate the mitogen-activated protein kinase/extracellular signal regulated kinase (MAPK/ERK) pathway in vivo. VEGF receptors 1-2 and co-receptors, neuropilins 1-2, were expressed both in mouse embryonic cultures and adult midbrains. In vivo, VEGF-C had a robust functional effect in the rat unilateral 6-hydroxydopamine (6-OHDA) model of PD and there was a small additive effect on the survival of tyrosine hydroxylase (TH)-positive cells with GDNF. The neuroprotective effect of VEGF-C is most likely due to a combination of direct and indirect neurotrophic effects because, VEGF-C, unlike GDNF, induced also angiogenesis in the striatum following 6-OHDA insult as it did in human umbilical vein endothelial cells (HUVEC). However, we detected activation of astroglia and microglia as well as blood–brain barrier disruption after intracerebral delivery of VEGF-C, raising a concern of its safe usage as a therapeutic molecule. Our results provide evidence of VEGF-C as a neurotrophic factor that influences the dopaminergic system through multiple mechanisms. | [M. Piltonena 1, A. Plankenb 1, O. Leskeläa, T.T. Myöhänena, A.-L. Hänninenb, P. Auvinenb, K. Alitaloc, J.-O. Andressoob, M. Saarmab, P.T. Männistöa] | Neuroscience | | |
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| sciencedirectS1567134811003182 | pknE, a serine/threonine kinase of Mycobacterium tuberculosis modulates multiple apoptotic paradigms | Mycobacterium tuberculosis, an intracellular pathogen that causes tuberculosis has developed multifactorial mechanisms to evade host signaling responses. Apoptosis, an important innate host immune response that clears the invading pathogen is suppressed by M. tuberculosis to gain persistence.Here, we examined the various apoptotic events suppressed by Protein Kinase E, (pknE) a Serine Threonine Protein Kinase (STPK) of M. tuberculosis in macrophages infected with ?pknE, a deletion mutant of pknE vs. the wild type strain H37Rv using microarray. The data showed increased expression of genes involved in apoptosis and chemokines with suppressed pro-inflammatory cytokines, co-stimulatory molecules, arginase1 and iNOS. The microarray data was validated using qRT-PCR, PCR array, oligoGE array, arginase assay and/or ELISA. Furthermore, we analyzed the phosphorylation of Akt that promotes cell survival using western blotting. ?pknE infected macrophages reduced the phosphorylation of Akt that correlates with the observed apoptotic responses.Experiments performed using exogenous nitrate donor, sodium nitro prusside to demonstrate the role of pknE during nitrate stress showed similar apoptotic responses to that of endogenous nitrate stress in ?pknE infected macrophages. Our data confirms the role of pknE in the intra cellular survival of M. tuberculosis by suppressing apoptosis during nitrate stress. | [Dinesh Kumar, Sujatha Narayanan] | Infection, Genetics and Evolution | | |
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| sciencedirectS0306452211007019 | MicroRNA machinery responds to peripheral nerve lesion in an injury-regulated pattern | Recently, functional and potent RNA interference (RNAi) has been reported in peripheral nerve axons transfected with short-interfering RNA (siRNA). In addition, components of RNA-induced silencing complex (RISC) have been identified in axotomized sciatic nerve fibers as well as in regenerating dorsal root ganglia (DRG) neurons in vitro. Based on these observations, and on the fact that siRNA and microRNA (miRNA) share the same effector enzymes, we hypothesized that the endogenous miRNA biosynthetic pathway would respond to peripheral nerve injury. To answer this question, we investigated changes in the expression of miRNA biosynthetic enzymes following peripheral nerve crush injury in mice. Here, we show that several pivotal miRNA biosynthetic enzymes are expressed in an injury-regulated pattern in sciatic nerve in vivo, and in DRG axons in vitro. Moreover, the sciatic nerve lesion induced expression of mRNA-processing bodies (P-bodies), which are the local foci of mRNA degradation in DRG axons. In addition, a group of injury-regulated miRNAs was identified by miRNA microarray and validated by real-time quantitative PCR (qPCR) and in situ hybridization analyses. Taken together, our data support the hypothesis that the peripheral nerve regeneration processes may be regulated by miRNA pathway. | [D. Wua, M. Raafata, E. Paka, S. Hammondb, A.K. Murashova] | Neuroscience | | |
| sciencedirectS0006291X11013660 | Chronic hypoxia upregulates adenosine 2a receptor expression in chromaffin cells via hypoxia inducible factor-2?: Role in modulating secretion | Catecholamine (CAT) release from chromaffin tissue plays an essential role in the fetus which develops in a low O2 environment (hypoxia). To address molecular mechanisms regulating CAT secretion in low O2, we exposed a fetal chromaffin-derived cell line (MAH cells) to chronic hypoxia (CHox; 2% O2, 24 h) and assessed gene expression using microarrays, quantitative RT-PCR, and western blot. CHox caused a dramatic ∼12× upregulation of adenosine A2a receptor (A2aR) mRNA, an effect critically dependent upon hypoxia-inducible factor (HIF)-2? which bound the promoter of the A2aR gene. In amperometric studies, acute hypoxia and high K+ (30 mM) evoked quantal CAT secretion that was enhanced after CHox, and further potentiated during simultaneous A2aR activation by adenosine. A2aR activation also enhanced stimulus-induced rise in intracellular Ca2+ in control, but not HIF-2?-deficient, MAH cells. Thus, A2aR, adenosine, and HIF-2? are key contributors to the potentiation of CAT secretion in developing chromaffin cells during chronic hypoxia. | [Stephen T. Brown, Edison P. Reyes1, Colin A. Nurse] | Biochemical and Biophysical Research Communications | 2 September 2011 | |
| sciencedirectS0142961211005151 | Reprogramming induced pluripotent stem cells in the absence of c-Myc for differentiation into hepatocyte-like cells | Induced pluripotent stem cells (iPSCs) with four reprogramming factors (Oct-4/Sox2/Klf-4/c-Myc) have been shown to differentiate into hepatic lineages. However, it was unclear whether obviation of the c-Myc oncogene in iPSCs affected hepatic differentiation or inhibited in vivo tumor formation. In this study, we demonstrated that iPSCs without c-Myc had the capacity to differentiate into hepatocyte-like cells (iPSC-Heps) with biological functions. As detected using planar-radionuclide imaging and Hoechst labeling assays, these iPSCs and iPSC-Heps tended to mobilize to the injured liver area in thioacetamide (TAA)-treated mice. Intravenous transplantation of both iPSCs and iPSC-Heps but not mouse embryonic fibroblasts (MEFs) reduced the hepatic necrotic area, improved liver functions, and rescued TAA-treated mice from lethal acute hepatic failure (AHF). In addition, microarray-based bioinformatics and quantitative RT-PCR showed high expression of antioxidant genes in iPSCs and iPSC-Heps compared to MEFs. In vivo and in vitro studies of NAC pretreatment confirmed that iPSCs and iPSC-Heps potentially suppressed ROS production and activated antioxidant enzymes in TAA-injured livers. Six months after transplantation in TAA-treated mice, tumor formation was not seen in non-c-Myc iPSC grafts. Therefore, reprogramming adult somatic cells without c-Myc may prevent oxidative stress-induced damage and provide a safer alternative for hepatic regeneration in AHF. | [Hsin-Yang Lia b f 1, Yueh Chiena g 1, Yi-Jen Chenb f, Szu-Fu Chenb d, Yuh-Lih Changa, Chih-Hung Chianga e, Shaw-Yeu Jengb e, Chia-Ming Changb f, Mong-Lien Wangb c, Liang-Kung Chenb h, Shuen-Iu Hunga c, Teh-Ia Huoa i, Shou-Dong Leeb, Shih-Hwa Chioua b c g] | Biomaterials | September 2011 | |
| sciencedirectS0142961211004984 | The use of nanoimprinted scaffolds as 3D culture models to facilitate spontaneous tumor cell migration and well-regulated spheroid formation | Two-dimensional (2D) cell cultures are essential for drug development and tumor research. However, the limitations of 2D cultures are widely recognized, and a better technique is needed. Recent studies have indicated that a strong physical contact between cells and 2D substrates induces cellular characteristics that differ from those of tumors growing in vivo. 3D cell cultures using various substrates are then developing; nevertheless, conventional approaches have failed in maintenance of cellular proliferation and viability, uniformity, reproducibility, and/or simplicity of these assays. Here, we developed a 3D culture system with inorganic nanoscale scaffolding using nanoimprinting technology (nano-culture plates), which reproduced the characteristics of tumor cells growing in vivo. Diminished cell-to-substrate physical contact facilitated spontaneous tumor cell migration, intercellular adhesion, and multi-cellular 3D-spheroid formation while maintaining cellular proliferation and viability. The resulting multi-cellular spheroids formed hypoxic core regions similar to tumors growing in vivo. This technology allows creating uniform and highly-reproducible 3D cultures, which is easily applicable for microscopic and spectrophotometric assays, which can be used for high-throughput/high-content screening of anticancer drugs and should accelerate discovery of more effective anticancer therapies. | [Yukie Yoshiia b, Atsuo Wakia b c, Kaori Yoshidac, Anna Kakezukac, Maki Kobayashic, Hideo Namikid, Yusei Kurodab, Yasushi Kiyonob, Hiroshi Yoshiie, Takako Furukawaa b, Tatsuya Asaib, Hidehiko Okazawab, Juri G. Gelovanif, Yasuhisa Fujibayashia b] | Biomaterials | September 2011 | |
| sciencedirectS0045653511006692 | Transcriptional profiles induced by the Aryl Hydrocarbon Receptor agonists 2,3,7,8-tetrachlorodibenzo-p-dioxin, 2,3,7,8-tetrachlorodibenzofuran and 2,3,4,7,8-pentachlorodibenzofuran in primary rat hepatocytes | Toxicogenomics was used to examine mRNA expression profiles obtained from primary rat hepatocytes treated for 24 h with 0.01 or 1.0 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), 0.02 or 2.0 nM 2,3,4,7,8-pentachlorodibenzofuran (2,3,4,7,8-PeCDF) and 0.1 or 10 nM 2,3,7,8-tetrachlorodibenzofuran (2,3,7,8-TCDF). The concentrations of 2,3,4,7,8-PeCDF and 2,3,7,8-TCDF were chosen to be equivalent to 2,3,7,8-TCDD’s concentration based on the toxic equivalency factor/toxic equivalent (TEF/TEQ) method for estimating biological potency. 2,3,7,8-TCDD at 1.0 nM altered the expression of 533 genes; 2,3,4,7,8-PeCDF at 2.0 nM altered 182 genes, and 2,3,7,8-TCDF at 10 nM altered 154 genes. Of these, 57 genes were affected by all three congeners. Agglomerative hierarchical clustering revealed distinct congener-dependent gene subclusters. Principal components analyses of the microarray data revealed that these congeners cluster independently of one another. Data presented here demonstrate that equivalent TEQ concentrations of 2,3,7,8-TCDD, 2,3,4,7,8-PeCDF and 2,3,7,8-TCDF, while altering the expression of a small battery of genes in common, also produce substantial congener specific alterations in gene expression. | [J. Craig Rowlandsa, Robert Budinskya, Bhaskar Gollapudia, Raymond Novakb, Mohamed Abdelmegeedb 1, Daniela Cukovicb, Alan Dombkowskib] | Chemosphere | September 2011 | |
| sciencedirectS1744117X11000268 | Genome-wide expression analysis of roxarsone-stimulated growth of broiler chickens (Gallus gallus) | Roxarsone is a commonly used additive in chicken (Gallus gallus) industry. However, little is known on the intrinsic molecular mechanism via which the growth performance of birds improves. This study was therefore performed to investigate the expression profiles of genes induced by roxarsone. Fifty-six broiler chickens were divided into two groups, namely treated and untreated with roxarsone. The treated group was provided a diet of 45.4 mg/kg roxarsone medication and the other group acted as control. Data analysis showed that roxarsone consistently and significantly (P < 0.05) increased chicken growth performance. In addition to this a significant (P < 0.05) increase of arsenic residue in liver has been seen. Microarray expression analysis of 8935 genes in liver showed that 22 genes (10 up- and 12 down-regulated) had altered expression throughout the experimental periods. Two novel genes (GenBank accession no. GU724343 and GU724344) were cloned through rapid amplification of cDNA ends (RACE). Gene GU724343 was predicted to encode an unidentified protein and the second gene GU724344 was presumed to encode a new member of immunoglobulin-like receptor (CHIR) family. Our results suggested for the first time that the role of roxarsone could be mainly to modify the expression levels of cell growth, immunity/defense and energy metabolism associated genes, as a result promoting animal growth. Further research on these genes should help to increase the knowledge of improving animal productivity safely and effectively. | [Changlu Lia b, Xiuli Wanga b 1, Gengyu Wanga, Changxin Wub, Ning Lia] | Comparative Biochemistry and Physiology Part D: Genomics and Proteomics | September 2011 | |
| sciencedirectS0301468111001071 | Isolation and cellular properties of mesenchymal cells derived from the decidua of human term placenta | The clinical promise of cell-based therapies is generally recognized, and has driven an intense search for good cell sources. In this study, we isolated plastic-adherent cells from human term decidua vera, called decidua-derived-mesenchymal cells (DMCs), and compared their properties with those of bone marrow-derived-mesenchymal stem cells (BM-MSCs). The DMCs strongly expressed the mesenchymal cell marker vimentin, but not cytokeratin 19 or HLA-G, and had a high proliferative potential. That is, they exhibited a typical fibroblast-like morphology for over 30 population doublings. Cells phenotypically identical to the DMCs were identified in the decidua vera, and genotyping confirmed that the DMCs were derived from the maternal components of the fetal adnexa. Flow cytometry analysis showed that the expression pattern of CD antigens on the DMCs was almost identical to that on BM-MSCs, but some DMCs expressed the CD45 antigen, and over 50% of them also expressed anti-fibroblast antigen. In vitro, the DMCs showed good differentiation into chondrocytes and moderate differentiation into adipocytes, but scant evidence of osteogenesis, compared with the BM-MSCs. Gene expression analysis showed that, compared with BM-MSCs, the DMCs expressed higher levels of TWIST2 and RUNX2 (which are associated with early mesenchymal development and/or proliferative capacity), several matrix metalloproteinases (MMP1, 3, 10, and 12), and cytokines (BMP2 and TGFB2), and lower levels of MSX2, interleukin 26, and HGF. Although DMCs did not show the full multipotency of BM-MSCs, their higher proliferative ability indicates that their cultivation would require less maintenance. Furthermore, the use of DMCs avoids the ethical concerns associated with the use of embryonic tissues, because they are derived from the maternal portion of the placenta, which is otherwise discarded. Thus, the unique properties of DMCs give them several advantages for clinical use, making them an interesting and attractive alternative to MSCs for regenerative medicine. | [Daisuke Kanematsua, Tomoko Shofudab, Atsuyo Yamamotob, Chiaki Band, Takafumi Uedae, Mami Yamasakic f, Yonehiro Kanemuraa f] | Differentiation | September 2011 | |
| sciencedirectS0147651311001308 | Transcriptional regulatory dynamics of the hypothalamic–pituitary–gonadal axis and its peripheral pathways as impacted by the 3-beta HSD inhibitor trilostane in zebrafish (Danio rerio) | To study mechanisms underlying generalized effects of 3? hydroxysteroid dehydrogenase (HSD3B) inhibition, reproductively mature zebrafish (Danio rerio) were exposed to trilostane at two dosages for 24, 48, or 96 h and their gonadal RNA samples profiled with Agilent zebrafish microarrays. Trilostane had substantial impact on the transcriptional dynamics of zebrafish, as reflected by a number of differentially expressed genes (DEGs) including transcription factors (TFs), altered TF networks, signaling pathways, and Gene Ontology (GO) biological processes. Changes in gene expression between a treatment and its control were mostly moderate, ranging from 1.3 to 2.0 fold. Expression of genes coding for HSD3B and many of its transcriptional regulators remained unchanged, suggesting transcriptional up-regulation is not a primary compensatory mechanism for HSD3B enzyme inhibition. While some trilostane-responsive TFs appear to share cellular functions linked to endocrine disruption, there are also many other DEGs not directly linked to steroidogenesis. Of the 65 significant TF networks, little similarity, and therefore little cross-talk, existed between them and the hypothalamic–pituitary–gonadal (HPG) axis. The most enriched GO biological processes are regulations of transcription, phosphorylation, and protein kinase activity. Most of the impacted TFs and TF networks are involved in cellular proliferation, differentiation, migration, and apoptosis. While these functions are fairly broad, their underlying TF networks may be useful to development of generalized toxicological screening methods. These findings suggest that trilostane-induced effects on fish endocrine functions are not confined to the HPG-axis alone. Its impact on corticosteroid synthesis could also have contributed to some system wide transcriptional changes in zebrafish observed in this study. | [Rong-Lin Wanga, David Bencica, Jim Lazorchaka, Daniel Villeneuveb, Gerald T. Ankleyb] | Ecotoxicology and Environmental Safety | September 2011 | |
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| sciencedirectS0301472X11002785 | Diagnostic microRNAs in myelodysplastic syndrome | ObjectiveThe myelodysplastic syndromes (MDS) are aging-associated disorders characterized by ineffective maturation of hematopoietic elements, which are often diagnostically challenging. This study identifies microRNAs (miRNA) and miRNA targets that might represent diagnostic markers for MDS.Materials and MethodsThis study utilized a total of 42 MDS samples and 45 controls. A discovery set of 20 frozen bone marrow mononuclear cell samples (10 MDS, 10 controls) was profiled on a custom Agilent miRNA microarray. Classifier miRNAs were validated in a separate set of 49 paraffin-embedded particle preparations by real-time polymerase chain reaction (24 MDS, 25 controls). Target prediction analysis was compared to a de novo transcriptional profile of MDS derived from the Microarray Innovations in Leukemia study. c-Myb and Sufu were further investigated by immunohistochemical stains on a set of 26 paraffin-embedded samples.ResultsWe identified 13 miRNAs of interest from the discovery set, 8 of which proved statistically significant on real-time polymerase chain reaction verification. These eight miRNAs were then examined in an independent real-time polymerase chain reaction validation set. Notably, hsa-miR-378, hsa-miR-632, and hsa-miR-636 demonstrated particularly high discrimination between MDS and normal controls. Target prediction identified potential targets of miRNA regulation that correspond to many of the genes that characterize MDS. Immunohistochemical staining performed on a third validation set confirmed that c-Myb and Sufu are differentially expressed in MDS.ConclusionsOur data utilize both discovery and validation sets and two complementary platforms to identify miRNAs associated with MDS. We have analyzed predicted targets and identified c-Myb and Sufu as potential diagnostic markers of MDS. | [Begum Erdogana, Crystal Faceyb, Julianne Qualtieria, Jason Tedescoa, Elizabeth Rinkera, R. Benjamin Isettc, John Tobiasc, Donald A. Baldwinc, James E. Thompsond e, Martin Carrolld, Annette S. Kima b f] | | September 2011 | |
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| sciencedirectS1874778711000055 | No chromosomal clustering of housekeeping genes in the marine chordate Ciona intestinalis | Housekeeping genes, widely expressed genes that are required for the basal function of most cell types, are clustered in the human and worm genomes. This arrangement suggests coordinate control of housekeeping gene expression at the chromosomal level. Here we examined whether this notion is applicable to a marine chordate, Ciona intestinalis. Using microarrays, we analyzed genes that were expressed in 11 organs of the adult, including the neural complex, branchial sac, esophagus, stomach, endostyle, intestine, body-wall muscle, heart, blood cells, ovary and testis. This analysis identified 158 genes that are expressed ubiquitously in these organs. These housekeeping genes could be classified into a range of Gene Ontology categories, in particular, ribosomal protein components. Of these 158 genes, we were able to map 141 genes onto the 14 pairs of the C. intestinalis chromosomes. They were distributed rather evenly over all the chromosomes, except for small clusters containing two or three genes. Therefore, the notion of chromosomal clustering of housekeeping genes is not applicable in this chordate. | [Eiichi Shoguchi, Manabu Fujie, Mayuko Hamada] | Marine Genomics | September 2011 | |
| sciencedirectS0161589011006584 | Molecular profiling of the gilthead sea bream (Sparus aurata L.) response to chronic exposure to the myxosporean parasite Enteromyxum leei | The aim of the present work was to investigate the transcriptome response of gilthead sea bream (Sparus aurata) after challenge with the myxosporean Enteromyxum leei, a wide-spread enteric parasite causing heavy economic losses in Mediterranean sparid farms. This parasite causes severe desquamative enteritis which usually leads to death of the fish, and there are no preventative or curative treatments for this enteromyxosis. After 113 days of exposure to parasite-contaminated effluent, fish were classified into three cohorts: control fish not exposed to parasite, those that were exposed and infected, and those that were exposed but not infected. In order to detect target genes that may be candidates for infective status or resistance, a cDNA microarray containing 18,490 cDNA clones enriched in genes differentially expressed after infection was hybridised with head kidney and intestine samples. In infected fish, 371 and 373 genes were differentially regulated at the >1.5-fold level in intestine and head kidney respectively, whereas in non-infected fish 175 and 501 genes were differentially regulated in these tissues, respectively. A global marked gene down-regulation was evident in infected fish, mainly in genes involved in the immune and acute phase response particularly complement and mannose binding lectin. Microarray analysis demonstrated a complex interplay between host and/or parasite derived proteases and protease inhibitors, apoptosis, cell proliferation and antioxidant defence genes in exposed fish. In the head kidney of non-infected fish a marked depression of genes involved in the acute phase response was evident. By contrast, in the intestine of non-infected fish, interferon-stimulated and MHC class II genes involved in antigen processing and presentation were up-regulated, possibly indicating that an active immune response at the local level is important to avoid infection with or proliferation of the parasite. | [Grace C. Daveya, Josep A. Calduch-Ginerb, Benoit Houeixa, Anita Talbota, Ariadna Sitjà-Bobadillac, Patrick Prunetd, Jaume Pérez-Sánchezb, Michael T. Cairnsa] | Molecular Immunology | September 2011 | |
| sciencedirectS0969996111001926 | Gene expression profiling of peripheral blood leukocytes identifies and validates ABCB1 as a novel biomarker for Alzheimer's disease | Increasing evidence has shown that the immunological reaction of leukocytes plays a crucial role in the development of neurodegenerative disorders. We conducted transcriptome analysis of leukocytes from patients of mild cognitive impairment (MCI), Alzheimer's disease (AD), as well as normal controls (NC) by oligonucleotide microarray. The differentially expressed genes of interest were selected by pathway-based functional enrichment and were then validated in 60 subjects (17 NC, 20 MCI and 23 AD) by quantitative PCR (QRT-PCR). Thirty-four differentially expressed genes between NC and AD were enriched in ATP-binding cassette (ABC) transporters, ascorbate and aldarate metabolism, Gly/Ser/Thr metabolism, transforming growth factor-? signaling, and extracellular matrix (ECM)-receptor interaction pathways (Welch t-test; p < 0.05). Comparison of NC, MCI and AD transcriptomes identified 8 genes significantly associated with purine metabolism and the ABC transporters. Furthermore, 13 out of 18 genes selected from the above lists were successfully validated by QRT-PCR (Mann–Whitney U-test), and only ABCB1 gene exhibited significantly positive correlation with MMSE scores among NC, MCI, and AD subjects (r = 0.3858, p = 0.0011). With a limited number of study population, our study may provide a novel direction for evaluating diagnostic biomarkers in monitoring AD progression. | [Kuang-Den Chena, Po-Tsung Changb, Yueh-Hsin Pingc, Hsin-Chen Leec, Chin-Wei Yeha, Pei-Ning Wangd e] | Neurobiology of Disease | September 2011 | |
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| sciencedirectS0378427411003262 | Integrated miRNA microarray analysis in the context of non-genotoxic rodent hepatocarcinogenesis | | [S. Plummer1, D. Dan1, J. Quinney1, C. Vacchi-Suzzi2, P. Couttet2] | Toxicology Letters | 28 August 2011 | |
| sciencedirectS0003267011000651 | Metabolomic approach based on liquid chromatography coupled to high resolution mass spectrometry to screen for the illegal use of estradiol and progesterone in cattle | Administration of hormonal compounds as growth promoters in livestock farming was banned by Council Directive 93/22/EC, however, this kind of substances are sometimes reported within the framework of European monitoring residue plans. Various analytical methods have been previously developed to screen for their misuse, and they are now especially efficient for monitoring the illegal administration of synthetic and semi-synthetic hormones. Nevertheless, proving an exogenous administration of hormones from natural origin (i.e. estradiol-17? or progesterone) still remains a challenging task for European authorities. As a result of their origin, these target compounds are indeed always present in the analytical matrix, and because the concentration levels of natural steroids are extremely variable from one animal to another, the establishment of reference thresholds appears very difficult. During this preliminary study, metabolomic data was acquired on a high performance liquid chromatography system coupled to high resolution mass spectrometer (HPLC–LTQ-Orbitrap). Serum samples were collected from dairy cows treated or not with sex steroid hormones commonly employed in animal husbandry: estradiol-17? (or its ester estradiol benzoate) and progesterone. After appropriate data processing and multivariate statistical analyses (OPLS-DA), it was possible to highlight significant metabolic modifications in serum consecutively to the administration of estradiol and/or progesterone. Those differences were used to build predictive models able to suspect illegal administration of these hormones in cattle. Potential biomarker candidates of estradiol and/or progesterone were pointed out, that remains to be structurally elucidated. | [Patricia Regala, Sébastien Anizanb, Jean-Philippe Antignacb c, Bruno Le Bizecb, Alberto Cepedaa, Cristina Fentea] | Analytica Chimica Acta | 26 August 2011 | |
| sciencedirectS0012160611009791 | Rex1 (Zfp42) null mice show impaired testicular function, abnormal testis morphology, and aberrant gene expression | Rex1 (Zfp42), GeneID 132625, is a gene whose expression is closely associated with pluripotency/multipotency in both mouse and human embryonic stem cells. To study the function of the murine Rex1 gene in vivo, we have used cre/lox technology to create Rex1(floxed) mice and mice deficient in Rex1 gene function. Rex1−/−males are characterized by an age-associated decrease in sperm counts, abnormal sperm morphology, and mild testicular atrophy. We characterized global patterns of gene expression in primary germ cells by microarray and identified the growth hormone responsive gene, GRTP1, as a transcript present at a 4.5 fold higher level in wild type (WT) compared to Rex1−/− mice. We analyzed immature germ cell (Dazl), proliferating (PCNA), and Sertoli cell populations, and quantitated levels of apoptosis in Rex1−/− as compared to WT testes. We evaluated the expression of proteins previously reported to correlate with Rex1 expression, such as STAT3, phospho-STAT3, p38, and phospho-p38 in the testis. We report a distinct cellular localization of total STAT3 protein in Rex1−/− affected testes. Our data suggest that loss of Rex1 leads to impaired testicular function. | [Naira C. Rezendea b 1, Mi-Young Leea 1, Sébastien Monettec, Willie Markd, Ailan Lua 2, Lorraine J. Gudasa b] | Developmental Biology | 15 August 2011 | |
| sciencedirectS0014482711001881 | The isolated muscle fibre as a model of disuse atrophy: Characterization using PhAct, a method to quantify f-actin | Research into muscle atrophy and hypertrophy is hampered by limitations of the available experimental models. Interpretation of in vivo experiments is confounded by the complexity of the environment while in vitro models are subject to the marked disparities between cultured myotubes and the mature myofibres of living tissues. Here we develop a method (PhAct) based on ex vivo maintenance of the isolated myofibre as a model of disuse atrophy, using standard microscopy equipment and widely available analysis software, to measure f-actin content per myofibre and per nucleus over two weeks of ex vivo maintenance. We characterize the 35% per week atrophy of the isolated myofibre in terms of early changes in gene expression and investigate the effects on loss of muscle mass of modulatory agents, including Myostatin and Follistatin. By tracing the incorporation of a nucleotide analogue we show that the observed atrophy is not associated with loss or replacement of myonuclei. Such a completely controlled investigation can be conducted with the myofibres of a single muscle. With this novel method we can distinguish those features and mechanisms of atrophy and hypertrophy that are intrinsic to the muscle fibre from those that include activities of other tissues and systemic agents. | [William J. Duddy, Tatiana Cohen, Stephanie Duguez, Terence A. Partridge] | Experimental Cell Research | 15 August 2011 | |
| sciencedirectS0378427411001974 | Gene expression profile of terminal end buds in rat mammary glands exposed to diethylstilbestrol in neonatal period | Diethlstilbestrol (DES) is a synthetic estrogen prescribed to several millions of pregnant women worldwide. The risk for breast cancer after age 40 in women prenatally exposed to DES has been reported; however, the precise mechanism of susceptibility to breast cancer remains to be resolved. We investigated the global gene expression profile of terminal end buds (TEBs), the target of carcinogen, in rat mammary glands neonatally exposed to a low- or high-dose DES at postnatal days (PND) 35 and 45, equivalent to the peripubertal stage in humans. In all groups, the number of TEBs gradually increased, peaked at PND35 and decreased at PND49. At PND35 and 49, the low-dose DES-treated group (low-DES group) showed the highest number of TEBs. In the low-DES group at PND35, ?-casein, ?-casein and whey acidic protein (WAP) mRNA expression increased 8.2-fold, 26.1-fold and 13.3-fold, respectively, whereas ?-casein and WAP mRNA decreased 17.6-fold and 27.7-fold, respectively, at PND49. The most significant network revealed by Ingenuity Pathway Analysis (IPA) software showed the relevance of NF-?B in low-DES group. The present findings suggest that the deregulation of mammary gland differentiation and development-related genes could be induced and cause the increased number of terminal duct lobular units (TDLUs) in human mammary glands of DES daughters in a critical period of mammary gland development. | [Yoshihisa Umekitaa, Masakazu Soudaa, Kazuhito Hatanakaa, Taiji Hamadaa, Takako Yoshiokaa, Hiroaki Kawaguchib, Akihide Tanimotoa] | Toxicology Letters | 10 August 2011 | |
| sciencedirectS0166445X11001147 | Transcriptional responses in neonate and adult Daphnia magna in relation to relative susceptibility to genotoxicants | Little information is available on the responses of lower animals to genotoxic chemicals or on their sensitivity for detecting genotoxic chemicals, especially at different life-stages, despite the established use of the water flea Daphnia magna in ecotoxicity testing. Comet assay methodology was developed and applied to daphnid cells but only limited, non-statistically significant responses to the genotoxicants sodium dichromate (0.2–1 ?M), chrysoidine (0.1–2 ?M), and mixtures of benzo-a-pyrene (BaP) and sodium dichromate were found (from 0.01 ?M BaP & 0.1 ?M sodium dichromate to 0.25 ?M BaP & 0.75 ?M sodium dichromate). Transcriptomic analyses using Agilent D. magna oligonucleotide microarrays were undertaken to assess the effect of a mixture of sodium dichromate and BaP (designed to produce both adducted and oxidised DNA) on gene transcription. Neonates (<24 h) and adults (day 7) were exposed for 6 h and 24 h at two combination concentration levels (0.02 ?M BaP & 0.15 ?M sodium dichromate and 0.1 ?M BaP & 0.75 ?M sodium dichromate). The greatest differences in transcriptional profile occurred between adults and neonates. Subsets of the transcriptional profiles distinguished genotoxicant-exposed animals from controls, both for neonates and adults. Higher transcript levels of DNA repair genes were found in adults and adults also displayed significant induction of DNA repair gene transcripts in response to exposure whereas neonates did not. Transcriptional changes in response to genotoxicant exposure proved more sensitive than measurement of DNA strand breaks by the Comet assay and the extensive differences in transcription between adults and neonates emphasized the importance of life stage in toxicant testing with Daphnia. | [Rhiannon M. Davida 1, Vanja Dakicb, Timothy D. Williamsa, Matthew J. Winterc, J. Kevin Chipmana] | Aquatic Toxicology | August 2011 | |
| sciencedirectS153204561100055X | Copper induces Cu-ATPase ATP7A mRNA in a fish cell line, SAF1 | Copper transporting ATPase, ATP7A, is an ATP dependent copper pump present in all vertebrates, critical for the maintenance of intracellular and whole body copper homeostasis. Effects of copper treatment on ATP7A gene expression in fibroblast cells (SAF1) of the sea bream (Sparus aurata) were investigated by qRT-PCR and by a medium density microarray from a closely related species, striped sea bream (Lithognathus mormyrus). To discriminate between the effects of Cu and other metals, SAF1 cells were exposed to sub-toxic levels of Cu, Zn and Cd. Expression of Cu homeostasis genes copper transporter 1 (CTR1), Cu ATPase (ATP7A), Cu chaperone (ATOX1) and metallothionein (MT) together with the oxidative stress markers glutathione reductase (GR) and Cu/Zn superoxide dismutase (CuZn/SOD) were measured 0, 4 and 24 hours post-exposure by qRT-PCR. Microarray was conducted on samples from 4 hours post Cu exposure. Cu, Zn and Cd increased MT and GR mRNA levels, while only Cu increased ATP7A mRNA levels. Microarray results confirmed the effects of Cu on ATP7A and MT and in addition showed changes in the expression of genes involved in protein transport and secretion. Results suggest that ATP7A may be regulated at the transcriptional level directly by Cu and by a mechanism that is different from that exerteted by metals on MT genes. | [Matteo Minghettia, Michael J. Leavera, John B. Taggarta, Elisa Casadeia, Meirav Auslanderb, Moshe Tomb, Stephen G. Georgea] | Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology | August 2011 | |
| sciencedirectS1438422111000063 | Transcriptome profiling of endothelial cells during infections with high and low densities of C. albicans cells | Systemic infections of Candida albicans, the most prevalent fungal pathogen in humans, are on the rise in recent years. However, the exact mode of pathogenesis of this fungus is still not well elucidated. Previous studies using C. albicans mutants locked into the yeast form via gene deletion found that this form was avirulent and did not induce significant differential expression of host genes in vitro. In this study, a high density of C. albicans was used to infect human umbilical vein endothelial cells (HUVEC), resulting in yeast-form infections, whilst a low density of C. albicans resulted in hyphae infections. Transcriptional profiling of HUVEC response to these infections showed that high densities of C. albicans induced a stronger, broader transcriptional response from HUVEC than low densities of C. albicans infection. Many of the genes that were significantly differentially expressed were involved in apoptosis and cell death. In addition, conditioned media from the high-density infections caused a significant reduction in HUVEC viability, suggesting that certain molecules released during C. albicans and HUVEC interactions were capable of causing cell death. This study has shown that C. albicans yeast-forms, at high densities, cannot be dismissed as avirulent, but instead could possibly contribute to C. albicans pathogenesis. | [Crystale S.Y. Lima, Rozita Roslib, Heng-Fong Seowc, Pei-Pei Chonga d] | International Journal of Medical Microbiology | August 2011 | |
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| sciencedirectS0041008X11001669 | Nickel differentially regulates NFAT and NF-?B activation in T cell signaling | Nickel is a potent hapten that induces contact hypersensitivity in human skin. While nickel induces the maturation of dendritic cells via NF-?B and p38 MAPK activation, it also exerts immunosuppressive effects on T cells through an unknown mechanism. To elucidate the molecular mechanisms of its effects on T cells, we examined the effects of NiCl2 on mRNA expression in human CD3+ T cells stimulated with CD3 and CD28 antibodies. Using a DNA microarray and Gene Ontology, we identified 70 up-regulated (including IL-1?, IL-6 and IL-8) and 61 down-regulated (including IL-2, IL-4, IL-10 and IFN-?) immune responsive genes in NiCl2-treated T cells. The DNA microarray results were verified using real-time PCR and a Bio-PlexTM suspension protein array. Suppression of IL-2 and IFN-? gene transcription by NiCl2 was also confirmed using Jurkat T cells transfected with IL-2 or IFN-? luciferase reporter genes. To explore the NiCl2-regulated signaling pathway, we examined the binding activity of nuclear proteins to NFAT, AP-1, and NF-?B consensus sequences. NiCl2 significantly and dose-dependently suppressed NFAT- and AP-1-binding activity, but augmented NF-?B-binding activity. Moreover, NiCl2 decreased nuclear NFAT expression in stimulated T cells. Using Jurkat T cells stimulated with PMA/ionomycin, we demonstrated that NiCl2 significantly suppressed stimulation-evoked cytosolic Ca2+ increases, suggesting that NiCl2 regulates NFAT signals by acting as a blocker of Ca2+ release-activated Ca2+ (CRAC) channels. These data showed that NiCl2 decreases NFAT and increases NF-?B signaling in T cells. These results shed light on the effects of nickel on the molecular regulation of T cell signaling. | [Rumiko Saitoa, Satoshi Hirakawaa b, Hiroshi Oharac, Makoto Yasudad, Tomomi Yamazakid, Shigeaki Nishiid, Setsuya Aibaa] | Toxicology and Applied Pharmacology | 1 August 2011 | |
| sciencedirectS0006291X11011004 | The pattern of gene expression and gene dose profiles of 6-Mercaptopurine- and 6-Thioguanine-resistant human leukemia cells | Exposure of MOLT4 human T-cell leukemia cells to 6-Mercaptopurine (6-MP) and 6-Thioguanine (6-TG) resulted in acquired resistance associated with attenuated expression of the genes encoding concentrative nucleoside transporter 3 (CNT3) and equilibrative nucleoside transporter 2 (ENT2). To identify other alterations at the RNA and DNA levels associated with 6-MP- and 6-TG resistance, we compared here the patterns of gene expression and DNA copy number profiles of resistant sublines to those of the parental wild-type cells. The mRNA levels for two nucleoside transporters were down-regulated in both of the thiopurine-resistant sublines. Moreover, both of these cell lines expressed genes encoding the enzymes of purine nucleotide composition and synthesis, including adenylate kinase 3-like 1 and guanosine monophosphate synthetase at significantly lower levels than wild-type cells. In addition, expression of the mRNA for a specialized DNA polymerase, human terminal transferase encoded by the terminal deoxynucleotidyl transferase (DNTT) gene, was 122- and 93-fold higher in 6-TG- and 6-MP-resistant cells, respectively. The varying responses to 6-MP- and 6-TG observed here may help identify novel cellular targets and modalities of resistance to thiopurines, as well as indicating new potential approaches to individualization therapy with these drugs. | [Hazhar Karima, Jamileh Hashemib, Catharina Larssonb, Ali Moshfeghc, Alan K. Fotoohia c, Freidoun Albertionic] | Biochemical and Biophysical Research Communications | 22 July 2011 | |
| sciencedirectS0955286311000994 | Quercetin accumulates in nuclear structures and triggers specific gene expression in epithelial cells ? | Quercetin is a flavonol modifying a number of cell processes in different cell lines. Here, we present evidence that nonconjugated quercetin enters cells possibly via organic anion transporter polypeptides and quickly accumulates in the nucleus where it concentrates at distinct foci. Furthermore, it induces major transcriptional events with a high number of transcripts being modified over time and about 2200 transcripts being continuously influenced by the agent. The latter transcripts are related to cell cycle and adhesion, xenobiotic metabolism, immune-related factors and transcription. In addition, quercetin up-regulates the expression of estrogen receptors ? and ?. The overall outcome on cell fate is reflected by an inhibition of cell proliferation, cell cycle arrest in the G1 phase and reduction of the cells' migratory potential due to actin cytoskeleton disorganization. Finally, we report that the flavonol modifies the transcription and/or activity of numerous transcription factors. In conclusion, our data support the idea that quercetin may actively accumulate in discrete cell structures and exert more than just antioxidant actions on epithelial cells by regulating mechanisms related to gene transcription. | [George Notasa 1, Artemisia-Phoebe Niflia 1 2, Marilena Kampaa, Vassiliki Pelekanoua 3, Vasileia-Ismini Alexakia, Panayiotis Theodoropoulosb, Joseph Vercauterenc, Elias Castanasa] | The Journal of Nutritional Biochemistry | | |
| sciencedirectS0012160611002478 | Protein deiminases: New players in the developmentally regulated loss of neural regenerative ability | Spinal cord regenerative ability is lost with development, but the mechanisms underlying this loss are still poorly understood. In chick embryos, effective regeneration does not occur after E13, when spinal cord injury induces extensive apoptotic response and tissue damage. As initial experiments showed that treatment with a calcium chelator after spinal cord injury reduced apoptosis and cavitation, we hypothesized that developmentally regulated mediators of calcium-dependent processes in secondary injury response may contribute to loss of regenerative ability. To this purpose we screened for such changes in chick spinal cords at stages of development permissive (E11) and non-permissive (E15) for regeneration. Among the developmentally regulated calcium-dependent proteins identified was PAD3, a member of the peptidylarginine deiminase (PAD) enzyme family that converts protein arginine residues to citrulline, a process known as deimination or citrullination. This post-translational modification has not been previously associated with response to injury. Following injury, PAD3 up-regulation was greater in spinal cords injured at E15 than at E11. Consistent with these differences in gene expression, deimination was more extensive at the non-regenerating stage, E15, both in the gray and white matter. As deimination paralleled the extent of apoptosis, we investigated the effect of blocking PAD activity on cell death and deiminated-histone 3, one of the PAD targets we identified by mass-spectrometry analysis of spinal cord deiminated proteins. Treatment with the PAD inhibitor, Cl-amidine, reduced the abundance of deiminated-histone 3, consistent with inhibition of PAD activity, and significantly reduced apoptosis and tissue loss following injury at E15. Altogether, our findings identify PADs and deimination as developmentally regulated modulators of secondary injury response, and suggest that PADs might be valuable therapeutic targets for spinal cord injury. | [Sigrun Langea, Stefanie Gögela, Kit-Yi Leungb, Bertrand Vernaya, Anthony P. Nicholasc, Corey P. Causeyd, Paul R. Thompsone, Nicholas D.E. Greeneb, Patrizia Ferrettia] | Developmental Biology | 15 July 2011 | |
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| sciencedirectS0034528811002104 | Virulence genes in blaCTX-MEscherichia coli isolates from chickens and humans | The aim of this study was to determine the presence of virulence genes in isolates of CTX-M Escherichia coli from diseased chickens, from healthy chickens and from urinary tract infections in people. Three CTX-M E. coli strains from three different instances of disease in poultry (two of which were E. coli related) were tested for blaCTX-M sequence type and replicon type. Additionally, they were tested for the presence of 56 virulence genes (encoding fimbriae, adhesins, toxins, microcins and iron acquisition genes) using a micro-array. Results were compared to the virulence genes present in isolates from 26 healthy chickens and from 10 people with urinary tract infections. All genes found in isolates from diseased birds, including the astA (heat stable toxin) and tsh (temperature sensitive haemagglutinin) genes which have previously been associated with colibacillosis in chickens, were also present in isolates from healthy birds. However, 6/13 of the virulence genes found were exclusive to isolates from humans. Genes exclusive to chicken isolates included ireA (sidephore receptor), lpfA (long polar fimbriae), mchF (microcin transporter protein) and tsh whilst genes exclusive to human isolates included ctdB (cytolethal distending toxin), nfaE (non-fimbrial adhesion), senB (plasmid encoded enterotoxin) and toxB (toxin B). The results support previous findings that CTX-M E. coli strains in chickens are generally different from those causing disease in humans, but genes such as astA and tsh in isolates from diseased birds with colisepticaemia were also present in isolates from healthy birds. | [Luke Randalla, Guanghui Wua, Neil Phillipsa, Nick Coldhama, Dik Meviusb, Chris Tealea] | Research in Veterinary Science | | |
| sciencedirectS0006291X11009144 | The TCP4 transcription factor of Arabidopsis blocks cell division in yeast at G1 → S transition | The TCP transcription factors control important aspects of plant development. Members of class I TCP proteins promote cell cycle by regulating genes directly involved in cell proliferation. In contrast, members of class II TCP proteins repress cell division. While it has been postulated that class II proteins induce differentiation signal, their exact role on cell cycle has not been studied. Here, we report that TCP4, a class II TCP protein from Arabidopsis that repress cell proliferation in developing leaves, inhibits cell division by blocking G1 → S transition in budding yeast. Cells expressing TCP4 protein with increased transcriptional activity fail to progress beyond G1 phase. By analyzing global transcriptional status of these cells, we show that expression of a number of cell cycle genes is altered. The possible mechanism of G1 → S arrest is discussed. | [Pooja Aggarwal1, Bhavna Padmanabhan, Abhay Bhat, Kavitha Sarvepalli, Parag P. Sadhale, Utpal Nath] | Biochemical and Biophysical Research Communications | 1 July 2011 | |
| sciencedirectS0012160611002582 | The molecular and cellular basis of variable craniofacial phenotypes and their genetic rescue in Twisted gastrulation mutant mice | The severity of numerous developmental abnormalities can vary widely despite shared genetic causes. Mice deficient in Twisted gastrulation (Twsg1−/−) display such phenotypic variation, developing a wide range of craniofacial malformations on an isogenic C57BL/6 strain background. To examine the molecular basis for this reduced penetrance and variable expressivity, we used exon microarrays to analyze gene expression in mandibular arches from several distinct, morphologically defined classes of Twsg1−/− and wild type (WT) embryos. Hierarchical clustering analysis of transcript levels identified numerous differentially expressed genes, clearly distinguishing severely affected and unaffected Twsg1−/− mutants from WT embryos. Several genes that play well-known roles in craniofacial development were upregulated in unaffected Twsg1−/− mutant embryos, suggesting that they may compensate for the loss of TWSG1. Imprinted genes were overrepresented among genes that were differentially expressed particularly between affected and unaffected mutants. The most severely affected embryos demonstrated increased p53 signaling and increased expression of its target, Trp53inp1. The frequency of craniofacial defects significantly decreased with a reduction of p53 gene dosage from 44% in Twsg1−/−p53+/+ pups (N = 675) to 30% in Twsg1−/−p53+/− (N = 47, p = 0.04) and 15% in Twsg1−/−p53−/− littermates (N = 39, p = 0.001). In summary, these results demonstrate that phenotypic variability in Twsg1−/− mice is associated with differential expression of certain developmentally regulated genes, and that craniofacial defects can be partially rescued by reduced p53 levels. We postulate that variable responses to stress may contribute to variable craniofacial phenotypes by triggering differential expression of genes and variable cellular apoptosis. | [Charles J. Billington Jr.a b c, Brandon Nga, Cynthia Forsmana b, Brian Schmidta, Anindya Bagchib, David E. Symerd e f g, Gunnar Schottah, Rajaram Gopalakrishnani, Aaron L. Sarverj, Anna Petryka b] | Developmental Biology | 1 July 2011 | |
| sciencedirectS0160412011000419 | Global gene expression and Ingenuity biological functions analysis on PCBs 153 and 138 induced human PBMC in vitro reveals differential mode(s) of action in developing toxicities | Several reports have indicated that low level of polychlorinated biphenyl (PCB) exposure can adversely affect a multitude of physiological disorders and diseases in in vitro, in vivo, and as reported in epidemiological studies. This investigation is focused on the possible contribution of two most prevalent PCB congeners in vitro in developing toxicities. We used PCBs 138 and 153 at the human equivalence level as model agents to test their specificity in developing toxicities. We chose a global approach using oligonucleotide microarray technology to investigate modulated gene expression for biological effects, upon exposure of PCBs, followed by Ingenuity Pathway Analysis (IPA), to understand the underlying consequence in developing disease and disorders. We performed in vitro studies with human peripheral blood mononuclear cells (PBMC), where PBMC cells were exposed to respective PCBs for 48 h. Overall, our observation on gene expression indicated that PCB produces a unique signature affecting different pathways, specific for each congener. While analyzing these data through IPA, the prominent and interesting disease and disorders were neurological disease, cancer, cardiovascular disease, respiratory disease, as well as endocrine system disorders, genetic disorders, and reproductive system disease. They showed strong resemblances with in vitro, in vivo, and in the epidemiological studies. A distinct difference was observed in renal and urological diseases, organisimal injury and abnormalities, dental disease, ophthalmic disease, and psychological disorders, which are only revealed by PCB 138 exposure, but not in PCB 153. The present study emphasizes the challenges of global gene expression in vitro and was correlated with the results of exposed human population. The microarray results give a molecular mechanistic insight and functional effects, following PCB exposure. The extent of changes in genes related to several possible mode(s) of action highlights the changes in cellular functions and signaling pathways that play major roles. In addition to understanding the pathways related to mode of action for chemicals, these data could lead to the identification of genomic signatures that could be used for screening of chemicals for their potential to cause disease and developmental disorders. | [Somiranjan Ghosha, Shizhu Zanga, Partha S. Mitraa, Svetlana Ghimbovschib, Eric P. Hoffmanb, Sisir K. Duttaa] | Environment International | July 2011 | |
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| sciencedirectS0022282811000915 | Inositol 1,4,5-trisphosphate receptors are essential for the development of the second heart field | Congenital heart defects (CHDs) occur in 0.5–1% of live births, yet the underlying genetic etiology remains mostly unknown. Recently, a new source of myocardial cells, namely the second heart field (SHF), was discovered in the splanchnic mesoderm. Abnormal development of the SHF leads to a spectrum of outflow tract defects, such as persistent truncus arteriosus and tetralogy of Fallot. Intracellular Ca2+ signaling is known to be essential for many aspects of heart biology including heart development, but its role in the SHF is uncertain. Here, we analyzed mice deficient for genes encoding inositol 1,4,5-trisphosphate receptors (IP3Rs), which are intracellular Ca2+ release channels on the endo/sarcoplasmic reticulum that mediate Ca2+ mobilization. Mouse embryos that are double mutant for IP3R type 1 and type 3 (IP3R1−/−IP3R3−/−) show hypoplasia of the outflow tract and the right ventricle, reduced expression of specific molecular markers and enhanced apoptosis of mesodermal cells in the SHF. Gene expression analyses suggest that IP3R-mediated Ca2+ signaling may involve, at least in part, the Mef2C–Smyd1 pathway, a transcriptional cascade essential for the SHF. These data reveal that IP3R type 1 and type 3 may play a redundant role in the development of the SHF. | [Maki Nakazawaa 1, Keiko Uchidaa 1, Megumi Aramakia, Kazuki Kodoa, Chihiro Yamagishia, Takao Takahashia, Katsuhiko Mikoshibab c, Hiroyuki Yamagishia] | Journal of Molecular and Cellular Cardiology | July 2011 | |
| sciencedirectS0141113611000535 | Integration of biochemical, histochemical and toxicogenomic indices for the assessment of health status of mussels from the Tamar Estuary, U.K. | The aim of this study was to examine whether a combination of biochemical, histopathological and toxicogenomic data could be used as a valuable tool for the assessment of biological risk associated with pollutants within the Tamar River and Estuary, S.W. England, U.K. Accordingly, biochemical and histopathological biomarkers (protein carbonyls, lipofuscin, neutral lipids, lysosomal stability [N-acetyl-?-hexosaminidase and neutral red], lysosomal volume, ferric reducing antioxidant power [FRAP] and malonaldehyde [MDA]) and gene expression profiles were assessed in 5 sites from the Tamar River and Estuary (Neal Point, Town Quay, Wilcove, Cremyll Ferry and Whitsand; and a reference site, Trebarwith Strand, N. Cornwall). PAHs were measured in mussel tissue and sediment and metals were measured in mussel tissue only. Data from the biomarkers was integrated into a Mussel Expert System (MES) model to produce a simple assessment of mussel stress. Clear gradients of mussel toxicity were identified by the biomarkers (with the exception of neutral lipids) with the highest impacted animals found furthest up the Tamar, whilst the MES was unable to identify a gradient of effect. Gene expression profiles also indicated a gradient of stress with the greatest number of significantly up- or down- regulated genes found at the uppermost 2 sites. The MES did, however, determine that mussels from all sites, except the reference site, were highly stressed; a conclusion that could not be inferred from the biomarker data alone. It is concluded that the MES is a valuable tool that permits integration and interpretation of complex sets of biomarker data by identifying the biological meaning of biomarker changes. | [J.P. Shawa, F. Donderob, M.N. Moorea, A. Negrib, A. Dagninob, J.W. Readmana, D.R. Lowea, P.E. Frickersa, A. Beesleya, J.E. Thainc, A. Viarengob] | Marine Environmental Research | July 2011 | |
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| sciencedirectS1537189111000589 | Estrogens and selective estrogen receptor modulators regulate gene and protein expression in the mesenteric arteries | Estrogen has both beneficial and detrimental effects on the cardiovascular system. Selective estrogen receptor modulators (SERMs) exhibit partial estrogen agonist/antagonist activity in estrogen target tissues. Gene targets of estrogen and SERMs in the vasculature are not well-known. Thus, the present study tested the hypothesis that estrogens (ethinyl estradiol, estradiol benzoate, and equilin) and SERMs (tamoxifen and raloxifene) cause differential gene and protein expression in the vasculature. DNA microarray and real-time RT-PCR were used to investigate gene expression in the mesenteric arteries of estrogen and SERM treated ovariectomized rats. The genes shown to be differentially expressed included stearoyl-CoA desaturase (SCD), soluble epoxide hydrolase (sEH), secreted frizzled related protein-4 (SFRP-4), insulin-like growth factor-1 (IGF-1), phospholipase A2 group 1B (PLA2-G1B), and fatty acid synthase (FAS). Western blot further confirmed the differential expression of sEH, SFRP-4, FAS, and SCD protein. These results reveal that estrogens and SERMs cause differential gene and protein expression in the mesenteric artery. Consequently, the use of these agents may be associated with a unique profile of functional and structural changes in the mesenteric arterial circulation. | [Connie J. Mark-Kappeler, Douglas S. Martin, Kathleen M. Eyster] | Vascular Pharmacology | July–September 2011 | |
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| sciencedirectS0006291X11008564 | Genes that integrate multiple adipogenic signaling pathways in human mesenchymal stem cells | Adipogenesis is a well-characterized cell differentiation process. A large body of evidence has revealed the core transcription factors and signaling pathways that govern adipogenesis, but cross-talks between these cellular signals and its functional consequences have not been thoroughly investigated. We, therefore, sought to identify genes that are regulated by multiple signaling pathways during adipogenesis of human mesenchymal stem cells. Focusing on the early stage of adipogenesis, microarray analysis and quantitative RT-PCR identified 12 genes whose transcription levels were dramatically affected by the complete adipogenic induction cocktail but not by the cocktail’s individual components. Expression kinetics of these genes indicate diverse mechanisms of transcriptional regulation during adipogenesis. Functional relationships between these genes and adipogenic differentiation were frequently unknown. This study thus provided novel adipogenic gene candidates that likely mediate communications among multiple signaling pathways within human mesenchymal stem cells. | [Tomoya Itoa, So Tsurutaa, Koki Tomitaa, Kunio Kikuchib 1, Takahide Yokoic, Yasunori Aizawaa b] | Biochemical and Biophysical Research Communications | 17 June 2011 | |
| sciencedirectS1383571810000768 | Lack of change in microRNA expression in adult mouse liver following treatment with benzo(a)pyrene despite robust mRNA transcriptional response | Benzo(a)pyrene (BaP) is a mutagenic and carcinogenic environmental contaminant. Metabolic activation of BaP is required for it to exert its mutagenic effects. Metabolism occurs via BaP interaction with the aryl hydrocarbon receptor (AHR) resulting in induction of phase 1 enzymes. Exposure to BaP is expected to cause differential regulation of AHR-responsive genes as well as pathways responding to DNA damage induced by its metabolites. MicroRNAs (miRNAs) are short non-coding molecules that control mRNA levels and protein translation. MiRNA regulation may also be affected by chemical insult. Here we investigate the correlation between hepatic mRNA and miRNA response to BaP in vivo. Mature male mice were orally exposed to 3 daily doses of 150 mg/kg BaP. DNA microarrays were used to profile gene and miRNA expression in the liver 4 and 24 h following the final dose. Despite widespread changes in gene expression (>400 genes) in pathways consistent with the known effects of BaP, we found no changes in miRNA. This was confirmed on two microarray platforms and by qRT-PCR. Analysis of positive controls (2 distinct reference pools) indicated that the Agilent technology could identify differences in miRNA. The effects of sample storage at −80 °C were also compared. We found little effect of prolonged freezing on the technical correlation between samples or on differential expression. Our results are consistent with the lack of response of miRNA in rodent liver to dioxin, another potent AHR-agonist. We conclude that hepatic miRNA in vivo is not directly responsive to BaP exposure. | [Carole Lyn Yauk, Kelly Jackson, Morie Malowany, Andrew Williams] | Mutation Research/Genetic Toxicology and Environmental Mutagenesis | 17 June 2011 | |
| sciencedirectS0012160611002107 | A search for factors specifying tonotopy implicates DNER in hair-cell development in the chick's cochlea ? | The accurate perception of sound frequency by vertebrates relies upon the tuning of hair cells, which are arranged along auditory organs according to frequency. This arrangement, which is termed a tonotopic gradient, results from the coordination of many cellular and extracellular features. Seeking the mechanisms that orchestrate those features and govern the tonotopic gradient, we used expression microarrays to identify genes differentially expressed between the high- and low-frequency cochlear regions of the chick (Gallus gallus). Of the three signaling systems that were represented extensively in the results, we focused on the notch pathway and particularly on DNER, a putative notch ligand, and PTP?, a receptor phosphatase that controls DNER trafficking. Immunohistochemistry confirmed that both proteins are expressed more strongly in hair cells at the cochlear apex than in those at the base. At the apical surface of each hair cell, the proteins display polarized, mutually exclusive localization patterns. Using morpholinos to decrease the expression of DNER or PTP? as well as a retroviral vector to overexpress DNER, we observed disturbances of hair-bundle morphology and orientation. Our results suggest a role for DNER and PTP? in hair-cell development and possibly in the specification of tonotopy. | [Lukasz Kowalik1, A.J. Hudspeth] | Developmental Biology | 15 June 2011 | |
| sciencedirectS0168165611001982 | Redundancy in putrescine catabolism in solvent tolerant Pseudomonas putida S12 | Pseudomonas putida S12 is a promising platform organism for the biological production of substituted aromatic compounds due to its extreme tolerance towards toxic chemicals. Solvent or aromatic stress tolerance may be due to membrane modifications and efflux pumps; however in general, polyamines have also been implicated in stressed cells. Previous transcriptomics results of P. putida strains producing an aromatic compound, or being exposed to the solvent toluene, indicated differentially expressed genes involved in polyamine transport and metabolism. Therefore, the metabolism of the polyamine, putrescine was investigated in P. putida S12, as no putrescine degradation pathways have been described for this strain. Via transcriptome analysis various, often redundant, putrescine-induced genes were identified as being potentially involved in putrescine catabolism via oxidative deamination and transamination. A series of knockout mutants were constructed in which up to six of these genes were sequentially deleted, and although putrescine degradation was affected in some of these mutants, complete elimination of putrescine degradation in P. putida S12 was not achieved. Evidence was found for the presence of an alternative pathway for putrescine degradation involving ?-glutamylation. The occurrence of multiple putrescine degradation routes in the solvent-tolerant P. putida S12 is indicative of the importance of controlling polyamine homeostasis, as well as of the high metabolic flexibility exhibited by this microorganism. | [Luaine Bandounasa b c d, Hendrik Ballerstedta c d, Johannes H. de Windea b c, Harald J. Ruijssenaarsa c d 1] | Journal of Biotechnology | 10 June 2011 | |
| sciencedirectS0168165611001714 | A high-density quantitative nuclease protection microarray platform for high throughput analysis of gene expression | The quantitative nuclease protection assay (qNPA) is a very simple and highly sensitive method for measuring mRNA transcripts, can be used on a variety of sample types, and is amenable to high-throughput sample processing. We have combined the power of the qNPA assay with the density of a DNA microarray to create a qNPA Microarray platform. This platform is compatible with common laboratory equipment: it uses fluorescence-based detection, can be analyzed with common microarray scanners, and is in an SBS footprint with 96-well layout for high-throughput applications. Here, we demonstrate the characteristics of a qNPA Microarray slide that contains up to 1700 gene elements per well. We show that the new platform can reliably detect transcripts at levels as low as 10 fM with median CVs below 12%. On a standardized set of samples, the qNPA Microarray detected the same trends in gene expression as the original qNPA technology, real time qPCR, and Affymetrix GeneChip DNA Microarrays. Given its ease of use, compatibility with multiple sample types, high-throughput capabilities, and its integration with standard laboratory equipment, the qNPA Microarray is a powerful new platform for gene expression research. | [K.M. Bourzaca 1, M.P. Rounsevilleb 1, X. Zaratea, V.S.R.K. Maddulaa b, D.C. Hendersona, J.A. Luckeyc, B. Seligmannb, D.W. Galbraitha d] | Journal of Biotechnology | 10 June 2011 | |
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| sciencedirectS1533002811000120 | Predicting Ulcerative Colitis-Associated Colorectal Cancer Using Reverse-Transcription Polymerase Chain Reaction Analysis | BackgroundWidespread genetic alterations are present not only in ulcerative colitis (UC)-associated neoplastic lesions but also in the adjacent normal colonic mucosa. This suggests that genetic changes in nonneoplastic mucosa might be effective markers for predicting the development of UC-associated cancer (UC-Ca). This study aimed to build a predictive model for the development of UC-Ca based on gene expression levels measured by reverse-transcription polymerase chain reaction (RT-PCR) analysis in nonneoplastic rectal mucosa.Patients and MethodsFifty-three UC patients were examined, of which 10 had UC-Ca and 43 did not (UC-NonCa). In addition to the 40 genes and transcripts previously shown to be predictive for developing UC-Ca in our microarray studies, 149 new genes, reported to be important in carcinogenesis, were selected for low density array (LDA) analysis. The expression of a total of 189 genes was examined by RT-PCR in nonneoplastic rectal mucosa.ResultsWe identified 20 genes showing differential expression in UC-Ca and UC-NonCa patients, including cancer-related genes such as CYP27B1, RUNX3, SAMSN1, EDIL3, NOL3, CXCL9, ITGB2, and LYN. Using these 20 genes, we were able to build a predictive model that distinguished patients with and without UC-Ca with a high accuracy rate of 83% and a negative predictive value of 100%.ConclusionThis predictive model suggests that it is possible to identify UC patients at a high risk of developing cancer. These results have important implications for improving the efficacy of surveillance by colonoscopy and suggest directions for future research into the molecular mechanisms of UC-associated cancer. | [Toshiaki Watanabe1, Takashi Kobunai1 2, Yoko Yamamoto1, Hiroki Ikeuchi3, Keiji Matsuda1, Soichiro Ishihara1, Keijiro Nozawa1, Hisae Iinuma1, Takamitsu Kanazawa4, Toshiaki Tanaka4, Tadashi Yokoyama4, Tsuyoshi Konishi4, Kiyoshi Eshima2, Yohichi Ajioka5, Toshifumi Hibi6, Mamoru Watanabe7, Tetsuichiro Muto8, Hirokazu Nagawa4] | Clinical Colorectal Cancer | June 2011 | |
| sciencedirectS1567133X11000457 | Genes expressed in Atoh1 neuronal lineages arising from the r1/isthmus rhombic lip | During embryogenesis, the rhombic lip of the fourth ventricle is the germinal origin of a diverse collection of neuronal populations that ultimately reside in the brainstem and cerebellum. Rhombic lip neurogenesis requires the bHLH transcription factor Atoh1 (Math1), and commences shortly after neural tube closure (E9.5). Within the rhombomere 1 – isthmus region, the rhombic lip first produces brainstem and deep cerebellar neurons (E9.5–E12), followed by granule cell precursors after E12. While Atoh1 function is essential for all of these populations to be specified, the downstream genetic programs that confer specific properties to early and late born Atoh1 lineages are not well characterized. We have performed a comparative microarray analysis of gene expression within early and later born cohorts of Atoh1 expressing neural precursors purified from E14.5 embryos using a transgenic labeling strategy. We identify novel transcription factors, cell surface molecules, and cell cycle regulators within each pool of Atoh1 lineages that likely contribute to their distinct developmental trajectories and cell fates. In particular, our analysis reveals new insights into the genetic programs that regulate the specification and proliferation of granule cell precursors, the putative cell of origin for the majority of medulloblastomas. | [R. Macholda, C. Kleinb 1, G. Fishellb] | Gene Expression Patterns | June–July 2011 | |
| sciencedirectS0171298510002159 | Dendritic cells matured by a prostaglandin E2-containing cocktail can produce high levels of IL-12p70 and are more mature and Th1-biased than dendritic cells treated with TNF-? or LPS | Dendritic cells (DCs) play a crucial role in the initiation of an immune response. As maturation is critical for effective antigen presentation, different methods have been used to generate mature DCs (mDCs) ex vivo. The use of a maturation cocktail (MC) consisting of IL-1?, IL-6, TNF-?, and prostaglandin E2 (PGE2) initially showed promising results, but then was challenged because of low production of IL-12p70 and the potential for induction of Th2-type immune responses. To investigate this contention, we compared two of the most commonly used maturation factors, TNF-? and LPS, with MC. Maturation cocktail was superior to TNF-? and LPS with respect to enhancement of mDC-specific surface marker expression (CD83, CD86, and HLA-DR), induction of T cell proliferation by mDCs, and directional motility of mDCs toward CCL19. These results were supported by increased expression of a significant number of additional maturation-related genes by MC in comparison to TNF-? and LPS. In addition, we did not observe a Th2-biased shift in the gene expression profile of mDCs generated by MC. Conversely, MC induced more Th1-promoting transcriptional changes than LPS or TNF-?, including increased transcript levels of Th1-type cytokines such as IL-15, IL-12?, and EBI3 (IL-27?) and MHC class I molecules, Th1-promoting changes in the transcripts of CXCL16, CCL13, and CCL18, and reduced transcript levels of MHC class II molecules. More interestingly, the Th1-promoting characteristics of MC-mDCs were confirmed by their potential to produce large amounts of IL-12p70 after effective stimulation simulating in vivo events. | [Abdolamir Landia d, Lorne A. Babiukc, Sylvia van Drunen Littel-van den Hurka b] | Immunobiology | June 2011 | |
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| sciencedirectS088240101100026X | Analysis on Actinobacillus pleuropneumoniae LuxS regulated genes reveals pleiotropic roles of LuxS/AI-2 on biofilm formation, adhesion ability and iron metabolism | LuxS is an enzyme involved in the activated methyl cycle and the by-product autoinducer-2 (AI-2) was a quorum sensing signal in some species. In our previous study, the functional LuxS in AI-2 production was verified in the porcine respiratory pathogen Actinobacillus pleuropneumoniae. Enhanced biofilm formation and reduced virulence were observed in the luxS mutant. To comprehensively understand the luxS function, in this study, the transcriptional profiles were compared between the A. pleuropneumoniae luxS mutant and its parental strain in four different growth phases using microarray. Many genes associated with infection were differentially expressed. The biofilm formation genes pgaABC in the luxS mutant were up-regulated in early exponential phase, while 9 genes associated with adhesion were down-regulated in late exponential phase. A group of genes involved in iron acquisition and metabolism were regulated in four growth phases. Phenotypic investigations using luxS mutant and both genetic and chemical (AI-2) complementation on these virulence traits were performed. The results demonstrated that the luxS mutant showed enhanced biofilm formation and reduced adhesion ability and these effects were not due to lack of AI-2. But AI-2 could increase biofilm formation and adhesion of A. pleuropneumoniae independent of LuxS. Growth under iron restricted condition could be controlled by LuxS through AI-2 production. These results revealed pleiotropic roles of LuxS and AI-2 on A. pleuropneumoniae virulence traits. | [Lu Li, Zhuofei Xu, Yang Zhou, Tingting Li, Lili Sun, Huanchun Chen, Rui Zhou] | Microbial Pathogenesis | June 2011 | |
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| sciencedirectS0168010211000514 | The ERBB4 intracellular domain (4ICD) regulates NRG1-induced gene expression in hippocampal neurons | The NRG1 growth factor and ERBB4 receptor have been identified as leading schizophrenia risk genes. Although NRG1 and ERBB4 have been shown to modulate neuronal functions involved in schizophrenia, including both GABAergic and glutamatergic synapses, the exact molecular mechanisms remain poorly understood. Here we investigated ERBB4 intracellular domain, 4ICD, transactivator function in rat hippocampal cultures by inhibiting ?-secretase mediated ERBB4 regulated intramembrane proteolysis (RIP). NRG1 stimulation resulted in a dramatic increase in the number of hippocampal cells displaying nuclear 4ICD which was abolished in cultures pretreated with the ?-secretase inhibitor compound E (CE). To identify NRG1-4ICD transactivated genes we compared global gene expression profiles of hippocampal cultures stimulated with NRG1 in the absence or presence of CE. In concordance with the contribution of NRG1-ERBB4 signaling to dendritic spine maturation and schizophrenia, global gene expression analysis followed by Ingenuity Pathway Analysis of the dataset identified NRG1-4ICD regulated genes significantly represented in semaphorin signaling and actin cytoskeletal plasticity and multiple genes with confirmed roles in dendritic spine morphogenesis. Using the power of global gene expression analysis our data provides a proof-of-concept supporting a role for non-canonical NRG1-4ICD signaling in the regulation of gene expression contributing to normal and schizophrenic neuronal function. | [June G. Allison1, Partha M. Das, Jingjing Ma, Fiona M. Inglis, Frank E. Jones] | Neuroscience Research | June 2011 | |
| sciencedirectS016801021100054X | Survey of the effect of genetic variations on gene expression in human prefrontal cortex and its application to genetics of psychiatric disorders | Identifying the genetic basis of gene expression variation in the human brain is important for understanding brain physiology and pathophysiology. We investigated the genetic basis of gene expression variation in human prefrontal cortex using single nucleotide polymorphisms (SNPs) and taking into consideration brain sample pH. From approximately 12,000 brain-expressed transcripts, we identified 187 cis-regulated transcripts. Some of the transcripts were identified as cis-regulated in the lymphoblastoid cells or lymphocytes, which suggests common cis-regulation across different tissues. Knowledge of genetic variations contributing to differences in gene expression in the brain would be particularly useful in the study of neuropsychiatric disorders in combination with a large-scale genome-wide association study. Using Wellcome Trust Case Control Consortium association study data, we identified SNPs associated with bipolar disorder and gene expression variation in the human brain. We found that SNPs in the AKAP10 and PRKCI genes are significantly associated with bipolar disorder and gene expression variation. | [Kazuya Iwamotoa b, Junko Uedaa, Miki Bundoa b, Toshio Kojimac d, Tadafumi Katoa] | Neuroscience Research | June 2011 | |
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| sciencedirectS0303720711001535 | Differential muscle gene expression as a function of disease progression in Goto-Kakizaki diabetic rats | The Goto-Kakizaki (GK) rat, a polygenic non-obese model of type 2 diabetes, is a useful surrogate for study of diabetes-related changes independent of obesity. GK rats and appropriate controls were killed at 4, 8, 12, 16 and 20 weeks post-weaning and differential muscle gene expression along with body and muscle weights, plasma hormones and lipids, and blood cell measurements were carried out. Gene expression analysis identified 204 genes showing 2-fold or greater differences between GK and controls in at least 3 ages. Array results suggested increased oxidative capacity in GK muscles, as well as differential gene expression related to insulin resistance, which was also indicated by HOMA-IR measurements. In addition, potential new biomarkers in muscle gene expression were identified that could be either a cause or consequence of T2DM. Furthermore, we demonstrate here the presence of chronic inflammation evident both systemically and in the musculature, despite the absence of obesity. | [Jing Niea, Bai Xuea, Siddharth Sukumarana, William J. Juskob c, Debra C. DuBoisa b, Richard R. Almona b c] | Molecular and Cellular Endocrinology | 16 May 2011 | |
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| sciencedirectS0142961211001074 | Modulation of immune responses by the antimicrobial peptide, epinecidin (Epi)-1, and establishment of an Epi-1-based inactivated vaccine | Current efforts to improve the effectiveness of vaccines include incorporating antimicrobial peptides mixed with a virus. The antimicrobial peptide, epinecidin (Epi)-1, was reported to have an antiviral function, and an Epi-1-based inactivated vaccine was postulated as a model and discussed. In this report, we demonstrated modulation of immune responses by Epi-1 and an Epi-1-based Japanese encephalitis virus (JEV)-inactivated vaccine against JEV infection in mice. Under in vitro conditions, Epi-1 prevented JEV infection-mediated loss of cell viability in BHK-21 cells. When Epi-1 and JEV were co-injected into mice and mice were re-challenged with JEV after 14 days, all mice survived. In addition, Epi-1 modulated the expressions of immune-responsive genes like interleukin (IL)-6, IL-10, MCP-1, tumor necrosis factor-?, interferon-? and IL-12, and elevated the levels of anti-JEV-neutralizing antibodies in the serum. The presence of Epi-1 suppressed the multiplication of JEV in brain sections at 4 days after an injection. Mice immunized with the developed vaccine showed complete survival against JEV infection, and it was superior to the traditional formalin-based JEV-inactivated vaccine. This study demonstrates the use of Epi-1 to develop an inactivated vaccine can provide guidelines for the future design of Epi-1-virus formulations for various in vivo applications. | [Han-Ning Huanga, Chieh-Yu Panb, Venugopal Rajanbabub, Yi-Lin Chanc, Chang-Jer Wua, Jyh-Yih Chenb] | Biomaterials | May 2011 | |
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| sciencedirectS0965174811000233 | Molecular analysis of nutritional and hormonal regulation of female reproduction in the red flour beetle, Tribolium castaneum | Female reproduction includes maturation of oocytes and the synthesis of yolk proteins (vitellogenin, Vg) in the fat body and their deposition into the oocytes. Our recent studies showed that juvenile hormone (JH) regulates Vg synthesis and 20-hydroxyecdysone (20E) regulates oocyte maturation in the red flour beetle (Tribolium castaneum). Here, we report on the role of nutritional signaling on vitellogenesis and oogenesis. Comparison of gene expression between fed and starved beetles by microarray analysis showed the up-regulation of genes involved in energy homeostasis and down-regulation of genes involved in egg production in the starved beetles. The RNA interference (RNAi) aided knock-down in the expression of genes involved in insulin and TOR signaling pathways showed that both these signaling pathways play key roles in Vg synthesis and oocyte maturation. Starvation of female beetles resulted in a block in Vg synthesis but not in the progression of primary oocyte development to the resting stage. Feeding after starvation induced Vg synthesis and the progression of primary oocytes from the resting stage to the mature stage. However, in the beetles where JH or 20E synthesis or action was blocked by RNAi, both Vg synthesis and oocyte maturation were affected suggesting that both these hormones (JH and 20E) and nutritional signaling and their cross-talk regulate vitellogenesis and oogenesis. | [R. Parthasarathy, Subba R. Palli] | Insect Biochemistry and Molecular Biology | May 2011 | |
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| sciencedirectS0161589011000599 | Influence of gut microbiota on mouse B2 B cell ontogeny and function | A complex interplay between the microbiota and the host immune system is evidenced to shape the immune system throughout life, but little is known about the microbial effect on key players of the adaptive immune system, the B2 B cells. In the presented study, we have evaluated the effect of commensal bacteria on B cell ontogeny and function, with the focus on B2 B cells of spleen and Peyer's patches. We have compared germ-free mice to mice that are exposed to a normal complex bacterial community from the day of birth and combined classical immunological assessment with advanced genome-wide expression profiling. Despite a preservation of all B cell subsets and phenotype, our results show that microbiota strongly impact mucosal B cell physiology and lead to higher serum Ig concentrations. We show that this microbial influence comprises downregulation of transcription factors involved in early B cell activation steps and upregulation of genes and proteins involved in later stages of B cell response. In summary, we show an influence of the gut microbiota on function of mucosal B2 B cells, involving mechanisms downstream of B cell activation and proliferation. | [Jenny Hanssona b, Nabil Boscoc, Laurent Favrec, Frederic Raymondb, Manuel Oliveirac, Sylviane Metaironb, Robert Mansourianb, Stephanie Blumc, Martin Kussmannb d, Jalil Benyacoubc] | Molecular Immunology | May 2011 | |
| sciencedirectS0923250811000209 | Profound differences in the transcriptome of Campylobacter jejuni grown in two different, widely used, microaerobic atmospheres | It was noted that quantitative and qualitative differences occurred between the growth of Campylobacter in microaerobic atmospheres provided by a gas replacement jar and that in a modular atmosphere controlled system cabinet, despite the fact that oxygen levels were comparable. Hydrogen was, however, only present in the replacement mixture (3%). Investigations were therefore carried out to examine any accompanying physiological or transcriptional differences. Growth curves and motility studies using Campylobacter jejuni HPC5 showed that cultures growing in the cabinet were impaired, but only in the early stages of growth compared to growth in the jar. However, transcriptome studies highlighted profound changes in the transcript profiles of exponential cultures grown in the cabinet compared to the jar, including genes indicative of oxidative stress. Genes involved in detoxification, synthesis and modification of macromolecules, probable prophage genes and genes associated with inhibition of natural transformation showed relative increases in expression in the cabinet. Conversely, genes that function in energy metabolism, chaperones, heat shock and motility were increased in the jar, which was indicative of balanced growth. This work highlights the need to carefully annotate the different methods of atmosphere generation in the description of experiments in microarray databases; the assessment of these experimental details is crucial to overcome difficulties in comparing transcriptomic studies of campylobacter cultures between different laboratories. | [Amy John, Phillippa Leigh Connerton, Nicola Cummings, Ian Frank Connerton] | Research in Microbiology | May 2011 | |
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| sciencedirectS016524781000297X | TOX regulates the differentiation of human natural killer cells from hematopoietic stem cells in vitro | Natural killer (NK) cells act important roles in innate immunity and adaptive immunity. However, the mechanisms governing NK cell development have not been clearly elucidated. Previous studies have shown that an HMG (high-mobility group) protein, TOX, is important for regulating the differentiation program of developing T cells in mice. In this study, we examined the role of TOX in differentiation of human NK cells. Knockdown of TOX in differentiating cells decreased the NK cell population identified by expression of NK surface markers and receptors. In addition, over-expression of TOX enhanced the differentiation of NK cells which give rise to a population showing effector functions of mature NK cells. Moreover, TOX influenced expression of T-bet (T-box expressed in T cells, also as known as Tbx21) during NK cell development. Overall, these results suggest that TOX is required for IL-15-mediated NK cell differentiation and affected expression of T-bet that plays critical roles in NK differentiation and maturation. | [Sohyun Yuna b, Suk Hyung Leea, Suk-Ran Yoona, Mi Sun Kima, Zheng-Hao Piaoa, Pyung-Keun Myungb, Tae-Don Kima, Haiyoung Junga, Inpyo Choia] | Immunology Letters | 30 April 2011 | |
| sciencedirectS0006291X11005638 | Identification of NDRG1-regulated genes associated with invasive potential in cervical and ovarian cancer cells | N-myc downstream regulated gene 1 (NDRG1) is an important gene regulating tumor invasion. In this study, shRNA technology was used to suppress NDRG1 expression in CaSki (a cervical cancer cell line) and HO-8910PM (an ovarian cancer cell line). In vitro assays showed that NDRG1 knockdown enhanced tumor cell adhesion, migration and invasion activities without affecting cell proliferation. cDNA microarray analysis revealed 96 deregulated genes with more than 2-fold changes in both cell lines after NDRG1 knockdown. Ten common upregulated genes (LPXN, DDR2, COL6A1, IL6, IL8, FYN, PTP4A3, PAPPA, ETV5 and CYGB) and one common downregulated gene (CLCA2) were considered to enhance tumor cell invasive activity. BisoGenet network analysis indicated that NDRG1 regulated these invasion effector genes/proteins in an indirect manner. Moreover, NDRG1 knockdown also reduced pro-invasion genes expression such as MMP7, TMPRSS4 and CTSK. These results suggest that regulation of invasion and metastasis by NDRG1 is a highly complicated process. | [Gang Zhaoa b, Jiawei Chena, Yanqiu Dengc, Feng Gaoa, Jiwei Zhud, Zhenzhong Fenga, Xiuhong Lva, Zheng Zhaoe] | Biochemical and Biophysical Research Communications | 29 April 2011 | |
| sciencedirectS0022283611002014 | Transcriptional and Cellular Responses to Defective Mitochondrial Proteolysis in Fission Yeast | Lon and m-AAA are the principal, regulated proteases required for protein maturation and turnover in the mitochondrial matrix of diverse species. To understand their roles in fission yeast (Schizosaccharomyces pombe) mitochondria, we generated deletion strains lacking Lon and m-AAA, individually (?lon1 and ?m-AAA) or together, ?lon1?m-AAA (?/?). All three strains were viable but incapable of respiratory growth on a non-fermentable carbon source due to mitochondrial dysfunction. Confocal and electron microscopy revealed a decrease in membrane potential and ultrastructural changes in ?lon1, ?m-AAA and ?/? mitochondria, consistent with a respiratory defect and aggregation of proteins in the mitochondrial matrix. To understand the global adaptations required for cell survival in the absence of Lon and m-AAA proteases, we compared genome-wide gene expression signatures of the deletion strains with the isogenic wild-type strain. Deletion of lon1 caused a distinctive transcriptional footprint of just 12 differentially expressed genes, 9 of which were up-regulated genes located on the proximal mitochondrial genome (mitochondrial DNA). In contrast, m-AAA deletion caused a much larger transcriptional response involving 268 almost exclusively nuclear genes. Genes ameliorating stress and iron assimilation were up-regulated, while diverse mitochondrial genes and other metabolic enzymes were down-regulated. The connection with iron dysregulation was further explored using biochemical, chemical and cellular assays. Although ?m-AAA and ?/? contained more cellular iron than the wild-type strain, their transcriptomes strongly resembled a signature normally evoked by iron insufficiency or disrupted assembly of iron–sulfur clusters in mitochondria. Based on these findings, we posit that excess iron accumulation could contribute to the pathology of human neurodegenerative disorders arising from defects in m-AAA function. | [Suranjana Guha1, Luis López-Maury2, Michael Shaw3, Jürg Bähler2, Chris J. Norbury3, Vishwas R. Agashe1] | Journal of Molecular Biology | 29 April 2011 | |
| sciencedirectS001429991100121X | A microarray based expression profiling of paclitaxel and vincristine resistant MCF-7 cells | Resistance to the broad spectrum of chemotherapeutic agents in cancer cell lines and tumors has been called multiple drug resistance (MDR). In this study, the molecular mechanisms of resistance to two anticancer agents (paclitaxel and vincristine) in mammary carcinoma cell line MCF-7 were investigated. Drug resistant sublines to paclitaxel (MCF-7/Pac) and vincristine (MCF-7/Vinc) that were developed from sensitive MCF-7 cells (MCF-7/S) were used. cDNA microarray analysis was performed for the RNA samples of sensitive and resistant cells in duplicate experiments. GeneSpring GX 7.3.1 Software was used in data analysis. The results indicated that the upregulation of MDR1 gene is the dominating mechanism of the paclitaxel and vincristine drug resistance. Additionally the upregulation of the genes encoding the detoxifying enzymes (i.e. GSTP1) was observed. Significant downregulation of apoptotic genes (i.e. PDCD2/4/6/8) and upregulation of some cell cycle regulatory genes (CDKN2A, CCNA2 etc.) was seen which may be in close relation to MDR in breast cancer. Drug resistant cancer cells exhibit different gene expression patterns depending on drug treatment, and each drug resistance phenotype is probably genetically different. Further functional studies are needed to demonstrate the complete set of genes contributing to the drug resistance phenotype in breast cancer cells. | [Meltem Demirel Karsa b, Özlem Darcansoy I?eric, Ufuk Gündüza] | European Journal of Pharmacology | 25 April 2011 | |
| sciencedirectS0014299911001087 | NF-?B-mediated anti-inflammatory activity of the sesquiterpene lactone 7-hydroxyfrullanolide | Microarray technology can be used to study the molecular mechanisms of new chemical entities with the aim to develop effective therapeutics. 7-Hydroxyfrullanolide (7HF) is a sesquiterpene lactone that was found to be efficacious in multiple animal models of inflammation by suppression of pro-inflammatory cytokines; however, its molecular mechanism of action remains unclear. We investigated the effects of 7HF on lipopolysaccharide (LPS)-stimulated human peripheral blood mononuclear cells using microarray-based gene expression studies and explored the molecular targets affected. Gene expression profiles and pathway analysis revealed that 7HF potently suppressed multiple inflammatory pathways induced by LPS. More importantly, 7HF was found to inhibit NF-?B related transcripts. These transcripts were further validated using freshly isolated synovial cells from rheumatoid arthritis patients, thus clinically validating our findings. Cell-based imaging and subsequent Western blot analysis demonstrated that 7HF inhibited the translocation of NF-?B into the nucleus by directly inhibiting the phosphorylation of IKK-?. Since the transcription of adhesion molecules is regulated by NF-?B, further investigation showed that 7HF dose-dependently suppressed ICAM-1, VCAM-1 and E-selectin expression on LPS-stimulated endothelial cells as well as inhibited the adhesion of monocytes to LPS-stimulated endothelial cells. Taken together, our results reveal that 7HF possesses NF-?B inhibitory potential and suggest a likely molecular mechanism of its anti-inflammatory activity. | [Lyle C. Fonsecaa, Shruta S. Dadarkara, Aurelio S. Loboa, Prabha B. Mishraa, Arvind D. Thakkara, Shanthi Chandrababub, Muralidhara Padigarua] | European Journal of Pharmacology | 25 April 2011 | |
| sciencedirectS0304394011002552 | Early changes of microRNAs expression in the dorsal root ganglia following rat sciatic nerve transection | MicroRNAs (miRNAs) are a novel class of small non-coding RNAs that regulate gene expression at the post-transcriptional level. Here we report early alterations of miRNAs expression following rat sciatic nerve injury using microarray analysis. We harvested dorsal root ganglia (DRG) tissues and identified 19 miRNAs that showed significant changes at four early time points after sciatic nerve transection. Subsequently, miR-188 and miR-500 microarray results were verified by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). The bioinformatics analysis indicated that the potential targets for these miRNAs were involved in the intracellular signaling cascade, the regulation of signal transduction, the regulation of cellular process and the response to cAMP that were known to play important roles in mobilizing the inherent capacity for neurite outgrowth and promoting regeneration during the early phase of sciatic nerve injury. Our results show that abnormal expression of miRNAs may contribute to illustrate the molecular mechanisms of nerve regeneration and miRNAs are potential targets for therapeutic interventions that may enhance intrinsic regenerative ability. | [Songlin Zhou1, Bin Yu1, Tianmei Qian, Dengbing Yao, Yongjun Wang, Fei Ding, Xiaosong Gu] | Neuroscience Letters | 25 April 2011 | |
| sciencedirectS0042682211000420 | The Epstein–Barr Virus BART microRNAs target the pro-apoptotic protein Bim | In Epstein–Barr Virus infected epithelial cancers, the alternatively spliced BamHI A rightward transcripts (BARTs) are abundantly expressed and are the template for two large clusters of miRNAs. This study indicates that both of these clusters independently can inhibit apoptosis in response to etoposide in an epithelial cell line. The Bcl-2 interacting mediator of cell death (Bim) was identified using gene expression microarrays and bioinformatic analysis indicated multiple potential binding sites for several BART miRNAs in the Bim 3′UTR. Bim protein was reduced by Cluster I and the individual expression of several miRNAs, while mRNA levels were unaffected. In reporter assays, the Bim 3′ untranslated region (UTR) was inhibited by both clusters but not by any individual miRNAs. These results are consistent with the BART miRNAs downregulating Bim post-transcriptionally in part through the 3′UTR and suggest that there are miRNA recognition sites within other areas of the Bim mRNA. | [Aron R. Marquitza, Anuja Mathura, Cyd Stacy Nama, Nancy Raab-Trauba b] | Virology | 10 April 2011 | |
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| sciencedirectS0171933510002426 | Homeodomain-only protein HOP is a novel modulator of late differentiation in keratinocytes | The homeodomain-only protein (HOP) contains an atypical homeodomain which is unable to bind to DNA due to mutations in residues important for DNA binding. Recently, HOP was reported to regulate proliferation/differentiation homeostasis in different cell types. In the present study, we performed transcriptional profiling of cultured primary human keratinocytes and noted a robust induction of HOP upon calcium-induced cell differentiation. Immunohistochemistry of human skin localized HOP to the granular layer in the epidermis. Overexpression of HOP using a lentiviral vector up-regulated FLG and LOR expression during keratinocyte differentiation. Conversely, decreasing HOP expression using small interfering RNA markedly reduced the calcium-induced expression of late markers of differentiation in vitro, with the most prominent effect on profilaggrin (FLG) mRNA. Moreover, mRNA levels of profilaggrin and loricrin were downregulated in the epidermis of HOP knockout mice. Analysis of skin disorders revealed altered HOP expression in lichen planus, psoriasis and squamous cell carcinoma (SCC). Our data indicate that HOP is a novel modulator of late terminal differentiation in keratinocytes. | [Magdalena Obarzanek-Fojt, Bertrand Favre, Magdalini Kypriotou, Stephan Ryser, Marcel Huber, Daniel Hohl] | European Journal of Cell Biology | April 2011 | |
| sciencedirectS0014483511000029 | Morphological, functional and gene expression analysis of the hyperoxic mouse retina | This study examined the impact of prolonged (up to 35 day) exposure to hyperoxia on the morphology and function of the retina, in the C57BL/6J mouse, as a basis for interpretation of gene expression changes. Mice of the C57BL/6J strain were raised from birth in dim cyclic illumination (12 h 5 lux, 12 h dark). Adult animals (90–110 days) were exposed to continuous hyperoxia (75% oxygen) for up to 35 d. Retinas were examined after 0 d (controls), 3 d, 7 d, 14 d and 35 d. Spatial and temporal patterns of photoreceptor death were mapped, using the TUNEL technique. Immunohistochemistry and a specific assay were used to assess the expression of a stress-related protein (GFAP) and the activity of key antioxidant enzymes (SOD). The dark-adapted flash electroretinogram was used to assess the function of rods and cones. RNA hybridized to Affymetrix Genechips was used to assess gene expression during the first 3 d of exposure. Photoreceptors were stable during the first 7 d exposure to hyperoxia, but thereafter showed progressive damage and degeneration, which began in a ‘hot-spot’ 0.5 mm inferior to the optic disc, then spread into surrounding retina. SOD activity was upregulated at 14 d, but not at earlier time points. GFAP expression was upregulated in Müller cells from 3 d. Rod and cone components of the ERG were supernormal at 3 d and 7 d, but then fell below control levels. Gene expression changes suggested possible mechanisms for this early supernormality of function. At 14 d exposure, damage to and death of photoreceptors were prominent and spreading, and function was correspondingly degraded. However at 3 d exposure, hyperoxia-induced supernormal functional responses in rods, while leaving their structure apparently undamaged. Variations in early (3 days) gene expression provide a partial insight into the mechanisms involved in this. | [Riccardo Natolia b c, Krisztina Valtera b, Vicki Chrysostomoua b, Jonathan Stonea d, Jan Provisa b c] | Experimental Eye Research | April 2011 | |
| sciencedirectS0378111910004531 | The amyloid precursor protein intracellular domain alters gene expression and induces neuron-specific apoptosis | Although amyloid precursor protein (APP) plays a central role in Alzheimer's disease, the physiological functions of this protein have yet to be fully elucidated. As previously reported, we established an embryonic carcinoma P19 cell line expressing the intracellular domain of APP (AICD). While neurons were differentiated from these cell lines with retinoic acid treatment, expression of AICD induced neuron-specific apoptosis. As the first step to identify the genes involved in this process, we evaluated AICD-induced changes in gene expression through cell death. The levels of expression of 41,256 transcripts were monitored by DNA microarray analysis. The expression of 277 genes showed up-regulation by more than 10-fold in the presence of AICD. Conversely, the expression of 341 genes showed down-regulation to less than one-tenth of the original level. Reverse transcription-polymerase chain reaction of 17 selected genes showed excellent agreement with the microarray results. These results suggest that AICD induces dynamic changes in gene expression, which may be closely correlated with AICD-induced neuron-specific apoptosis. | [Takeshi Ohkawaraa 1 2, Hisashi Nagaseb 2, Chang-Sung Kohc, Kohzo Nakayamaa] | Gene | 1 April 2011 | |
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| sciencedirectS0022282811000034 | Increased lysyl oxidase expression and collagen cross-linking during atrial fibrillation | The aim of the study is to characterize the signal transduction leading to interstitial fibrosis in the pathogenesis of atrial fibrillation (AF) and atrial remodeling.Samples of the left atrial appendage (LA) from patients with AF showed higher collagen content (73 ± 5 vs. 38 ± 2 ?g/mg protein) and 2.5-fold increased collagen crosslinking compared to patients with sinus rhythm (SR). Affymetrix-assays, RT-PCR and western Blot analysis revealed that LA of AF patients are characterized by increased lysyl oxidase (LOX) mRNA (218 ± 42%) and protein (253 ± 11%) expression. This was associated with increased expression of connective tissue growth factor (CTGF), fibronectin and Rac1 activity compared to SR. In neonatal cardiac fibroblasts, the Rac1 specific small molecule inhibitor NSC23766 prevented angiotensin II (AngII) induced upregulation of LOX (214 ± 16%) expression. Inhibition of CTGF by siRNA transfections completely inhibited AngII induced LOX expression. The LOX specific small molecule inhibitor BAPN prevented AngII and CTGF induced fibronectin expression. Left atria of transgenic mice with cardiac overexpression of Rac1 (RacET) that develop AF at high age exhibited upregulation of CTGF as well as LOX (187 ± 7%) and fibronectin (627 ± 146%) expression. Atria of RacET showed increased collagen content (28 ± 2 ?g/mg protein) and crosslinking (10 ± 0.7) compared to wildtypes (20 ± 0.4 ?g/mg protein; 5 ± 0.9).Left atrial myocardium of patients with atrial fibrillation is characterized by increased lysyl oxidase and fibronectin expression as well as collagen cross-linking. In cardiac fibroblasts, Rac1 GTPase mediates upregulation of fibronectin via LOX and CTGF. Inhibition of this signaling pathway may therefore represent a target for the prevention of fibrotic atrial remodeling. | [Oliver Adama 1, Katharina Theobalda 1, Daniel Lavalla, Markus Grubeb, Heyo K. Kroemerb, Sabine Amelingc, Hans-Joachim Schäfersd, Michael Böhma, Ulrich Laufsa] | Journal of Molecular and Cellular Cardiology | April 2011 | |
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| sciencedirectS0042682211000110 | Comprehensive analysis of host gene expression in Autographa californica nucleopolyhedrovirus-infected Spodoptera frugiperda cells | Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) is the best-studied baculovirus and most commonly used virus vector for baculovirus expression vector systems. The effect of AcMNPV infection on host cells is incompletely understood. A microarray based on Spodoptera frugiperda ESTs was used to investigate the impact of AcMNPV on host gene expression in cultured S. frugiperda, Sf21 cells. Most host genes were down-regulated over the time course of infection, although a small number were up-regulated. The most highly up-regulated genes encoded heat shock protein 70s and several poorly characterized proteins. Regulated genes with the highest score identified by functional annotation clustering included primarily products required for protein expression and trafficking in the ER and golgi. All were significantly down-regulated by approximately 12 h post-infection. Microarray data were validated by qRT-PCR. This study provides the first comprehensive host transcriptome overview of Sf21 cells during AcMNPV infection. | [Tamer Z. Salema d, Fengrui Zhanga, Yan Xieb, Suzanne M. Thiema c] | Virology | 30 March 2011 | |
| sciencedirectS0024320511000671 | Aberrant expression of imprinted genes in post-implantation rat embryos | AimImprinted genes are known regulators of embryo growth. Studies from our laboratory have demonstrated that treatment of adult male rats with tamoxifen increased post-implantation loss at around midgestation. Expression of insulin like growth factor 2 (Igf2), a paternally expressed imprinted gene was down-regulated in the resorbing embryos obtained at embryonic day 13. Hypomethylation of Igf2-H19 imprint control region was observed in the resorbing embryo sires and spermatozoa obtained from tamoxifen-treated rats thereby suggesting that errors in imprint acquisition during spermatogenesis can result in embryo loss. The present study aims at studying the expression of other imprinted genes, besides Igf2 in the embryos sired by tamoxifen-treated males.Main methodsGene expression profiles of resorbing versus normal embryos were assessed by microarrays. Real time quantitative RT-PCR for six imprinted genes and four genes involved in cell cycle was done to validate gene expression data. The affected pathways and functions were identified in the resorbing embryos and effect on cell cycle was confirmed by flow cytometry.Key findingsAberrant expression of a number of imprinted genes was observed in the resorbing embryos when compared to the normal embryos at embryonic days 11 and 13. Down-regulation of Notch signaling, Wnt signaling and cell cycle pathway was observed in the resorbing embryos.SignificanceThe study suggests that exposure of male germ cells to tamoxifen during adulthood results in aberrant expression of imprinted genes and down-regulation of development associated pathways in the F1 progeny thereby causing embryo loss. | [Neelam A. Kedia-Mokashia, Raja Mugasimangalamb, Mohammed Aiyazb, Srabani Mukherjeea, N.H. Balasinora] | Life Sciences | 28 March 2011 | |
| sciencedirectS0006291X11002506 | Arabidopsis HDA6 is required for freezing tolerance | Many plants exhibit altered gene expression patterns in response to low nonfreezing temperatures and an increase in freezing tolerance in a phenomenon known as cold acclimation. Here we show, for the first time, that the histone deacetylase gene HDA6 is required for cold acclimation and freezing tolerance in Arabidopsis. HDA6 is transcriptionally upregulated during long-term cold treatment. Cold-treated hda6 mutants showed reduced freezing tolerance compared with the cold-treated wild-type plants. Freezing-caused electrolyte leakage increased in the cold-treated hda6 mutant. In contrast, the non-cold-treated hda6 mutants showed no significant difference in survivability and electrolyte leakage compared to wild-type plants. Transcriptome analysis identified the genes that showed aberrant expression in the hda6 mutant after cold acclimation. We conclude that HDA6 plays a critical role in regulating cold acclimation process that confers freezing resistance on Arabidopsis. | [Taiko Kim Toa b, Kentaro Nakaminamia, Jong-Myong Kima, Taeko Morosawaa, Junko Ishidaa, Maho Tanakaa, Shigeyuki Yokoyamab, Kazuo Shinozakic, Motoaki Sekia d] | Biochemical and Biophysical Research Communications | 18 March 2011 | |
| sciencedirectS0273117710007131 | Expression of p53-regulated genes in human cultured lymphoblastoid TSCE5 and WTK1 cell lines after spaceflight in a frozen state | The 53 kDa tumor suppressor protein p53 is generally thought to contribute to the genetic stability of cells and to protect cells from DNA damage through the activity of p53-centered signal transduction pathways. To clarify the effect of space radiation on the expression of p53-dependent regulated genes, gene expression profiles were compared between two human cultured lymphoblastoid cell lines: one line (TSCE5) has a wild-type p53 gene status, and the other line (WTK1) has a mutated p53 gene status. Frozen human lymphoblastoid cells were stored in a freezer in the International Space Station (ISS) for 133 days. Gene expression was analyzed using DNA chips after culturing the space samples for 6 h on the ground after their return from space. Ground control samples were also cultured for 6 h after being stored in a frozen state on the ground for the same time period that the frozen cells were in space. p53-Dependent gene expression was calculated from the ratio of the gene expression values in wild-type p53 cells and in mutated p53 cells. The expression of 50 p53-dependent genes was up-regulated, and the expression of 94 p53-dependent genes was down-regulated after spaceflight. These expression data identified genes which could be useful in advancing studies in basic space radiation biology. The biological meaning of these results is discussed from the aspect of gene functions in the up- and down-regulated genes after exposure to low doses of space radiation. | [A. Takahashia b, H. Suzukic d, K. Omorib, M. Sekid e, T. Hashizumed e, T. Shimazuc, N. Ishiokab d, T. Ohnishib f] | Advances in Space Research | 15 March 2011 | |
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| sciencedirectS0891584910014450 | A global transcriptomic view of the multifaceted role of glutathione peroxidase-1 in cerebral ischemic–reperfusion injury | Transient cerebral ischemia often results in secondary ischemic/reperfusion injury, the pathogenesis of which remains unclear. This study provides a comprehensive, temporal description of the molecular events contributing to neuronal injury after transient cerebral ischemia. Intraluminal middle cerebral artery occlusion (MCAO) was performed to induce a 2-h ischemia with reperfusion. Microarray analysis was then performed on the infarct cortex of wild-type (WT) and glutathione peroxidase-1 (a major antioxidant enzyme) knockout (Gpx1−/−) mice at 8 and 24 h postreperfusion to identify differential gene expression profile patterns and potential alternative injury cascades in the absence of Gpx1, a crucial antioxidant enzyme, in cerebral ischemia. Genes with at least ± 1.5-fold change in expression at either time point were considered significant. Global transcriptomic analyses demonstrated that 70% of the WT-MCAO profile overlapped with that of Gpx1−/−-MCAO, and 28% vice versa. Critical analysis of the 1034 gene probes specific to the Gpx1−/−-MCAO profile revealed regulation of additional novel pathways, including the p53-mediated proapoptotic pathway and Fas ligand (CD95/Apo1)-mediated pathways; downplay of the Nrf2 antioxidative cascade; and ubiquitin–proteasome system dysfunction. Therefore, this comparative study forms the foundation for the establishment of screening platforms for target definition in acute cerebral ischemia intervention. | [Minghui Jessica Chena 1, Connie H.Y. Wongb 1, Zhao Feng Pengc d, Jayapal Manikandane, Alirio J. Melendeze, Theresa M. Tand, Peter J. Crackb, Nam Sang Cheunga f] | Free Radical Biology and Medicine | 15 March 2011 | |
| sciencedirectS0048969711000507 | Hepatic gene expression profile in brown trout (Salmo trutta) exposed to traffic related contaminants | In recent decades there has been growing concern about highway runoff as a potential threat and a significant source of diffuse pollution to the aquatic environment. However, identifying ecotoxicological effects might be challenging, especially at sites where the traffic density is modest to low. Hence, there is a need for alternatives e.g. small-scale toxicity tests using conventional endpoints such as mortality and growth. The present paper presents result from a transcriptional (microarray) screening performed on liver from brown trout (Salmo trutta) acutely exposed (4 h) to traffic-related contaminants during washing of a highway tunnel outside the city of Oslo, Norway. The results demonstrated that traffic-related contaminants caused a plethora of molecular changes that persisted several hours after the exposure (i.e. during recovery). Beside an evident transcriptional up-regulation of e.g. cytochrome P450 1A1 (CYP1A1), cytochrome P450 1B1 (CYP1B1), and cytosolic sulfotransferase (SULT) involved in xenobiotic biotransformation, the observed responses were predominantly associated with immunosuppression, oxidative damage, and endocrine modulation. The observed responses were likely caused by an interaction of several contaminants including trace metals and organic micro-pollutants such as PAHs. | [Sondre Melanda b, Eivind Farmenc, Lene S. Heiera, Bjørn Olav Rosselandd, Brit Salbua, You Songa, Knut Erik Tollefsena c] | Science of The Total Environment | 15 March 2011 | |
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| sciencedirectS0968089611000022 | Antitumor agents 283. Further elaboration of Desmosdumotin C analogs as potent antitumor agents: Activation of spindle assembly checkpoint as possible mode of action | In our ongoing study of the desmosdumotin C (1) series, twelve new analogues, 21–32, mainly with structural modifications in ring-A, were prepared and evaluated for in vitro antiproliferative activity against several human tumor cell lines. Among them, the 4′-iodo-3,3,5-tripropyl-4-methoxy analogue (31) showed significant antiproliferative activity against multiple human tumor cell lines with ED50 values of 1.1–2.8 ?M. Elongation of the C-3 and C-5 carbon chains reduced activity relative to propyl substituted analogues; however, activity was still better than that of natural compound 1. Among analogues with various ether groups on C-4, compounds with methyl (2) and propyl (26) ethers inhibited cell growth of multiple tumor cells lines, while 28 with an isobutyl ether showed selective antiproliferative activity against lung cancer A549 cells (ED50 1.7 ?M). The gene expression profiles showed that 3 may modulate the spindle assembly checkpoint (SAC) and chromosome separation, and thus, arrest cells at the G2/M-phase. | [Kyoko Nakagawa-Gotoa, Pei-Chi Wua, Kenneth F. Bastowb, Shuenn-Chen Yangc, Sung-Liang Yud, Hsuan-Yu Chene, Jau-Chen Linf, Masuo Gotog, Susan L. Morris-Natschkea, Pan-Chyr Yangc d h, Kuo-Hsiung Leea i] | Bioorganic & Medicinal Chemistry | 1 March 2011 | |
| sciencedirectS088915911000574X | Suppressed monocyte gene expression profile in men versus women with PTSD | There have been several attempts to use gene microarrays from peripheral blood mononuclear cells to identify new biological pathways or targets for therapy in Posttraumatic Stress Disorder (PTSD). The few studies conducted to date have yielded an unclear pattern of findings, perhaps reflecting the use of heterogeneous samples of circulating immune cells for analysis. We used gene microarrays on a homogeneous sample of circulating monocytes to test the hypothesis that chronic PTSD would be associated with elevated inflammatory activity and to identify new pathways dysregulated in the disorder. Forty-nine men (24 PTSD+ and 25 age-matched trauma-exposed PTSD− controls) and 18 women (10 PTSD+ and 8 age-matched PTSD− controls) were recruited. Gene expression microarray analysis was performed on CD14+ monocytes, immune cells that initiate and respond to inflammatory signaling. Male subjects with PTSD had an overall pattern of under-expression of genes on monocytes (47 under-expressed versus 4 over-expressed genes). A rigorous correction for multiple comparisons and verification with qPCR showed that of only 3 genes that were differentially expressed, all were under-expressed. There was no transcriptional evidence of chronic inflammation in male PTSD+ subjects. In contrast, preliminary data from our pilot female PTSD+ subjects showed a relatively balanced pattern of increased and decreased expression of genes and an increase in activity of pathways related to immune activation. The results indicate differential patterns of monocyte gene expression in PTSD, and the preliminary data from our female pilot subjects are suggestive of gender dimorphism in biologic pathways activated in PTSD. Changes in immune cell gene expression may contribute to medical morbidity in PTSD. | [Thomas C. Neylana b c, Bing Suna b, Hans Rempela b, Jessica Rossa c, Maryann Lenocia b, Aoife O’Donovana b c, Lynn Pulliama b d] | Brain, Behavior, and Immunity | March 2011 | |
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| sciencedirectS1533002811700639 | Correlation of Overall Survival With Gene Expression Profiles in a Prospective Study of Resectable Esophageal Cancer | Purpose: Preoperative chemotherapy has demonstrated a survival benefit for patients with potentially resectable esophageal cancer; however, currently it is not possible to predict the benefit of this treatment for an individual patient. This prospective study was designed to correlate gene expression profiles with clinical outcome in this setting.Patients and MethodsEligible patients were deemed to have resectable disease after staging by computed tomography, endoscopic ultrasound, and laparoscopy as indicated and following discussion at the multidisciplinary team meeting. All patients received neoadjuvant platinum and fluoropyrimidine-based chemotherapy; and clinical data were entered prospectively onto a study-specific database. Total RNA was isolated from pretreatment tumor biopsies obtained at baseline endoscopy and analyzed using a cDNA array consisting of 22,000 cDNA clones.ResultsOf the patients with adequate follow-up accrued between 2002 and 2005, 35 satisfied the quality control measures for the microarray profiling. Median follow-up was 938 days. Supervised hierarchical clustering of normalized data revealed 165 significantly differentially expressed genes based on overall survival (OS; P < .01) with 2 distinct clusters: a poor outcome group: N = 17 (1 year OS 46.2%) and a good outcome group: N = 18 (1 year OS 100%). Genes identified included those previously associated with esophageal cancer and, interestingly, a group of genes encoding proteins involved in the regulation of the TOLL receptor-signaling pathway.ConclusionThis initial study has highlighted groups of tumors with distinct gene expression profiles based on survival and warrants further validation in a larger cohort. This approach may further our understanding of individual tumor biology and thus facilitate the development of tailored treatment. | [Sheela Raoa, Lyndsey Welshb, David Cunninghama, Robert H. te-Poeleb, Martin Bensona, Andrew Normana, Claire Safferya, Ian Giddingsc, Paul Workmanb, Paul A. Clarkeb] | Clinical Colorectal Cancer | March 2011 | |
| sciencedirectS1744117X10000341 | Heritability and mechanisms of n− 3 long chain polyunsaturated fatty acid deposition in the flesh of Atlantic salmon ? | n− 3 long chain polyunsaturated fatty acids (n− 3LC-PUFA) are essential components of vertebrate membrane lipids and are now at critically low levels in modern Western diets. The main human dietary source for n− 3LC-PUFA is fish and seafood, and over 50% of global fish production is currently supplied by aquaculture. However, increasing pressure to include vegetable oils, which are devoid of n− 3LC-PUFA, in aquaculture feeds reduces their content in farmed fish flesh. The aim of this study was to measure the heritability and infer mechanisms determining flesh n− 3LC-PUFA content in Atlantic salmon. This was achieved by analysing flesh lipid parameters in 48 families of Atlantic salmon and by measuring differences, by high density microarray, in hepatic mRNA expression in families with high and low flesh n− 3LC-PUFA. The results show that flesh n− 3LC-PUFA composition is a highly heritable trait (h2 = 0.77 ± 0.14). Gene ontology analysis of differentially expressed genes indicates increased hepatic lipid transport, likely as very low density lipoprotein (VLDL), and implicates family differences in transforming growth factor ?1 (Tgf?1) signalling, activities of a transcription factor Snai1, and considered together may indicate alterations in hepatic nuclear factor 4? (HNF4?), a master controller of lipid homeostasis. This study paves the way for identification of quantitative trait loci and gene interaction networks that are associated with flesh n− 3LC-PUFA composition, which will assist the sustainable production of Atlantic salmon and provide optimal levels of critical nutrients for human consumers. | [Michael J. Leavera, John B. Taggarta, Laure Villeneuvea, James E. Brona, Derrick R. Guyb, Stephen C. Bishopc, Ross D. Houstonc, Oswald Matikac, Douglas R. Tochera] | Comparative Biochemistry and Physiology Part D: Genomics and Proteomics | March 2011 | |
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| sciencedirectS016816051000499X | Effect of chicken meat environment on gene expression of Campylobacter jejuni and its relevance to survival in food | Poultry meat is the major food source responsible for gastrointestinal infections caused by the human pathogen Campylobacter jejuni. Even though C. jejuni does not grow below 30 °C, the bacterium survives on raw meat surfaces at refrigerated temperatures and thus poses a risk to the consumer. Previously, we have shown that chicken meat juice prolongs survival of C. jejuni at 5 °C compared to laboratory medium, suggesting that compounds present in meat juice influence adaptation to low temperatures. In the present study we have used chicken meat juice to identify C. jejuni genes that are differentially expressed in a typical chicken meat environment encountered by consumers. The analysis showed that chicken meat juice increased expression of luxS involved in quorum sensing, as well as a gene involved in O-linked flagellin glycosylation in C. jejuni, while expression of haemin uptake and the peroxide stress response genes were reduced. Furthermore, we propose that LuxS may play a key role in adaptation to the chicken meat juice environment, as lack of the luxS gene reduces the ability of C. jejuni to survive in chicken meat juice at low temperature. Finally, our data suggest that part of an ABC transport system is induced and we speculate that uptake of cryoprotectants may be important for C. jejuni to adapt to low temperature. In summary, we found that C. jejuni has a specific but limited transcriptional response to chicken meat juice and that luxS has an impact on the prolonged survival of C. jejuni in this important environment in the food chain. | [Ma?gorzata Ligowskaa, Marianne Thorup Cohna, Richard A. Stablerb, Brendan W. Wrenb, Lone Brøndsteda] | International Journal of Food Microbiology | 1 March 2011 | |
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| sciencedirectS0882401010001968 | Genomic comparisons of USA300 Staphylococcus aureus colonizating the nose and rectum of children with skin abscesses | USA300 Staphylococcus aureus is responsible for the current outbreak of skin abscesses in the United States. Unlike other USA types, USA300 colonizes the rectum at rates higher than the nose. The reason for the difference in colonization site preference may be related to specific adherence or attachment factors contained in the genome of these strains. Additional knowledge in this field may help design novel prophylactic and therapeutic strategies to combat staphylococcal infections. Strains of USA300 MSSA and MRSA colonizing the nose and/or rectum from children with staphylococcal skin abscesses were compared by whole genome array technology to identify bacterial genetic determinants associated with site-specific colonization. Strains isolated from different colonization sites were indistinguishable by genomic content. Site-specific colonization traits were not detected in the colonizing bacteria by this array. Either host characteristics associated with staphylococcal carriage or under represented bacterial genomic constructions need to be examined to determine the etiology of this site-specific colonization. | [Nicole Lemmensa, Willem van Wamela, Susan Snijdersa, Alan J. Lesseb c, Howard Fadenb d, Alex van Belkuma] | Microbial Pathogenesis | March–April 2011 | |
| sciencedirectS0163725810002068 | Single cell transcriptomics of hypothalamic warm sensitive neurons that control core body temperature and fever response: Signaling asymmetry and an extension of chemical neuroanatomy | We report on an ‘unbiased’ molecular characterization of individual, adult neurons, active in a central, anterior hypothalamic neuronal circuit, by establishing cDNA libraries from each individual, electrophysiologically identified warm sensitive neuron (WSN). The cDNA libraries were analyzed by Affymetrix microarray. The presence and frequency of cDNAs were confirmed and enhanced with Illumina sequencing of each single cell cDNA library. cDNAs encoding the GABA biosynthetic enzyme Gad1 and of adrenomedullin, galanin, prodynorphin, somatostatin, and tachykinin were found in the WSNs. The functional cellular and in vivo studies on dozens of the more than 500 neurotransmitters, hormone receptors and ion channels, whose cDNA was identified and sequence confirmed, suggest little or no discrepancy between the transcriptional and functional data in WSNs; whenever agonists were available for a receptor whose cDNA was identified, a functional response was found. Sequencing single neuron libraries permitted identification of rarely expressed receptors like the insulin receptor, adiponectin receptor 2 and of receptor heterodimers; information that is lost when pooling cells leads to dilution of signals and mixing signals. Despite the common electrophysiological phenotype and uniform Gad1 expression, WSN transcriptomes show heterogeneity, suggesting strong epigenetic influence on the transcriptome. Our study suggests that it is well-worth interrogating the cDNA libraries of single neurons by sequencing and chipping. | [James Eberwinea b, Tamas Bartfaic] | Pharmacology & Therapeutics | March 2011 | |
| sciencedirectS0981942811000088 | Microarray analysis of ripening-regulated gene expression and its modulation by 1-MCP and hexanal | Hexanal, an inhibitor of phospholipase D, has been successfully applied for the pre- and post-harvest treatment of fruits, vegetables and flowers. Changes in gene expression induced by hexanal and the ethylene antagonist 1-MCP, were analyzed by microarray using TOM2 tomato oligo-array containing approximately 12 000 unigenes. Mature green tomato fruits were treated with 1-MCP and hexanal, RNA isolated after 10 days of storage, and labeled cDNA synthesized for microarray analysis. A large variation in gene expression profile was observed in 1-MCP-treated fruits. Genes for ethylene biosynthetic pathway enzymes such as ACC- synthase/oxidase, ethylene receptor and ethylene response factors were heavily down-regulated in 1-MCP-treated fruits. In addition, genes for key enzymes involved in cell wall degradation and carotenoid development pathways were down-regulated. Hexanal treatment significantly down-regulated ACC-synthase, and to a lesser extent, other components of ethylene signal transduction. By contrast to MCP-treated fruits, hexanal-treated fruits gradually ripened and showed higher levels of lycopene and ?-carotene. GC–MS analysis of volatiles showed a higher level of major volatile components in hexanal-treated fruits. Similarities in the modulation of gene expression by hexanal and 1-MCP suggest that hexanal, in addition to being a PLD inhibitor, may also act as a weak ethylene inhibitor. | [Krishnaraj Tiwari, Gopinadhan Paliyath] | Plant Physiology and Biochemistry | March 2011 | |
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| sciencedirectS0049384810006481 | Gene expression analysis of HUVEC in response to TF-binding | IntroductionTissue factor (TF), the cofactor for factor VII/VIIa (FVII/FVIIa) and initiator of the extrinsic pathway, is transiently expressed on intravascular cells under control of cytokines and growth factors. In addition, endothelial cells express a binding site for external TF. In the present study, we investigated gene expression of endothelial cells derived from human umbilical veins (HUVEC) in response to TF-binding to identify differentially expressed genes.Materials and methodsHUVEC were treated with recombinant relipidated TF (Innovin) versus nontreated cells, as well as TF/FVIIa versus FVIIa alone. TF binding was measured by ELISA. Gene expression profiles were examined using HG-U133 plus 2.0 arrays (Affymetrix).ResultsGene expression analysis of HUVEC showed 148 up-regulated and 29 down-regulated genes 4 h after TF binding. Notably, the genes, which were significantly up- and down-regulated, either by TF alone or by the complex of TF/FVIIa, exhibited a complete overlap, indicating that activation of endothelial cells after binding of external added TF does not depend on FVIIa as has been demonstrated for TF-expressing cells. TF-mediated regulation of gene expression of several genes, involved in regulation of apoptosis, cell adhesion, cell motility, and angiogenesis, was confirmed by qPCR. Furthermore, in case of SELE, TGFB2, TNFAIP3, TNFSF4, TNFSF18, TAGLN, CXCL1, PCF11 antibodies directed to TF clearly inhibited TF-mediated regulation of gene expression.ConclusionsThe results demonstrate that interaction of TF with HUVEC via a binding site, independent from FVIIa, may result in regulation of a variety of genes involved in arteriosclerosis, cancer, and cardiovascular diseases. | [Marianne Grossera, Viktor Magdolenb, Gustavo Barettona, Thomas Lutherc, Sybille Albrechta] | Thrombosis Research | March 2011 | |
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| sciencedirectS0006291X11001549 | Microarray analysis of differentially regulated genes in human neuronal and epithelial cell lines upon exposure to type A botulinum neurotoxin | Among the seven serotypes (A–G), type A botulinum neurotoxin (BoNT/A) is the most prevalent etiologic agent and the most potent serotype to cause foodborne botulism, characterized by flaccid muscle paralysis. Upon ingestion, BoNT/A crosses epithelial cell barriers to reach lymphatic and circulatory systems and blocks acetylcholine release at the pre-synaptic cholinergic nerve terminals of neuromuscular junctions (NMJs) resulting in paralysis. One of the unique features of BoNT/A intoxication is its neuroparalytic longevity due to its persistent catalytic activity. The persistent presence of the toxin inside the cell can induce host cell responses. To understand the pathophysiology and host response at the cellular level, gene expression changes upon exposure of human HT-29 colon carcinoma (epithelial) and SH-SY5Y neuroblastoma cell lines to BoNT/A complex were investigated using microarray analysis. In HT-29 cells, 167 genes were up-regulated while 60 genes were down-regulated, whereas in SH-SY5Y cells about 223 genes were up-regulated and 18 genes were down-regulated. Modulation of genes and pathways involved in neuroinflammatory, ubiquitin–proteasome degradation, phosphatidylinositol, calcium signaling in SH-SY5Y cells, and genes relevant to focal adhesion, cell adhesion molecules, adherens and gap junction related pathways in HT-29 cells suggest a massive host response to BoNT/A. A clear differential response in epithelial and neuronal cells indicates that the genes affected may play a distinct role in BoNTs cellular mode of action, involving these two types of host cells. | [Nagarajan Thirunavukkarasusxa, Koyel J. Ghosala, Roshan Kukrejaa, Yu Zhoua, Alan Dombkowskib, Shuowei Caia, Bal Ram Singha] | Biochemical and Biophysical Research Communications | 25 February 2011 | |
| sciencedirectS0006291X11001252 | ER stress-induced protein, VIGG, disturbs plant cation homeostasis, which is correlated with growth retardation and robustness to ER stress | VIGG is a putative endoplasmic reticulum (ER) resident protein induced by virus infection and ER stress, and is correlated with fruit quality in grapevine. The present study was undertaken to determine the biological function of VIGG in grapevine. Experiments using fluorescent protein-VIGG fusion protein demonstrated that VIGG is localized in ER and the ER targeting sequence is in the N-terminus. The overexpression of VIGG in Arabidopsis plant led to growth retardation. The rosette leaves of VIGG-overexpressing plants were smaller than those of the control plants and rolled at 42 days after seeding. VIGG-overexpressing plants revealed robustness to ER stress as well as the low expression of ER stress marker proteins, such as the luminal binding proteins. These characteristics of VIGG-overexpressing plants were supported by a microarray experiment that demonstrated the disruption of genes related to ER stress response and flowering, as well as cation mobility, in the plants. Finally, cation homeostasis in the plants was disturbed by the overexpression of VIGG. Taken together, these results suggest that VIGG may disturb cation homeostasis in plant, which is correlated with the robustness to ER stress and growth retardation. | [Hironori Katoha, Keiko Fujitaa, Yuki Takuharaa, Atsushi Ogawab, Shunji Suzukia] | Biochemical and Biophysical Research Communications | 18 February 2011 | |
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| sciencedirectS003991401000826X | Urinary signature of anabolic steroids and glucocorticoids in humans by LC–MS | A metabonomic strategy based on LC–MS was employed to investigate the metabolic profile of urine samples from 20 athletes who had been tested positive for corticoids and anabolic steroids and 29 controls. In this aim, different sample preparations and chromatographic conditions were compared. The acquired LC–MS data of doped athletes and controls were subjected to analysis of variance (ANOVA) and principal component analysis (PCA). Using this approach, molecular signature of human urine was obtained showing that metabonomics could be a complementary tool to discriminate different urinary profiles and to track down metabolic changes in humans. | [Agneta Kissa, Anne-Laure Jacqueta, Olivier Paissea, Marie-Magdeleine Flament-Watona, Jacques de Ceaurrizb, Claire Bordesc, Jean-Yves Gauvritc, Pierre Lantéric, Cécile Cren-Olivéa] | Talanta | 15 February 2011 | |
| sciencedirectS0006899310026144 | Dynamic variation of genes profiles and pathways in the hippocampus of ischemic mice: A genomic study | ObjectiveTo reveal the potential time-sequential molecular mechanism in the hippocampus of ischemia-reperfusion mice, so as to provide pertinent evidence for differential treatment during different phases after cerebral ischemia-reperfusion injury. Methods Seventy-five male Kunming mice were randomly divided into four groups: sham, ischemia and reperfusion for 3 h, 12 h, and 24 h, respectively. A cDNA microarray involving 374 cDNA ischemia-related genes, selected from the Science STKE database, was performed to detect the gene expression profiles. All data analyses were performed in the FDA ArrayTrack system. Data were also uploaded to the KEGG database (http://www.genome.jp/kegg/) to analyze the genetic pathways. Results Clustering and principal component analyses showed clear boundaries in the differentially expressed genes among the 3 h, 12 h, and 24 h groups. Although 56 overlapping up-regulated genes and 2 down-regulated genes were identified in 3 h, 12 h, and 24 h groups, the sequence variation of CA1 neurons and gene expression profiles also existed in all groups. Based on the total number of altered genes, the top 3 GO categories were metabolism, signal and cell cycle, which shared 8, 11 and 5 overlapping genes in 3 h, 12 h, and 24 h groups, respectively. As for metabolism, there were 2 specific altered genes in the 3 h group (casp8ap2 and mmp2), 6 in the 24 h group (daxx, gadd45a, adamts1, adcy8, cyp51, dusp16), but none in the 12 h group. Based on the KEGG database analysis, 18 overlapping pathways were detected in the three groups; and 1, 12 and 2 overlapping pathways were noted between the 3 h and 12 h, 12 h and 24 h, and 3 h and 24 h comparisons, respectively. The gene expressions of Caspase 2 and Rgs6 were identified by real-time RT-PCR, which was consistent with the results of microarray analysis. Conclusion Overlapping and variable genes and pathways demonstrate the time-sequential molecular mechanism in the hippocampus of ischemic mice, which may provide evidence for rational treatment during different phases after cerebral ischemia-reperfusion injury. | [Liying Wanga, Caixiu Zhoua, Zhong Wanga, Jun Liua, Zhiwei Jinga, Zhanjun Zhangb, Yongyan Wanga] | Brain Research | | |
| sciencedirectS0167527311000052 | Effects of exercise and antioxidant supplementation on endothelial gene expression ? | BackgroundThe molecular mechanisms of exercise training induced cardiovascular protection are poorly understood. There is growing evidence that reactive oxygen species may be involved in a number of these adaptations and that antioxidants may be used to investigate this effect.ObjectiveTo determine the effects of exercise training and/or antioxidant supplementation on myocardial endothelium and vascular endothelium gene expression.MethodsMale Wistar rats were divided into four groups: i) control; ii) exercise trained (90 min of treadmill running 4d per week, 14 weeks); iii) antioxidant-supplemented (?-tocopherol 1000 IU kg− 1 diet and ?-lipoic acid 1.6 g kg− 1 diet, mixed with rat chow) and iv) exercise trained and antioxidant-supplemented.ResultscDNA microarray analysis showed diverse expression changes in both left ventricular and coronary artery endothelial cells. In particular, RT-PCR analysis showed that a gene involved in cardiovascular disease progression, Ras homolog gene family member A, was down-regulated by exercise, and up-regulated by antioxidant supplementation in left ventricular endothelial cells. Furthermore, an important gene involved in inflammation, IL-6, was down-regulated by all treatments.ConclusionsExercise training and/or antioxidant supplementation affects cardiac endothelial cell gene expression, and their effects on genes such as ras homolog gene family member A and IL-6 provides insight into the molecular mechanisms of their influences on cardiovascular diseases. | [Aya Matsumotoa, Steven R. Masonb, Traute Flatscher-Baderb, Leigh C. Wardb, Susan A. Marshc, Peter A. Wilceb, Robert G. Fassetta d e, Judy B. de Haanf, Jeff S. Coombesa] | International Journal of Cardiology | | |
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| sciencedirectS1050464810004079 | Microarray analysis of gene expression in disk abalone Haliotis discus discus after bacterial challenge | In this study, we investigated the gene expression profiling of disk abalone, Haliotis discus discus challenged by a mixture of three pathogenic bacteria Vibrio alginolyticus, Vibrio parahemolyticus, and Listeria monocytogenes using a cDNA microarray. Upon bacteria challenge, 68 (1.6%) and 112 (2.7%) gene transcripts changed their expression levels ≥2 or ≤2 -fold in gills and digestive tract, respectively. There were 46 tissue-specific transcripts that up-regulated specifically in the digestive tract. In contrast, only 13 transcripts showed gill-specific up-regulation. Quantitative real-time PCR was performed to verify microarray data and results revealed that candidate genes namely Krüppell-like factor (KLF), lachesin, muscle lim protein, thioredoxin-2 (TRx-2), nuclear factor interleukin 3 (NFIL-3) and abalone protein 38 were up-regulated. Also, our results further indicated that bacteria challenge may activate the transcription factors or their activators (Krüppell-like factor, inhibitor of NF-?B or Ik-B), inflammatory cytokines (IL-3 regulated protein, allograft inflammatory factor), other cytokines (IFN-44-like protein, SOCS-2), antioxidant enzymes (glutathione-S-transferase, thioredoxin-2 and thioredoxin peroxidase), and apoptosis-related proteins (TNF-?, archeron) in abalone. The identification of immune and stress response genes and their expression profiles in this microarray will permit detailed investigation of the stress and immune responses of abalone genes. | [Mahanama De Zoysaa 1, Chamilani Nikapitiyaa, Chulhong Ohb, Youngdeuk Leea, Ilson Whangc, Jae-Seong Leed, Cheol Young Choie, Jehee Leea f] | Fish & Shellfish Immunology | February 2011 | |
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| sciencedirectS0969996110003463 | Citron kinase regulates axon growth through a pathway that converges on cofilin downstream of RhoA | Axon regeneration in the adult central nervous system (CNS) is prevented by inhibitory molecules present in myelin, which bind to a receptor complex that leads to downstream RhoGTP activation and axon growth cone collapse. Here, we compared expression of Citron kinase (Citron-K), a target molecule of RhoGTP in non-regenerating dorsal root ganglion neurons (DRGN) after dorsal column (DC) injury, and in regenerating DRGN after either sciatic nerve (SN) injury or preconditioning SN + DC lesion models. We show by microarray that Citron-K mRNA levels in DRGN of a non-regenerating DC injury model were elevated 2-fold compared to those of intact control DRGN. Conversely, Citron-K levels were reduced by 2 and 2.4-fold at 10 days post lesion in the regenerating SN and preconditioning SN + DC lesion models, respectively, compared to levels in control intact DRGN. Western blotting and immunohistochemistry confirmed these observations and localised Citron-K immunostaining to both DRGN and satellite glia. In dissociated, adult rat DRG cell cultures, 80% knockdown of Citron-K, in the presence of inhibitory concentrations of CNS myelin extract (CME), promoted significant disinhibited DRGN neurite outgrowth, only when cells were stimulated with neurotrophic factors. The levels of RhoGTP remained unchanged after Citron-K knockdown in the presence of CME while enhanced cofilin levels correlated with disinhibited DRGN neurite outgrowth. This observation suggests that Citron-K plays a role in axon growth downstream of Rho activation. We conclude that Citron-K regulates actin polymerisation downstream of RhoA and may offer a potentially novel therapeutic approach for promoting CNS axon regeneration. | [Zubair Ahmeda, Michael R. Douglasa b, Martin L. Reada, Martin Berrya, Ann Logana] | Neurobiology of Disease | February 2011 | |
| sciencedirectS0890623810003175 | TGF?-1 and Wnt-3a interact to induce unique gene expression profiles in murine embryonic palate mesenchymal cells | Development of the secondary palate in mammals is a complex process under the control of numerous growth and differentiation factors that regulate key processes such as cell proliferation, synthesis of extracellular matrix molecules, and epithelial–mesenchymal transdifferentiation. Alterations in any one of these processes either through genetic mutation or environmental insult have the potential to lead to clefts of the secondary palate. Members of the TGF? family of cytokines are crucial mediators of these processes and emerging evidence supports a pivotal role for members of the Wnt family of secreted growth and differentiation factors. Previous work in this laboratory demonstrated cross-talk between the Wnt and TGF? signaling pathways in cultured mouse embryonic palate mesenchymal cells. In the current study we tested the hypothesis that unique gene expression profiles are induced in murine embryonic palate mesenchymal cells as a result of this cross-talk between the TGF? and Wnt signal transduction pathways. | [Dennis R. Warnera, Partha Mukhopadhyaya, Guy N. Brockb, Vasyl Pihurb, M. Michele Pisanoa, Robert M. Greenea] | Reproductive Toxicology | February 2011 | |
| sciencedirectS0960076010003948 | Persistent and non-persistent changes in gene expression result from long-term estrogen exposure of MCF-7 breast cancer cells | Life-long estrogen exposure is recognized as a major risk factor for the development of breast cancer. While the initial events in the regulation of gene expression by estrogen have been described in detail, far less is known of the role of estrogen in the long-term regulation of gene expression. In this study, we investigated the effects of long-term exposure of MCF-7 breast cancer cells to 1 nM 17?-estradiol on gene expression with the goal of distinguishing between gene expression that is continually reliant on estrogen receptor (ER) function as opposed to secondary and persistent effects that are downstream of ER. To assess the direct involvement of ER in the differential gene expression of long-term estrogen exposed (LTEE) cells in comparison with that of control cells, we exposed cultures to the selective estrogen receptor modulator raloxifene (RAL). cDNA microarray analysis showed that exposure to RAL inhibited expression of numerous characterized estrogen-regulated genes, including PGR, GREB1, and PDZK1. Genes that were increased in expression in LTEE cells yet were unaffected by RAL exposure included the aryl hydrocarbon receptor (AHR) and numerous other genes that were not previously reported to be regulated by estrogen. Epigenetic regulation was evident for the AHR gene; AhR transcript levels remained elevated for several cell passages after the removal of estrogen. Signal transducer and activator of transcription 1 (STAT1); STAT1-regulated genes including ISG15, IFI27, and IFIT1; and MHC class I genes were also up-regulated in LTEE cells and were unaffected by RAL exposure. STAT1 is commonly overexpressed in breast and other cancers, and is associated with increased resistance to radiation and chemotherapy. This is the first study to relate estrogen exposure to increased STAT1 expression in breast cancer cells, an effect that may represent an additional role of estrogen in the pathogenesis of breast cancer. | [Neal A. Englerta b, Barbara C. Spinka, David C. Spinka b] | The Journal of Steroid Biochemistry and Molecular Biology | February 2011 | |
| sciencedirectS0303720710004922 | miR-29a levels are elevated in the db/db mice liver and its overexpression leads to attenuation of insulin action on PEPCK gene expression in HepG2 cells | MicroRNAs comprise a class of small (∼22 nucleotide) non-coding RNA species and they bind to their complementary sequence on the 3′UTR of target genes and cause translational repression. In the present study, we report that miR-29a levels are significantly elevated in the diabetic db/db mice liver. Further, we report the effects of such elevation on insulin action in HepG2 cells. Overexpression of miR-29a narrowed down insulin mediated Akt phosphorylation without altering the total Akt levels presumably due to another upstream mediator being directly targeted by miR-29a. This hunt led us to the discovery that the p85? subunit of PI3K (phosphoionositide-3-kinase), the upstream molecule in the insulin signaling cascade harbors the miR-29a binding site on its 3′UTR and a marked inhibition of PI3Kp85? was observed by this microRNA. This was consequently accompanied by attenuation of insulin inhibition of PEPCK gene expression. All these events could be significantly prevented in the presence of the miR-29a inhibitor. Our results, for the first time, show the effect of miR-29a in counteracting insulin action on PEPCK gene expression by primarily targeting PI3K and abrogating downstream insulin signaling in HepG2 cells. | [Amit K. Pandeya, Gaurav Vermaa, Saurabh Viga, Swayamprakash Srivastavab, Arvind K. Srivastavab, Malabika Dattaa] | Molecular and Cellular Endocrinology | 30 January 2011 | |
| sciencedirectS0166445X1000408X | Gene expression profiling of the androgen receptor antagonists flutamide and vinclozolin in zebrafish (Danio rerio) gonads | The studies presented in this manuscript focus on characterization of transcriptomic responses to anti-androgens in zebrafish (Danio rerio). Research on the effects of anti-androgens in fish has been characterized by a heavy reliance on apical endpoints, and molecular mechanisms of action (MOA) of anti-androgens remain poorly elucidated. In the present study, we examined effects of a short term exposure (24–96 h) to the androgen receptor antagonists flutamide (FLU) and vinclozolin (VZ) on gene expression in gonads of sexually mature zebrafish, using commercially available zebrafish oligonucleotide microarrays (4 × 44 K platform). We found that VZ and FLU potentially impact reproductive processes via multiple pathways related to steroidogenesis, spermatogenesis, and fertilization. Observed changes in gene expression often were shared by VZ and FLU, as demonstrated by overlap in differentially-expressed genes and enrichment of several common key pathways including: (1) integrin and actin signaling, (2) nuclear receptor 5A1 signaling, (3) fibroblast growth factor receptor signaling, (4) polyamine synthesis, and (5) androgen synthesis. This information should prove useful to elucidating specific mechanisms of reproductive effects of anti-androgens in fish, as well as developing biomarkers for this important class of endocrine-active chemicals. | [Dalma Martinovi?-Weigelta b, Rong-Lin Wangc, Daniel L. Villeneuvea, David C. Bencicc, Jim Lazorchakc, Gerald T. Ankleya] | Aquatic Toxicology | 25 January 2011 | |
| sciencedirectS0014299910010927 | Histamine H4 receptor antagonism inhibits allergen-specific T-cell responses mediated by human dendritic cells | Dendritic cells are potential targets in allergy therapy as they, under the influence of their microenvironment, regulate T-cell responses. Histamine has been shown to promote Th2 polarization by dendritic cells. However, neither the mechanism nor the functionality of the different histamine receptors in this process has been fully elucidated. The aim of the present study was to identify factors involved in histamine-mediated dendritic cell activation as well as to study dendritic cell expression of histamine H1 and H4 receptors and their influence on allergen-specific T-cell responses in grass pollen allergy. Assessment of dendritic cell gene regulation by histamine using mRNA microarrays demonstrated that histamine alters many immunoregulatory genes of which the majority are novel in this context. Additionally, immunocytochemical stainings showed protein expression of histamine H1 and H4 receptors on dendritic cells from healthy and allergic donors. Furthermore, histamine H1 and H4 receptor antagonists (pyrilamine/N-(4-methoxybenzyl)-N′,N′-dimethyl-N-pyridin-2-ylethane-1,2-diamine and JNJ7777120/1-[(5-chloro-1H-indol-2-yl)carbonyl]-4-methylpiperazine, respectively) were shown to influence histamine-induced dendritic cell maturation. Interestingly, JNJ7777120 inhibited dendritic cells’ capacity to induce allergen-specific T-cell proliferation. In conclusion, H4 receptor antagonism suppressed DC-induced, allergen-specific T-cell responses in humans and might thus inhibit allergic responses. This finding indicates that the H4 receptor is a potential treatment target in human allergic conditions. | [Kristina Lundberga, Sissela Broosa, Lennart Greiffb, Carl A.K Borrebaecka, Malin Lindstedta] | European Journal of Pharmacology | 25 January 2011 | |
| sciencedirectS0167011510003526 | Adrenomedullin reduces expression of adhesion molecules on lymphatic endothelial cells | Adrenomedullin (AM) is a novel vasoactive peptide which regulates vascular tone and vascular endothelial cell growth. We recently reported that lymphatic endothelial cells (LECs) are also an attractive target of AM and concluded that AM is a potent mediator of lympangiogenesis. In the present study, we conducted a genome-wide analysis of genes that are regulated by AM in LECs. AM profoundly suppressed gene expression of cell adhesion receptors and inflammatory factors in LECs, such as intercellular adhesion molecule-1 (ICAM-1), vascular adhesion molecule-1 (VCAM-1), endothelial adhesion molecule-1 (E-selectin), interleukin-8, and chemokines, QRT-PCR and flow cytometry analysis showed that AM dose-dependently suppressed the TNF-a-induced mRNA and protein expression of ICAM-1 and VCAM-l. Treatment of LECs with a cell permeable cyclic adenosine monophosphate (cAMP) analog, 8-Br-cAMP, mimicked the suppressive effect of AM on the expression of adhesion molecules. Moreover, both AM and 8-Br-cAMP suppressed TNF-?-induced NF-?B activation in LECs, indicating that AM reduces expression of adhesion molecules in LECs via a cAMP/NF-kB dependent pathway. These results suggest that AM may have an important role in the regulation of the expression of adhesion molecules in lymphatic endothelium, which is critical in the control of immune and inflammatory responses. | [Donghao Jina, Kentaro Otania, Kenichi Yamaharaa, Tomoaki Ikedaa, Noritoshi Nagayaa, Kenji Kangawab] | Regulatory Peptides | 17 January 2011 | |
| sciencedirectS0012160610011383 | Adipocyte derived paracrine mediators of mammary ductal morphogenesis controlled by retinoic acid receptors ? | We generated a transgenic (Tg)-mouse model expressing a dominant negative-(DN)-RAR?, (RAR?G303E) under adipocytes-specific promoter to explore the paracrine role of adipocyte retinoic acid receptors (RARs) in mammary morphogenesis. Transgenic adipocytes had reduced level of RAR?, ? and ?, which coincided with a severely underdeveloped pubertal and mature ductal tree with profoundly decreased epithelial cell proliferation. Transplantation experiments of mammary epithelium and of whole mammary glands implicated a fat-pad dependent paracrine mechanism in the stunted phenotype of the epithelial ductal tree. Co-cultures of primary adipocytes, or in vitro differentiated adipocyte cell line, with mammary epithelium showed that when activated, adipocyte-RARs contribute to generation of secreted proliferative and pro-migratory factors. Gene expression microarrays revealed a large number of genes regulated by adipocyte-RARs. Among them, pleiotrophin (PTN) was identified as the paracrine effectors of epithelial cell migration. Its expression was found to be strongly inhibited by DN-RAR?, an inhibition relieved by pharmacological doses of all-trans retinoic acid (atRA) in culture and in vivo. Moreover, adipocyte-PTHR, another atRA responsive gene, was found to be an up-stream regulator of PTN. Overall, these results support the existence of a novel paracrine loop controlled by adipocyte-RAR that regulates the mammary ductal tree morphogenesis. | [Christine V. Marzan, Tara S. Kupumbati1, Silvina P. Bertran, TraceyAnn Samuels, Boris Leibovitch, Rafael Mira-y-Lopez, Liliana Ossowski, Eduardo F. Farias] | Developmental Biology | 15 January 2011 | |
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| sciencedirectS0378427410017388 | Circulating microRNAs, possible indicators of progress of rat hepatocarcinogenesis from early stages | MicroRNAs (miRNAs), a class of small noncoding RNAs that regulate gene expression at the posttranscriptional level, are believed promising biomarkers for several diseases as well as a novel target of drugs, including cancer. In particular, miRNAs might allow detection of early stages of carcinogenesis. The present study was conducted to provide concrete evidence using chemical-induced hepatocarcinogenesis in rat as a model. We thereby observed aberrant fluctuation of circulating miRNAs in the serum of rats not only with neoplastic lesions such as hepatocellular adenoma (HCA) and hepatocellular carcinoma (HCC), but also with preneoplastic lesions, such as foci of hepatocellular alteration (FHA). Additional qRT-PCR analysis revealed gradual elevation of some circulating miRNAs (i.e., let-7a, let-7f, miR-34a, miR-98, miR-331, miR-338 and miR-652) with progress of hepatocarcinogenesis. Interestingly, increased levels of let-7a, let-7f and miR-98 were statistically significant even in the serum of rats at very early stages. These findings provide the first evidences that circulating miRNAs have the potential to predict carcinogenesis at earlier stages, preneoplastic lesions than with previous biomarkers and that they might be utilized to monitor the progress of tumor development. | [Tokuo Sukata, Kayo Sumida, Masahiko Kushida, Keiko Ogata, Kaori Miyata, Setsuko Yabushita, Satoshi Uwagawa] | Toxicology Letters | 15 January 2011 | |
| sciencedirectS0006291X10022576 | The effect of CD4 receptor downregulation and its downstream signaling molecules on HIV-1 latency | HIV-1 can establish a latent infection in memory CD4 + T cells to evade the host immune response. CD4 molecules can act not only as the HIV-1 receptor for entry but also as the trigger in an intracellular signaling cascade for T-cell activation and proliferation via protein tyrosine kinases. Novel chronic HIV-1-infected A3.01-derived (NCHA) cells were used to examine the involvement of CD4 downstream signaling in HIV-1 latency. CD4 receptors in NCHA cells were dramatically downregulated on its surface but were slightly decreased in whole-cell lysates. The expression levels of CD4 downstream signaling molecules, including P56Lck, ZAP-70, LAT, and c-Jun, were sharply decreased in NCHA cells. The lowered histone modifications of H3K4me3 and H3K9ac correlated with the downregulation of P56Lck, ZAP-70, and LAT in NCHA cells. AP-1 binding activity was also reduced in NCHA cells. LAT and c-Jun suppressed in NCHA cells were highly induced after PMA treatment. In epigenetic analysis, other signal transduction molecules which are associated with active and/or latent HIV-1 infection showed normal states in HIV-1 latently infected cells compared to A3.01 cells. In conclusion, we demonstrated that the HIV-1 latent state is sustained by the reduction of downstream signaling molecules via the downregulation of CD4 and the attenuated activity of transcription factor as AP-1. The HIV-1 latency model via T-cell deactivation may provide some clues for the development of the new antireservoir therapy. | [Kyung-Chang Kima b 1, Hyeon Guk Kima 1, Tae-Young Rohc d, Jihwan Parkc, Kyung-Min Junga, Joo-Shil Leea, Sang-Yun Choib, Sung Soon Kima, Byeong-Sun Choia] | Biochemical and Biophysical Research Communications | 14 January 2011 | |
| sciencedirectS0306452210013564 | Transcription factor Sox11b is involved in spinal cord regeneration in adult zebrafish | Adult zebrafish have the ability to recover from spinal cord injury and exhibit re-growth of descending axons from the brainstem to the spinal cord. We performed gene expression analysis using microarray to find damage-induced genes after spinal cord injury, and found that Sox11b mRNA is up-regulated at 11 days after injury. However, the functional relevance of Sox11b for regeneration is not known. Here, we report that the up-regulation of Sox11b mRNA after spinal cord injury is mainly localized in ependymal cells lining the central canal and in newly differentiating neuronal precursors or immature neurons. Using an in vivo morpholino-based gene knockout approach, we demonstrate that Sox11b is essential for locomotor recovery after spinal cord injury. In the injured spinal cord, expression of the neural stem cell associated gene Nestin, and the proneural gene Ascl1a (Mash1a), which are involved in the self-renewal and cell fate specification of endogenous neural stem cells, respectively, is regulated by Sox11b. Our data indicate that Sox11b promotes neuronal determination of endogenous stem cells and regenerative neurogenesis following spinal cord injury in the adult zebrafish. Enhancing Sox11b expression to promote proliferation and neurogenic determination of endogenous neural stem cells after injury may be a promising strategy in restorative therapy after spinal cord injury in mammals. | [Y. Guoa b, L. Maa, M. Cristofanillia 1, R.P. Harta, A. Haob, M. Schachnera] | Neuroscience | | |
| sciencedirectS0300483X10004853 | Gene expression profiling of DEHP-treated cardiomyocytes reveals potential causes of phthalate arrhythmogenicity | BackgroundDi-(2-ethylhexyl)-phthalate (DEHP) is a widely used plasticizer that imparts flexibility to polyvinyl chloride. We have recently reported that clinically relevant concentrations of DEHP can affect electrical coupling between cardiac myocytes causing significant rhythm disturbances. The underlying causes for this effect are currently unknown.ObjectivesTo use data on global mRNA expression as a tool to reveal possible pathways leading to arrhythmogenic effects of DEHP.MethodsRat neonatal cardiomyocytes were treated with 50 ?g/mL DEHP for 72 h. Extracted RNA samples were hybridized onto Affymetrix Rat Gene 1.0 ST arrays. The mRNA expression of a subset of genes was validated by qRT-PCR. In a second set of experiments, cells were treated in a concentration dependent manner to identify genes affected by low DEHP concentrations.ResultsDEHP exposure is associated with global changes in mRNA expression, with differentially expressed genes overrepresented in 47 Gene Ontology categories. Modified expression was detected for genes associated with cell electrical activity, calcium handling, adhesion and microtubular transport. For a number of key proteins, including kinesin, TGF?2, ?-tubulin, and ?1 & ?1 integrins, changes in mRNA levels were confirmed on the level of the protein expression. A number of genes associated with cell adhesion and electrical activity were identified as early DEHP targets as they were affected by concentrations as low as 1 ?g/mL.ConclusionsExposure of neonatal rat cardiomyocytes to clinically relevant DEHP concentrations leads to global changes in mRNA expression. These changes help to explain the arrhythmogenic effects of phthalates on these cells. | [Nikki Gillum Posnacka, Norman H. Leea, Ronald Brownb, Narine Sarvazyana] | Toxicology | 11 January 2011 | |
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| sciencedirectS0024320510004807 | Role of dipeptidyl peptidase IV (DPP4) in the development of dyslipidemia: DPP4 contributes to the steroid metabolism pathway | AimsWe previously reported that dipeptidyl peptidase IV (DPP4)-deficient rats were susceptible to dyslipidemia induced by streptozotocin (STZ). Hence, it is suggested that DPP4 is important for lipid metabolism.Main methodsIn this study, to verify the role of DPP4 in the development of dyslipidemia, we carried out a microarray analysis of the livers of STZ-treated wild-type and DPP4-deficient rats and showed that the expression levels of genes involved in metabolic processes (steroid metabolic processes and cellular lipid metabolic processes) were significantly altered by STZ treatment.Key findingsIn the wild-type rats, the expression of hydroxysteroid (17-beta) dehydrogenase 2 (Hsd7b2), which catalyzes sex steroid synthesis from cholesterol, was significantly increased by about 15-fold after STZ treatment; however, it did not change in the DPP4-deficient rats. In the STZ untreated group of DPP4-deficient rats, the expression levels of cytochrome P450, subfamily 51 (Cyp51) and sterol-C4-methyl oxidase-like (Sc4mol), which catalyze intermediate steps in cholesterol synthesis, were significantly elevated compared to those of other groups. Similar results were demonstrated in HuH7-cells after DPP4 overexpression or the addition of human sera containing DPP4.SignificanceDPP4 is crucial for regulating the expression of factors related to steroid metabolism such as Cyp51, Sc4mol, and Hsd17b2, and DPP4 deficiency or inhibition may cause dyslipidemia. | [Youichi Satoa b, Sakura Koshiokab c, Yasushi Kirinob c, Takayuki Kamimotob c, Kazuyoshi Kawazoec, Shinji Abec, Kazuo Minakuchic, Yutaka Nakahorib] | Life Sciences | 3 January 2011 | |
| sciencedirectS0006295210006647 | UDP-glucuronosyltransferase 1A6 overexpression in breast cancer cells resistant to methotrexate | Methotrexate is a chemotherapeutic agent used in breast cancer treatment, but the occurrence of resistance limits its therapeutic use. A microarrays analysis between sensitive and methotrexate resistant MCF7 and MDA-MB-468 breast cancer cells pointed out the UDP-glucuronosyltransferase 1A (UGT1A) family as a common deregulated node in both cell lines. This family of genes is involved in Phase II metabolism. UGT1A6 was the main isoform responsible for UGT1A family overexpression in these cells. Its overexpression was not due to gene amplification. Transfection of a vector encoding for UGT1A6 in sensitive cells counteracted the cytotoxicity caused by methotrexate. Methotrexate increased the transcriptional activity from a luciferase reporter driven by the UGT1A6 promoter and induced UGT1A6 mRNA and enzymatic activity. Promoter analysis suggested that UGT1A6 induction by methotrexate could be driven by the transcription factors ARNT (HIF-1) and AhR/ARNT. Cells incubated with anticancer drugs susceptible to glucuronidation, such as tamoxifen or irinotecan, together with methotrexate, showed a lesser degree of cytotoxicity, due to UGT1A6 induction. The pharmacological effect of this induction should be taken into account when combining methotrexate with other drugs that are glucuronidated. | [M. Cristina de Almagroa, Elisabet Selgaa 1, Rémi Thibautb, Cinta Porteb, Véronique Noéa, Carlos J. Ciudada] | Biochemical Pharmacology | 1 January 2011 | |
| sciencedirectS0142961210011804 | The influence of surface microroughness and hydrophilicity of titanium on the up-regulation of TGF?/BMP signalling in osteoblasts. | The topography of titanium implants has been identified as an important factor affecting the osseointegration of surgically placed dental implants. Further modification to produce a hydrophilic microrough titanium implant surface has been shown to increase osseointegration compared with microrough topology alone. This study aimed to determine possible molecular mechanisms to explain this clinical observation by examining differences in the whole genome mRNA expression profile of primary human osteoblasts in response to sand-blasted acid-etched (SLA) and hydrophilic SLA (modSLA) titanium surfaces. A decrease in osteoblast proliferation associated with the titanium surfaces (modSLA > SLA > control) correlated with an increase in expression of the osteogenic differentiation markers BSPII and osteocalcin. Pathway analysis demonstrated that a number of genes associated with the TGF??BMP signalling cascade (BMP2, BMP6, SP1, CREBBP, RBL2, TBS3, ACVR1 and ZFYVE16) were significantly differentially up-regulated with culture on the modSLA surface. BMP2 was shown to have the largest fold change increase in expression which was subsequently confirmed at the protein level by ELISA. Several other genes associated with the functionally important mechanisms relevant to bone healing, such as Wnt signalling (CTNNA1, FBX4, FZD6), angiogenesis (KDR), osteoclastogenesis (HSF2, MCL1) and proteolysis (HEXB, TPP1), were also differentially regulated. These results suggest that chemical (hydrophilic) modification of the SLA surface may result in more successful osseointegration through BMP signalling. | [J. Vlacic-Zischkea, S.M. Hamleta, T. Friisb, M.S. Tonettic, S. Ivanovskia] | Biomaterials | January 2011 | |
| sciencedirectS0045653510011343 | Transcriptome analysis provides insights for understanding the adverse effects of endosulfan in Drosophila melanogaster | Indiscriminate use of agrochemicals worldwide, particularly, persistent organic pollutants (POPs), is of concern. Endosulfan, a POP, is used by various developing/developed nations and is known to adversely affect the development and the hormonal profiles of humans and animals. However, little is known about the molecular players/pathways underlying the adverse effects of endosulfan. We therefore analyzed the global gene expression changes and subsequent adverse effects of endosulfan using Drosophila. We used Drosophila melanogaster keeping in view of its well annotated genome and the wealth of genetic/molecular reagents available for this model organism. We exposed third instar larvae of D. melanogaster to endosulfan (2.0 ?g mL−1) for 24 h and using microarray, we identified differential expression of 256 genes in exposed organisms compared to controls. These genes are associated with cellular processes such as development, stress and immune response and metabolism. Microarray results were validated through quantitative PCR and biochemical assay on a subset of genes/proteins. Taking cues from microarray data, we analyzed the effect of endosulfan on development, emergence and survival of the organism. In exposed organisms, we observed deformities in hind-legs, reminiscent of those observed in higher organisms exposed to endosulfan. In addition, we observed delayed and/or reduced emergence in exposed organisms when compared to their respective controls. Together, our studies not only highlight the adverse effects of endosulfan on the organism but also provide an insight into the possible genetic perturbations underlying these effects, which might have potential implications to higher organisms. | [Anurag Sharmaa c, M. Mishraa c, K. Ravi Rama c, R. Kumarb c, M.Z. Abdind, D. Kar Chowdhuria c] | Chemosphere | January 2011 | |
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| sciencedirectB9780080885049002531 | 4.12 – Plant Bioinformatics and Microarray Technologies | Plants regulate gene transcription to initiate proper developmental programs, to respond to environmental changes, and to maintain homeostasis. Microarrays and other technologies have fundamentally advanced plant biology research by enabling the simultaneous investigation of the transcript abundance of thousands to tens of thousands of genes. This article discusses microarray technology and gives a brief description of the high-throughput sequencing technology that complements and may supersede microarray technology. Microarray data are highly processed to accurately represent gene transcript abundance levels on an array and to enable comparisons among samples, and a number of processing steps are described. The remaining components of the article focus on gene expression analysis. Microarrays are often utilized to compare gene transcript levels between different biological treatments, and we discuss methods for identifying differentially expressed genes in simple and more complex experiments. Finally, microarray data can reveal groups of genes, groups of samples, and groups of genes and samples with similar transcriptional profiles. Clusters of samples reveal shared attributes among experimental treatments. Clusters of genes define novel transcription networks and may be correlated with trait values to identify transcriptional profiles that predict positive or negative outcomes. | [L. Lukens [Author Vitae], S. Zhan [Author Vitae]] | Comprehensive Biotechnology (Second Edition) | | |
| sciencedirectS0014488610003973 | Altered microRNA regulation in Huntington's disease models | Huntington's disease (HD) is a genetic neurodegenerative disease caused by abnormal CAG expansion. MicroRNAs (miRNAs) are short RNA molecules regulating gene expression, and are implicated in a variety of diseases including HD. However, the profiles and regulation of miRNAs in HD are not fully understood. Here, we analyzed the miRNA expression and miRNA regulators in two transgenic models of HD, YAC128 and R6/2 mice, and in a 3-nitropropionic acid (3NP)-induced striatal degeneration rat model. After characterizing the phenotypes by behavioral tests and histological analyses, we profiled striatal miRNAs using a miRNA microarray and we measured the key molecules involved in miRNA biogenesis and function. YAC128 mice showed upregulation-dominant miRNA expressions at 5 months and downregulation-dominant expressions at 12 months. Concomitantly, the expressions of Drosha-DGCR8, Exportin-5, and Dcp1 were increased at 5 months, and the expression of Dicer was decreased at 12 months. In 10-week-old R6/2 mice, downregulation was dominant in the miRNA expressions and the level of Drosha decreased concomitantly. Nine miRNAs (miR-22, miR-29c, miR-128, miR-132, miR-138, miR-218, miR-222, miR-344, and miR-674*) were commonly down-regulated in both the 12-month-old YAC128 and 10-week-old R6/2 mice. Meanwhile, 3NP rats showed dynamic changes in the miRNA profiles during disease development and a few miRNAs with altered expression. Our results show that transgenic HD mice have abnormal miRNA biogenesis. This information should aid in future studies on therapeutic application of miRNAs in HD. | [Soon-Tae Leea b 1, Kon Chua b 1, Woo-Seok Ima, Hye-Jin Yoona, Ji-Yeon Ima, Jung-Eun Parka, Ki-Ho Parkc, Keun-Hwa Junga b, Sang Kun Leea b, Manho Kima b, Jae-Kyu Roha b] | Experimental Neurology | January 2011 | |
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| sciencedirectS1546509811310011 | 1 – An introduction to metals in fish physiology and toxicology: basic principles | A brief history of metals, their early investigation in fish by physiologists and toxicologists, and current terminology are presented. The conceptual basis for the topics explored in each of the metal-specific chapters of these two volumes is then described. These include sources of metals, their economic importance, environmental situations of concern, essentiality or non-essentiality, bioconcentration or lack thereof, and the overarching importance of chemical speciation in understanding their effects on fish. The techniques used to derive ambient water quality criteria for metals are explained. Key mechanisms of acute and chronic toxicity are reviewed, as well as recent findings on the mechanisms and sites of uptake, internal handling, biotransformation, subcellular partitioning, detoxification, storage, and excretion. Important new research fronts focus on behavioral effects, molecular and omic analyses of cellular responses, and the effects of interacting metals in fish. Similarities and differences among the metals dealt with in these volumes are highlighted. | [Chris M. Wood] | Fish Physiology | 2011 | |
| sciencedirectS0090825810007183 | The expression of the miRNA-200 family in endometrial endometrioid carcinoma | Objective.Recent reports suggest that targeting the unique miRNAs highly expressed in several cancers may be a promising approach in the development of new cancer therapeutic tools. The purpose of this study was to evaluate the roles of miRNAs as therapeutic targets in human endometrial endometrioid carcinomas (EECs).Methods.We evaluated the differential expressions of miRNAs in EECs and normal endometrial tissues using microarrays and cluster analysis. After validation of differentially expressed miRNAs in another set of EECs and normal endometrial tissues, we performed the in vitro experiment using endometrial cancer cells with anti-miRNA (anti-miR) to evaluate the roles of miRNAs that are highly expressed in EECs for cell proliferation and chemosensitivity.Results.A miRNA microarray showed that the miR-200 family, including hsa-miR-141, hsa-miR-200a, hsa-miR-200b, hsa-miR-200c, and hsa-miR-429, was up-regulated in EECs as compared with that in normal endometrial tissues. When we treated endometrial cancer cells with specific anti-miRs, including anti-miR-141, -200a, -200b, -200c, or -429, we found that anti-miR-200a, -200b, -200c, and -429 significantly inhibited the growth of HEC-1A cells and anti-miR-141, -200c, and -429 significantly inhibited the growth of Ishikawa cells. Moreover, transfection with anti-miR-429 enhanced the cytotoxic effect of cisplatin in HEC-1A cells.Conclusions.These results indicate that the miR-200 family is highly expressed in EECs compared with that of normal endometrial tissues and could play an important role in cancer growth. Specifically, anti-miR-429 could enhance the cytotoxic activity with cisplatin in EECs. Therefore, the miR-200 family may offer new candidate targets to be exploited in therapeutic strategies for patients with these carcinomas. | [Jeong-Won Leea 1, Young-Ae Parka 1, Jung-Joo Choia, Yoo Young Leea, Chul-Jung Kima, ChelHun Choia, Tae-Joong Kima, Nak Woo Leeb, Byoung-Gie Kima, Duk-Soo Baea] | Gynecologic Oncology | January 2011 | |
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| sciencedirectS1389172310002604 | Long-term continuous adaptation of Escherichia coli to high succinate stress and transcriptome analysis of the tolerant strain | To understand the responses of Escherichia coli to high succinate stress and to determine the roles of upregulated genes in high succinate tolerance, a continuous culture of wild-type E. coli W3110 was performed for 268 days in a gradually increasing concentration of succinate. Growth of the final adapted strain, designated DST160, proceeded growth rate of 0.20 h− 1 without a lag phase in medium containing 0.592 M succinate, while the wild-type strain showed 0.02 h− 1 in 38 h. The growth rates of DST160 in media containing either 0.61 M NaCl, 0.61 M KCl, or at pH 4.5 were 25% higher, 18% lower, and 57% higher than those of wild-type, respectively, implying DST160 acquired salt tolerance and pH shock tolerance as well as succinate tolerance. DNA microarray and real-time PCR results indicated that genes controlling active transport and biosynthesis of osmoprotectants were upregulated in DST160 compared to W3110. When ygjE, encoding a putative tartrate/succinate antiporter, and betA, encoding betaine biosynthesis, were expressed in a wild-type E. coli as represent genes for active transport and osmoprotectant synthesis, respectively, greater growth rates were achieved under 0.592 M succinate stress conditions (seven times higher due to ygjE expression and six times higher due to betA expression) than wild-type. The potential to design a metabolic engineering for microbial succinate production is suggested based on the transcriptional regulation of the long-term adapted DST160. | [Yeong-Deok Kwon1 § †, Susie Kim1 †, Sang Yup Lee2, Pil Kim1] | Journal of Bioscience and Bioengineering | January 2011 | |
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| sciencedirectS0022191010003100 | Changes in oxygen and carbon dioxide environment alter gene expression of cowpea bruchids | Hermetic storage is a widely adopted technique for preventing stored grain from being damaged by storage insect pests. In the air-tight container, insects consume oxygen through metabolism while concomitantly raising carbon dioxide concentrations through respiration. Previous studies on the impact of hypoxia and hypercapnia on feeding behavior of cowpea bruchids have shown that feeding activity gradually decreases in proportion to the changing gas concentrations and virtually ceases at approximately 3–6% (v/v) oxygen and 15–18% carbon dioxide. Further, a number of bruchid larvae are able to recover their feeding activity after days of low oxygen and high carbon dioxide, although extended exposure tends to reduce survival. In the current study, to gain insight into the molecular mechanism underpinning the hypoxia-coping response, we profiled transcriptomic responses to hypoxia/hypercapnia (3% oxygen, 17% carbon dioxide for 4 and 24 h) using cDNA microarrays, followed by quantitative RT-PCR verification of selected gene expression changes. A total of 1046 hypoxia-responsive cDNAs were sequenced; these clustered into 765 contigs, of which 645 were singletons. Many (392) did not show homology with known genes, or had homology only with genes of unknown function in a BLAST search. The identified differentially-regulated sequences encoded proteins presumptively involved in nutrient transport and metabolism, cellular signaling and structure, development, and stress responses. Gene expression profiles suggested that insects compensate for lack of oxygen by coordinately reducing energy demand, shifting to anaerobic metabolism, and strengthening cellular structure and muscular contraction. | [Yong Hun Chia b, Ji-Eun Ahna, Dae-Jin Yunb, Sang Yeol Leeb, Tong-Xian Liuc, Keyan Zhu-Salzmana d] | Journal of Insect Physiology | January 2011 | |
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| sciencedirectB9780123748140000173 | Chapter 17 – Data Extraction, Transformation, and Dissemination through ZFIN | The publication of a research article is the beginning of the digital life of its associated data. In this article, we will present an overview of how data are incorporated into ZFIN, with a particular emphasis on helping researchers make their work accessible to online databases. | [Douglas G. Howe, Ken Frazer, David Fashena, Leyla Ruzicka, Yvonne Bradford, Sridhar Ramachandran, Barbara J. Ruef, Ceri Van Slyke, Amy Singer, Monte Westerfield] | Methods in Cell Biology | | |
| sciencedirectS0168945210002013 | Identification of candidate genes important for frost tolerance in Festuca pratensis Huds. by transcriptional profiling | Studies of differential gene expression between cold acclimated (CA) and non-cold acclimated (NA) plants yield insight into how plants prepare for cold stress at the transcriptional level. Furthermore genes involved in the cold acclimation process are good candidate loci for genetic variation in frost tolerance and winter survival. In this study we combine different approaches to try to decode the genetics of cold acclimation and frost tolerance in meadow fescue (Festuca pratensis Huds). An EST library of cold acclimation responsive genes was established by suppression subtractive hybridization (SSH), and a microarray experiment was used to identify gene expression differences between high and low frost tolerance genotypes in response to cold acclimation. Many genes known to be involved in CA in other species were confirmed to be involved in CA in F. pratensis, however, 18% of the ESTs did not show significant homology to any database proteins. Seven genes were found to be differentially expressed (>2-fold) between high and low frost tolerance genotypes. Two of these genes, FpQM and FpTPT, represent interesting candidate genes for frost tolerance in perennial forage grasses. | [Heidi Rudia, Simen R. Sandvea, Lars M. Opsetha, Arild Larsenb, Odd Arne Rognlia] | Plant Science | January 2011 | |
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| sciencedirectS0041008X10003625 | Reactive oxygen species and oxidative DNA damage mediate the cytotoxicity of tungsten–nickel–cobalt alloys in vitro | Tungsten alloys (WA) have been introduced in an attempt to find safer alternatives to depleted uranium and lead munitions. However, it is known that at least one alloy, 91% tungsten–6% nickel–3% cobalt (WNC-91–6–3), causes rhabdomyosarcomas when fragments are implanted in rat muscle. This raises concerns that shrapnel, if not surgically removable, may result in similar tumours in humans. There is therefore a clear need to develop rapid and robust in vitro methods to characterise the toxicity of different WAs in order to identify those that are most likely to be harmful to human health and to guide development of new materials in the future. In the current study we have developed a rapid visual in vitro assay to detect toxicity mediated by individual WA particles in cultured L6-C11 rat muscle cells. Using a variety of techniques (histology, comet assay, caspase-3 activity, oxidation of 2′7′-dichlorofluorescin to measure the production of reactive oxygen species and whole-genome microarrays) we show that, in agreement with the in vivo rat carcinogenicity studies, WNC-91–6–3 was the most toxic of the alloys tested. On dissolution, it produces large amounts of reactive oxygen species, causes significant amounts of DNA damage, inhibits caspase-3, triggers a severe hypoxic response and kills the cells in the immediate vicinity of the alloy particles within 24 h. By combining these in vitro data we offer a mechanistic explanation of the effect of this alloy in vivo and show that in vitro tests are a viable alternative for assessing new alloys in the future. | [R.M. Harris, T.D. Williams, N.J. Hodges, R.H. Waring] | Toxicology and Applied Pharmacology | 1 January 2011 | |
| sciencedirectB978012381978910085X | Chapter 85 – Vitamin D Actions in Mammary Gland and Breast Cancer | SummaryThe vitamin D receptor (VDR) is highly expressed in breast tissue, suggesting that vitamin D status may directly influence physiology or pathology of the mammary gland. Consistent with this concept, complete disruption of VDR function in mice alters the balance between proliferation and apoptosis in the mammary gland and is associated with enhanced susceptibility to carcinogenesis. In vitro studies have demonstrated that the VDR ligand, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), exerts growth inhibitory effects on normal human mammary epithelial cells that contribute to maintenance of the differentiated phenotype and protection of the genome. Mammary cells also express Cyp27B1 and have the ability to internalize the major circulating vitamin D metabolite, 25-hydroxyvitamin D3 (25(OH)D3), and convert it to 1,25(OH)2D3. Dietary vitamin D supplementation, or chronic treatment with synthetic VDR agonists, alters mammary gland morphology and reduces the incidence of carcinogen-induced mammary tumors in rodents. VDR expression is often retained in transformed cells, and VDR agonists elicit anti-proliferative and pro-apoptotic signaling in human breast cancer cells in vitro and in animal models of breast cancer. Based on these observations, clinical trials are ongoing to assess the effectiveness of dietary or supplemental vitamin D and synthetic VDR agonists in the prevention or treatment of human breast cancer. Collectively, these observations have reinforced the need to further define the human requirement for vitamin D and the molecular actions of the VDR in relation to prevention and treatment of breast cancer. | [JoEllen Welsh] | Vitamin D (Third Edition) — Vitamin D | | |
| sciencedirectS0306452210013485 | Genetic and histologic evidence implicates role of inflammation in traumatic brain injury-induced apoptosis in the rat cerebral cortex following moderate fluid percussion injury | Traumatic brain injury (TBI) causes massive brain damage. However, the secondary injury and temporal sequence of events with multiple mechanisms after the insult has not been elucidated. Here, we examined the occurrence of apoptosis and a causal relationship between inflammation and apoptosis in the TBI brain. Following a lateral moderate fluid percussion injury model of TBI in adult rats, microarray analyses detected apparent changes in the expression levels of apoptosis-related genes which revealed time-dependent expression patterns for 23 genes in the lateral cortex. The upregulated 23 genes included inflammatory cytokines such as interleukin 1 (IL-1) ?, IL-1?, and tumor necrotic factor (TNF) which immediately increased at 3 h following the injury. Time-dependent gene expression profile analyses showed that apoptosis was subsequently induced following inflammation. These results taken together suggested changes in expression of apoptosis-related genes may be associated with inflammatory response. Accompanying this surge of cell death genes after TBI was a neurostructural pathologic hallmark of apoptosis characterized by leakage of cytochrome c into cytoplasm, DNA fragmentation and apoptotic cells in the lateral cortex of the impacted hemisphere. Caspase-3 positive cells in the TBI brain were initially sporadic after 3 h, but these apoptotic cells subsequently increased and populated the cerebral cortex at 6 and 12 h, and gradually reached a plateau by 48 h. Interestingly, the expression profile of CD68 macrophage labeled cells closely resembled that of apoptotic cells after TBI, including the role of inflammatory signaling pathway in the progression of apoptotic cell death. These results taken together suggest that TBI induced upregulation of apoptosis-related genes, concomitant with the detection of apoptotic brain pathology during the 3–48 h post-injury period, which may be likely mediated by inflammation. Therapies designed at abrogating apoptosis and/or inflammation may prove effective when initiated at this subacute TBI phase. | [H. Shojoa b, Y. Kanekob, T. Mabuchic, K. Kibayashid, N. Adachia, C.V. Borlonganb] | Neuroscience | 29 December 2010 | |
| sciencedirectS0014299910008411 | Irbesartan enhances GLUT4 translocation and glucose transport in skeletal muscle cells | Irbesartan, an angiotensin II type 1 receptor blocker has been reported to alleviate metabolic disorder in animal studies and human clinical trials. Although this effect may be related to the ability of irbesartan to serve as a partial agonist for the peroxisome proliferator-activated receptor (PPAR)-?, the target tissues on which irbesartan acts remain poorly defined. As muscle glucose transport plays a major role in maintaining systemic glucose homeostasis, we investigated the effect of irbesartan on glucose uptake in skeletal muscle cells. In C2C12 myotubes, 24-h treatment with irbesartan significantly promoted both basal and insulin-stimulated glucose transport. In L6-GLUT4myc myoblasts, irbesartan caused a significant increase in glucose transport and GLUT4 translocation to the cell surface in a concentration-dependent manner. Valsartan, another angiotensin II type 1 receptor blocker had no effect on either glucose uptake or GLUT4 translocation, implying that these actions on glucose transport are independent of angiotensin II receptor blockade. Moreover, irbesartan exerted these effects in an additive manner with insulin, but not with acute treatment for 3 h, suggesting that they may require the synthesis of new proteins. Finally, in insulin-resistant Zucker fatty rat, irbesartan (50 mg/kg/day for 3 weeks) significantly ameliorated insulin resistance without increasing weight gain. We conclude that irbesartan has a direct action, which can be additive to insulin, of promoting glucose transport in skeletal muscle. This may be beneficial for ameliorating obesity-related glucose homeostasis derangement. | [Tatsuo Kobayashi, Yuko Akiyama, Nobuteru Akiyama, Hideaki Katoh, Sachiko Yamamoto, Kenzo Funatsuki, Toru Yanagimoto, Mitsuru Notoya, Kenji Asakura, Toshihiro Shinosaki, Kohji Hanasaki] | European Journal of Pharmacology | 15 December 2010 | |
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| sciencedirectS0165242710003429 | Methods for transcriptomic analyses of the porcine host immune response: Application to Salmonella infection using microarrays | Technological developments in both the collection and analysis of molecular genetic data over the past few years have provided new opportunities for an improved understanding of the global response to pathogen exposure. Such developments are particularly dramatic for scientists studying the pig, where tools to measure the expression of tens of thousands of transcripts, as well as unprecedented data on the porcine genome sequence, have combined to expand our abilities to elucidate the porcine immune system. In this review, we describe these recent developments in the context of our work using primarily microarrays to explore gene expression changes during infection of pigs by Salmonella. Thus while the focus is not a comprehensive review of all possible approaches, we provide links and information on both the tools we use as well as alternatives commonly available for transcriptomic data collection and analysis of porcine immune responses. Through this review, we expect readers will gain an appreciation for the necessary steps to plan, conduct, analyze and interpret the data from transcriptomic analyses directly applicable to their research interests. | [C.K. Tugglea, S.M.D. Bearsonb, J.J. Uthea, T.H. Huanga, O.P. Couturea, Y.F. Wanga, D. Kuharc, J.K. Lunneyc, V. Honavard] | Veterinary Immunology and Immunopathology | 15 December 2010 | |
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| sciencedirectS159086581000160X | Molecular mechanisms underlying human adipose tissue-derived stromal cells differentiation into a hepatocyte-like phenotype | BackgroundAdipose tissue-derived stromal cells (ATSCs) hold great promises in regenerative medicine. In the last decade, several studies have reported the plasticity of ATSCs toward a hepatocyte-like phenotype. Nonetheless, the molecular mechanisms underlying the conversion from a mesenchymal to an epithelial phenotype remain poorly understood.AimIn this study, we compared the full genome expression profiles of ATSCs cultured for 4 weeks under pro-hepatogenic conditions to undifferentiated ATSCs, in order to depict the molecular events involved in ATSC hepatic transdifferentiation.MethodsAnalysis was performed using the Affymetrix human focus arrays. Sets of differentially expressed genes were functionally categorized in order to understand which pathways drive the hepatic conversion and interesting targets were validated by Q-PCR.ResultsATSC-derived hepatocyte-like cells activate several genes associated with specific liver functions, including protein metabolism, innate immune response regulation, and biodegradation of toxic compounds. Furthermore, microarray analysis highlighted downregulation of transcripts associated with the mesenchymal lineage, while epithelial-related genes were overexpressed.ConclusionOur data suggest that the in vitro system used in this study drove ATSCs toward a hepatic conversion through a subtle regulation of molecular pathways controlling lineage commitment that promote mesenchymal-epithelial transition. | [Nathalie Saulniera, Anna Chiara Piscagliaa, Maria Ausiliatrice Puglisia, Marta Barbaa, Vincenzo Arenab, Giovambattista Panic, Sergio Alfierid, Antonio Gasbarrinia] | Digestive and Liver Disease | December 2010 | |
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| sciencedirectS0163725810001737 | Information technology solutions for integration of biomolecular and clinical data in the identification of new cancer biomarkers and targets for therapy | The quest for new cancer biomarkers and targets for therapy requires not only the aggregation and analysis of heterogeneous biomolecular data but also integration of clinical data. In this review we highlight information technology solutions for the integration of biomolecular and clinical data and focus on a solution at the departmental level, i.e., decentralized and medium-scale solution for groups of labs working on a specific topic. Both, hardware and software requirements are described as well as bioinformatics methods and tools for the data analysis. The highlighted IT solutions include storage architecture, high-performance computing, and application servers. Additionally, following computational approaches for data integration are reviewed: data aggregation, integrative data analysis including methodological aspects as well as examples, biomolecular pathways and network reconstruction, and mathematical modelling. Finally, a case study in cancer immunology including the used computational methods is shown, demonstrating how IT solutions for integrating biomolecular and clinical data can help to identify new cancer biomarkers for improving diagnosis and predicting clinical outcome. | [Hubert Hackla, Gernot Stockera, Pornpimol Charoentonga, Bernhard Mlecnikb, Gabriela Bindeab, Jerome Galonb, Zlatko Trajanoskia] | Pharmacology & Therapeutics | December 2010 | |
| sciencedirectS1357272510003286 | The existence of multipotent stem cells with epithelial–mesenchymal transition features in the human liver bud | During early stage of embryonic development, the liver bud, arising from the foregut endoderm, is the beginning for the formation of future liver three-dimensional structure. While the gene expression profiles associated with this developmental stage have been well explored, the detailed cellular events are not as clear. Epithelial–mesenchymal transition (EMT) was thought to be essential for cell migration in the early vertebrate embryo but seldom demonstrated in human liver development. In this study, we tried to identify the cell populations with both stem cell and EMT features in the human liver bud. Our in situ studies show that the phenotype of EMT occurs at initiation of human liver development, accompanied by up-regulation of EMT associated genes. A human liver bud derived stem cell line (hLBSC) was established, which expressed not only genes specific to both mesenchymal cells and hepatic cells, but also octamer-binding protein 4 (OCT4) and nanog. Placed in appropriate media, hLBSC differentiated into hepatocytes, adipocytes, osteoblast-like cells and neuron-like cells in vitro. When transplanted into severe combined immunodeficiency mice pre-treated by carbon tetrachloride, hLBSC engrafted into the liver parenchyma and proliferated. These data suggests that there are cell populations with stem cell and EMT-like properties in the human liver bud, which may play an important role in the beginning of the spatial structure construction of the liver. | [Juan Sua, Pu Youa, Wen-Lin Lia, Xin-Rong Taoa, Hai-Ying Zhua, Yu-Cheng Yaoa b, Hong-Yu Yuc, Qing-Wang Hana, Bing Yua, Fang-Xia Liua, Jun Xud, Joseph T.Y. Laue, Yi-Ping Hua] | The International Journal of Biochemistry & Cell Biology | December 2010 | |
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| sciencedirectS1090023309003566 | Equine transcriptome quantification using human GeneChip arrays can be improved using genomic DNA hybridisation and probe selection | Affymetrix GeneChip arrays are a powerful tool for transcriptome profiling and have been applied to a wide range of species. A genomic DNA (gDNA)-based probe selection method has been developed which broadens the range of species to which GeneChips may be successfully applied. This study demonstrated that gDNA-based probe selection on the Affymetrix U133 + 2 GeneChip array can be used to study the equine transcriptome which, to date, has received only limited attention. More than 29,000 transcripts can be detected in equine brain and liver and in primary cultures of equine articular chondrocytes. Gene ontology analysis of differentially expressed genes revealed the presence of expected categories within each tissue. The level of gene expression could also be correlated with the phenotypes and specialised functions of each tissue. The results demonstrated that probe selection on a human chip can be successfully used to study the equine transcriptome. | [Neil S. Grahama, Abigail L. Clutterbuckb, Nicholas Jamesa, Richard G. Leab, Ali Mobasherib, Martin R. Broadleya, Sean T. Maya] | The Veterinary Journal | December 2010 | |
| sciencedirectS0043135410004719 | Monitoring of bacterial communities during low temperature thermal treatment of activated sludge combining DNA phylochip and respirometry techniques | Sludge reduction is one of the major challenges in biological wastewater treatment. One approach is to increase the sludge degradation yield together with the biodegradation kinetics. Among the various sludge pretreatment strategies proposed, thermal pretreatment at around 65 °C was described as promising. The enhancement in the biodegradation activity due to the selection of thermophilic hydrolytic bacteria was proposed, but further experiments are needed to demonstrate the specific role of these bacteria. In this study, concentrated activated sludge grown at 20 °C was subjected to thermal treatment at 65 °C for different periods. The originality of the work relied on a polyphasic approach based on the correlation between kinetics (chemical oxygen demand, COD; mixed liquor suspended solids, MLSS), bacterial activity (respirometry) and bacterial community structure (phylochip monitoring) in order to characterize the mechanisms involved in the thermal reduction of sludge. The bacterial activity in the aeration basin decreased to a very low level when recycling sludge was treated at 65 °C from 13 to 60 h, but then, started to increase after 60 h. In parallel to these fluctuations in activity, a drastic shift occurred in the bacterial community structure with the selection of thermophilic bacteria (mainly related to genera Paenibacillus and Bacillus), which are known for their specific hydrolases. | [Marina Hérya b 1, Hervé Sanguinc d e 1, Sergio Perez Fabiela b, Xavier Lefebvrea b, Timothy M. Vogelf, Etienne Paula b, Sandrine Alfenorea b] | Water Research | December 2010 | |
| sciencedirectS0378427410016681 | Arsenite exposure in human lymphoblastoid cell lines induces autophagy and coordinated induction of lysosomal genes | Chronic exposure to inorganic arsenic is associated with diverse, complex diseases, making the identification of the mechanism underlying arsenic-induced toxicity a challenge. An increasing body of literature from epidemiological and in vitro studies has demonstrated that arsenic is an immunotoxicant, but the mechanism driving arsenic-induced immunotoxicity is not well established. We have previously demonstrated that in human lymphoblastoid cell lines (LCLs), arsenic-induced cell death is strongly associated with the induction of autophagy. In this study we utilized genome-wide gene expression analysis and functional assays to characterize arsenic-induced effects in seven LCLs that were exposed to an environmentally relevant, minimally cytotoxic, concentration of arsenite (0.75 ?M) over an eight-day time course. Arsenic exposure resulted in inhibition of cellular growth and induction of autophagy (measured by expansion of acidic vesicles) over the eight-day exposure duration. Gene expression analysis revealed that arsenic exposure increased global lysosomal gene expression, which was associated with increased functional activity of the lysosome protease, cathepsin D. The arsenic-induced expansion of the lysosomal compartment in LCL represents a novel target that may offer insight into the immunotoxic effects of arsenic. | [Alicia M. Bolt, Randi M. Douglas, Walter T. Klimecki] | Toxicology Letters | 30 November 2010 | |
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| sciencedirectS0022283610009794 | The Roles of Stress-Activated Sty1 and Gcn2 Kinases and of the Protooncoprotein Homologue Int6/eIF3e in Responses to Endogenous Oxidative Stress during Histidine Starvation | In fission yeast, Sty1 and Gcn2 are important protein kinases that regulate gene expression in response to amino acid starvation. The translation factor subunit Int6/eIF3e promotes Sty1-dependent response by increasing the abundance of Atf1, a transcription factor targeted by Sty1. While Gcn2 promotes expression of amino acid biosynthesis enzymes, the mechanism and function of Sty1 activation and Int6/eIF3e involvement during this nutrient stress are not understood. Here we show that mutants lacking sty1+ or gcn2+ display reduced viabilities during histidine depletion stress in a manner suppressible by the antioxidant N-acetyl cysteine, suggesting that these protein kinases function to alleviate endogenous oxidative damage generated during nutrient starvation. Int6/eIF3e also promotes cell viability by a mechanism involving the stimulation of Sty1 response to oxidative damage. In further support of these observations, microarray data suggest that, during histidine starvation, int6? increases the duration of Sty1-activated gene expression linked to oxidative stress due to the initial attenuation of Sty1-dependent transcription. Moreover, loss of gcn2 induces the expression of a new set of genes not activated in wild-type cells starved for histidine. These genes encode heatshock proteins, redox enzymes, and proteins involved in mitochondrial maintenance, in agreement with the idea that oxidative stress is imposed on gcn2? cells. Furthermore, early Sty1 activation promotes rapid Gcn2 activation on histidine starvation. These results suggest that Gcn2, Sty1, and Int6/eIF3e are functionally integrated and cooperate to respond to oxidative stress generated during histidine starvation. | [Naoki Nemoto1 †, Tsuyoshi Udagawa1 †, Takahiro Ohira1 †, Li Jiang2, Kouji Hirota3, Caroline R.M. Wilkinson4, Jürg Bähler5, Nic Jones4, Kunihiro Ohta6, Ronald C. Wek2, Katsura Asano1] | Journal of Molecular Biology | 26 November 2010 | |
| sciencedirectS0303720710002868 | Chronology and complexities of ovarian tumorigenesis in FORKO mice: Age-dependent gene alterations and progressive dysregulation of Major Histocompatibility Complex (MHC) Class I and II profiles | Among gynecologic malignancies ovarian cancer is the deadliest and most difficult to detect at early stages. As ovarian tumors have long latency and are relatively more frequent in postmenopausal women, revealing chronological changes in model systems might help in the discovery of novel molecular targets and diagnostic biomarkers for disease detection and management. Follitropin receptor knockout (FORKO) mice with early and sustained sex steroid hormone disharmony develop various age-dependent ovarian abnormalities including increased incidence ovarian tumors in complete absence of ovulation. These mutants show various tumor cell types including those related to ovarian surface epithelium around 12–15 months of age. To explore why the FORKO mice develop ovarian tumors later in life, we assessed global gene expression changes during the pre-tumor period (at 8 months). Age-matched wild-type and FORKO mice were compared to gain a comprehensive view of genes that are misregulated, even before overt tumors appear in mutants. Applying a conservative 2-fold change to detect changes, our study identified 476 genes (338 upregulated and 138 downregulated) to be altered between 8-month-old FORKO and wild-type ovaries. Using Ingenuity Pathway Analysis (IPA), we found highly significant alterations in five functional networks in pre-tumor stage FORKO ovaries. Notably, the top network to change in 8-month-old FORKO ovaries was associated with functions implicated in immune system development and function. We selected 9 immune related genes that are reportedly altered in Epithelial Ovarian Cancer (EOC) in women and confirmed their expression and chronology of changes in FORKO ovaries before and after tumor development. Our data indicate that immune surveillance mechanisms are compromised with in a 4-month window of tumorigenic alterations. In addition, expression of previously unrecognized genes misregulated in the dysfunctional FORKO ovaries suggests mechanisms not yet appreciated to date. We propose that a better understanding of genes that change before overt tumors develop could provide useful insights into ovarian carcinogenesis and open the door to additional new targets for treating ovarian cancers. | [J. Aravindakshan, X.L. Chen, M.R. Sairam] | Molecular and Cellular Endocrinology | 25 November 2010 | |
| sciencedirectS0042682210004769 | Clonal expansion of HTLV-1 positive CD8+ cells relies on cIAP-2 but not on c-FLIP expression | Here we investigate the mechanisms by which HTLV-1 infection prevents the cell death of CD8+ T cells in vivo. We show that upon natural infection, cloned CD8+ but not CD4+ cells from patients without malignancy become resistant to Fas-mediated cell death and acquire an antiapoptotic transcriptome that includes the overexpression of cIAP-2 and c-FLIP(L). CD8+ lymphocyte-restricted cIAP-2 overexpression correlates with resistance to Fas-mediated apoptosis and depends on tax expression via NF-KappaB. In contrast, in the same CD8+ cells, the HTLV-1-dependent overexpression of c-FLIP(L) does not correlate with resistance to Fas-mediated cell death nor with tax expression. In the present model, infected CD8+ clones are the only cell subtype in which cIAP-2 expression correlates with resistance to cell death. These results support a role for Tax-dependent cIAP-2 expression in preventing the death of naturally infected CD8+ cells and thereby in their clonal expansion in vivo. | [Linda Zanea, David Sibona b 1, Catherine Legrasc, Joël Lachuerc, Anne Wierinckxc, Patrick Mehlend, Marie-Hélène Delfau-Laruee, Antoine Gessainf, Olivier Goutg, Christiane Pinatela, Agnès Lançona, Franck Mortreuxa, Eric Wattela b] | Virology | 25 November 2010 | |
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| sciencedirectS0012160610010407 | Protein kinase A regulates GDNF/RET-dependent but not GDNF/Ret-independent ureteric bud outgrowth from the Wolffian duct | Embryonic kidney development begins with the outgrowth of the ureteric bud (UB) from the Wolffian duct (WD) into the adjacent metanephric mesenchyme (MM). Both a GDNF-dependent and GDNF-independent (Maeshima et al., 2007) pathway have been identified. In vivo and in vitro, the GDNF-dependent pathway is inhibited by BMPs, one of the factors invoked to explain the limitation of UB formation in the unbudded regions of the WD surrounding the UB. However, the exact mechanism remains unknown. Here a previously described in vitro system that models UB budding from the WD was utilized to study this process. Because Protein kinase A (PKA) activation has been shown to prevent migration, morphogenesis and tubulogenesis of epithelial cells (Santos et al., 1993), its activity in budded and non-budded portions of the GDNF-induced WD was analyzed. The level of PKA activity was 15-fold higher in the unbudded portions of the WD compared to budded portions, suggesting that PKA activity plays a key role in controlling the site of UB emergence. Using well-characterized PKA agonists and antagonists, we demonstrated that at various levels of the PKA-signaling hierarchy, PKA regulates UB outgrowth from the WD by suppressing budding events. This process appeared to be PKA-2 isoform specific, and mediated by changes in the duct rather than the surrounding mesenchyme. In addition, it was not due to changes in either the sorting of junctional proteins, cell death, or cell proliferation. Furthermore, the suppressive effect of cAMP on budding did not appear to be mediated by spread to adjacent cells via gap junctions. Conversely, antagonism of PKA activity stimulated UB outgrowth from the WD and resulted in both an increase in the number of buds per unit length of WD as well as a larger surface area per bud. Using microarrays, analysis of gene expression in GDNF-treated WDs in which the PKA pathway had been activated revealed a nearly 14-fold decrease in Ret, a receptor for GDNF. A smaller decrease in GFR?1. a co-receptor for GDNF, was also observed. Using Ret-null WDs, we were able to demonstrate that PKA regulated GDNF-dependent budding but not GDNF-independent pathway for WD budding. We also found that BMP2 was higher in unbudded regions of the GDNF-stimulated WD. Treatment of isolated WDs with BMP2 suppressed budding and resulted in a 3-fold increase in PKA activity. The data suggests that the suppression of budding by BMPs and possibly other factors in non-budded zones of the WD may be regulated in part by increased PKA activity, probably partially through downregulation of Ret/GFR?1 coreceptor expression. | [James B. Teeb, Yohan Choia, Mita M. Shaha, Ankur Dnyanmotea, Derina E. Sweeneya, Tom F. Gallegosa, Kohei Johkuraa, Chiharu Itoa, Kevin T. Busha, Sanjay K. Nigama] | Developmental Biology | 15 November 2010 | |
| sciencedirectS0041008X10003157 | Preferential induction of the AhR gene battery in HepaRG cells after a single or repeated exposure to heterocyclic aromatic amines | 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) and 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) are two of the most common heterocyclic aromatic amines (HAA) produced during cooking of meat, fish and poultry. Both HAA produce different tumor profiles in rodents and are suspected to be carcinogenic in humans. In order to better understand the molecular basis of HAA toxicity, we have analyzed gene expression profiles in the metabolically competent human HepaRG cells using pangenomic oligonucleotide microarrays, after either a single (24-h) or a repeated (28-day) exposure to 10 ?M PhIP or MeIQx. The most responsive genes to both HAA were downstream targets of the arylhydrocarbon receptor (AhR): CYP1A1 and CYP1A2 after both time points and CYP1B1 and ALDH3A1 after 28 days. Accordingly, CYP1A1/1A2 induction in HAA-treated HepaRG cells was prevented by chemical inhibition or small interference RNA-mediated down-regulation of the AhR. Consistently, HAA induced activity of the CYP1A1 promoter, which contains a consensus AhR-related xenobiotic-responsive element (XRE). In addition, several other genes exhibited both time-dependent and compound-specific expression changes with, however, a smaller magnitude than previously reported for the prototypical AhR target genes. These changes concerned genes mainly related to cell growth and proliferation, apoptosis, and cancer. In conclusion, these results identify the AhR gene battery as the preferential target of PhIP and MeIQx in HepaRG cells and further support the hypothesis that intake of HAA in diet might increase human cancer risk. | [Julie Dumont1, Rozenn Jossé, Carine Lambert, Sébastien Anthérieu, Véronique Laurent, Pascal Loyer, Marie-Anne Robin, André Guillouzo] | Toxicology and Applied Pharmacology | 15 November 2010 | |
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| sciencedirectS0143416010001466 | RANKL-induced TRPV2 expression regulates osteoclastogenesis via calcium oscillations | The receptor activator of NF?B ligand (RANKL) induces Ca2+ oscillations and activates the Nuclear Factor of Activated T cells 1 (NFATc1) during osteoclast differentiation (osteoclastogenesis). Ca2+ oscillations are an important trigger signal for osteoclastogenesis, however the molecular basis of Ca2+ permeable influx pathways serving Ca2+ oscillations has not yet been identified. Using a DNA microarray, we found that Transient Receptor Potential Vanilloid channels 2 (TRPV2) are expressed significantly in RANKL-treated RAW264.7 cells (preosteoclasts) compared to untreated cells. Therefore, we further investigated the expression and functional role of TRPV2 on Ca2+ oscillations and osteoclastogenesis. We found that RANKL dominantly up-regulates TRPV2 expression in preosteoclasts, and evokes spontaneous Ca2+ oscillations and a transient inward cation current in a time-dependent manner. TRPV inhibitor ruthenium red and tetracycline-induced TRPV2 silencing significantly decreased both the frequency of Ca2+ oscillations and the transient inward currents in RANKL-treated preosteoclasts. Silencing of store-operated Ca2+ entry (SOCE) proteins similarly suppressed both RANKL-induced oscillations and currents in preosteoclasts. Furthermore, suppression of TRPV2 also reduced RANKL-induced NAFTc1 expression, its nuclear translocation, and osteoclastogenesis. In summary, Ca2+ oscillations in preosteoclasts are triggered by RANKL-dependent TRPV2 and SOCE activation and intracellular Ca2+ release. Subsequent activation of NFATc1 promotes osteoclastogenesis. | [Hiroshi Kajiya, Fujio Okamoto, Tetsuomi Nemoto, Keiichiro Kimachi, Kazuko Toh-Goto, Shuji Nakayana, Koji Okabe] | Cell Calcium | November 2010 | |
| sciencedirectS0160412010001121 | PCB congener specific oxidative stress response by microarray analysis using human liver cell line | In this study we have examined the effect of exposure to different congeners of PCBs and their role in oxidative stress response. A metabolically competent human liver cell line (HepG2) was exposed with two prototype congeners of PCBs: coplanar PCB-77 and non-coplanar PCB-153. After the predetermined times of exposure (0–24 h) at 70 ?M concentration, the HepG2 cells showed significant apoptotic changes by fluorescent microscopy after 12 h of exposure. Gene set enrichment analysis (GSEA) identified oxidative stress as the predominant enrichment. Further, paraquat assay showed that PCB congeners lead to oxidative stress to different extents, PCB-77 being more toxic. This study, with emphasis on all recommended microarray quality control steps, showed that apoptosis was one of the most significant cellular processes as a result of oxidative stress, but each of these congeners had a unique signature gene expression, which was further validated by Taqman real time PCR and immunoblotting. The pathways involved leading to the common apoptotic effect were completely different. Further in-silico analysis showed that PCB-153 most likely acted through the TNF receptor, leading to oxidative stress involving metallothionein gene families, and causing apoptosis mainly by the Fas receptor signaling pathway. In contrast, PCB-77 acted through the aryl hydrocarbon receptor. It induced oxidative stress through the involvement of cytochrome P450 (CYP1A1) leading to apoptosis through AHR/ARNT pathway. | [Supriyo Dea, Somiranjan Ghosha, Raghunath Chatterjeea, Y-Q Chena, Linda Mosesb, Akanchha Kesarib, Eric P. Hoffmanb, Sisir K. Duttaa] | Environment International | November 2010 | |
| sciencedirectS0098847210000651 | Transcriptome analysis of gene expression during the hydrotropic response in Arabidopsis seedlings | Because of their sessile nature, plants require appropriate strategies to adapt to the surrounding environment. Tropism is a directional growth in response to environmental stimulus that allows plants to adapt to changes in sunlight, nutrients and water. Plant roots display hydrotropism in response to a moisture gradient, and this phenomenon is believed to play an important role in the ability of the plant to obtain water. However, the molecular mechanism underlying hydrotropism has yet to be fully elucidated. To investigate the transcriptional changes associated with root hydrotropism, we performed a whole-genome microarray analysis of Arabidopsis to monitor the transcription levels of 22,810 genes during the early phase of the hydrotropic response. The transcript levels of 793 genes were significantly changed 1 or 2 hours (h) after hydrotropic stimulation. A large number of genes responsive to abscisic acid (ABA) or water-stress were among the hydrostimulation-responsive genes. In contrast, there appeared to be little overlap in transcript abundance between hydrostimulation-responsive and gravistimulation-responsive genes. Our results suggest that ABA and water-stress responses are important signal transduction mechanisms involved in the root hydrotropic response, and that the signaling pathways involved in hydrotropism differ from those of gravitropism. | [Teppei Moriwaki, Yutaka Miyazawa, Hideyuki Takahashi] | Environmental and Experimental Botany | November 2010 | |
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| sciencedirectS1389172310001933 | Toxicogenomics using yeast DNA microarrays | Development of genomics and bioinformatics enable us to analyze the global gene expression profiles of cells by DNA microarray. Changes in gene expression patterns indicate changes in its physiological conditions. Following the exposure of an organism or cell to toxic chemicals or other environmental stresses, the global genetic responses can be expeditiously and easily analyzed. Baker's yeast, Saccharomyces cerevisiae, is one of the most studied and useful model eukaryotes. The biggest advantage of yeast genomics is the available functional information for each gene and a considerable number of data are accumulating in the field of toxicity assessment using yeast DNA microarray. In this review, we discuss the toxicogenomics of metal ions, alcohols and aldehydes, and other chemicals. | [Daisuke Yasokawa1, Hitoshi Iwahashi2] | Journal of Bioscience and Bioengineering | November 2010 | |
| sciencedirectS0168010210022443 | Behavioral and gene expression analyses in heterozygous XBP1 knockout mice: Possible contribution of chromosome 11qA1 locus to prepulse inhibition | The Xbp1 gene, located on chromosome 11qA1 in Mus musculus, encodes a key transcription factor in the endoplasmic reticulum stress response pathway. XBP1 play a role in brain development and implicated in pathogenesis of neurodegenerative and psychiatric diseases. To evaluate the role of Xbp1 in behavioral phenotypes, we subjected heterozygous Xbp1 knockout (Xbp1+/−) mice to a battery of behavioral tests. Xbp1+/− mice showed enhanced prepulse inhibition (PPI). We also examined gene expression profiles in frontal cortex and hippocampus of Xbp1+/− mice to investigate the molecular basis that could underlie behavioral phenotypes. Gene expression analysis showed that several genes located on chromosome 11qA1 were differentially expressed. Among them, Uqcr10 and Nipsnap1 were strongly up-regulated. Significant up-regulation of these genes in 129S compared with BALB/c as well as higher PPI in 129S than BALB/c was previously reported. The ES cells used to generation of XBP1 knockout mice were derived from 129S and the founder was backcrossed with BALB/c. Thus, these findings would be accounted for by 129S-derived chromosomal region flanking Xbp1. These results support the contribution of chromosome 11qA1 locus to the amount of PPI. Uqcr10 and Nipsnap1 are good candidate genes that could impact PPI. | [Atsushi Takataa b, Chihiro Kakiuchic, Mizuho Ishiwataa, Shigenobu Kanbab, Tadafumi Katoa] | Neuroscience Research | November 2010 | |
| sciencedirectS0890623810001954 | Alterations in the developing testis transcriptome following embryonic vinclozolin exposure | The current study investigates the direct effects of in utero vinclozolin exposure on the developing F1 generation rat testis transcriptome. Previous studies have demonstrated that exposure to vinclozolin during embryonic gonadal sex determination induces epigenetic modifications of the germ line and transgenerational adult onset disease states. Microarray analyses were performed to compare control and vinclozolin treated testis transcriptomes at embryonic days 13, 14 and 16. A total of 576 differentially expressed genes were identified and the major cellular functions and pathways associated with these altered transcripts were examined. The sets of regulated genes at the different development periods were found to be transiently altered and distinct. Categorization by major known functions of altered genes was performed. Specific cellular process and pathway analyses suggest the involvement of Wnt and calcium signaling, vascular development and epigenetic mechanisms as potential mediators of the direct F1 generation actions of vinclozolin. | [Tracy M. Clement2, Marina I. Savenkova, Matthew Settles, Matthew D. Anway1, Michael K. Skinner] | Reproductive Toxicology | November 2010 | |
| sciencedirectS0048969710009381 | A microarray data analysis method to evaluate the impact of contaminants on wild animals | Here we propose a novel microarray data analysis method applicable to evaluation of the chemical effects on wild animals. First, we analyzed correlations between log-transformed hepatic 2,3,7,8-tetrachlorodibenzo-p-dioxin toxic equivalent (TEQ) levels and probe signals detected in wild cormorant liver to screen contaminant-responsive genes. Second, principal component analysis (PCA) was conducted using the screened probes. Third, these probes were divided into two groups based on our PCA result. Finally, we calculated Euclidian distance of signals, which is equivalent to variance of gene expressions, in each probe set, and analyzed the relationship between log-transformed hepatic TEQ levels and Euclidian distances. A probe set whereby the calculated Euclidian distance was positively correlated with TEQ levels, could indicate genes that were directly affected by dioxins or other persistent organic pollutants (POPs), hence they can be used as biomarkers. By contrast, there were a number of probes whereby the Euclidian distance was negatively correlated with TEQ levels. In the latter probe group, the smaller Euclidian distances in highly contaminated individuals could point to changes in physiological activities of wild cormorants. Therefore, our microarray data analysis method will provide new insights into POPs-responsive genes in field-collected samples for toxicogenomics studies. | [Kei Nakayama, Itsuki C. Handoh, Shin-Ichi Kitamura, Eun-Young Kim, Hisato Iwata, Shinsuke Tanabe] | Science of The Total Environment | 1 November 2010 | |
| sciencedirectS0006291X10017778 | The absence of the luxS gene increases swimming motility and flagella synthesis in Escherichia coli K12 | Despite the significant role of S-ribosylhomocysteinase (LuxS) in the activated methyl cycle pathway and quorum sensing, the connectivity between luxS and other cellular functions remains incomplete. Herein, we show that luxS deletion significantly increases swimming motility and flagella synthesis in Escherichia coli K12 using motility, transcriptome, and scanning electron microscopy assays. Further, based on the transcriptome and network component analyses, and known regulatory relations, we propose a conceptual genetic regulatory network underlying the increased flagella synthesis in response to luxS deletion. | [Hua Ling1, Aram Kang1, Mui Hua Tan, Xiaobao Qi, Matthew Wook Chang] | Biochemical and Biophysical Research Communications | 29 October 2010 | |
| sciencedirectS0304394010010773 | Brief naturalistic stress induces an alternative splice variant of SMG-1 lacking exon 63 in peripheral leukocytes | Alternative splicing (AS) not only regulates the gene expression program in response to surrounding environment, but also produces protein isoforms with unique properties under stressful conditions. However, acute psychological stress-initiated AS events have not been documented in human studies. After assessments of changes in salivary cortisol levels and anxiety among 28 fourth-grade medical students 7 weeks prior to, 1 day before, immediately after, and 1 week after an examination for promotion, we selected 5 male students, who showed a typical stress response, and screened AS events in their circulating leukocytes using the GeneChip human exon 1.0 ST array. AS events of 27 genes with splicing indices >1.0 could be detected between immediately after and either 7 weeks before, 1 day before, or 1 week after the examination. The examination stress preferentially caused skipping rather than inclusion: 21 out of the 27 pre-mRNAs underwent skipping of exons, and skipping in 3′UTR was observed in 8 genes. Among the candidate genes, real-time reverse transcription PCR validated the stress-initiated skipping of exon 63 of SMG-1 that encodes a phosphatidylinositol 3-kinase-related protein kinase crucial for activations of p53-dependent pathways and nonsense-mediated mRNA decay. Our results indicate a significant impact of brief naturalistic stressors on AS-mediated regulation of gene expression in peripheral leukocytes, and suggest the SMG-1 splice variant as a potential biomarker for acute psychological stress. | [Ken Kurokawa, Yuki Kuwano, Kumiko Tominaga, Tomoko Kawai, Sakurako Katsuura, Naoko Yamagishi, Yuzuru Satake, Keisuke Kajita, Toshihito Tanahashi, Kazuhito Rokutan] | Neuroscience Letters | 29 October 2010 | |
| sciencedirectS0006291X10017237 | Effect of nephrotoxicants and hepatotoxicants on gene expression profile in human peripheral blood mononuclear cells | Studying peripheral blood transcriptome in the quest for translational markers of toxicity is considered to be an attractive offshoot in the field of toxicogenomics. Moreover, it is acknowledged that, xenobiotics which cause a toxic response through similar mechanisms lead to distinctive gene expression patterns. The current study was undertaken to gauge the response of an accessible surrogate tissue, such as blood, to drug-induced perturbations aimed at deriving gene expression patterns. Human peripheral blood mononuclear cells (hPBMC) were exposed to conventional drugs, with reported kidney and/or liver injury, in order to determine their transcriptomic response. Test drugs were divided into two classes viz., drugs affecting kidney (cyclophosphamide, amphotericin B, gentamicin and cisplatin) and liver (acetaminophen, rosiglitazone, fluconazole and isoniazid). After performing gene expression analysis and hierarchical clustering, signature patterns for the two classes were obtained, with a set of 365 genes that can discriminate the two classes of drugs. Our results imply that transcriptional profile of hPBMC get altered as a consequence of drug exposure and unique patterns indicative of specific organ toxicity can hence be deduced. These signature patterns obtained for drugs could be studied for their qualification to identify drug-induced toxicity. | [Shruta S. Dadarkara, Lyle C. Fonsecaa, Arvind D. Thakkara, Prabha B. Mishraa, Ashok K. Rangasamyb, Muralidhara Padigarua] | Biochemical and Biophysical Research Communications | 15 October 2010 | |
| sciencedirectS0306452210009437 | Persistent gene expression changes in ventral tegmental area of adolescent but not adult rats in response to chronic nicotine | Because adolescent brains are undergoing extensive developmental changes, they may be uniquely sensitive to effects of addictive drugs like nicotine. We exposed adolescent and adult rats to nicotine infusion for two weeks, and then used whole genome microarray analysis to determine effects on gene expression in the ventral tegmental area. We examined brains immediately after two weeks of nicotine or saline, and also four weeks after termination of nicotine exposure. After identifying genes with a significant age×treatment interaction, we employed template matching to find specific patterns of expression across age and treatment. Of those genes that were transiently regulated (up- or down-regulated immediately following the end of nicotine treatment, but back to saline baseline 30 days later), two-thirds were specific to adult animals, while only 30% were specific to adolescents and 4% were shared across the two ages. In contrast, significant genes that were persistently regulated (altered following nicotine treatment and still altered 30 days later) were more likely (59%) to be adolescent, with only 32% in adults and 8% shared. The greatest number of significant genes was late-regulated (no change immediately after nicotine, but regulated 30 days later). Again, most were in adolescents (54%), compared to adults (10%) or shared (36%). Pathway analysis revealed that adolescent-specific genes were over-represented in several biological functions and canonical pathways, including nervous system development and function and long-term potentiation. Furthermore, adolescent-specific genes formed extensive interaction networks, unlike those specific for adults or shared. This age-specific expression pattern may relate to the heightened vulnerability of adolescents to the effects of addictive drugs. In particular, the propensity of adolescents to show persistent alterations in gene expression corresponds to the persistence of drug dependence among smokers who began their habit as adolescents. These findings support a model whereby adolescent brains are uniquely vulnerable to long-term changes in gene expression in the brain's reward pathway caused by early exposure to nicotine. | [M.B. Doura, T.V. Luu, N.H. Lee, D.C. Perry] | Neuroscience | 13 October 2010 | |
| sciencedirectS0042682210004381 | The hemagglutinin protein of influenza A/Vietnam/1203/2004 (H5N1) contributes to hyperinduction of proinflammatory cytokines in human epithelial cells | Live attenuated influenza A/Vietnam/1203/04 (H5N1) (VN04 cold adapted [ca]) and A/Hong Kong/213/03 (H5N1) (HK03 ca) vaccine viruses were compared with the A/New Caledonia/20/99 (H1N1) (NC99 ca) seasonal vaccine virus for induction of host gene expression in infected human epithelial cells. Levels of proinflammatory cytokines and interferon-related genes were significantly upregulated in VN04 ca virus-infected A549 cells compared to cells infected with the HK03 ca and NC99 ca viruses as examined by microarray analysis and confirmed by quantitative RT–PCR and ELISA assays. Further mapping studies demonstrated that the hemagglutinin (HA) protein of the VN04 ca virus contributed to the hyperinduction of cytokines. The inactivated viruses could also induce the production of the cytokines and chemokines, albeit at a much lower level than live viruses. Compared to HK03 ca virus, VN04 ca virus differs by 9 amino acids including an additional glycosylation site at residue 158N of the HA protein and a shortened stalk in the neuraminidase (NA) protein. Increased cytokine production by HK03 ca virus was only observed when HK03 ca virus acquired an additional glycosylation in the HA protein and when its NA protein was replaced by that of VN04. Thus, our data indicate that the HA protein and its interaction with the NA protein play a role in triggering cytokine responses. The full implications of cytokine induction in vaccine virus-induced immune responses remain to be explored. | [Xing Cheng, Qi Xu, Eyun Song, Chin-Fen Yang, George Kemble, Hong Jin] | Virology | 10 October 2010 | |
| sciencedirectS0024320510003747 | Temporal transcriptomic profiling reveals cellular targets that govern survival in HOCl-mediated neuronal apoptosis | AimsWith the identification of hypochlorous acid (HOCl) as a biomarker in diseased brains and endogenous detection of its modified proteins, HOCl might be implicated in the development of neurodegenerative disorders. However, its effect on neuronal cell death has not yet been investigated at gene expression level.Main methodsTherefore, DNA microarray was performed for screening of HOCl-responsive genes in primary mouse cortical neurons. Neurotoxicity caused by physiological relevant HOCl (250 ?M) exhibited several biochemical markers of apoptosis.Key findingsThe biological processes affected during HOCl-mediated apoptosis included cell death, response to stress, cellular metabolism, and cell cycle. Among them, mRNAs level of cell death and stress response genes were up-regulated while expression of metabolism and cell cycle genes were down-regulated.SignificanceOur results showed, for the first time, that HOCl induces apoptosis in cortical neurons by upregulating apoptotic genes and gene expression of stress response such as heat shock proteins and antioxidant proteins were enhanced to provide protection. These data form a foundation for the development of screening platforms and define targets for intervention in HOCl neuropathologies where HOCl-mediated injury is causative. | [Yann Wan Yapa 1, Minghui Jessica Chenb 1, Meng Shyan Choya, Zhao Feng Penga c, Matthew Whitemand, Jayapal Manikandane, Alirio J. Melendeze, Nam Sang Cheungb] | Life Sciences | 9 October 2010 | |
| sciencedirectS157096391000107X | Gaining insights into the Bcr-Abl activity-independent mechanisms of resistance to imatinib mesylate in KCL22 cells: A comparative proteomic approach | Imatinib mesylate is a potent inhibitor of Bcr-Abl tyrosine kinase, an oncoprotein that plays a key role in the development of chronic myeloid leukemia. Consequently, imatinib is used as front-line therapy for this disease. A major concern in imatinib treatment is the emergence of resistance to the drug. Here we used the imatinib-resistant KCL22R and imatinib-sensitive KCL22S cells in which none of the known resistance mechanisms has been detected and hence novel Bcr-Abl activity-independent mechanisms could be envisaged. We characterized proteins that were differentially expressed between the KCL22R and KCL22S cells. Using two-dimensional differential gel electrophoresis coupled with mass spectrometry and Western blot analysis we identified 51 differentially expressed proteins: 27 were over-expressed and 24 were under-expressed in KCL22R versus KCL22S cells. Several of these proteins are likely to be involved in such survival mechanisms as modulation of redox balance and activation of anti-apoptotic pathways mediated by NF-?B and Ras-MAPK signaling. The data reported may be useful for further studies on mechanisms of imatinib resistance and for the screening of biomarkers to develop new combinatorial therapeutic approaches. | [Irene Colavitaa b, Nicola Espositoa c, Rosanna Martinellia c, Francesca Catanzanoa d, Junia V. Meloe, Fabrizio Panea c, Margherita Ruoppoloa c, Francesco Salvatorea c] | Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics | October 2010 | |
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| sciencedirectS0145305X10001266 | Effects of Salmonella on spatial-temporal processes of jejunal development in chickens | To study effects of Salmonella enteritidis on morphological and functional changes in chicken jejunal development, we analysed gene expression profiles at seven points post-infection in 1–21 day-old broiler chickens. Nine clusters with different gene expression patterns were identified, and the genes in each cluster were further analyzed by a functional annotation clustering method (DAVID). Functional and morphological developmental processes dominated in all the nine clusters. Salmonella infection caused delays in several intestinal-morphological processes, whereas functional metabolic processes occurred in a similar spatial-temporal frame compared to normal jejunum development. A clear difference between normal developing- and Salmonella disturbed jejunum was the higher expression of genes involved in cell turn-over at early stages in the infected jejunum. Surprisingly, we found no clustered immune related processes in the infected birds. To compare the immunological processes between control and Salmonella infected chickens, the gene expression data was superimposed on known immunological KEGG pathways. Furthermore an in-depth analysis on the immune gene level was performed. As expected, we did find immunological processes in the Salmonella infected jejunum. Several of these processes could be verified by immunohistochemistry measurements of different immunological cell types. However, the well-ordered spatial-temporal development of the immune system, as observed in control non-infected animals, was completely abolished in the infected animals. Several immunological processes started much earlier in time, whereas other processes are disorganised. These data indicate that normal morphological and immunological development of jejunum is changed dramatically by a disturbance due to Salmonella infection. Due to the disturbance, the well-organized spatial-temporal development of morphological processes are delayed, those of the immunological development are scattered, whereas metabolic functional processes are almost not affected. This demonstrates the flexibility of developmental processes in the broiler chicken intestine. | [Dirkjan Schokkera, Mari A. Smitsa, Arjan J.W. Hoekmana, Henk K. Parmentierc, Johanna M.J. Rebelb] | Developmental & Comparative Immunology | October 2010 | |
| sciencedirectS1590865810605270 | OC5 The natural history of autoimmune hepatitis/primary sclerosing cholangitis (AIH/PSC) overlap syndrome | | [S. Antoniazzi, N. Cazzagon, J. Egoue, R. Lazzari, A. Floreani] | Digestive and Liver Disease | October 2010 | |
| sciencedirectS1590865810605282 | OC6 In vitro and in vivo demonstration of multipotent cells isolated from human extrahepatic bile ducts (hEHBDs) | | [V. Cardinale, Y. Wang, G. Carpino, M. Gatto, A. Cantafora, I. Blotta, A. Torrice, R. Semeraro, J. Dominguez-Bendala, L. Inverardi, C. Ricordi, E. Gaudio, L.M. Reid, D. Alvaro] | Digestive and Liver Disease | October 2010 | |
| sciencedirectS1590865810605294 | OC7 Intrahepatic cholestasis of pregnancy: new insights into its pathogenesis | | [R. Lazzari, M.T. Gervasi, D. Caroli, A. Memmo, E. Vidali, D. Colavito, A. D'Arrigo, A. Leon, A. Floreani] | Digestive and Liver Disease | October 2010 | |
| sciencedirectS1590865810605300 | OC8 Defective progenitor cells activation and biliary tubule formation in liver conditional RBP-Jk-knock out mice exposed to cholestatic injuries reveals a key role for Notch signaling in liver repair | | [R. Fiorotto, C. Spirli, R. Scirpo, T. Gridley, S. Huppert, B. Torsello, C. Ferrero, M. Strazzabosco] | Digestive and Liver Disease | October 2010 | |
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| sciencedirectS1567133X10000827 | stac1 and stac2 genes define discrete and distinct subsets of dorsal root ganglia neurons | Deciphering the precise in vivo function of a particular neuronal subpopulation is one of the most challenging issues in neurobiology. Dorsal root ganglia (DRG) neurons represent a powerful model system to address this fundamental question. These neurons display many morphological, anatomical and few molecular characteristics. With the aim of expanding the molecular description of the primary sensory neurons, we used Affimetrix microarrays to compare global gene expression profiles of DRG of wild type and trkAtrkC/trkC knock-in mice at birth and identified several hundred potential markers of nociceptive neurons and few markers of proprioceptive neurons. Here, we describe the identification of two members of a family of putative adapter proteins STAC1 and STAC2. We found STAC1 and STAC2 being expressed in a mutually exclusive fashion in adult DRG neurons. STAC1 mainly marks peptidergic nociceptive neurons while STAC2 is expressed in a subset of nonpeptidergic nociceptors, in all trkB+ neurons and in a subpopulation of proprioceptive neurons. Our expression data demonstrate that STAC proteins identify four categories of primary sensory neurons; one class of peptidergic neurons, a subset of nonpeptidergic neurons, all TrkB + neurons and a subset of proprioceptive neurons. Genetic marking of STACs-expressing sensory neurons will lend significant advance into our understanding of DRG neuronal functional diversity. | [Wassim Legha, Stéphane Gaillard, Eduardo Gascon, Pascale Malapert, Mélanie Hocine, Serge Alonso, Aziz Moqrich] | Gene Expression Patterns | October–December 2010 | |
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| sciencedirectS0161589010004992 | SARS spike protein induces phenotypic conversion of human B cells to macrophage-like cells | Massive aggregations of macrophages are frequently detected in afflicted lungs of patients with severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection. In vitro, ectopic expression of transcription factors, in particular CCAAT/enhancer-binding protein alpha (C/EBP?) and C/EBP?, can convert B cells into functional macrophages. However, little is known about the specific ligands responsible for such phenotype conversion. Here, we investigated whether spike protein of SARS-CoV can act as a ligand to trigger the conversion of B cells to macrophages. We transduced SARS-CoV spike protein-displayed recombinant baculovirus (SSDRB), vAtEpGS688, into peripheral B cells and B lymphoma cells. Cell surface expression of CD19 or Mac-1 (CD11b) was determined by flow cytometry. SSDRB-mediated changes in gene expression profiles of B lymphoma cells were analyzed by microarray. In this report, we showed that spike protein of SARS virus could induce phenotypic conversion of human B cells, either from peripheral blood or B lymphoma cells, to macrophage-like cells that were steadily losing the B-cell marker CD19 and in turn expressing the macrophage-specific marker Mac-1. Furthermore, we found that SSDRB enhanced the expression of CD86, hypoxia-inducible factor-1? (HIF1?), suppressor of cytokine signaling (SOCS or STAT-induced STAT inhibitor)-3, C/EBP?, insulin-like growth factor-binding protein 3 (IGFBP3), Krüpple-like factor (KLF)-5, and CD54, without marked influence on C/EBP? or PU.1 expression in transduced cells. Prolonged exposure to hypoxia could also induce macrophage-like conversion of B cells. These macrophage-like cells were defective in phagocytosis of red fluorescent beads. In conclusion, our results suggest that conversion of B cells to macrophage-like cells, similar to a pathophysiological response, could be mediated by a devastating viral ligand, in particular spike protein of SARS virus, or in combination with severe local hypoxia, which is a condition often observed in afflicted lungs of SARS patients. | [Shu-Fen Chianga 1, Tze-Yi Linb 1, Kuan-Chih Chowc, Shiow-Her Chioua] | Molecular Immunology | October 2010 | |
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| sciencedirectS0038071710002269 | Direct detection of soil mRNAs using targeted microarrays for genes associated with lignin degradation | Microarrays have become established tools for describing microbial systems, however the direct assessment of expression profiles for uncharacterized environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. Thus we applied a target labeling and amplification approach based on the Klenow fragment and signal amplification approach to detect expression of fungally-derived lignin-degrading enzymes in soil. Known amplicons and cDNA from Phanerochaete chrysosporium were mixed with the soil cDNA both before and after the signal amplification in order to assess the dynamic range of the microarray. The addition of control cDNA with soil cDNA interfered with detection of the low-abundance transcripts. Nevertheless this microarray approach consistently reported the higher-abundance transcripts which presented more robust signals. | [Vanessa L. Baileya, Sarah J. Fanslera, Somnath Bandyopadhyaya 1, Jeffrey L. Smithb, Katrina M. Watersa, Harvey Boltona] | Soil Biology and Biochemistry | October 2010 | |
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| sciencedirectS1357272510002347 | Transcriptome atlas of aromatic amino acid family metabolism-related genes in eight liver cell types uncovers the corresponding metabolic pathways in rat liver regeneration | To explore gene expression of aromatic amino acid family metabolism and their metabolic pathways of eight liver cell types in rat liver regeneration, eight kinds of rat regenerating liver cells were isolated by using the combination of percoll density gradient centrifugation and immunomagnetic bead methods. Rat Genome 230 2.0 Array was used to detect the expression changes of genes associated with aromatic amino acid family metabolism. The transcriptome atlas showed that the metabolic pathway of phenylalanine was mainly catalyzed into tyrosine in hepatic stellate cells in the initiation stage, tyrosine was oxidized into dopa and norepinephrine in biliary epithelia cells and dendritic cells, and norepinephrine was finally catalyzed into adrenaline in biliary epithelia cells and pit cells in the progress stage. Thyroid hormone of tyrosine catabolites was synthesized from tyrosine in almost all cells in different stage of LR, among which genes of T3 biosynthesis were increased in HCs, BECs, SECs and DCs in the progress stage. Tryptophan was decarboxylated to 5-hydroxytryptamine in dendritic cells in the progress stage. Based on the results as above, we concluded that phenylalanine is the major source of tyrosine, proliferation of biliary epithelia cells and dendritic cells maybe promote by tyrosine catabolites—dopa and norepinephrine, biliary epithelia cells and pit cells maybe promote by adrenaline. T3 maybe play a major role on proliferation of HCs, BECs, SECs and DCs in the progress stage. The proliferation of dendritic cells maybe promote by tryptophan catabolites—5-hydroxytryptamine. | [Cuifang Changa b, CunShuan Xub c] | The International Journal of Biochemistry & Cell Biology | October 2010 | |
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| sciencedirectS0306452210008778 | Id1, Id2 and Id3 are induced in rat melanotrophs of the pituitary gland by dopamine suppression under continuous stress | In rats under continuous stress (CS) there is decreased hypothalamic dopaminergic innervation to the intermediate lobe (IL) of the pituitary gland, which causes hyperactivation and subsequent degeneration of melanotrophs in the IL. In this study, we investigated the molecular basis for the changes that occur in melanotrophs during CS. Using microarray analysis, we identified several genes differentially expressed in the IL under CS conditions. Among the genes up-regulated under CS conditions, we focused on the inhibitor of DNA binding/differentiation (Id) family of dominant negative basic helix-loop-helix (bHLH) transcription factors. RT-PCR, Western blotting and in situ hybridization confirmed the significant inductions of Id1, Id2 and Id3 in the IL of CS rats. Administration of the dopamine D2 receptor agonist bromocriptine prevented the inductions of Id1–3 in the IL of CS rats, whereas application of the dopamine D2 antagonist sulpiride induced significant expressions of Id1–3 in the IL of normal rats. Moreover, an in vitro study using primary cultured melanotrophs demonstrated a direct effect on Id1–3 inductions by dopamine suppression. These results suggest that the decreased dopamine levels in the IL during CS induce Id1–3 expressions in melanotrophs. Because Id family members inhibit various bHLH transcription factors, it is conceivable that the induced Id1–3 would cooperatively modulate gene expressions in melanotrophs under CS conditions to induce hormone secretion. | [H. Konishia b, T. Ogawaa b, S. Nakagomia, K. Inouec 1, M. Tohyamac, H. Kiyamaa b] | Neuroscience | 15 September 2010 | |
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| sciencedirectS0006291X10014567 | Differential gene expression profiling in blood from patients with digestive system cancers | To develop a non-invasive and sensitive diagnostic test for cancer using peripheral blood, we evaluated gene expression profiling of blood obtained from patients with cancer of the digestive system and normal subjects. The expression profiles of blood-derived total RNA obtained from 39 cancer patients (11 colon cancer, 14 gastric cancer, and 14 pancreatic cancer) was clearly different from those obtained from 15 normal subjects. By comparing the gene expression profiles of cancer patients and normal subjects, 25 cancer-differentiating genes (p < 5.0 × 10−6 and fold differences >3) were identified and an “expression index” deduced from the expression values of these genes differentiated the validation cohort (11 colon cancer, 8 gastric cancer, 18 pancreatic cancer, and 15 normal subjects) into cancer patients and normal subjects with 100% (37/37) and 87% (13/15) accuracy, respectively. Although, the expression profiles were not clearly different between the cancer patients, some characteristic genes were identified according to the stage and species of the cancer. Interestingly, many immune-related genes such as antigen presenting, cell cycle accelerating, and apoptosis- and stress-inducing genes were up-regulated in cancer patients, reflecting the active turnover of immune regulatory cells in cancer patients. These results showed the potential relevance of peripheral blood gene expression profiling for the development of new diagnostic examination tools for cancer patients. | [Masao Hondaa b, Yoshio Sakaia, Taro Yamashitaa, Tatsuya Yamashitaa, Akito Sakaia, Eishiro Mizukoshia, Yasunari Nakamotoa, Isamu Tatsumia, Yoshitaka Miyazakia, Hiroshi Tannoa, Shuichi Kanekoa, Hokuriku Liver Study Group1] | Biochemical and Biophysical Research Communications | 10 September 2010 | |
| sciencedirectS0006291X1001466X | Osteogenic differentiation of mouse mesenchymal progenitor cell, Kusa-A1 is promoted by mammalian transcriptional repressor Rbpj | Pluripotent mesenchymal stem cells possess the ability to differentiate into many cell types, but the precise mechanisms of differentiation are still unclear. Here, we provide evidence that Rbpj (recombination signal-binding protein for immunoglobulin kappa j region) protein, the primary nuclear mediator of Notch, is involved in osteogenesis. Overexpression of Rbpj promoted osteogenic differentiation of mouse Kusa-A1 cells in vitro and in vivo. Transient transfection of an Rbpj expression vector into Kusa-A1 cells upregulated promoter activities of Runx2 and Ose2. Enhanced osteogenic potentials including high alkaline phosphatase activity, rapid calcium deposition, and increased calcified nodule formation, were observed in established stable Rbpj-overexpressing Kusa-A1 (Kusa-A1/Rbpj) cell line. In vivo mineralization by Kusa-A1/Rbpj was promoted compared to that by Kusa-A1 host cells. Histological findings revealed that expression of Rbpj was primarily observed in osteoblasts. These results suggest that Rbpj may play essential roles in osteoblast differentiation. | [Shengchao Wanga, Nobuyuki Kawashimab, Kei Sakamotoc, Ken-ichi Katsubec, Akihiro Umezawad, Hideaki Sudab e] | Biochemical and Biophysical Research Communications | 10 September 2010 | |
| sciencedirectS0006291X10014580 | The HPV-16 E5 protein represses expression of stress pathway genes XBP-1 and COX-2 in genital keratinocytes | The HPV-16 E5 protein resides in membranes of the endoplasmic reticulum (ER) and modulates cell growth and viral replication. In order to help define its biological activities, we analyzed E5-induced changes in human keratinocyte gene expression. Our studies identified the downregulation of spliced XBP-1 transcripts, a key player in the ER stress response, as a biochemical marker of E5 expression. IRE1?, the endoribonuclease responsible for XBP-1 RNA splicing, was also downregulated. Furthermore, cDNA microarray analysis revealed the repression of COX-2, another member of the ER stress pathway. In contrast, these genes were not altered either by the low-risk HPV-6b E5, or a C-terminal HPV-16 E5 mutant, in which the histidine and alanine residues (conserved in high-risk HPVs) were replaced with tyrosine and isoleucine (conserved in low-risk HPVs). HPV-16 E5 was also able to lower COX-2 mRNA levels in cells co-expressing E6/E7, suggesting that it might exert similar activity during viral replication. Interestingly, the E6/E7 genes were independently able to lower COX-2 transcripts compared to vector cells, indicating that multiple pathways of COX-2 repression exist. COX-2 downregulation by E5 could be overcome by thapsigargin or tunicamycin treatments, which initiate ER stress via calcium fluxes and abnormal protein glycosylation respectively, making it unlikely that E5 specifically tempers these pathways. Overall, our data indicate that E5 represses the cellular ER stress response and suggest a potential role for E5 during productive HPV infection. | [Sawali R. Sudarshan, Richard Schlegel, Xuefeng Liu] | Biochemical and Biophysical Research Communications | 3 September 2010 | |
| sciencedirectS0166445X10001943 | Temporal patterns in the transcriptomic response of rainbow trout, Oncorhynchus mykiss, to crude oil | Time is often not characterized as a variable in ecotoxicogenomic studies. In this study, temporal changes in gene expression were determined during exposure to crude oil and a subsequent recovery period. Juvenile rainbow trout, Oncorhynchus mykiss, were exposed for 96 h to the water accommodated fractions of 0.4, 2 or 10 mg l−1 crude oil loadings. Following 96 h of exposure, fish were transferred to recovery tanks. Gill and liver samples were collected after 24 and 96 h of exposure, and after 96 h of recovery for RNA extraction and microarray analysis. Fluorescently labeled cDNA was hybridized against matched controls, using salmonid cDNA arrays. Each exposure scenario generated unique patterns of altered gene expression. More genes responded to crude oil in the gill than in the liver. In the gill, 1137 genes had altered expression at 24 h, 2003 genes had altered expression levels at 96 h of exposure, yet by 96 h of recovery, no genes were significantly altered in expression. In the liver at 10 mg l−1, only five genes were changed at 24 h, yet 192 genes had altered expression after 96 h recovery. At 2 mg l−1 in the liver, many genes had altered regulation at all three time points. The 0.4 mg l−1 loading also showed 289 genes upregulated at 24 h after exposure. The Gene Ontology terms associated with altered expression in the liver suggested that the processes of protein synthesis, xenobiotic metabolism, and oxidoreductase activity were altered. The concentration-responsive expression profile of cytochrome P450 1A, a biomarker for oil exposure, did not predict the majority of gene expression profiles in any tissue or dose, since direct relationships with dose were not observed for most genes. While the genes and their associated functions agree with known modes of toxic action for crude oil, the gene lists obtained do not match our previously published work, presumably due to array analysis procedures. These results demonstrate that changes in gene expression with time and dose may be complicated, and should be characterized in controlled laboratory settings before attempts are made to interpret responses in field-collected organisms. Further, processes for analyzing microarray data need to be developed such that standardized gene lists are developed, or that analysis does not rely on lists of significantly altered genes before arrays can be further evaluated as a monitoring tool. | [Sharon E. Hooka, Mark A. Lampib, Eric J. Febbob, Jeff A. Warda, Thomas F. Parkertonb] | Aquatic Toxicology | 1 September 2010 | |
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| sciencedirectS0171933510001044 | Initial receptor–ligand interactions modulate gene expression and phagosomal properties during both early and late stages of phagocytosis | The receptors engaged during recognition and phagocytic uptake of microorganisms and particles influence signaling events and diverse subcellular responses that occur during phagosome formation and maturation. However, pathogens generally have multiple ligands on their surface, making it difficult to dissect the roles of individual receptors during phagocytosis. Moreover, it remains elusive to which extent receptor–ligand interactions and early binding events define the subsequent intracellular fate of phagosomes. Here, we used latex beads coupled to single ligands, focusing on immunoglobulin G, mannan, bacterial lipopolysaccharides and avidin, and monitored: (1) phagocytic uptake rates, (2) fusion of phagosomes with lysosomal compartments, (3) the gene expression profile during phagocytosis, (4) the protein composition of mature phagosomes and (5) time-dependent dynamics of protein association with phagosomes in J774.A1 mouse macrophages. The differently coated latex beads were internalized at different rates and exhibited different kinetics of phagolysosomal fusion events dependent on their specific ligand. Furthermore, less than 60% of identified phagosomal proteins and only 10–15% of changes in gene expression were common to all investigated ligands. These findings demonstrate that each single ligand induced a distinct pattern of genes and a different protein composition of phagosomes. Taken together, our data argue that phagocytic receptor-specific programs of signaling events direct phagosomes to different physiological states and support the existence of a specific receptor–ligand ‘signature’ during the whole process of phagocytosis. | [Eik Hoffmanna b 1, Sabrina Marionb 2, Bibhuti Bhusan Mishrac 3, Mathias Johnd, Ramona Kratzkea, Syed Furquan Ahmada, Daniela Holzerb, Paras Kumar Anandb, Dieter G. Weissa, Gareth Griffithsb 4, Sergei A. Kuznetsova] | European Journal of Cell Biology | September 2010 | |
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| sciencedirectS0198885910001515 | Transcript abundance patterns in Kawasaki disease patients with intravenous immunoglobulin resistance | Intravenous immunoglobulin (IVIG)–resistant Kawasaki disease (KD) patients comprise at least 20% of treated patients and are at high risk for coronary artery abnormalities. If identified early in the course of the disease, such patients may benefit from additional anti-inflammatory therapy. The aim of this study was to compare the transcript abundance between IVIG resistant and -responsive KD patients, to identify biomarkers that might differentiate between these two groups and to generate new targets for therapies in IVIG resistant KD patients. We compared the transcript abundance profiles of whole-blood RNA on Agilent arrays from acute and convalescent KD subjects and age-similar, healthy controls. KD subjects were stratified as IVIG resistant or –responsive based on response to initial IVIG therapy. Transcript abundance was higher for IL-1 pathway genes (IL-1 receptor, interleukin receptor associated kinase, p38 mitogen-activated protein kinase), and MMP-8. These findings point to candidate biomarkers that may predict IVIG resistance in acute KD patients. The results also underscore the importance of the IL-1 pathway as a mediator of inflammation in KD and suggest that IL-1 or its receptor may be reasonable targets for therapy, particularly for IVIG resistant patients. | [Wen Furya, Adriana H. Tremouletb, Virginia E. Watsonb, Brookie M. Bestb c, Chisato Shimizub, Jennifer Hamiltona, John T. Kanegayeb, Yi Weia, Chiayi Kaoa, Scott Mellisa, Calvin Lina, Jane C. Burnsb] | Human Immunology | September 2010 | |
| sciencedirectS0171298510000987 | Comprehensive analysis of TLR4-induced transcriptional responses in interleukin 4-primed mouse macrophages ? | Interferon (IFN)? and interleukin (IL)-4 are central regulators of T helper 1 (Th1) and T helper 2 (Th2) immune responses, respectively. Both cytokines have a major impact on macrophage phenotypes: IFN?-priming and subsequent TLR4 activation induces so-called “classically activated” macrophages that are characterized by pronounced pro-inflammatory responses, whereas IL-4-treated macrophages, commonly called “alternatively activated”, are known to develop enhanced capacity for endocytosis, antigen presentation and tissue repair and are generally considered anti-inflammatory. Considering IL-4 as priming rather than activating stimulus, we now compared the TLR4-dependent global gene activation program in IFN?- versus IL-4-pretreated mouse macrophages, which has rarely been studied so far. Although both cytokines frequently induced opposing effects on gene transcription, the subsequent activation of bone marrow-derived macrophages by lipopolysaccharide (LPS) produced a strong, priming-dependent pro-inflammatory response in both macrophage types. For example, the production of key pro-inflammatory cytokines IL-6 and IL-12 was significantly higher in IL-4- versus IFN?-primed macrophages and several cytokine genes, including Il19, Ccl17, Ccl22, Ccl24 and Cxcl5, were preferentially induced in “alternatively” primed and LPS activated mouse macrophages. In a subset of genes, including IL12a, IFN?-priming was actually found to suppress LPS-induced gene expression in a Stat1-dependent manner. Our data suggest that IL-4-priming is not per se anti-inflammatory but generates a macrophage that is “tissue protective” but still capable of mounting a strong inflammatory response after TLR4-dependent activation. | [Carol El Chartouni, Michael Rehli] | Immunobiology | September–October 2010 | |
| sciencedirectS0171298510000975 | Interleukin-4 induced interferon regulatory factor (Irf) 4 participates in the regulation of alternative macrophage priming | Interleukin (IL)-4 is a central regulator of T helper 2 (Th2) immune responses, and also has a major impact on innate immune cells. This cytokine primes macrophages for immune responses to parasites and induces a distinct macrophage phenotype that may also promote tissue repair. IL-4 signaling in macrophages is primarily mediated by the transcription factor signal transducer and activator of transcription 6 (Stat6), which in turn regulates a number of secondary DNA binding proteins that may participate in shaping the resulting phenotype. The impact of secondary transcription factors on IL-4-treated macrophages, however, is largely unknown. Here we show that interferon regulatory factor 4 (Irf4) is strongly induced on RNA and protein level in bone marrow-derived macrophages upon priming with IL-4. Using microarray-based whole genome expression analysis, we also demonstrate that a subset of IL-4 regulated genes, including several MHC-II genes, Ciita, Cyp1b1, and Il1rn, are dysregulated in Irf4-deficient macrophages. The presented data suggests a non-redundant role for Irf4 in shaping the phenotype of alternatively primed macrophages. | [Carol El Chartouni, Lucia Schwarzfischer, Michael Rehli] | Immunobiology | September–October 2010 | |
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| sciencedirectS0176161710001203 | Global analysis of the root hair morphogenesis transcriptome reveals new candidate genes involved in root hair formation in barley | Root hairs are long tubular outgrowths of specialized root epidermal cells that play an important role in plant nutrition and water uptake. They are also an important model in studies of higher plant cell differentiation. In contrast to the model dicot Arabidopsis thaliana, currently very little is known about the genetic and molecular basis of root hair formation in monocots, including major cereals. To elucidate candidate genes controlling this developmental process in barley, we took advantage of the recently established Affymetrix GeneChip Barley1 Genome Array to carry out global transcriptome analyses of hairless and root hair primordia-forming roots of two barely mutant lines. Expression profiling of the root-hairless mutant rhl1.a and its wild type parent variety ‘Karat’ revealed 10 genes potentially involved in the early step of root hair formation in barley. Differential expression of all identified genes was confirmed by quantitative reverse transcription-polymerase chain reaction. The genes identified encode proteins associated with the cell wall and membranes, including one gene for xyloglucan endotransglycosylase, three for peroxidase enzymes and five for arabinogalactan protein, extensin, leucine-rich-repeat protein, phosphatidylinositol phosphatidylcholine transfer protein and a RhoGTPase GDP dissociation inhibitor, respectively. The molecular function of one gene is unknown at present. The expression levels of these genes were strongly reduced in roots of the root-hairless mutant rhl1.a compared to the parent variety, while expression of all 10 genes was similar in another mutant, i.e. rhp1.b, that has lost its ability to develop full root hairs but still forms hairs blocked at the primordium stage, and its wild type relative. This clearly indicates that the new genes identified are involved in the initiation of root hair morphogenesis in barley. | [Miroslaw Kwasniewskia, Agnieszka Janiaka, Bernd Mueller-Roeberb, Iwona Szarejkoa] | Journal of Plant Physiology | 1 September 2010 | |
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| sciencedirectS0969996110001294 | Satellite glia not DRG neurons constitutively activate EGFR but EGFR inactivation is not correlated with axon regeneration | To test the possibility that phosphorylated epidermal growth factor receptor (pEGFR) mediates axon growth inhibition, we determined if pEGFR levels were raised in dorsal root ganglia (DRG) after non-regenerating dorsal column (DC) lesions and suppressed in regenerating sciatic nerve (SN) and preconditioning (P) SN + DC lesioned DRG. Levels of EGFR mRNA and protein in DRG were unchanged between control and all injury models. Satellite glia and not DRG neurons (DRGN) constitutively contained pEGFR and, only in PSN + DC rats, were levels significantly reduced in these cells. In vitro, siRNA mediated knockdown of EGFR (siEGFR) mRNA and protein was associated with suppressed RhoA activation, but fibroblast growth factor-2 (FGF2) was a mandatory requirement for DRGN neuritogenesis after addition of inhibitory concentrations of CNS myelin. Thus, EGFR activation in satellite glia was not consistently correlated with DRGN axogenesis and siEGFR reduction of pEGFR with attenuated Rho-GTP signalling did not promote DRGN disinhibited neurite outgrowth without exogenous FGF2 stimulation. Together, these data argue against a direct intra-axonal involvement of pEGFR in axon regeneration. | [Zubair Ahmed, Martin L. Read, Martin Berry, Ann Logan] | Neurobiology of Disease | September 2010 | |
| sciencedirectS0306452210008110 | Epigenetic modification of vomeronasal (V2r) precursor neurons by histone deacetylation | Vomeronasal neurons undergo continuous neurogenesis throughout development and adult life. These neurons originate as stem cells in the apical zone of the lumen of the vomeronasal organ (VNO) and are described as nestin-expressing glia-like progenitor cells (Murdoch and Roskams, 2008). They then migrate horizontally along the basal zone where they differentiate into functional VNO neurons (Kaba et al., 1988). We harvested progenitor cells from the adult VNO and, after 3–6 months of invitro culture, these VNO neurons remained in a stable undifferentiated state expressing nestin, ?-tubulin III and vomeronasal type 2 (V2r), but not vomeronasal type 1 (V1r) receptors. Application of histone-deacetylase inhibitors induced development of a neural phenotype that expressed V2r receptors, a down-regulation of nestin expression and no change in any specific genetic markers associated with glial cells. Treatment with valproic acid induced extensive changes in gene expression in the axon guidance pathway. The adult VNO is known to functionally adapt throughout life as a consequence of changes in both a mouse's physiological status and its social environment. These pluripotent cultured neurons may provide valuable insights into how changes in both physiology and environment, exert epigenetic effects on vomeronasal neurons as they undergo continuous neurogenesis and development throughout the life of a mouse. | [J. Xiaa c, K.D. Broadb, P.C. Emsona, E.B. Keverneb] | Neuroscience | 1 September 2010 | |
| sciencedirectS0264410X10009400 | Reduced immune reaction prevents immunopathology after challenge with avian influenza virus: A transcriptomics analysis of adjuvanted vaccines | To gain more insight in underlying mechanisms correlating to protection against avian influenza virus (AIV) infection, we investigated correlates of protection after AIV H9N2 infection and studied the contribution of different adjuvants to a protective response at host transcriptional level. One-day-old chickens were immunised with inactivated H9N2 supplemented with w/o, Al(OH)3, CpG or without adjuvant. Two weeks later, birds were homologously challenged and at 1–4 days post challenge (d.p.c.) trachea and lung were collected. Birds immunised with H9N2 + w/o or H9N2 + Al(OH)3 were protected against challenge infection and had lower viral RNA expression, less immune related genes induced after challenge, a lower amplitude of change of gene expression and smaller cellular influxes compared to the higher and prolonged gene expression in unprotected birds. We show that a limited number of differentially expressed genes correlates with reduced immune activation and subsequently reduced immunopathology after challenge with AIV. | [Sylvia S. Reemersa, Christine Jansena, Marian J. Groot Koerkampb, Daphne van Haarlema, Peter van de Haara, Winfried G.J. Degenc, Willem van Edena, Lonneke Verveldea] | Vaccine | 31 August 2010 | |
| sciencedirectS0378113510000234 | A time-course study of gene responses of chicken granulosa cells to Salmonella Enteritidis infection | Consumption of eggs contaminated with Salmonella Enteritidis (SE) has been recognized as one of the important causes of human foodborne salmonellosis. Chicken granulosa cells (cGCs) comprise the last tissue layer surrounding the yolk in preovulatory follicles and are a preferred site for SE invasion. To understand the cGC response to SE infection, we conducted an in vitro time-course study to identify cGC transcriptional changes using chicken whole genome microarrays. The expression of 135 (4 h postinfection) and 120 cGC genes (48 h postinfection) were altered (P < .01) compared to uninfected cells. Many of the altered genes were related to immune response, physiological processes, signal transduction, and transcription. Furthermore, we also found that the Jak-STAT pathway, which is essential in the regulation of cellular cytokines and growth factors, was highly active in this study. Among the genes identified by microarray, the mRNA levels of TLR15, IL-6, CXCLi1, CXCLi2, and K203 were shown to be upregulated by real-time RT-PCR (qRT-PCR). In contrast, the mRNA levels of RASD1 and HB-EGF decreased according to both microarray and qRT-PCR analyses. These results suggest that during the SE infection, cGCs recruit cells of the innate immune responses; the infection may also induce suppression of cGC cell proliferation, which alters follicular development and ovulation. | [Hsiang-Jung Tsaia, Chih-Hsien Chiub, Chia-Lan Wanga, Chung-Hsi Choua] | Veterinary Microbiology | 26 August 2010 | |
| sciencedirectS0006291X10013203 | Immediate and gradual gene expression changes in telomerase over-expressing fibroblasts | Most human somatic cells contain no or very low levels of telomerase. The over-expression of the catalytic subunit (hTERT) of human telomerase is a common method to generate cells with a greatly prolonged lifespan. These cells serve as models for cells that are either difficult to cultivate or have a limited lifespan in vitro. In addition, hTERT over-expressing cells are thought to be a useful resource for tissue engineering and regenerative medicine.While tumour suppressors and cell cycle checkpoints are maintained for an extended period in most hTERT over-expressing cells we found that there is a gradual change in gene expression over a range of 130 population doublings (PD) for the majority of genes analysed. Seven genes were significantly down-regulated with increasing population doublings (PDs), while only two were up-regulated. One gene, stanniocalcin 2, was highly expressed in parental fibroblasts but completely diminished as a consequence of hTERT transgene expression.These data demonstrate that in hTERT over-expressing cells two different types of expression changes occur: one can be directly associated with hTERT transgene expression itself, while others might occur more gradual and with varying kinetics. These changes should be taken into account when these cells are used as functional models or for regenerative purposes. | [Darren J. Danielsa b, Christopher Clothiera, Daniel C. Swanc, Gabriele Saretzkia b] | Biochemical and Biophysical Research Communications | 13 August 2010 | |
| sciencedirectS0027510710000692 | Investigating micronutrients and epigenetic mechanisms in relation to inflammatory bowel disease | Epigenomic regulation, via DNA methylation, histone modification and non-coding RNA, is increasingly recognised as having a key role in normal development and function of an organism, acting to control cellular and tissue growth and differentiation. It is also thought to be involved in many complex diseases now common in the Western world, including cardiovascular disease, type 2 diabetes, obesity and inflammatory bowel disease (IBD). There is a range of evidence to suggest that nutrition plays a vital role in the protection from such diseases. However, there is little information about the role of nutrition on the epigenetic regulation of IBD. This review aims to elucidate the interactions of nutrients and the epigenome in IBD. More specifically, the plasticity of epigenetic modifications that occur due to low selenium and folate levels in the diet during gestation and lactation will be discussed. A better understanding of this plasticity, and of nutrient–epigenome interactions, will have important implications for enhancing human health through foods. | [Matthew Barnetta c, Emma Berminghama c, Warren McNabbb c d, Shalome Bassetta c, Kelly Armstronga c, John Rouncea c, Nicole Roya c] | Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis | 7 August 2010 | |
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| sciencedirectS0828282X10704177 | Increased myocardial expression of angiopoietin-2 in patients undergoing urgent surgical revascularization for acute coronary syndromes | BackgroundMyocardial ischemia triggers the expression of multiple angiogenic factors including vascular endothelial growth factor and its receptors. However, vascular endothelial growth factor does not act in isolation.ObjectiveTo identify other genes important in the angiogenic response to clinically relevant myocardial ischemia.Methods and ResultsPaired intraoperative biopsies of ischemic and nonischemic myocardium were obtained from 12 patients with acute coronary syndromes (ACS) undergoing urgent coronary artery bypass graft surgery. Real-time polymerase chain reaction demonstrated significant upregulation of angiopoietin-2 (Ang-2) in ischemic myocardium, to a greater extent than other classical angiogenic factors. Microarray gene profiling identified Ang-2 to be among the top 10 differentially upregulated genes, in addition to genes involved in inflammation, cell signalling, remodelling and apoptosis.ConclusionsThe present document is the first report of microarray analysis of patients with ACS, and supports an important role for Ang-2 in the angiogenic response to severe ischemia in the human heart. Common gene expression patterns in ACS may provide opportunities for targeted pharmacological and cellular intervention. | [Neil P. Fam MD MSc1, Sara Arab PhD2 4, Filio Billia MD PhD5, Robin Han MD PhD1, Gerald Proteau PhD1, David Latter MD1, Lee Errett MD1, Daniel Bonneau MD1, Rosemary Dunne RN1, Peter P. Liu MD2 4, Duncan J. Stewart MD1 3 4 5] | Canadian Journal of Cardiology | August–September 2010 | |
| sciencedirectS0012160610002897 | Functional characterization of bursicon receptor and genome-wide analysis for identification of genes affected by bursicon receptor RNAi | Bursicon is an insect neuropeptide hormone that is secreted from the central nervous system into the hemolymph and initiates cuticle tanning. The receptor for bursicon is encoded by the rickets (rk) gene and belongs to the G protein-coupled receptor (GPCR) superfamily. The bursicon and its receptor regulate cuticle tanning as well as wing expansion after adult eclosion. However, the molecular action of bursicon signaling remains unclear. We utilized RNA interference (RNAi) and microarray to study the function of the bursicon receptor (Tcrk) in the model insect, Tribolium castaneum. The data included here showed that in addition to cuticle tanning and wing expansion reported previously, Tcrk is also required for development and expansion of integumentary structures and adult eclosion. Using custom microarrays, we identified 24 genes that are differentially expressed between Tcrk RNAi and control insects. Knockdown in the expression of one of these genes, TC004091, resulted in the arrest of adult eclosion. Identification of genes that are involved in bursicon receptor mediated biological processes will provide tools for future studies on mechanisms of bursicon action. | [Hua Bai, Subba R. Palli] | Developmental Biology | 1 August 2010 | |
| sciencedirectS0014483510001612 | Impaired function of circulating CD34+ CD45− cells in patients with proliferative diabetic retinopathy | Proliferative diabetic retinopathy is a consequence of retinal ischemia due to capillary occlusion resulting from damage to the retinal microvascular endothelium. Recent evidence suggests that high levels of bone-marrow derived circulating endothelial progenitor cells (EPCs) contribute to the pathological neovascularization of ischemic tissues and are a critical risk factor for the development of these complications. In the absence of a consensus definition of a circulating EPC and its surface markers in humans we evaluated the functional properties of CD34+ CD45− endothelial colony forming cells (ECFCs) in patients with proliferative diabetic retinopathy (PDR). Higher levels of circulating CD34+ CD45− cells were observed in patients with PDR compared to controls. However, ECFCs from patients with PDR were impaired in their ability to migrate towards SDF-1 and human serum, incorporate into and form vascular tubes with human retinal endothelial cells. The results from these pilot studies suggest that ECFCs from patients with PDR are mobilized into the circulation but may be unable to migrate and repair damaged capillary endothelium. This suggests that ECFCs may be a potential therapeutic target in the prevention and treatment of diabetic vascular complications. | [Kevin Tana, Emma Lessieura, Alecia Cutlera, Patrice Neronea, Amit Vasanjib, Kewal Asosinghb, Serpil Erzurumb, Bela Anand-Aptea b] | Experimental Eye Research | August 2010 | |
| sciencedirectS187861461000084X | Microarray analysis of differential gene expression elicited in Trametes versicolor during interspecific mycelial interactions | Trametes versicolor is an important white rot fungus of both industrial and ecological interest. Saprotrophic basidiomycetes are the major decomposition agents in woodland ecosystems, and rarely form monospecific populations, therefore interspecific mycelial interactions continually occur. Interactions have different outcomes including replacement of one species by the other or deadlock. We have made subtractive cDNA libraries to enrich for genes that are expressed when T. versicolor interacts with another saprotrophic basidiomycete, Stereum gausapatum, an interaction that results in the replacement of the latter. Expressed sequence tags (ESTs) (1920) were used for microarray analysis, and their expression compared during interaction with three different fungi: S. gausapatum (replaced by T. versicolor), Bjerkandera adusta (deadlock) and Hypholoma fasciculare (replaced T. versicolor). Expression of significantly more probes changed in the interaction between T. versicolor and S. gausapatum or B. adusta compared to H. fasciculare, suggesting a relationship between interaction outcome and changes in gene expression. | [Catherine Eyre, Wafa Muftah, Jennifer Hiscox, Julie Hunt, Peter Kille, Lynne Boddy, Hilary J. Rogers] | Fungal Biology | August 2010 | |
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| sciencedirectS0039128X09002232 | Conjugated and non-conjugated androgens differentially modulate specific early gene transcription in breast cancer in a cell-specific manner | The role of androgen in breast cancer development is not fully understood, although androgen receptors (ARs) have been identified in breast cancer clinical samples and cell lines. However the whole spectrum of androgen actions cannot be accounted to the classic AR activation and the possible existence of a cell surface-AR has been suggested. Indeed, androgen, like all steroids, has been reported to trigger membrane-initiated signaling activity and exert specific actions, including ion channels and kinase signaling pathway activation, ultimately affecting gene expression. However, the molecular nature of membrane androgen sites represents another major persisting question. In the present study, we investigated early transcriptional effects of testosterone and the impermeable testosterone–BSA conjugate, in two breast cancer cell lines (T47D and MDA-MB-231), in an attempt to decipher specific genes modified in each case, providing evidences about specific membrane-initiating actions. Our data indicate that the two agents affect the expression of several genes. A group of genes were commonly affected while others were uniquely modified by each agent, including interaction with growth factors and K+-channels. In MDA-MB-231 cells, that are AR negative, the majority of genes affected by testosterone were also affected by testosterone–BSA indicating a membrane-initiated action. Subsequent analysis revealed that the two agents trigger different molecular pathways and cellular/molecular functions, suggestive of a molecular or functional heterogeneity of membrane and intracellular AR. In addition, the reported phenotypic interactions of membrane-acting androgen with growth factor were verified at the transcriptomic level, as well as their ion channel-modifying effects. Finally an interesting interplay between membrane-acting androgen with inflammation-related molecules, with potential clinical implications was revealed. | [George Notas, Vassiliki Pelekanou1, Elias Castanas, Marilena Kampa] | Steroids | August–September 2010 | |
| sciencedirectS0006899310012400 | Profiles of oxidative stress-related microRNA and mRNA expression in auditory cells | Oxidative stress and high levels of reactive oxygen species (ROS) are risk factors of auditory cell injury and hearing impairment. MicroRNAs (miRNAs) are critical for the post-transcriptional regulation of gene expression and cell proliferation and survival. However, little is known about the impact of oxidative stress on the expression of miRNAs and their targeted mRNAs in auditory cells. We employed a cell model of oxidative stress by treatment of House Ear Institute-Organ of Corti 1 (HEI-OC1) cells with different concentrations of tert-butyl hydroperoxide (t-BHP) to examine the t-BHP-induced production of ROS and to determine the impact of t-BHP treatment on the relative levels of miRNA and mRNA transcripts in HEI-OC1 cells. We found that treatment with different concentrations of t-BHP promoted the production of ROS, but inhibited the proliferation of HEI-OC1 cells in a dose- and time-dependent manner. Furthermore, treatment with t-BHP induced HEI-OC1 cell apoptosis. Further microarray analyses revealed that treatment with t-BHP increased the transcription of 35 miRNAs, but decreased the expression of 40 miRNAs. In addition, treatment with t-BHP up-regulated the transcription of 2076 mRNAs, but down-regulated the levels of 580 mRNA transcripts. Notably, the up-regulated (or down-regulated) miRNAs were associated with the decreased (or increased) expression of predicted targeted mRNAs. Importantly, these differentially expressed mRNAs belonged to different functional categories, forming a network participating in the oxidative stress-related process in HEI-OC1 cells. Therefore, our findings may provide new insights into understanding the regulation of miRNAs on the oxidative stress-related gene expression and function in auditory cells. | [Zhi Wanga b 1, Yimin Liub 1, Ning Hanc, Xuemei Chena, Wei Yub, Weisen Zhangb, Fei Zoua] | Brain Research | | |
| sciencedirectS0006899310012709 | Gene expression profiling in progressively MPTP-lesioned macaques reveals molecular pathways associated with sporadic Parkinson's disease | Parkinson's disease (PD) is a common neurodegenerative disease characterized by progressive loss of midbrain dopaminergic neurons. To gain an insight into the mechanisms underlying the progression of PD, gene expression analysis was performed using two different brain regions, the substantia nigra pars compacta (SN) and the striatum (STR), of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-lesioned monkey model of PD. 230 genes were differentially expressed in the MPTP-treated SN compared to control, whereas 452 genes showed altered expression in the MPTP-treated STR, implying that MPTP elicits more damages in the striatal gene expression than in the SN. Comparative data analysis of the transcription profiles on the PD patients and MPTP monkey models, and pathway analysis indicated several signaling pathways as possible routes to MPTP-induced neurodegeneration. Interestingly, the networks which associated with cytoskeletal stability, ubiquitin–proteasome system (UPS) and Wnt signaling gained prominence in our study. Further transcriptional regulatory network analysis suggested the association of the neuronal repressor REST (RE1-silencing transcription factor; NRSF) and androgen receptor with the dysregulation of the striatal genes. Our study suggests the possibility that the dysfunction of multi-network signaling may induce abnormalities in a diverse range of biological processes, such as synaptic function, cytoskeletal stability, survival and differentiation. | [Tatsuya Ohnukia b, Atsushi Nakamuraa, Shigeru Okuyamaa, Shoji Nakamurab] | Brain Research | | |
| sciencedirectS0303720710001280 | Large scale analysis of transcription factor TTF-1/NKX2.1 target genes in GnRH secreting cell line GT1-7 | TTF-1/Nkx2.1 is a homeodomain-containing transcription factor required for the proper development of ventral forebrain, including some structures of the hypothalamus. TTF-1/Nkx2.1 remains expressed in the hypothalamus after birth and it plays a crucial role during sexual development. To identify putative TTF-1/Nkx2.1 target genes in GnRH neurons, we have studied the gene expression profile of the GT1-7 cells exogenously expressing TTF-1/Nkx2.1 coding gene. Our transcriptome analysis confirms that TTF-1/Nkx2.1 is involved in neuron morphogenesis and differentiation. Many of the newly identified TTF-1/Nkx2.1 target genes have a direct involvement with the central regulation of sexual maturity. In particular, we have identified Sparc as a gene directly regulated by TTF-1/Nkx2.1 at the promoter level. To further support the role of TTF-1 in GnRH neurons, we show that Sparc is involved in the regulation of the GnRH secretion in GT1-7 cells. | [Claudia Provenzanoa 1, Barbara Pascuccib, Eliana Luparia 2, Donato Civitarealea] | Molecular and Cellular Endocrinology | 29 July 2010 | |
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| sciencedirectS0924203110000214 | Neural network algorithm for the early detection of Parkinson's disease from blood plasma by FTIR micro-spectroscopy | Parkinson's disease (PD) is a progressive bradykinetic disorder. Diagnosis of PD is entirely clinical, no biochemical parameters exist to diagnose PD. The diagnostic problem associated with the early detection has led to an interest in the development of spectroscopic based diagnostic techniques. Fourier-transform infrared micro-spectroscopy analysis (FTIR) was applied to analyze human plasma samples of 69 healthy and 61 drug-naive PD patients in order to detect spectral parameters, which serve as biomarkers for monitoring and identification of PD. The analysis showed the bands at 1078, 1169 and 1244 cm−1 corresponding to carbohydrates, significantly increased in all tested patient samples (p ≤ 0.01). Several other spectral regions that attribute to amino acids, lipids and proteins indicate the unique detection of disease stages. Cluster analysis of variable regions provided excellent grouping of the healthy and the patient samples, which correlate completely with the clinical diagnosis. For automatic detection, artificial neural network (ANN) was implemented on the variable regions showed 96.29% accuracy in the detection of disease progression. These parameters could be used, as a basis for developing a spectral method for detecting PD. Execution of neural network will be useful in clinical screening and rapid detection of PD. | [Shiek S.S.J. Ahmeda, Winkins Santosha, Suresh Kumarb, T. Hema Thanka Christletc] | Vibrational Spectroscopy | 20 July 2010 | |
| sciencedirectS0378427410007733 | Post-transcriptional effect of endocrine disruptors in mouse testicular Sertoli cells | | [S.Y. Hwang1, S.J. Kim1, H.W. Park1, Y.R. An1, H. Cho1, M.J. Oh2, J.H. Oh3, S.J. Yoon3] | Toxicology Letters | 17 July 2010 | |
| sciencedirectS0378427410010106 | Study using differential gene expression analysis of the toxic responses in bladder from male and female dogs after treatment with a new anticholinesterasic compound for 28 days. An activity of the Melius project | | [A. García1, I. Amann1, M. Betanzos1, N. Fabre2, I. Anglade2, J.A. Vericat2] | Toxicology Letters | 17 July 2010 | |
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| sciencedirectS0166445X10000913 | Influence of ovarian stage on transcript profiles in fathead minnow (Pimephales promelas) ovary tissue | Interpretation of toxicogenomic experiments conducted with ovary tissue from asynchronous-spawning small fish species is complicated by background variation in the relative abundance and proportion of follicles at different stages within the ovary tissue sample. This study employed both real-time quantitative polymerase chain reaction and a 15,000 gene oligonucleotide microarray to examine variation in the fathead minnow (Pimephales promelas) ovarian transcriptional profile as a function of quantitative and qualitative differences in ovarian histology. The objectives were to provide data that could potentially aid interpretation of future toxicogenomics experiments, identify putative stage-related transcriptional markers, and generate insights into basic biological regulation of asynchronous oocyte development. Multiple lines of evidence from the present study indicate that variation in the transcriptional profile is primarily dependent on the relative abundance of previtellogenic versus vitellogenic follicles in the ovary. Due to the relatively small proportions of mature ovulated follicles or atretic follicles in the overall follicle population, few potential transcriptional markers of maturation, ovulation, or atresia could be identified. However, among the 460 differentially expressed genes identified in the present study, several targets, including HtrA serine peptidase 3 (htra3), tissue inhibitor of metalloproteinase 3 (timp3), aquaporin 8 (aqp8), transgelin 2 like (tagln2), Nedd4 family interacting protein 2 (ndfip2), chemokine ligand 12a (cxcl12a), midkine-related growth factor (mdka), and jagged 1b (jag 1b) exhibited responses and functional properties that support them as candidate molecular markers of significant shift in gross ovarian stage. Genes associated with a diversity of functions including cellular development, morphogenesis, coated vesicle transport, sexual reproduction, and neuron development, among others, were statistically enriched within the list of 460 genes differentially expressed among different ovarian classes. Overall, results of this study provide insights into background variation in ovary transcript profiles that should aid and enhance the interpretation of toxicogenomic data generated in experiments conducted with small, asynchronous-spawning fish species. | [Daniel L. Villeneuvea, Natàlia Garcia-Reyerob, Dalma Martinovi?a c, Jenna E. Cavallina, Nathaniel D. Muellera, Leah C. Wehmasa, Michael D. Kahla, Anne L. Linnuma, Edward J. Perkinsd, Gerald T. Ankleya] | Aquatic Toxicology | 15 July 2010 | |
| sciencedirectS0264410X10006663 | Immunomodulatory nanoparticles as adjuvants and allergen-delivery system to human dendritic cells: Implications for specific immunotherapy | Novel adjuvants and antigen-delivery systems with immunomodulatory properties that shift the allergenic Th2 response towards a Th1 or regulatory T cell response are desired for allergen-specific immunotherapy. This study demonstrates that 200-nm sized biodegradable poly(?-glutamic acid) (?-PGA) nanoparticles (NPs) are activators of human monocyte-derived dendritic cells (MoDCs). ?-PGA NPs are efficiently internalized by immature MoDCs and strongly stimulate production of chemokines and inflammatory cytokines as well as up-regulation of co-stimulatory molecules and immunomodulatory mediators involved in efficient T cell priming. Furthermore, MoDCs from allergic subjects stimulated in vitro with a mixture of ?-PGA NPs and extract of grass pollen allergen Phleum pratense (Phl p) augment allergen-specific IL-10 production and proliferation of autologous CD4+ memory T cells. Thus, ?-PGA NPs are promising as sophisticated adjuvants and allergen-delivery systems in allergen-specific immunotherapy. | [Sissela Broosa, Kristina Lundberga, Takami Akagib, Koji Kadowakib, Mitsuru Akashib, Lennart Greiffc, Carl A.K. Borrebaecka, Malin Lindstedta] | Vaccine | 12 July 2010 | |
| sciencedirectS0006899310009789 | VTA neurons show a potentially protective transcriptional response to MPTP | Parkinson's disease and its characteristic symptoms are thought to arise from the progressive degeneration of specific midbrain dopamine (DA) neurons. In humans, DA neurons of the substantia nigra (SN) and their projections to the striatum show selective vulnerability, while neighboring DA neurons of the ventral tegmental area (VTA) are relatively spared from degeneration. This pattern of cell loss is mimicked in humans, primates, and certain rodents by the neurotoxin MPTP. In this study, we aimed to test the hypothesis that there are factors in the VTA that are potentially neuroprotective against MPTP and that these factors change over time. We have found a dynamic transcriptional response within the cells of the VTA to sustained exposure to a low dose of MPTP. Specifically, the VTA has increased expression of 148 genes as an early response to MPTP and 113 genes as a late response to MPTP toxicity. This response encompasses many areas of cellular function, including protein regulation (Phf6) and ion/metal regulation (PANK2 and Car4). Notably, these responses were largely absent from the cells of the SN. Our data show a clear dynamic response in maintaining the homeostasis and viability of the neurons in the VTA that is lacking in the SN after neurotoxin challenge. | [Sudarshan Phania, Gregory Gonyec, Lorraine Iacovittia b] | Brain Research | | |
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| sciencedirectS0166445X10000834 | A transcriptomics-based biological framework for studying mechanisms of endocrine disruption in small fish species | This study sought to construct a transcriptomics-based framework of signal transduction pathways, transcriptional regulatory networks, and the hypothalamic-pituitary gonadal (HPG) axis in zebrafish (Danio rerio) to facilitate formulation of specific, testable hypotheses regarding the mechanisms of endocrine disruption in fish. For the analyses involved, we used data from a total of more than 300 microarrays representing 58 conditions, which encompassed 4 tissue types from zebrafish of both genders exposed for 1 of 3 durations to 10 different test chemicals (17?-ethynyl estradiol, fadrozole, 17?-trenbolone, fipronil, prochloraz, flutamide, muscimol, ketoconazole, trilostane, and vinclozolin). Differentially expressed genes were identified by one class t-tests for each condition, and those with false discovery rates of less than 40% and treatment/control ratios ≥1.3-fold were mapped to orthologous human, mouse, and rat pathways by Ingenuity Pathway Analysis to look for overrepresentation of known biological pathways. To complement the analysis of known biological pathways, the genes regulated by approximately 1800 transcription factors were inferred using the ARACNE mutual information-based algorithm. The resulting gene sets for all transcriptional factors, along with a group of compiled HPG-axis genes and approximately 130 publicly available biological pathways, were analyzed for their responses to the 58 treatment conditions by Gene Set Enrichment Analysis (GSEA) and its variant, Extended-GSEA. The biological pathways and transcription factors associated with multiple distinct treatments showed substantial interactions among the HPG-axis, TGF-beta, p53, and several of their cross-talking partners. These candidate networks/pathways have a variety of profound impacts on such cellular functions as stress response, cell cycle, and apoptosis. | [Rong-Lin Wanga, David Bencica, Daniel L. Villeneuveb, Gerald T. Ankleyb, Jim Lazorchaka, Stephen Edwardsc] | Aquatic Toxicology | 1 July 2010 | |
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| sciencedirectS0022282809005574 | Tumor necrosis factor-? produced in cardiomyocytes mediates a predominant myocardial inflammatory response to stretch in early volume overload | Acute stretch caused by volume overload (VO) of aorto-caval fistula (ACF) induces a variety of myocardial responses including mast cell accumulation, matrix metalloproteinase (MMP) activation, and collagen degradation, all of which are critical in dictating long-term left ventricle (LV) outcome to VO. Meanwhile, these responses can be part of myocardial inflammation dictated by tumor necrosis factor-? (TNF-?), which is elevated after acute ACF. However, it is unknown whether TNF-? mediates a major myocardial inflammatory response to stretch in early VO. In 24-h ACF and sham rats, microarray gene expression profiling and subsequent Ingenuity Pathway Analysis identified a predominant inflammatory response and a gene network of biologically interactive genes strongly linked to TNF-?. Western blot demonstrated increased local production of TNF-? in the LV (1.71- and 1.66-fold in pro- and active-TNF-? over control, respectively, P < 0.05) and cardiomyocytes (2- and 4-fold in pro- and active-TNF-? over control, respectively, P < 0.05). TNF-? neutralization with infliximab (5.5 mg/kg) attenuated the myocardial inflammatory response to acute VO, as indicated by inhibition of inflammatory gene upregulation, myocardial infiltration (total CD45+ cells, mast cells, and neutrophils), MMP-2 activation, collagen degradation, and cardiac cell apoptosis, without improving LV remodeling and function. These results indicate that TNF-? produced by cardiomyocytes mediates a predominant inflammatory response to stretch in the early VO in the ACF rat, suggesting an important role of TNF-? in initiating pathophysiological response of myocardium to VO. | [Yuanwen Chena b, Betty Patb, Junying Zhengb, Laura Cainb, Pamela Powellb, Ke Shib, Abdelkarim Sabrid, Ahsan Husainb e, Louis J. Dell'Italiab c] | Journal of Molecular and Cellular Cardiology | July 2010 | |
| sciencedirectS0882401010000586 | The cvfC operon of Staphylococcus aureus contributes to virulence via expression of the thyA gene | The cvfC operon of Staphylococcus aureus comprises four genes, cvfC1, cvfC2, cvfC3, and cvfC4. The cvfC3-disrupted mutant, M1262, produces less hemolysin and has attenuated virulence in silkworms and mice. Although introduction of the cvfC3 gene restores the decreased hemolysin production of M1262, the cvfC operon is more effective for the complementation, suggesting that cvfC operon function is impaired in M1262. In this study, we performed a microarray analysis and identified 21 genes with altered expression in M1262. The expression of virulence genes and metabolic genes, including thyA, was changed in M1262. The decreased expression of thyA in M1262 was restored by introducing a plasmid containing the cvfC operon. Introduction of a thyA gene-containing plasmid in M1262 restored hemolysin production and virulence against silkworms. Both M1262 and a thyA-deletion mutant exhibited slow growth in the presence of the detergent Triton-X 100. The growth defect of M1262 in the presence of Triton-X 100 was restored by the introduction of thyA. These results suggest that the cvfC operon contributes to hemolysin production, detergent resistance, and virulence of S. aureus in host animals via thyA expression. | [Mariko Ikuo, Chikara Kaito, Kazuhisa Sekimizu] | Microbial Pathogenesis | July–August 2010 | |
| sciencedirectS0196978110001567 | Antimicrobial peptide of an anti-lipopolysaccharide factor modulates of the inflammatory response in RAW264.7 cells | In this study, to clarify the protective mechanism of a peptide from shrimp anti-lipopolysaccharide (LPS) factor (SALF) against endotoxin shock, we evaluated the effects of the SALF and LPS on the production and release of tumor necrosis factor (TNF)-? in vitro using the RAW264.7 murine macrophage cell line. Stimulation by LPS induced the production of inflammatory cytokines, and the SALF was able to modulate TNF-? production in LPS-stimulated RAW264.7 cells. Microarray studies revealed a transcriptional profile which was assessed in the presence or absence of the SALF by a quantitative real-time polymerase chain reaction. Pretreatment with the SALF significantly downregulated the expression of nuclear factor (NF)-?B in the presence of LPS. In contrast, pretreatment with the SALF significantly elevated the expressions of Anp32a, CLU, and SLPI, which are considered to be immune-related genes in the presence of LPS. Inhibitor studies suggested that the SALF's modulation of LPS-induced TNF-? production involved a complex mechanism with mitogen-activated protein kinase kinase, calcium, and protein kinase C. The data from this study, which imply that the SALF can suppress TNF-? production, suggest a role for the SALF in the defense mechanism which can potentially be applied to mammals for endotoxin treatment. | [Ming-Ching Lina b 1, Shih-Bin Linb c 1, Shang-Chun Leea, Ching-Chun Lind, Cho-Fat Huid, Jyh-Yih Chena] | Peptides | July 2010 | |
| sciencedirectS1873506110000206 | The HOX Code as a “biological fingerprint” to distinguish functionally distinct stem cell populations derived from cord blood | Mesenchymal stem cells (MSC) have been isolated from almost every adult tissue. In cord blood (CB), different non-hematopoietic CD45-, CD34− adherent cell populations can be generated: the cord blood derived MSC (CB-MSC), that behave almost like MSC from bone marrow (BM-MSC), and unrestricted somatic stem cells (USSC) which show a distinct differentiation potential into all three germ layers. However, distinguishing these populations easily by molecular markers is still a concern. In this study we were able to present the HOX expression pattern of USSC, CB-MSC and BM-MSC, which in fact allows a discrimination of these populations.Briefly, RT-PCR analysis of the HOX code revealed a high similarity between BM-MSC and CB-MSC, which are both HOX-positive, whereas USSC resembled H9 embryonic stem cells HOX-negative.Especially HOXA9, HOXB7, HOXC10 and HOXD8 are good candidate markers to discriminate MSC from USSC. Thus, our data suggest that the "biological fingerprint" based on the HOX code can be used to distinguish functionally distinct MSC populations derived from bone marrow and cord blood. | [Stefanie Liedtkea 1 2, Anja Buchheisera 2 3, Julia Boscha 2 4, Frank Bosseb 5 6, Fabian Kruseb 5 6, Xiaoyi Zhaoa 2 7, Simeon Santourlidisa 2 7, Gesine Köglera 8] | Stem Cell Research | July 2010 | |
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| sciencedirectS0960076010001500 | Human breast tumor slices: A model for identification of vitamin D regulated genes in the tumor microenvironment ? | While many studies have addressed the direct effects of 1?,25(OH)2D3 on breast cancer (BC) cells, stromal–epithelial interactions, which are important for the tumor development, have been largely ignored. In addition, high concentrations of the hormone, which cannot be attained in vivo, have been used. Our aim was to establish a more physiological breast cancer model, represented by BC tissue slices, which maintain epithelial–mesenchymal interactions, cultured with a relatively low 1?,25(OH)2D3 concentration, in order to evaluate the vitamin D pathway. Freshly excised human BC samples were sliced and cultured in complete culture media containing vehicle, 0.5 nM or 100 nM 1?,25(OH)2D3 for 24 h. BC slices remained viable for at least 24 h, as evaluated by preserved tissue morphology in hematoxylin and eosin (HE) stained sections and bromodeoxyuridine (BrdU) incorporation by 10% of tumor cells. VDR mRNA expression was detected in all samples and CYP24A1 mRNA expression was induced by 1?,25(OH)2D3 in both concentrations (but mainly with 100 nM). Our results indicate that the vitamin D signaling pathway is functional in BC slices, a model which preserves stromal–epithelial interactions and mimics in vivo conditions. | [C. Milania, J. Welshb, M.L.H. Katayamaa, E.C. Lyrac, M.S. Macield, M.M. Brentania, M.A.A.K. Folgueiraa] | The Journal of Steroid Biochemistry and Molecular Biology | July 2010 | |
| sciencedirectS0960076010001603 | Genomic vitamin D signaling in breast cancer: Insights from animal models and human cells ? | These studies focus on identification of vitamin D regulated pathways that impact development or progression of breast cancer. In mouse experiments, we assessed genomic profiles of glandular tissue and established tumors from MMTV-neu mice fed adequate (250 IU/kg) or high (5000 IU/kg) vitamin D (cholecalciferol). Genomic profiles were also obtained in murine mammary cells that differentially express VDR that were cultured in vitro with 100 nM 1,25-dihydroxyvitamin D (1,25D). Ten candidate genes were identified that were commonly regulated in murine cells treated with 1,25D in vitro and in mammary gland of mice fed high dietary vitamin D. In complementary studies, the vitamin D pathway was evaluated in human mammary epithelial cells as a function of transformation. Genes regulated by 1,25D in human mammary epithelial cells included those involved in innate immunity (CD14), differentiation (Bmp6), extracellular matrix remodeling (Plau) and cell survival (Birc3). Transformation reduced VDR content and blunted the induction of some, but not all, target genes by 1,25D in human mammary cells. Collectively, these in vivo and in vitro data demonstrate that vitamin D signaling impacts on common pathways that drive differentiation, alter metabolism, remodel the extracellular matrix and trigger innate immunity in mammary tissue. | [Donald Matthewsa, Erika LaPortaa, Glendon M. Zinserb, Carmen J. Narvaezc, JoEllen Welshc d] | The Journal of Steroid Biochemistry and Molecular Biology | July 2010 | |
| sciencedirectS0960076010000981 | Actions of vitamin D are mediated by the TLR4 pathway in inflammation-induced colon cancer ? | Many chronic inflammatory diseases are associated with increased risk of developing cancer. In the colon, strong support for a link between chronic inflammation and cancer extends, in part, from population-based studies of persons with inflammatory bowel disease (IBD). Patients with IBD are at increased risk of developing colorectal cancer (CRC). The general consensus is that IBD results from the combined effects of genetics and environment factors known to affect the immune system. Vitamin D, an important regulator of the immune system, has been linked to IBD. Despite the strong potential reported for 1,25-dihydroxyvitamin D (1,25-OH)2D), its effects on calcium metabolism limits its application. Recently, less active vitamin D metabolites, cholecalciferol and 25-hydroxyvitamin D (25(OH)D), have gained considerable attention as promising agents against IBD-related colon cancer. Yet, their anti-proliferative properties and mechanism of action remain to be better defined. We present several signaling pathways commonly regulated by vitamin D compounds and highlight their regulation on TLR4. The efficacy of 25(OH)D and 1?-hydroxyviatmin D5 are evaluated using the azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced IBD-related colon carcinogenesis model. In summary, vitamin D supplementation may provide a cost-effective approach to reduce IBD related colon cancer. | [G. Murilloa b, V. Nagpala b, N. Tiwaria b, R.V. Benyac, R.G. Mehtaa b] | The Journal of Steroid Biochemistry and Molecular Biology | July 2010 | |
| sciencedirectS0300483X10002222 | Identification of potential biomarkers from gene expression profiles in rat lungs intratracheally instilled with C60 fullerenes | The use of C60 fullerenes is expected to increase in various industrial fields. Little is known about the potential toxicological mechanism of action of water-soluble C60 fullerenes. In our previous research, gene expression profiling of the rat lung was performed after whole-body inhalation exposure to C60 fullerenes to gain insights into the molecular events. These DNA microarray-based data closely matched the pathological findings that C60 fullerenes caused no serious adverse pulmonary effects under the inhalation exposure condition. Taking advantage of this, we attempted to characterize time-dependent changes in the gene expression profiles after intratracheal instillation with C60 fullerenes at different dosages and to identify the candidate expressed genes as potential biomarkers. The hierarchical cluster analysis revealed that the up- or downregulation of genes after intratracheal instillation with 1.0 mg C60 fullerene particles in rat lung tissue was significantly over-represented in the “response to stimulus” and “response to chemical stimulus” categories of biological processes and in the “extracellular space” category of the cellular component. These results were remarkable for 1 week after the instillation with C60 fullerenes. In the lung tissues instilled with 1.0 mg C60 fullerene particles, many representative genes involved in “inflammatory response,” such as the Cxcl2, Cxcl6, Orm1, and Spp1 genes, and in “matrix metalloproteinase activity,” such as the Mmp7 and Mmp12 genes, were upregulated for over 6 months. The expression levels of 89 and 21 genes were positively correlated with the C60 fullerene dose at 1 week and 6 months after the instillation, respectively. Most of them were involved in “inflammatory response”, and the Ccl17, Ctsk, Cxcl2, Cxcl6, Lcn6, Orm1, Rnase9, Slc26a4, Spp1, Mmp7, and Mmp12 genes were overlapped. Meanwhile, the expression levels of 16 and 4 genes were negatively correlated with the C60 fullerene dose at 1 week and 6 months after the instillation, respectively. Microarray-based gene expression profiling suggested that the expression of some genes is correlated with the dose of intratracheally instilled C60 fullerenes. We propose that these genes are useful for identifying potential biomarkers in acute-phase or persistent responses to C60 fullerenes in the lung tissue. | [Katsuhide Fujitaa b, Yasuo Morimotoc, Shigehisa Endohd, Kunio Uchidad, Hiroko Fukuib, Akira Ogamic, Isamu Tanakac, Masanori Horieb, Yasukazu Yoshidab, Hitoshi Iwahashib, Junko Nakanishia] | Toxicology | July–August 2010 | |
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| sciencedirectS0006899310006372 | Genome-wide gene expression analysis identifies K-ras as a regulator of alcohol intake | Adaptations in the anterior cingulate cortex (ACC) have been implicated in alcohol and drug addiction. To identify genes that may contribute to excessive drinking, here we performed microarray analyses in laser microdissected rat ACC after a single or repeated administration of an intoxicating dose of alcohol (3 g/kg). Expression of the small G protein K-ras was differentially regulated following both single and repeated alcohol administration. We also observed that voluntary alcohol intake in K-ras heterozygous null mice (K-ras+/−) did not increase after withdrawal from repeated cycles of intermittent ethanol vapor exposure, unlike in their wild-type littermates. To identify K-ras regulated pathways, we then profiled gene expression in the ACC of K-ras+/−, heterozygous null mice for the K-ras negative regulator Nf1 (Nf1+/−) and wild-type mice following repeated administration of an intoxicating dose of alcohol. Pathway analysis showed that alcohol differentially affected various pathways in a K-ras dependent manner – some of which previously shown to be regulated by alcohol – including the insulin/PI3K pathway, the NF-?B, the phosphodiesterases (PDEs) pathway, the Jak/Stat and the adipokine signaling pathways. Altogether, the data implicate K-ras-regulated pathways in the regulation of excessive alcohol drinking after a history of dependence. | [Vez Repunte-Canonigoa, Lena D. van der Stapa, Jihuan Chena, Valentina Sabinob c, Ulrich Wagnera, Eric P. Zorrillab, Gunter Schumannd, Amanda J. Robertsa, Pietro Paolo Sannaa] | Brain Research | | |
| sciencedirectS002196731000258X | Comprehensive blood plasma lipidomics by liquid chromatography/quadrupole time-of-flight mass spectrometry | A lipidomics strategy, combining high resolution reversed-phase liquid chromatography (RPLC) with high resolution quadrupole time-of-flight mass spectrometry (QqTOF), is described. The method has carefully been assessed in both a qualitative and a quantitative fashion utilizing human blood plasma. The inherent low technical variability associated with the lipidomics method allows to measure 65% of the features with an intensity RSD value below 10%. Blood plasma lipid spike-in experiments demonstrate that relative concentration differences smaller than 25% can readily be revealed by means of a t-test. Utilizing an advanced identification strategy, it is shown that the detected features mainly originate from (lyso-)phospholipids, sphingolipids, mono-, di- and triacylglycerols and cholesterol esters. The high resolution offered by the up-front RPLC step further allows to discriminate various isomeric species associated with the different lipid classes. The added value of utilizing a Jetstream electrospray ionization (ESI) source over a regular ESI source in lipidomics is for the first time demonstrated. In addition, the application of ultra high performance LC (UHPLC) up to 1200 bar to extend the peak capacity or increase productivity is discussed. | [Koen Sandraa b, Alberto dos Santos Pereirab, Gerd Vanhoenackerb, Frank Davidb, Pat Sandraa b] | Journal of Chromatography A | 18 June 2010 | |
| sciencedirectS0264410X10005852 | A general method for characterization of humoral immunity induced by a vaccine or infection | A universal system to diagnose disease, characterize infection or evaluate the response to a vaccine would be useful. Towards this end we introduce a machine-readable platform that we term “Immunosignaturing”. Rather than attempt to identify antibodies one by one, we splay the entire immune response across an array of 10,000 random sequence peptides. This segregates serum antibodies sufficiently to group and characterize responses caused by disease or vaccination. In the present study, we explore in detail the murine immunosignature to influenza A/PR/8/34 immunization and subsequent challenge. Even though the peptides are random sequence, the response to immunization and challenge is quite apparent. We find that the immunosignatures contained information not evident in whole virus ELISA. Antibody recognition of 283 influenza-specific peptides increased upon immunization and remained elevated for 211 days post-challenge. A set of 65 peptides, which overlapped 39 of the peptides that were consistent across time, was capable of distinguishing mice based on infectious dose, while whole virus ELISA could not. These peptide populations are consistently recognized in independent biological replicates of infection and are largely, but not solely, composed of virus reactive antibodies. The immunosignaturing analysis was expanded to analysis of human recipients of the 2006/2007 seasonal influenza vaccine. We find that 30 peptides are significantly recognized by all donors 21 days post-immunization and have the power to distinguish immune from pre-immune samples. Taken together the data suggest that immunosignaturing on a random peptide array can serve as a universal platform to assess antibody status in ways that cannot be replicated by conventional immunological assays. | [Joseph Barten Legutki, D. Mitchell Magee1, Phillip Stafford, Stephen Albert Johnston] | Vaccine | 17 June 2010 | |
| sciencedirectS0006291X10009137 | Expression of the Argonaute protein PiwiL2 and piRNAs in adult mouse mesenchymal stem cells | Piwi (P-element-induced wimpy testis) first discovered in Drosophila is a member of the Argonaute family of micro-RNA binding proteins with essential roles in germ-cell development. The murine homologue of PiwiL2, also known as Mili is selectively expressed in the testes, and mice bearing targeted mutations of the PiwiL2 gene are male-sterile. PiwiL2 proteins are thought to protect the germ line genome by suppressing retrotransposons, stabilizing heterochromatin structure, and regulating target genes during meiosis and mitosis. Here, we report that PiwiL2 and associated piRNAs (piRs) may play similar roles in adult mouse mesenchymal stem cells. We found that PiwiL2 is expressed in the cytoplasm of metaphase mesenchymal stem cells from the bone marrow of adult and aged mice. Knockdown of PiwiL2 with a specific siRNA enhanced cell proliferation, significantly increased the number of cells in G1/S and G2/M cell cycle phases and was associated with increased expression of cell cycle genes CCND1, CDK8, microtubule regulation genes, and decreased expression of tumor suppressors Cables 1, LATS, and Cxxc4. The results suggest broader roles for Piwi in genome surveillance beyond the germ line and a possible role in regulating the cell cycle of mesenchymal stem cells. | [Qiuling Wu1, Qi Ma, Lina A. Shehadeh, Amber Wilson, Linghui Xia1, Hong Yu, Keith A. Webster] | Biochemical and Biophysical Research Communications | 11 June 2010 | |
| sciencedirectS0006291X10008168 | TGF-? superfamily regulates a switch that mediates differentiation either into adipocytes or myocytes in left atrium derived pluripotent cells (LA-PCS) | Many stem cell studies have focused on the subject of cell fate and the signal molecules that modulate the regulatory switches for a given differentiation pathway. Genome-wide screens for cell fate determination signals require a cell source that differentiates purely into a single cell type. From adult rat left atrium, we established LA-PCs that differentiates into cardiac/skeletal myocytes or adipocytes with almost 100% purity. In this study, we compared gene expression profiles of undifferentiated LA-PCs with those of differentiated cells [adipocytes (Adi) or cardiac/skeletal myocytes (Myo)] to identify the signals that set the regulatory switch for adipocyte or myocyte differentiation. Microarray analysis verified the feasibility of genome-wide screening by this method. Using a pathway analysis screen, we found that members of the TGF-? superfamily signal transduction pathways modulate the adipocyte/myocyte differentiation switch. Further analysis determined that recombinant TGF-? inhibits adipogenesis and induces myogenesis simultaneously in a dose-dependent manner. Moreover, noggin induces differentiation into fully developed beating cardiac myocytes in vitro. These results provided new insight into the molecules that modulate the differentiation switch and validated a screening method for their identification. | [Nanako Kawaguchi, Ryota Nakao, Makoto Yamaguchi, Daisuke Ogawa, Rumiko Matsuoka] | Biochemical and Biophysical Research Communications | 4 June 2010 | |
| sciencedirectS1075996409001358 | Identification of a two-component VirR/VirS regulon in Clostridium perfringens | Clostridium perfringens, a Gram-positive anaerobic pathogen, is a causative agent of human gas gangrene that leads to severe rapid tissue destruction and can cause death within hours unless treated immediately. Production of several toxins is known to be controlled by the two-component VirR/VirS system involving a regulatory RNA (VR-RNA) in C. perfringens. To elucidate the precise regulatory network governed by VirR/VirS and VR-RNA, a series of microarray screening using VirR/VirS and VR-RNA-deficient mutants was performed. Finally, by qRT-PCR analysis, 147 genes (30 single genes and 21 putative operons) were confirmed to be under the control of the VirR/VirS-VR-RNA regulatory cascade. Several virulence-related genes for alpha-toxin, kappa-toxin, hyaluronidases, sialidase, and capsular polysaccharide synthesis were found. Furthermore, some genes for catalytic enzymes, various genes for transporters, and many genes for energy metabolism were also found to be controlled by the cascade. Our data indicate that the VirR/VirS-VR-RNA system is a global gene regulator that might control multiple cellular functions to survive and multiply in the host, which would turn out to be a lethal flesh-eating infection. | [Kaori Ohtania, Hideki Hirakawab, Kousuke Tashirob, Satoko Yoshizawaa, Satoru Kuharab, Tohru Shimizua] | Anaerobe | June 2010 | |
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| sciencedirectS0011224010000027 | Comparative analysis of transcriptional responses to the cryoprotectants, dimethyl sulfoxide and trehalose, which confer tolerance to freeze–thaw stress in Saccharomyces cerevisiae ? | We have used microarray analysis to monitor the gene expression profile of Saccharomyces cerevisiae BY4743 in the presence of the cryoprotectants, dimethyl sulfoxide (Me2SO) and trehalose. Analysis of these profiles suggests that both cryoprotectants increased the expression of genes involved in protein synthesis, ribosomal biogenesis, fatty acid biosynthesis, ergosterol biosynthesis, cell wall biosynthesis, and cellular accumulation of low molecular compounds such as glycerol, arginine and proline. Cryoprotectant treatment reduced the expression of genes involved in the ?-oxidation of fatty acids. In addition, Me2SO increased the expression of genes involved in protein refolding and trehalose increased the expression of genes involved in spore formation. This study supported that exposure to cryoprotectants prior to freezing not only reduce the freeze–thaw damage but also provide various process to the recovery from freeze–thaw damage. | [Yuko Momose, Rena Matsumoto, Akihiko Maruyama, Masakazu Yamaoka] | Cryobiology | June 2010 | |
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| sciencedirectS1087184510000460 | Identification of modules in Aspergillus niger by gene co-expression network analysis | The fungus Aspergillus niger has been studied in considerable detail with respect to various industrial applications. Although its central metabolic pathways are established relatively well, the mechanisms that control the adaptation of its metabolism are understood rather poorly. In this study, clustering of co-expressed genes has been performed on the basis of DNA microarray data sets from two experimental approaches. In one approach, low amounts of inducer caused a relatively mild perturbation, while in the other approach the imposed environmental conditions including carbon source starvation caused severe perturbed stress. A set of conserved genes was used to construct gene co-expression networks for both the individual and combined data sets. Comparative analysis revealed the existence of modules, some of which are present in all three networks. In addition, experimental condition-specific modules were identified. Module-derived consensus expression profiles enabled the integration of all protein-coding A. niger genes to the co-expression analysis, including hypothetical and poorly conserved genes. Conserved sequence motifs were detected in the upstream region of genes that cluster in some modules, e.g., the binding site for the amino acid metabolism-related transcription factor CpcA as well as for the fatty acid metabolism-related transcription factors, FarA and FarB. Moreover, not previously described putative transcription factor binding sites were discovered for two modules: the motif 5′-CGACAA is overrepresented in the module containing genes encoding cytosolic ribosomal proteins, while the motif 5′-GGCCGCG is overrepresented in genes related to ‘gene expression’, such as RNA helicases and translation initiation factors. | [Robert A. van den Bergb c 1, Machtelt Braaksmab 1, Douwe van der Veena 1, Mariët J. van der Werfb, Peter J. Puntb, John van der Oosta, Leo H. de Graaffa] | Fungal Genetics and Biology | June 2010 | |
| sciencedirectS0171298509001417 | Transcriptional effects of Colony-stimulating factor-1 in mouse macrophages | Colony-stimulating factor-1 (CSF-1) is a major regulator of macrophage development. CSF-1-dependent signalling has been implicated in proliferation, survival, and differentiation of mononuclear phagocytes, however, relatively little is known about the effects of CSF-1 on macrophage gene transcription and on CSF-1-responsive gene promoters. We used a combination of transcription profiling and in silico motif search to characterize genes that are regulated in mature bone marrow-derived macrophages cultured in the presence or absence of CSF-1. The expression of many known differentiation-associated macrophage markers was not significantly affected in the absence of CSF-1. Genes repressed by CSF-1 comprised a considerable number of granulocyte-specific genes. The respective gene promoters; however, were not significantly enriched for specific DNA patterns, suggesting that these genes are regulated by promoter-distal elements or at a post-transcriptional level. Genes downregulated upon CSF-1 deprivation showed a highly significant association with cell division which is in line with the known role of CSF-1 as a proliferation stimulus for mouse macrophages. Interestingly, three DNA patterns were significantly co-enriched in CSF-1-dependent gene promoters, including motifs related to NFY, CHR, and E2F sites. These motifs showed a strong positional preference on target promoters at −60, −30 and 0 bp upstream of the transcription start site, and define the common promoter structure of CSF-1-responsive genes. | [Carol El Chartounia, Chris Bennerb, Monika Eignera, Monika Lichtingera, Michael Rehlia] | Immunobiology | June 2010 | |
| sciencedirectS0965174810000846 | Ecdysteroid regulation of ovarian growth and oocyte maturation in the red flour beetle, Tribolium castaneum | Previous studies from our laboratory showed the involvement of juvenile hormone (JH) and ecdysteroid signaling in the regulation of female reproduction in the red flour beetle, Tribolium castaneum. JH regulates vitellogenin (Vg) synthesis in the fat body but the role of ecdysteroid signaling is not known. Here, we report on ecdysteroid regulation of ovarian growth and oocyte maturation. Microarray analysis of RNA isolated from ovaries showed the up-regulation of several genes coding for proteins involved in ecdysteroid signaling on the 4th day after female adult eclosion. The functional analyses of genes coding for proteins involved in ecdysteroid and JH signaling pathways by RNA interference (RNAi) revealed that ecdysteroids but not JH regulate ovarian growth and primary oocyte maturation. Ultrastructural studies showed the temporal sequences of key events in oogenesis including the development of primary oocytes, the differentiation and development of follicle epithelial cells, and the formation of intercellular spaces to facilitate uptake of Vg protein. RNAi studies showed that ecdysone receptor (EcR) and ultraspiracle (USP) are required for the ovarian growth, primary oocyte maturation and the growth and migration of the follicle cells. These studies suggest important roles for ecdysteroids in the regulation of oocyte maturation in the beetle ovaries. | [R. Parthasarathy, Zhentao Sheng, Zhiyuan Sun, Subba R. Palli] | Insect Biochemistry and Molecular Biology | June 2010 | |
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| sciencedirectS0022282809005689 | Derivation and characterization of human fetal MSCs: An alternative cell source for large-scale production of cardioprotective microparticles | The therapeutic effects of mesenchymal stem cells (MSCs) transplantation are increasingly thought to be mediated by MSC secretion. We have previously demonstrated that human ESC-derived MSCs (hESC-MSCs) produce cardioprotective microparticles in pig model of myocardial ischemia/reperfusion (MI/R) injury. As the safety and availability of clinical grade human ESCs remain a concern, MSCs from fetal tissue sources were evaluated as alternatives. Here we derived five MSC cultures from limb, kidney and liver tissues of three first trimester aborted fetuses and like our previously described hESC-derived MSCs; they were highly expandable and had similar telomerase activities. Each line has the potential to generate at least 1016–19 cells or 107–10 doses of cardioprotective secretion for a pig model of MI/R injury. Unlike previously described fetal MSCs, they did not express pluripotency-associated markers such as Oct4, Nanog or Tra1-60. They displayed a typical MSC surface antigen profile and differentiated into adipocytes, osteocytes and chondrocytes in vitro. Global gene expression analysis by microarray and qRT-PCR revealed a typical MSC gene expression profile that was highly correlated among the five fetal MSC cultures and with that of hESC-MSCs (r2 > 0.90). Like hESC-MSCs, they produced secretion that was cardioprotective in a mouse model of MI/R injury. HPLC analysis of the secretion revealed the presence of a population of microparticles with a hydrodynamic radius of 50–65 nm. This purified population of microparticles was cardioprotective at ∼1/10 dosage of the crude secretion. | [Ruenn Chai Laia b, Fatih Arslanc, Soon Sim Tana, Betty Tand, Andre Chooe, May May Leee, Tian Sheng Chena, Bao Ju Teha, John Kun Long Engf, Harwin Sidika, Vivek Tanavded, Wei Sek Hwangg, Chuen Neng Leeh, Reida Menshawe El Oakleyh, Gerard Pasterkampc, Dominique P.V. de Kleijnc i, Kok Hian Tanj, Sai Kiang Lima h] | Journal of Molecular and Cellular Cardiology | June 2010 | |
| sciencedirectS0022282810000398 | X-box binding protein 1 regulates brain natriuretic peptide through a novel AP1/CRE-like element in cardiomyocytes | The unfolded protein response (UPR) is triggered to assist protein folding when endoplasmic reticulum (ER) function is impaired. Recent studies demonstrated that ER stress can also induce cell-specific genes. In this study, we examined whether X-box binding protein 1 (XBP1), a major UPR-linked transcriptional factor, regulates the expression of brain natriuretic peptide (BNP) in cardiomyocytes. In samples from failing human hearts, extensive splicing of XBP1 was observed along with increased expression of glucose-regulated protein of 78 kDa (GRP78), a target of spliced XBP1 (sXBP1), suggesting that the UPR was induced in heart failure in humans. Interestingly, quantitative real-time PCR revealed a positive correlation between cardiac expression of GRP78 and BNP, leading us to test the hypothesis that sXBP1 regulates BNP as well as GRP78 in cardiomyocytes. A pharmacological ER stressor caused a dose-dependent increase in the expression of sXBP1 and BNP by cultured cardiomyocytes. Short interfering RNA targeting XBP1 suppressed the induction of BNP expression by a pharmacological ER stressor or norepinephrine, which was rescued by the adenovirus-mediated overexpression of sXBP1. The promoter assay with overexpression of sXBP1 or norepinephrine showed that the proximal AP1/CRE-like element in the promoter region of BNP was critical for transcriptional regulation of BNP by sXBP1. Direct binding of sXBP1 to this element was confirmed by the chromatin immunoprecipitation assay. These findings suggest that ER stress observed in failing hearts regulates cardiac BNP expression through a novel promoter region of the AP1/CRE-like element. | [Tamaki Sawadaa, Tetsuo Minaminoa, Hai Ying Fua, Mitsutoshi Asaia, Keiji Okudaa, Tadashi Isomurab, Satoru Yamazakic, Yoshihiro Asanoa, Ken-ichiro Okadaa, Osamu Tsukamotod, Shoji Sanadad, Hiroshi Asanumae, Masanori Asakurad, Seiji Takashimaa, Masafumi Kitakazed, Issei Komuroa] | Journal of Molecular and Cellular Cardiology | June 2010 | |
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| sciencedirectS0969996110000550 | Genes regulated in MPTP-treated macaques and human Parkinson's disease suggest a common signature in prefrontal cortex ? | The presymptomatic phase of Parkinson's disease (PD) is now recognized as a prodromal phase, with compensatory mechanism masking its progression and non-motor early manifestations, such as depression, cognitive disturbances and apathy. Those mechanisms were thought to be strictly dopamine-mediated until recent advances have shed light upon involvement of putative outside-basal ganglia, i.e. cortical, structures. We took advantage of our progressive 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated macaque model to monitor whole genome transcriptional changes in several brain areas. Our data reveals that transcriptomic activity changes take place from early stages, suggesting very early compensatory mechanisms or pathological activity outside the basal ganglia, including the PFC. Specific transcriptomic changes occurring in the PFC of fully parkinsonian MPTP-treated macaques have been identified. Interestingly, a large part of these transcriptomic changes were also observed in human post-mortem samples of patients with neurodegenerative diseases analysed by quantitative PCR. These results suggest that the PFC is able to detect the progression of dopamine denervation even at very early time points. There are therefore mechanisms, within the PFC, leading to compensatory alterations and/or participating to pathophysiology of prodromal PD manifestations. | [Markus Storvika 1, Marie-Jeanne Arguelb c 1, Sandra Schmiederb, Audrey Delerue-Audegondb c, Qin Lid, Chuan Qind, Anne Vitale, Bernard Bioulace, Christian E. Grosse, Garry Wonga, Jean-Louis Nahonb c 2, Erwan Bezardc d e 2] | Neurobiology of Disease | June 2010 | |
| sciencedirectS089062381000002X | In utero and lactational exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induces disruption of glands of the prostate and fibrosis in rhesus monkeys | We investigated the effects that 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure has on the prostate in rhesus monkey offspring. Dams received 0, 30 or 300 ng/kg TCDD subcutaneously on Day 20 of gestation, and then 5% of the initial dose was injected every 30 days until Day 90 after delivery. The offspring were maintained until reaching sexual maturity, and examined histopathologically. Dose-dependent decreases in glands of the prostate and widespread fibrosis were observed in offspring. It is noteworthy that 7 years from the final lactational TCDD exposure, inflammatory cell infiltration and disruption of glands of the prostate were still observed. Differential mRNA expression associated with fibrosis, inflammatory response and disruption of cell components were demonstrated by microarray analysis, with up-regulation of TGM4, TGFB1, COL1A1 and MMP2 confirmed. In conclusion, in utero and lactational exposure to TCDD induced dose-related prostatic fibrosis, indicating prostatic dysfunction and inducible semen quality reduction in second-generation rhesus monkeys. | [Akihiro Arimaa b, Hirohito Katoa, Ryota Isea, Yojiro Ooshimaa, Ayumi Inouea, Atsunobu Muneokaa, Shunichi Kamimurab c, Toshio Fukusatod, Shunichiro Kubotae, Hiroshi Sumidaf, Mineo Yasudaf] | Reproductive Toxicology | June 2010 | |
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| sciencedirectS0168170210000845 | Insect response to alphavirus infection—Establishment of alphavirus persistence in insect cells involves inhibition of viral polyprotein cleavage | Alphavirus persistence in the insect vector is an essential element in the vector–host transmission cycle of the virus and provides a model to study the biochemical and molecular basis for virus–vector coexistence. The prototype alphavirus Sindbis (SV) establishes persistent infections in invertebrate cell cultures which are characterized by low levels of virus production. We hypothesized that antiviral factors may be involved in decreasing the virus levels as virus persistence is established in invertebrate cells. Transcription profiles in Drosophila S2 cells at 5 days post-infection with SV identified families of gene products that code for factors that can explain previous observations seen in insect cells infected with alphaviruses. Genomic array analysis identified up-regulation of gene products involved in intracellular membrane vesicle formation, cell growth rate changes and immune-related functions in S2 cells infected with SV. Transcripts coding for factors involved in different aspects of the Notch signaling pathway had increased in expression. Increased expression of ankyrin,plap,syx13, unc-13, csp, rab1 and rab8 may aid in formation of virus containing vesicles and in intracellular transport of viral structural proteins. Possible functions of these gene products and relevant hypotheses are discussed. We confirmed the up-regulation of a wide-spectrum protease inhibitor, Thiol-ester containing Protein (TEP) II. We report inhibition of the viral polyprotein cleavage at 5 days post-infection (dpi) and after superinfection of SV-infected cells at 5 dpi. We propose that inefficient cleavage of the polyprotein may, at least in part, lead to reduced levels of virus seen as persistence is established. | [Usharani Mudiganti, Raquel Hernandez, Dennis T. Brown] | Virus Research | June 2010 | |
| sciencedirectS0006291X10006479 | Adhesion-mediated self-renewal abilities of Ph+ blastoma cells | The Philadelphia chromosome-positive blastoma, maintained by serial subcutaneous transplantation in nude mice, is a highly proliferating biological mass consisting of homogenous CD34+CD38− myeloblastoid cells. These cells newly evolved from pluripotent leukemia stem cells of chronic myeloid leukemia in the chronic phase. Therefore, this mass may provide a unique tool for better understanding cellular and molecular mechanisms of self-renewal of leukemia stem cells. In this paper, we demonstrated that intravenously injected blastoma cells can cause Ph+ blastic leukemia with multiple invasive foci in NOD/SCID mice but not in nude mice. In addition, using an in vitro culture system, we clearly showed that blastoma cell adhesion to OP9 stromal cells accelerates blastoma cell proliferation that is associated with up-regulation of BMI1 gene expression; increased levels of ?-catenin and the Notch1 intra-cellular domain; and changed the expression pattern of variant CD44 forms, which are constitutively expressed in these blastoma cells. These findings strongly suggest that adhesion of leukemic stem cells to stromal cells via CD44 might be indispensable for their cellular defense against attack by immune cells and for maintenance of their self-renewal ability. | [Keiji Funayamaa, Yumi Saito-Kurimotoa, Yasuhiro Ebiharab, Miyuki Shimanea, Hitoshi Nomuraa, Ko-ichiro Tsujib, Shigetaka Asanoa] | Biochemical and Biophysical Research Communications | 28 May 2010 | |
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| sciencedirectS0168165610001550 | Conditional cell-wall mutants of Saccharomyces cerevisiae as delivery vehicles for therapeutic agents in vivo to the GI tract | Strains of Saccharomyces cerevisiae capable of lysis upon conditional down-regulation of cell-wall biogenesis genes (SRB1 and PKC1) have been reported. Here, we show that they lyse and release recombinant protein not only under laboratory conditions, but (more importantly) under conditions found in the human stomach and duodenum. These findings provide proof that, in principle, such conditional lysis strains could be used as an integral part of a system for the oral delivery of therapeutic proteins. However, the current mechanism of conditional lysis is based on the use of the MET3 promoter which requires addition of methionine and cysteine for down-regulation of SRB1 and PKC1. This requirement makes it difficult to apply in vivo. We reasoned that promoters, suitable for in vivo down-regulation of lysis-inducing genes, could be identified amongst yeast genes whose transcript abundance is reduced under conditions found in the human gut. A microarray experiment identified a number of candidate genes with significantly reduced transcript levels under simulated human gut conditions. The greatest effects were seen with ANB1, TIR1, and MF(ALPHA)2), and we propose that their promoters have the potential to be used in vivo to achieve yeast lysis in the gut. | [Walid A.M. Omaraa 1, Bharat M. Rasha, Andrew Hayesa, Martin S.J. Wickhamb, Stephen G. Olivera c, Lubomira I. Statevaa] | Journal of Biotechnology | 17 May 2010 | |
| sciencedirectS0166445X09002306 | Hepatic transcriptomic and metabolomic responses in the Stickleback (Gasterosteus aculeatus) exposed to ethinyl-estradiol ? | An established three-spined stickleback (Gasterosteus aculeatus) cDNA array was expanded to 14,496 probes with the addition of hepatic clones derived from subtractive and normalized libraries from control males and males exposed to model toxicants. Microarrays and one-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy, together with individual protein and gene biomarkers were employed to investigate the hepatic responses of the stickleback to ethinyl-estradiol (EE2) exposure. Male fish were exposed via the water to EE2, including environmentally relevant concentrations (0.1–100 ng/l) for 4 days, and hepatic transcript and metabolite profiles, kidney spiggin protein and serum vitellogenin concentrations were determined in comparison to controls. EE2 exposure did not significantly affect spiggin concentration but significantly induced serum vitellogenin protein at the threshold concentration of 32 ng/l. 1H NMR coupled with robust univariate testing revealed only limited changes, but these did support the predicted modulation of the amino acid profile by transcriptomics. Transcriptional induction was found for hepatic vitellogenins and choriogenins as expected, together with a range of other EE2-responsive genes. Choriogenins showed the more sensitive responses with statistically significant induction at 10 ng/l. Real-time polymerase chain reaction (PCR) confirmed transcriptional induction of these genes. Phosvitinless vitellogenin C transcripts were highly expressed and represent a major form of the egg yolk precursors, and this is in contrast to other fish species where it is a minor component of vitellogenic transcripts. Differences in inducibility between the vitellogenins and choriogenins appear to be in accordance with the sequential formation of chorion and yolk during oogenesis in fish. | [Ioanna Katsiadakia 1, Tim D. Williamsb 1, Jonathan S. Ballc, Tim P. Beana, Matthew B. Sandersa, Huifeng Wub, Eduarda M. Santosc, Margaret M. Brownd, Paul Bakerd, Fernando Ortegab, Francesco Falcianib, John A. Craftd, Charles R. Tylerc, Mark R. Viantb, James K. Chipmanb] | Aquatic Toxicology | 5 May 2010 | |
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| sciencedirectS0306452210001533 | The effects of alcoholism on the human basolateral amygdala | Alcohol affects gene expression in several brain regions. The amygdala is a key structure in the brain's emotional system and in recent years the crucial importance of the amygdala in drug-seeking and relapse has been increasingly recognized. In this study gene expression screening was used to identify genes involved in alcoholism in the human basolateral amygdala of male patients. The results show that alcoholism affects a broad range of genes and many systems including genes involved in synaptic transmission, neurotransmitter transport, structural plasticity, metabolism, energy production, transcription and RNA processing and the circadian cycle. In particular, genes involved in the glutamate system were affected in the alcoholic patients. In the amygdala the glutamate system is involved in the acquisition, consolidation, expression and extinction of associative learning, which is a vital part of addiction, and in alcohol abusers it is associated with withdrawal anxiety and neurodegeneration. Downregulation of the excitatory amino acid transporters GLAST, GLT-1 and the AMPA glutamate receptor 2 (GluR2) revealed by the microarray were confirmed by Western blots. The decreased expression of GLAST, GLT-1 and GluR2 in the alcoholic patients may increase glutamate tone and activity in the basolateral amygdala and this may contribute to neurodegeneration as well as the expression of associative memories and anxiety which underlie continued drug-seeking and chronic relapse. | [R. Kryger, P.A. Wilce] | Neuroscience | 5 May 2010 | |
| sciencedirectS0306452210000916 | Gene expression profiling following short-term and long-term morphine exposure in mice uncovers genes involved in food intake | Addictive drugs including opioids activate signal transduction pathways that regulate gene expression in the brain. However, changes in CNS gene expression following morphine exposure are poorly understood. We determined changes in gene expression following short- and long-term morphine treatment in the hypothalamus and pituitary using genome-wide DNA microarray analysis and confirmed those alterations in gene expression by real-time reverse transcriptase polymerase chain reaction (RT-PCR) analysis. In the hypothalamus, short-term morphine administration up-regulated (at least twofold) 39 genes and down-regulated six genes. Long-term morphine treatment up-regulated 35 genes and down-regulated 51 genes. In the pituitary, short-term morphine administration up-regulated 110 genes and down-regulated 29 genes. Long-term morphine treatment up-regulated 85 genes and down-regulated 37 pituitary genes. Microarray analysis uncovered several genes involved in food intake (neuropeptide Y, agouti-related protein, and cocaine and amphetamine-regulated transcript) whose expression was strongly altered by morphine exposure in either the hypothalamus or pituitary. Subsequent RT-PCR analysis confirmed similar regulation in expression of these genes in the hypothalamus and pituitary. Finally, we found functional correlation between morphine-induced alterations in food intake and regulation of genes involved in this process. Changes in genes related to food intake may uncover new pathways related to some of the physiological effects of opioids. | [A. Anghela b, C.A.M. Jamiesonc d, X. Rena, J. Younga e, R. Porchea, E. Ozigboa, D.E. Ghodsa, M.L. Leea, Y. Liua, K. Lutfya f, T.C. Friedmana] | Neuroscience | 5 May 2010 | |
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| sciencedirectS0012160610000643 | Targeted deletion of Hand2 in cardiac neural crest-derived cells influences cardiac gene expression and outflow tract development | The basic helix–loop–helix DNA binding protein Hand2 has critical functions in cardiac development both in neural crest-derived and mesoderm-derived structures. Targeted deletion of Hand2 in the neural crest has allowed us to genetically dissect Hand2-dependent defects specifically in outflow tract and cardiac cushion independent of Hand2 functions in mesoderm-derived structures. Targeted deletion of Hand2 in the neural crest results in misalignment of the aortic arch arteries and outflow tract, contributing to development of double outlet right ventricle (DORV) and ventricular septal defects (VSD). These neural crest-derived developmental anomalies are associated with altered expression of Hand2-target genes we have identified by gene profiling. A number of Hand2 direct target genes have been identified using ChIP and ChIP-on-chip analyses. We have identified and validated a number of genes related to cell migration, proliferation/cell cycle and intracellular signaling whose expression is affected by Hand2 deletion in the neural crest and which are associated with development of VSD and DORV. Our data suggest that Hand2 is a multifunctional DNA binding protein affecting expression of target genes associated with a number of functional interactions in neural crest-derived cells required for proper patterning of the outflow tract, generation of the appropriate number of neural crest-derived cells for elongation of the conotruncus and cardiac cushion organization. Our genetic model has made it possible to investigate the molecular genetics of neural crest contributions to outflow tract morphogenesis and cell differentiation. | [Kristen L. Hollera, Tyler J. Hendershota, Sophia E. Troya, Joshua W. Vincentzb, Anthony B. Firullib, Marthe J. Howarda] | Developmental Biology | 1 May 2010 | |
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| sciencedirectS0965174810000822 | Juvenile hormone regulation of vitellogenin synthesis in the red flour beetle, Tribolium castaneum | To elucidate the endocrine regulation of vitellogenin (Vg) synthesis in the red flour beetle, Tribolium castaneum, the titers of juvenile hormone (JH) and ecdysteroids in the whole body of female beetles were measured and compared with Vg mRNA levels. Juvenile hormone levels remained high while the ecdysteroid levels declined steadily during 1–5 days post adult emergence (PAE). The Vg mRNA levels began to increase by the end of 3rd day PAE and peaked by the 4th–5th day PAE. Gene expression profiling by microarray and quantitative real-time PCR analyses of RNA isolated from 1 to 5 days PAE beetles revealed that the genes coding for proteins involved in JH biosynthesis and action, but not those involved in 20-hydroxyecdysone (20E) biosynthesis and action had similar expression patterns as the genes coding for Vg. RNA interference (RNAi)-aided knock-down in the expression of these genes showed that both JH and 20E were required for Vg gene expression. However, Vg mRNA was induced by the application of JH III but not by the injection of 20E into the previtellogenic females. These data suggest that JH is required for Vg synthesis in the fat body and 20E influences Vg synthesis through its action on oocyte maturation. | [R. Parthasarathy, Zhiyuan Sun, Hua Bai, Subba R. Palli] | Insect Biochemistry and Molecular Biology | May 2010 | |
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| sciencedirectS096999610900374X | Expression profiling in peripheral blood reveals signature for penetrance in DYT1 dystonia | DYT1 dystonia is an autosomal-dominantly inherited movement disorder, which is usually caused by a GAG deletion in the TOR1A gene. Due to the reduced penetrance of ∼ 30–40%, the determination of the mutation in a subject is of limited use with regard to actual manifestation of symptoms.In the present study, we used Affymetrix oligonucleotide microarrays to analyze global gene expression in blood samples of 15 manifesting and 15 non-manifesting mutation carriers in order to identify a susceptibility profile beyond the GAG deletion which is associated with the manifestation of symptoms in DYT1 dystonia.We identified a genetic signature which distinguished between asymptomatic mutation carriers and symptomatic DYT1 patients with 86.7% sensitivity and 100% specificity. This genetic signature could correctly predict the disease state in an independent test set with a sensitivity of 87.5% and a specificity of 85.7%.Conclusively, this genetic signature might provide a possibility to distinguish DYT1 patients from asymptomatic mutation carriers. | [M. Waltera b, M. Bonina b, R. Saunders Pullmanc d, E.M. Valentee f, M. Loig, M. Gambarinh, D. Raymondc, M. Tinazzih, C. Kammi, N. Glöcklea, S. Pothsa b, T. Gasseri, S.B. Bressmanc, C. Kleinj, L.J. Ozeliusk, O. Riessa, K. Grundmanna] | Neurobiology of Disease | May 2010 | |
| sciencedirectS0197018610001142 | Genome-wide microarray analysis of brain gene expression in mice on a short-term high iron diet | The effects of systemic iron overload on the brain are unclear. Microarray analysis of brain gene expression in mice following short-term iron supplementation revealed altered expression of 287 genes, although most changes were small. Transcripts for the iron storage protein ferritin light chain increased 20% (p = 0.002) and transcripts for iron regulatory protein 1, which negatively regulates ferritin translation, decreased 28% (p = 0.048). There were expression changes for genes involved in important brain functions such as neurotransmission and nitric oxide signaling, which is dependent on iron. Few changes related to reactive oxygen species, inflammation or apoptosis, however expression changes were observed for genes causatively linked to neurological disorders, including Charcot-Marie-Tooth disease, neuronal ceroid lipofuscinosis and mucolipidosis. The latter involve intralysosomal lipofuscin build-up that may reflect lysosomal iron accumulation. The findings suggest that high iron intake may cause subtle brain effects of clinical relevance in some circumstances. | [Daniel Johnstone, Elizabeth A. Milward] | Neurochemistry International | May–June 2010 | |
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| sciencedirectS0012160610000370 | Hes1 expression is reduced in Tbx1 null cells and is required for the development of structures affected in 22q11 deletion syndrome | 22q11 deletion syndrome (22q11DS) is characterised by aberrant development of the pharyngeal apparatus and the heart with haploinsufficiency of the transcription factor TBX1 being considered the major underlying cause of the disease. Tbx1 mutations in mouse phenocopy the disorder. In order to identify the transcriptional dysregulation in Tbx1-expressing lineages we optimised fluorescent-activated cell sorting of ?-galactosidase expressing cells (FACS-Gal) to compare the expression profile of Df1/Tbx1lacZ (effectively Tbx1 null) and Tbx1 heterozygous cells isolated from mouse embryos. Hes1, a major effector of Notch signalling, was identified as downregulated in Tbx1−/− mutants. Hes1 mutant mice exhibited a partially penetrant range of 22q11DS-like defects including pharyngeal arch artery (PAA), outflow tract, craniofacial and thymic abnormalities. Similar to Tbx1 mice, conditional mutagenesis revealed that Hes1 expression in embryonic pharyngeal ectoderm contributes to thymus and pharyngeal arch artery development. These results suggest that Hes1 acts downstream of Tbx1 in the morphogenesis of pharyngeal-derived structures. | [Kelly Lammerts van Buerena 1, Irinna Papangelia 1, Francesca Rochaisb, Kerra Pearcea, Catherine Robertsa, Amelie Calmonta, Dorota Szumskac, Robert G. Kellyb, Shoumo Bhattacharyac, Peter J. Scamblera] | Developmental Biology | 15 April 2010 | |
| sciencedirectS0012160610000722 | Genetic heterogeneity of skin microvasculature | Angiogenesis, the formation of new blood vessels from existing vasculature, is a complex process that is essential for normal embryonic development. Current models for experimental evaluation of angiogenesis often use tissue from large vessels like the aorta and umbilical vein, which are phenotypically distinct from microvasculature. We demonstrate that the utilization of skin to measure microvascular angiogenesis in embryonic and adult tissues is an efficient way to quantify microvasculature angiogenesis. We validate this approach and demonstrate its added value by showing significant differences in angiogenesis in monogenic and polygenic mouse models. We discovered that the pattern of angiogenic response among inbred mouse strains in this ex vivo assay differs from the strain distributions of previous in vivo angiogenesis assays. The difference between the ex vivo and in vivo assays may be related to systemic factors present in whole animals. Expression analysis of cultured skin biopsies from strains of mice with opposing angiogenic response was performed to identify pathways that contribute to differential angiogenic response. Increased expression of negative regulators of angiogenesis in C57Bl/6J mice was associated with lower growth rates. | [Fang Liua b, Jason Smitha, Zhen Zhanga, Richard Colea b, Bruce J. Herrona b] | Developmental Biology | 15 April 2010 | |
| sciencedirectS0303720709006534 | Androgen receptor and androgen-dependent gene expression in lung | The androgen receptor (AR) mediates the effects of male sex steroids. There are major sex differences in lung development and pathologies, including lung cancer. In this report, we show that Ar is mainly expressed in type II pneumocytes and the bronchial epithelium of murine lung and that androgen treatment increases AR protein levels in lung cells. Androgen administration altered significantly murine lung gene expression profiles; for example, by up-regulating transcripts involved in oxygen transport and down-regulating those in DNA repair and DNA recombination. Androgen exposure also affected the gene expression profile in a human lung adenocarcinoma-derived cell line, A549, by up- or down-regulating significantly some 200 transcripts, including down-regulation of genes involved in cell respiration. Dexamethasone treatment of A549 cells augmented expression of transcript sets that overlapped in part with those up-regulated by androgen in these cells. Moreover, a human lung cancer tissue array revealed that different lung cancer types are all AR-positive. Our results indicate that adult lung is an AR target tissue and suggest that AR plays a role in lung cancer biology. | [Laura Mikkonena, Päivi Pihlajamaaa, Biswajyoti Sahua, Fu-Ping Zhanga, Olli A. Jännea b] | Molecular and Cellular Endocrinology | 12 April 2010 | |
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| sciencedirectS1532045609002609 | Fatty acid composition and gene expression profiles are altered in aryl hydrocarbon receptor-1 mutant Caenorhabditis elegans | The aryl hydrocarbon receptor (AHR) is a eukaryotic transcription factor that plays an essential role in neuronal, immune, vascular, hepatic and hematopoietic development. In mammals, AHR induces metabolism-associated genes in response to xenobiotics. AHR is evolutionarily conserved, and the C. elegans AHR ortholog likely shares many physiologic functions with the mammalian version. While the role of AHR in development is known, the molecular basis of AHR action is less well understood. To understand the physiologic role of AHR in C. elegans, a combination of fatty acid profiling, transcriptomics, and phenotyping approaches was used. Fatty acid profiles from L4 larval stage whole animals indicated that C17isoA, C18:1n9t, C20:3n6 and C20:4n6 were significantly increased in an ahr-1 mutant compared to wild-type. Consistent with these changes, we observed a significant 5.8 fold increase in fat-7, and 1.7–1.9 fold increases in elo-5, nhr-49, and mdt-15 gene expression during the L4 stage. The ahr-1(ju145) mutant displayed deficits in growth and development including a reduced number of eggs laid, a higher proportion of dead embryos, delay in time to reach L4 stage, and movement deficits including a fewer number of body bends and a longer defecation cycle. To understand global effects of AHR-1 on transcription, microarray analysis was performed on L1 stage animals. Expression changes (324 under- and 238 over-expressed) were found in genes associated with metabolism, growth, and development. These results indicate a role for C. elegans AHR in regulating fatty acid composition and in contributing to some aspects of development. Since the transcriptional control of AHR targets may be evolutionarily conserved, these results provide a deeper understanding of the molecular actions of AHR in a model invertebrate system that may be informative for higher organisms. | [Vuokko Aarnioa b, Markus Storvika c, Marko Lehtonend, Suvi Asikainena b, Kaja Reisnera b e, James Callawaya b, Martina Rudgalvytea b, Merja Laksoa b, Garry Wonga b] | Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology | April 2010 | |
| sciencedirectS0301468110000149 | Redirection of renal mesenchyme to stromal and chondrocytic fates in the presence of TGF-?2 | Many members of the transforming growth factor-? (TGF-?) superfamily have been shown to be important regulators of metanephric development. In this study, we characterized the effect of TGF-?2 on metanephric development. Rat and mouse metanephroi cultured in the presence of exogenous TGF-?2 for up to 15 days were small, and contained rudimentary ureteric branches and few glomeruli. These metanephroi were mostly comprised of mesenchymal cells, with two cell populations (designated Type 1 and Type 2 cells) evident. Type 1 cells were only observed when TGF-?2 was added from the commencement of culture, they resembled chondroblasts and were Alcian Blue and Col IIB positive. Type 2 cells were observed whenever TGF-?2 was added to the media, formed a band at the periphery of the explants consisting of 5–10 layers of spindle-shaped cells, and were alpha-smooth muscle actin positive. Molecular and RNA in situ hybridization analysis of metanephroi cultured in the presence of TGF-?2 for 6 days demonstrated that Type 1 and 2 cells were negative for Pax2, WT1, GDNF and FoxD1. Gene expression profiling demonstrated an upregulation of chondrocyte, myogenic and stromal genes, some of which were identified as markers of Type 1 and Type 2 cells. In addition, TGF-?2 was capable of maintaining the survival of mouse isolated metanephric mesenchyme (iMM) in the absence of serum or inductive signals from the ureteric epithelium. TGF-?2 also induced the differentiation of iMM into Type 1 and 2 cells. The presence of chondrocytes and muscle in these cultures is reminiscent of the cell types found in some Wilms' tumors. These studies demonstrate that TGF-?2 is capable of differentiating metanephric mesenchyme away from a renal cell fate. | [Sunder Sims-Lucasa 1 2, Richard J. Younga 3 1, Gemma Martinezb 4, Darrin Taylorb, Sean M. Grimmondb, Rohan Teasdaleb, Melissa H. Littleb, John F. Bertrama, Georgina Caruanaa] | Differentiation | April–June 2010 | |
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| sciencedirectS0090825810000235 | Low malignant potential tumors with micropapillary features are molecularly similar to low-grade serous carcinoma of the ovary | Objective.Low-grade serous carcinoma (LGSC) is a chemoresistant ovarian neoplasm thought to potentially arise in a background of low malignant potential tumors (LMP), which are typically non-aggressive. However, LMP with micropapillary features (LMP-MP) have more aggressive clinical behavior and may represent an intermediate in progression to LGSC. The objective of this study was to obtain and compare gene expression profiles of LMP, LMP-MP and LGSC to determine if LMP-MP more closely resembles LGSC, and to identify genes involved in LGSC carcinogenesis.Methods.Epithelial cells from LMP (n = 17), LMP-MP (n = 9) and LGSC (n = 11) were isolated by laser capture microdissection. RNA was extracted, reverse transcribed to cDNA, amplified and hybridized to Affymetrix U133 Plus2 genechip arrays. Gene expression data were checked for quality, filtered and significantly altered genes between subgroups were identified. Differential expression of selected genes was verified by RT-qPCR and immunohistochemistry.Results.Gene expression analysis identified differential expression between LMP and LMP-MP, LMP and LGSC but not LMP-MP and LGSC. Integration of differentially expressed genes into the protein interaction database CytoScape highlighted gene products in the MAPK pathway as differentially regulated between LMP and LGSC. Four genes were selected and validated by RT-qPCR performed on microarray samples (n = 15) and immunohistochemistry on a representative microarray (n = 57).Conclusion.The gene expression profile of LMP-MP is similar to LGSC and distinct from LMP, reflecting their more aggressive clinical behavior. Candidate genes in the MAPK pathway were highlighted which may play a role in LGSC carcinogenesis and indicate potential therapeutic targets. | [Taymaa Maya b c, Carl Virtanend, Monika Sharmad, Anca Mileae, Heather Begleye, Barry Rosena f, K. Joan Murphya f, Theodore J. Browna b c 1, Patricia A. Shawe 1] | Gynecologic Oncology | April 2010 | |
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| sciencedirectS0022282809005586 | Glycolytic network restructuring integral to the energetics of embryonic stem cell cardiac differentiation | Decoding of the bioenergetic signature underlying embryonic stem cell cardiac differentiation has revealed a mandatory transformation of the metabolic infrastructure with prominent mitochondrial network expansion and a distinctive switch from glycolysis to oxidative phosphorylation. Here, we demonstrate that despite reduction in total glycolytic capacity, stem cell cardiogenesis engages a significant transcriptome, proteome, as well as enzymatic and topological rearrangement in the proximal, medial, and distal modules of the glycolytic pathway. Glycolytic restructuring was manifested by a shift in hexokinase (Hk) isoforms from Hk-2 to cardiac Hk-1, with intracellular and intermyofibrillar localization mapping mitochondrial network arrangement. Moreover, upregulation of cardiac-specific enolase 3, phosphofructokinase, and phosphoglucomutase and a marked increase in glyceraldehyde 3-phosphate dehydrogenase (GAPDH) phosphotransfer activity, along with apparent post-translational modifications of GAPDH and phosphoglycerate kinase, were all distinctive for derived cardiomyocytes compared to the embryonic stem cell source. Lactate dehydrogenase (LDH) isoforms evolved towards LDH-2 and LDH-3, containing higher proportions of heart-specific subunits, and pyruvate dehydrogenase isoforms rearranged between E1? and E1?, transitions favorable for substrate oxidation in mitochondria. Concomitantly, transcript levels of fetal pyruvate kinase isoform M2, aldolase 3, and transketolase, which shunt the glycolytic with pentose phosphate pathways, were reduced. Collectively, changes in glycolytic pathway modules indicate active redeployment, which would facilitate connectivity of the expanding mitochondrial network with ATP utilization sites. Thus, the delineated developmental dynamics of the glycolytic phosphotransfer network is integral to the remodeling of cellular energetic infrastructure underlying stem cell cardiogenesis. | [Susan Chung, D. Kent Arrell, Randolph S. Faustino, Andre Terzic, Petras P. Dzeja] | Journal of Molecular and Cellular Cardiology | April 2010 | |
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| sciencedirectS0168945210000373 | Gene expression profiling of developing Brassica napus seed in relation to changes in major storage compounds | Seed development is controlled by a complex network of spatially and temporally expressed genes. We previously reported that carotenoid accumulation in Brassica napus seeds was developmentally regulated, with the highest levels detected at 35–40 days post-anthesis (DPA). To investigate accompanying changes in gene expression, we conducted a microarray study during the early- to middle stage of B. napus (spring cv.) seed development. Compared to seeds 35 DPA, seeds 20 DPA had 1851 genes up-regulated 2-fold or greater and 1641 genes down-regulated 2-fold or greater. Genes related to the biosynthesis of storage reserve compounds (starch, lipid, and protein), four genes involved in carotenoid biosynthesis, and seven genes involved in isoprenoid biosynthesis showed differential expression between the two developmental stages. In addition, the array provided information on molecular factors which are similar to those regulating seed reserve compounds in other plant species, and may have the potential to include transcriptional networks controlling the biosynthesis of seed carotenoids. | [Bianyun Yua b, Margaret Grubera, George G. Khachatouriansb, Dwayne D. Hegedusa b, Abdelali Hannoufac] | Plant Science | April 2010 | |
| sciencedirectS0890623809003451 | Prenatal exposure to environmental tobacco smoke alters gene expression in the developing murine hippocampus | BackgroundLittle is known about the effects of passive smoke exposures on the developing brain.ObjectiveThe purpose of the current study was to identify changes in gene expression in the murine hippocampus as a consequence of in utero exposure to sidestream cigarette smoke (an experimental equivalent of environmental tobacco smoke (ETS)) at exposure levels that do not result in fetal growth inhibition.MethodsA whole body smoke inhalation exposure system was utilized to deliver ETS to pregnant C57BL/6J mice for 6 h/day from gestational days 6–17 (gd 6–17) [for microarray] or gd 6–18.5 [for fetal phenotyping].ResultsThere were no significant effects of ETS exposure on fetal phenotype. However, 61 “expressed” genes in the gd 18.5 fetal hippocampus were differentially regulated (up- or down-regulated by 1.5-fold or greater) by maternal exposure to ETS. Of these 61 genes, 25 genes were upregulated while 36 genes were down-regulated. A systems biology approach, including computational methodologies, identified cellular response pathways, and biological themes, underlying altered fetal programming of the embryonic hippocampus by in utero cigarette smoke exposure.ConclusionsResults from the present study suggest that even in the absence of effects on fetal growth, prenatal smoke exposure can alter gene expression during the “early” period of hippocampal growth and may result in abnormal hippocampal morphology, connectivity, and function. | [Partha Mukhopadhyay1, Kristin H. Horn1, Robert M. Greene, M. Michele Pisano] | Reproductive Toxicology | April 2010 | |
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| sciencedirectS0009279709005675 | Benzene-induced bone-marrow toxicity: A hematopoietic stem-cell-specific, aryl hydrocarbon receptor-mediated adverse effect | Benzene-induced hematopoietic toxicity is an aryl hydrocarbon receptor (AhR)-related adverse effect that is not exhibited in AhR-knockout (KO) mice. In the hematopoietic system, the steady-state expression of AhRs is limited in the hematopoietic progenitor cells; thus, a hierarchical hematopoietic impairment starts from hematopoietic progenitor cells after benzene exposure. When one looks at wild-type recipient mice that have been lethally irradiated and repopulated with AhR-KO bone marrow cells, owing to reconstruction by the marrow from AhR-KO mice, no impairment is observed in the assay of granulo-macrophage colony-forming units (CFU-GMs) in the bone marrow after benzene exposure of the reconstituted mice. In contrast, in mature white blood cells concern, benzene-induced hematopoietic cytotoxicity is observed in the same reconstituted mice; however, this benzene-induced hematopoietic cytotoxicity in mature white blood cells is not induced in the case of AhR-KO mice repopulated with wild-type bone marrow cells after a lethal dose of irradiation. The mechanism of benzene-induced hematopoietic toxicity in the mature blood cells in AhR-KO mice is assumed to be based on metabolites such as phenol and hydroquinone derived from hepatic AhR. Thus, the former toxicity in mature white blood cells is assumed to be based on the metabolites of the wild-type hepatic AhR, whereas the latter lack of toxicity in mature blood cells in AhR-KO mice is due to the lack of benzene-induced metabolism in the liver. Global gene expression analysis of bone marrow cells after benzene exposure reveals that MEF2c, the functions of which are known to maintain lymphocyte differentiation and promote proliferation of hematopoietic progenitor cells, is commonly downmodulated not only in C57BL/6 but also in C3H/He mice. In response to these impairments of the hematopoietic progenitor cells and the niches, stochastic and reciprocal upregulations of integrin beta 2 and the Runx family are observed, which are known to stabilize hematopoietic niches during the steady-state. Direct observation of the hematopoietic progenitor cells, particularly the Lin−c-kit+Sca-1+ (LKS) fraction, after benzene exposure revealed an increased amount of intracytoplasmic reactive oxygen species (ROS) detected by ROS-reacting dye as compared with other blood cell fractions. | [Yoko Hirabayashia, Tohru Inoueb] | Chemico-Biological Interactions | 19 March 2010 | |
| sciencedirectS0012160609014390 | Gp93, the Drosophila GRP94 ortholog, is required for gut epithelial homeostasis and nutrient assimilation-coupled growth control | GRP94, the endoplasmic reticulum Hsp90, is a metazoan-restricted chaperone essential for early development in mammals, yet dispensable for mammalian cell viability. This dichotomy suggests that GRP94 is required for the functional expression of secretory and/or membrane proteins that enable the integration of cells into tissues. To explore this hypothesis, we have identified the Drosophila ortholog of GRP94, Gp93, and report that Gp93 is an essential gene in Drosophila. Loss of zygotic Gp93 expression is late larval-lethal and causes prominent defects in the larval midgut, the sole endoderm-derived larval tissue. Gp93 mutant larvae display pronounced defects in the midgut epithelium, with aberrant copper cell structure, markedly reduced gut acidification, atypical septate junction structure, depressed gut motility, and deficits in intestinal nutrient uptake. The metabolic consequences of the loss of Gp93-expression are profound; Gp93 mutant larvae exhibit a starvation-like metabolic phenotype, including suppression of insulin signaling and extensive mobilization of amino acids and triglycerides. The defects in copper cell structure/function accompanying loss of Gp93 expression resemble those reported for mutations in labial, an endodermal homeotic gene required for copper cell specification, and ?-spectrin, thus suggesting an essential role for Gp93 in the functional expression of secretory/integral membrane protein-encoding lab protein target genes and/or integral membrane protein(s) that interact with the spectrin cytoskeleton to confer epithelial membrane specialization. | [Jason C. Maynarda, Trang Phamb, Tianli Zhenga, Angela Jockheck-Clarka, Helen B. Rankinc, Christopher B. Newgardb, Eric P. Spanac, Christopher V. Nicchittaa] | Developmental Biology | 15 March 2010 | |
| sciencedirectS0012160609014584 | Hs2st mediated kidney mesenchyme induction regulates early ureteric bud branching | Heparan sulfate proteoglycans (HSPGs) are central modulators of developmental processes likely through their interaction with growth factors, such as GDNF, members of the FGF and TGF? superfamilies, EGF receptor ligands and HGF. Absence of the biosynthetic enzyme, heparan sulfate 2-O-sulfotransferase (Hs2st) leads to kidney agenesis. Using a novel combination of in vivo and in vitro approaches, we have reanalyzed the defect in morphogenesis of the Hs2st−/− kidney. Utilizing assays that separately model distinct stages of kidney branching morphogenesis, we found that the Hs2st−/− UB is able to undergo branching and induce mesenchymal-to-epithelial transformation when recombined with control MM, and the isolated Hs2st null UB is able to undergo branching morphogenesis in the presence of exogenous soluble pro-branching growth factors when embedded in an extracellular matrix, indicating that the UB is intrinsically competent. This is in contrast to the prevailing view that the defect underlying the renal agenesis phenotype is due to a primary role for 2-O sulfated HS in UB branching. Unexpectedly, the mutant MM was also fully capable of being induced in recombination experiments with wild-type tissue. Thus, both the mutant UB and mutant MM tissue appear competent in and of themselves, but the combination of mutant tissues fails in vivo and, as we show, in organ culture. We hypothesized a 2OS-dependent defect in the mutual inductive process, which could be on either the UB or MM side, since both progenitor tissues express Hs2st. In light of these observations, we specifically examined the role of the HS 2-O sulfation modification on the morphogenetic capacity of the UB and MM individually. We demonstrate that early UB branching morphogenesis is not primarily modulated by factors that depend on the HS 2-O sulfate modification; however, factors that contribute to MM induction are markedly sensitive to the 2-O sulfation modification. These data suggest that key defect in Hs2st null kidneys is the inability of MM to undergo induction either through a failure of mutual induction or a primary failure of MM morphogenesis. This results in normal UB formation but affects either T-shaped UB formation or iterative branching of the T-shaped UB (possibly two separate stages in collecting system development dependent upon HS). We discuss the possibility that a disruption in the interaction between HS and Wnts (e.g. Wnt 9b) may be an important aspect of the observed phenotype. This appears to be the first example of a defect in the MM preventing advancement of early UB branching past the first bifurcation stage, one of the limiting steps in early kidney development. | [Mita M. Shahb, Hiroyuki Sakuraib 1, Derina E. Sweeneyb c, Thomas F. Gallegosc d, Kevin T. Bushb, Jeffrey D. Eskoc, Sanjay K. Nigama b c] | Developmental Biology | 15 March 2010 | |
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| sciencedirectS0344033810000440 | CAP Program 2009 Abstracts | | [] | Pathology - Research and Practice | 15 March 2010 | |
| sciencedirectS0304423809005676 | Oligoarray analysis of gene expression in ripening Japanese pear fruit | A custom oligoarray of Japanese pear (Pyrus pyrifolia) based on 9812 independent ESTs from different tissues (fruits at various growth stages, vegetative and flower tissues) was designed and used for comprehensive investigation of gene expression before and during ripening (105–147 days after full bloom). Results of one-way ANOVA test indicated that the expression of about 30% of the genes (corresponding to 3062 independent ESTs) showed a significant difference between 105 (before ripening) and 147 (ripened) days after full bloom. Classification of expression pattern of those 3062 ESTs showed 11 sets, five of them contain 545 up-regulated ESTs and the other six sets contain 1920 down-regulated ones. Among them, 16 genes showed remarkable increase of more than 100 fold from 105 to 147 days after full bloom. The largest increase (more than 9000 fold) was exhibited by the glutathione S-transferase gene. The major functional group of remarkably up-regulated genes was in a glycosyl hydrolase family such as polygalacturonase. Genes participating in ethylene metabolism and sulfate transport were also identified. On the contrary, 18 genes were down-regulated to less than 1% during the same period. Glycosyl hydrolase family genes, invertase/pectin methylesterase inhibitor genes, and genes involved in secondary metabolism were the major groups identified. In addition, putative regulatory genes such as bHLH transcription factor also showed remarkable decreasing in expression. The cDNA oligoarray analysis efficiently provided individual gene expression profiles and new insights for elucidating the biological mechanisms responsible for fruit ripening in Japanese pear. | [Chikako Nishitania, Tokurou Shimizua, Hiroshi Fujiia, Fumiko Hosakaa, Shingo Terakamia, Yuri Nakamuraa, Akihiro Itaib, Ayako Yamaguchi-Nakamuraa, Toshiya Yamamotoa] | Scientia Horticulturae | 15 March 2010 | |
| sciencedirectS0041008X09004943 | Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning | Identification of carcinogenic activity is the primary goal of the 2-year bioassay. The expense of these studies limits the number of chemicals that can be studied and therefore chemicals need to be prioritized based on a variety of parameters. We have developed an ensemble of support vector machine classification models based on male F344 rat liver gene expression following 2, 14 or 90 days of exposure to a collection of hepatocarcinogens (aflatoxin B1, 1-amino-2,4-dibromoanthraquinone, N-nitrosodimethylamine, methyleugenol) and non-hepatocarcinogens (acetaminophen, ascorbic acid, tryptophan). Seven models were generated based on individual exposure durations (2, 14 or 90 days) or a combination of exposures (2 + 14, 2 + 90, 14 + 90 and 2 + 14 + 90 days). All sets of data, with the exception of one yielded models with 0% cross-validation error. Independent validation of the models was performed using expression data from the liver of rats exposed at 2 dose levels to a collection of alkenylbenzene flavoring agents. Depending on the model used and the exposure duration of the test data, independent validation error rates ranged from 47% to 10%. The variable with the most notable effect on independent validation accuracy was exposure duration of the alkenylbenzene test data. All models generally exhibited improved performance as the exposure duration of the alkenylbenzene data increased. The models differentiated between hepatocarcinogenic (estragole and safrole) and non-hepatocarcinogenic (anethole, eugenol and isoeugenol) alkenylbenzenes previously studied in a carcinogenicity bioassay. In the case of safrole the models correctly differentiated between carcinogenic and non-carcinogenic dose levels. The models predict that two alkenylbenzenes not previously assessed in a carcinogenicity bioassay, myristicin and isosafrole, would be weakly hepatocarcinogenic if studied at a dose level of 2 mmol/kg bw/day for 2 years in male F344 rats; therefore suggesting that these chemicals should be a higher priority relative to other untested alkenylbenzenes for evaluation in the carcinogenicity bioassay. The results of the study indicate that gene expression-based predictive models are an effective tool for identifying hepatocarcinogens. Furthermore, we find that exposure duration is a critical variable in the success or failure of such an approach, particularly when evaluating chemicals with unknown carcinogenic potency. | [Scott S. Auerbacha, Ruchir R. Shahb, Deepak Mavb, Cynthia S. Smitha, Nigel J. Walkera, Molly K. Vallanta, Gary A. Boormana, Richard D. Irwina] | Toxicology and Applied Pharmacology | 15 March 2010 | |
| sciencedirectS0304394010000571 | VMH lesions downregulate the expression of Per2 gene in the pancreas in the rat ? | The mammalian circadian system contains both central and peripheral oscillators. It was reported that the rhythmic expressions of period homolog 2 (per2) mRNA in peripheral tissues were abolished by the suprachiasmatic nucleus (SCN) lesions. However, there are no reports that ventromedial hypothalamic (VMH) lesions can directly affect the expression of clock genes in pancreas and liver. In the present study, we examined whether VMH lesions can affect the expression of the clock gene, per2 in these organs. Total RNA was extracted from rat pancreas and liver tissues, and differences in the gene expression profiles between rats at day 3 after VMH lesioning and sham-VMH-lesioned rats were investigated using DNA microarray and real-time quantitative analysis. These results showed that VMH lesions downregulated the expression of the clock gene, per2 in the pancreas, but not the liver in the morning. There is a possibility that VMH lesions may affect the expression of the clock gene, per2 in the pancreas. | [Takayoshi Kibaa, Yuri Kintakab, Yoko Suzukia, Noriko Ishizukaa, Yasuhito Ishigakic, Shuji Inouea] | Neuroscience Letters | 8 March 2010 | |
| sciencedirectS0166432809006652 | Gene expression profiling in brain regions of a rat model displaying schizophrenia-related features | Animal models allow insights into complex neurodevelopmental disorders. Apomorphine-susceptible rats (so-called APO-SUS rats) provide a model that displays a complex phenotype with schizophrenia-related features and together with its phenotypic counterpart (APO-UNSUS rats) has been independently generated twice (original and replicate rat lines). To understand the molecular basis underlying this phenotype, we here performed mRNA expression profiling in various APO-SUS and APO-UNSUS rat brain regions. The expression of only the previously reported Aph-1b and the newly discovered KCnIP1 (a member of the potassium channel-interacting protein family that is known to modulate neuronal channel activity) was significantly different in the APO-SUS and APO-UNSUS rats from both the original and replicate rat lines. Thus, KCnIP1 may constitute a novel candidate gene playing a role in the complex phenotype of the APO-SUS/APO-UNSUS rat model and further studies on this gene are warranted. | [Jessica E. Van Schijndel, Martine Van Zweeden, Karen M.J. Van Loo, Gerard J.M. Martens] | Behavioural Brain Research | 5 March 2010 | |
| sciencedirectS0304416509003420 | Insulin alters the expression of components of the Wnt signaling pathway including TCF-4 in the intestinal cells | BackgroundEpidemiological and experimental evidence that support the correlation between Type 2 diabetes mellitus (T2D) and increased risks of colorectal cancer formation have led us to hypothesize the existence of molecular crosstalk between insulin and canonical Wnt signaling pathways. Insulin was shown to stimulate Wnt target gene expression, utilizing the effector of the Wnt signaling pathway. Whether insulin affects expression of components of Wnt pathway has not been extensively examined.MethodscDNA microarray was utilized to assess the effect of insulin on gene expression profile in the rat intestinal non-cancer IEC-6 cell line, followed by real-time RT-PCR, Western blotting and reporter gene analyses in intestinal cancer and non-cancer cells.ResultsInsulin was shown to alter the expression of a dozen of Wnt pathway related genes including TCF-4 (= TCF7L2) and frizzled- (Fzd-4). The stimulatory effect of insulin on TCF-4 expression was then confirmed by real-time RT-PCR, Western blotting and luciferase reporter analyses, while the activation on Fzd-4 was confirmed by real-time PCR.General significanceOur observations suggest that insulin may crosstalk with the Wnt signaling pathway in a multi-level fashion, involving insulin regulation of the expression of Wnt target genes, a Wnt receptor, as well as mediators of the Wnt signaling pathway. | [Jane Suna d, Dingyan Wangd, Tianru Jina b c d e] | Biochimica et Biophysica Acta (BBA) - General Subjects | March 2010 | |
| sciencedirectS0142961209013234 | Biodistribution of gold nanoparticles and gene expression changes in the liver and spleen after intravenous administration in rats | Biodistribution of gold nanoparticles (AuNPs) in more than 25 organs were examined on 1 day, 1 week, 1 month and 2 months after a single intravenous (i.v.) injection in rats. Au was rapidly and consistently accumulated in liver (49.4 ± 50.4–72.2 ± 40.5 ng/g) and spleen (8.4 ± 5.0–9.5 ± 6.4 ng/g) throughout the entire timeframe of the study (2 months). Significant accumulation of Au in kidney (up to 5.5 ± 2.5 ng/g) and testis (up to 0.6 ± 0.1 ng/g) occurred from 1 month post-injection when Au level in urine and feces decreased. Significant increase of Au in blood occurred 2 months after injection, coincident with the delayed accumulation in kidney. Au accumulation in lungs was found at 1 day post-injection but decreased within a week. No accumulation of Au was found in the brain. Microarray results of liver and spleen point to significant effects on genes related to detoxification, lipid metabolism, cell cycle, defense response, and circadian rhythm. These results demonstrate that significant biodistribution of Au occurs in the body over 2 months after a single i.v. injection of AuNPs, accompanied by gene expression changes in target organs. | [Suresh K. Balasubramaniana, Jinatta Jittiwatb, Jayapal Manikandanc, Choon-Nam Ongd e f, Liya E. Yua e f, Wei-Yi Ongb e f] | Biomaterials | March 2010 | |
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| sciencedirectS0145305X09002444 | Comparison of global transcriptional responses to primary and secondary Eimeria acervulina infections in chickens | In the current study, we compared chicken gene transcriptional profiles following primary and secondary infections with Eimeria acervulina using a 9.6K avian intestinal intraepithelial lymphocyte cDNA microarray (AVIELA). Gene Ontology analysis showed that primary infection significantly modulated the levels of mRNAs for genes involved in the metabolism of lipids and carbohydrates as well as those for innate immune-related genes. By contrast, secondary infection increased the levels of transcripts encoded by genes related to humoral immunity and reduced the levels of transcripts for the innate immune-related genes. Because the observed modulation in transcript levels for gene related to energy metabolism and immunity occurred concurrent with the clinical signs of coccidiosis, these results suggest that altered expression of a specific set of host genes induced by Eimeria infection may be responsible, in part, for the observed reduction in body weight gain and inflammatory gut damage that characterizes avian coccidiosis. | [Chul-Hong Kima 1, Hyun S. Lillehoja, Yeong-Ho Honga 2, Calvin L. Keeler Jr.b, Erik P. Lillehojc] | Developmental & Comparative Immunology | March 2010 | |
| sciencedirectS0965174810000202 | Identification, mRNA expression and functional analysis of several yellow family genes in Tribolium castaneum | Querying the genome of the red flour beetle, Tribolium castaneum, with the Drosophila melanogaster Yellow-y (DmY-y) protein sequence identified 14 Yellow homologs. One of these is an ortholog of DmY-y, which is required for cuticle pigmentation (melanization), and another is an ortholog of DmY-f/f2, which functions as a dopachrome conversion enzyme (DCE). Phylogenetic analysis identified putative T. castaneum orthologs for eight of the D. melanogaster yellow genes, including DmY-b, -c, -e, -f, -g, -g2, -h and -y. However, one clade of five beetle genes, TcY-1-5, has no orthologs in D. melanogaster. Expression profiles of all T. castaneum yellow genes were determined by RT-PCR of pharate pupal to young adult stages. TcY-b and TcY-c were expressed throughout all developmental stages analyzed, whereas each of the remaining yellow genes had a unique expression pattern, suggestive of distinct physiological functions. TcY-b, -c and -e were all identified by mass spectrometry of elytral proteins from young adults. Eight of the 14 genes showed differential expression between elytra and hindwings during the last three days of the pupal stage when the adult cuticle is synthesized. Double-stranded RNA (dsRNA)-mediated transcript knockdown revealed that TcY-y is required for melanin production in the hindwings, particularly in the region of the pterostigma, while TcY-f appears to be required for adult cuticle sclerotization but not pigmentation. | [Yasuyuki Arakanea, Neal T. Dittmera, Yoshinori Tomoyasub, Karl J. Kramera c, Subbaratnam Muthukrishnana, Richard W. Beemanc, Michael R. Kanosta] | Insect Biochemistry and Molecular Biology | March 2010 | |
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| sciencedirectS1873506109001214 | Fourier transform infrared microspectroscopy identifies early lineage commitment in differentiating human embryonic stem cells | Human ESCs (hESCs) are a valuable tool for the study of early human development and represent a source of normal differentiated cells for pharmaceutical and biotechnology applications and ultimately for cell replacement therapies. For all applications, it will be necessary to develop assays to validate the efficacy of hESC differentiation. We explored the capacity for FTIR spectroscopy, a technique that rapidly characterises cellular macromolecular composition, to discriminate mesendoderm or ectoderm committed cells from undifferentiated hESCs. Distinct infrared spectroscopic “signatures” readily distinguished hESCs from these early differentiated progeny, with bioinformatic models able to correctly classify over 97% of spectra. These data identify a role for FTIR spectroscopy as a new modality to complement conventional analyses of hESCs and their derivatives. FTIR spectroscopy has the potential to provide low-cost, automatable measurements for the quality control of stem and differentiated cells to be used in industry and regenerative medicine. | [Philip Herauda b, Elizabeth S. Nga, Sally Cainea b, Qing C. Yua, Claire Hirsta, Robyn Mayberrya, Amanda Brucea, Bayden R. Woodb, Don McNaughtonb, Edouard G. Stanleya, Andrew G. Elefantya] | Stem Cell Research | March 2010 | |
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| sciencedirectS1090023308004103 | Molecular and cellular insights into a distinct myopathy of Great Dane dogs | A myopathy in the Great Dane dog with characteristic pathological and molecular features is reported. Young adults present with progressive weakness and generalised muscle atrophy. To better define this condition, an investigation using histopathology, confocal microscopy, biochemistry and microarray analysis was undertaken. The skeletal muscles of affected dogs exhibited increased oxidative fibre phenotype and core fibre lesions characterised by the disruption of the sarcomeric architecture and the accumulation of mitochondrial organelles. Affected muscles displayed co-ordinated expression of genes consistent with a slow-oxidative phenotype, which was possibly a compensatory response to chronic muscle damage. There was disruption of Z-lines in affected muscles which, at the molecular level, manifested as transcriptional dysregulation of several Z-line associated genes, including ?-actinin, myotilin, desmin, vimentin and telethonin. The pathology of this canine myopathy is distinct from that of human central core myopathies that are characterised by cores devoid of mitochondria and by the presence of myofibrillar breakdown products. | [Kin-Chow Changa, Maj-Lis C. McCullochb, Thomas James Andersonb] | The Veterinary Journal | March 2010 | |
| sciencedirectS0378113509003538 | Involvement of NF-?B and MAP-kinases in the transcriptional response of alveolar macrophages to Streptococcus suis | Interaction of Streptococcus suis with primary porcine alveolar macrophages was studied using transcriptomics. Transcriptional response of macrophages to two different S. suis strains was studied: wild-type S10 that is resistant to phagocytosis, and its non-encapsulated mutant that is phagocytosed efficiently. The macrophages’ transcriptional response was observed only after 60 min of incubation. Eleven genes were expressed significantly different between macrophages infected with streptococci and control mock-infected macrophages. These genes include IL-1-?, MIP-2-? and TNF-?. When gene expression was studied as a function of time, transcriptional changes occurred in all macrophages independent of streptococci. The fold induction of induced genes however, was much stronger in macrophages incubated with the non-encapsulated S. suis strain that was phagocytosed. The genes that were higher induced due to S. suis suggest an innate immune response is induced in macrophages. Pathway analysis revealed that genes that are part of the putative MAP-kinase signal transduction system are over-represented among the regulated genes. Using an immortalized alveolar macrophage cell line it was shown that macrophages respond to interaction with S. suis by the translocation of NF-?B to the nucleus, independent of phagocytosis. This translocation subsequently induced expression of innate immune genes. This strongly suggests besides the MAP-kinase signaling pathway, NF-?B signaling is also induced upon interaction with S. suis. | [Astrid de Greeffa, Laurentiu Bengab, Paul J. Wichgers Schreura, Peter Valentin-Weigandb, Johanna M.J. Rebela, Hilde E. Smitha] | Veterinary Microbiology | 24 February 2010 | |
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| sciencedirectS0166445X09003798 | Hepatic gene expression in flounder chronically exposed to multiply polluted estuarine sediment: Absence of classical exposure ‘biomarker’ signals and induction of inflammatory, innate immune and apoptotic pathways | The effects of chronic long-term exposure to multiply polluted environments on fish are not well understood, but environmental surveys suggest that such exposure may cause a variety of pathologies, including cancers. Transcriptomic profiling has recently been used to assess gene expression in European flounder (Platichthys flesus) living in several polluted and clean estuaries. However, the gene expression changes detected were not unequivocally elicited by pollution, most likely due to the confounding effects of natural estuarine ecosystem variables. In this study flounder from an uncontaminated estuary were held on clean or polluted sediments in mesocosms, allowing control of variables such as salinity, temperature, and diet. After 7 months flounder were removed from each mesocosm and hepatocytes prepared from fish exposed to clean or polluted sediments. The hepatocytes were treated with benzo(a)pyrene (BAP), estradiol (E2), copper, a mixture of these three, or with the vehicle DMSO. A flounder cDNA microarray was then used to measure hepatocyte transcript abundance after each treatment. The results show that long-term chronic exposure to a multiply polluted sediment causes increases in the expression of mRNAs coding for proteins of the endogenous apoptotic programme, of innate immunity and inflammation. Contrary to expectation, the expression of mRNAs which are commonly used as biomarkers of environmental exposure to particular contaminants were not changed, or were changed contrary to expectation. However, acute treatment of hepatocytes from flounder from both clean and polluted sediments with BAP or E2 caused the expected changes in the expression of these biomarkers. Thus transcriptomic analysis of flounder exposed long-term to chronic pollution causes a different pattern of gene expression than in fish acutely treated with single chemicals, and reveals novel potential biomarkers of environmental contaminant exposure. These novel biomarkers include Diablo, a gene involved in apoptotic pathways and highly differentially regulated by both chronic and acute exposure to multiple pollutants. | [Michael J. Leavera, Amer Diaba, Evridiki Boukouvalaa b c 1, Tim D. Williamsb, J. Kevin Chipmanb, Colin F. Moffatd, Craig D. Robinsond, Stephen G. Georgea] | Aquatic Toxicology | 18 February 2010 | |
| sciencedirectS0006295209008053 | A novel anti-neuroinflammatory pyridylimidazole compound KR-31360 | Excessive microglial activation with overexpression of proinflammatory cytokines and oxidative stress products is linked to the progression of several neurodegenerative diseases; therefore, suppression of microglial activation is a potential therapeutic approach against these diseases. Since nitric oxide (NO) is one of the major inflammatory mediators that are produced by activated microglia, inhibitory effects of novel synthetic compounds on microglial NO production were investigated. From the mouse microglia cell-based assays, an imidazo [4,5-b] pyridine compound KR-31360 was identified as an inhibitor of microglial NO production with an IC50 value of 2 ?M. Structure–activity relationship study indicated that 5-position of imidazo [4,5-b] pyridine ring is critical for the activity. KR-31360 also inhibited lipopolysaccharide (LPS)-induced secretion of tumor necrosis factor alpha (TNF-?) and transcription of TNF-?, interleukin-1 beta, and inducible nitric oxide synthase as well as activation of nuclear factor kappa B and mitogen-activated protein kinases. KR-31360 was neuroprotective by suppressing microglial neurotoxicity in a microglia–neuron coculture. The neuroprotective activity of the compound was most effective when microglia were pretreated with the compound prior to LPS challenge. The inhibitory effect of KR-31360 on microglial activation was further demonstrated in a mouse neuroinflammation model in vivo: compared to vehicle-injected animals, KR-31360 injection attenuated LPS-induced microglial activation as evidenced by isolectin B4 staining and proinflammatory gene expression of brain sections. DNA microarray analysis supported that KR-31360 targeted Toll-like receptor 4 pathways. In addition to being a new drug candidate against neuroinflammatory diseases, the compound may be a powerful tool for the better understanding of microglia biology and neuroinflammation. | [Jiyeon Ocka, Sangseop Kima 1, Kyu-Yang Yib, Nak-Jung Kimb, Hyung Soo Hanc, Je-Yoel Chod, Kyoungho Suka] | Biochemical Pharmacology | 15 February 2010 | |
| sciencedirectS0012160609013864 | Six1 and Six4 gene expression is necessary to activate the fast-type muscle gene program in the mouse primary myotome | While the signaling pathways and transcription factors active in adult slow- and fast-type muscles begin to be characterized, genesis of muscle fiber-type diversity during mammalian development remains unexplained.We provide evidence showing that Six homeoproteins are required to activate the fast-type muscle program in the mouse primary myotome. Affymetrix transcriptomal analysis of Six1−/−Six4−/− E10.5 somites revealed the specific down-regulation of many genes of the fast-type muscle program. This data was confirmed by in situ hybridization performed on Six1−/−Six4−/− embryos. The first mouse myocytes express both fast-type and slow-type muscle genes. In these fibers, Six1 and Six4 expression is required to specifically activate fast-type muscle genes. Chromatin immunoprecipitation experiments confirm the binding of Six1 and Six4 on the regulatory regions of these muscle genes, and transfection experiments show the ability of these homeoproteins to activate specifically identified fast-type muscle genes.This in vivo wide transcriptomal analysis of the function of the master myogenic determinants, Six, identifies them as novel markers for the differential activation of a specific muscle program during mammalian somitic myogenesis. | [Claire Niroa b, Josiane Demignona b, Stéphane Vincentc, Yubing Liud, Julien Giordania b, Nicolas Sgariotoa b, Maryline Faviera b, Isabelle Guillet-Deniaua b, Alexandre Blaisd, Pascal Mairea b] | Developmental Biology | 15 February 2010 | |
| sciencedirectS0006291X10000045 | An evidence for adhesion-mediated acquisition of acute myeloid leukemic stem cell-like immaturities | For long-term survival in vitro and in vivo of acute myeloid leukemia cells, their adhesion to bone marrow stromal cells is indispensable. However, it is still unknown if these events are uniquely induced by the leukemic stem cells. Here we show that TF-1 human leukemia cells, once they have formed a cobblestone area by adhering to mouse bone marrow-derived MS-5 cells, can acquire some leukemic stem cell like properties in association with a change in the CD44 isoform-expression pattern and with an increase in a set of related microRNAs. These findings strongly suggest that at least some leukemia cells can acquire leukemic stem cell like properties in an adhesion-mediated stochastic fashion. | [Keiji Funayama, Miyuki Shimane, Hitoshi Nomura, Shigetaka Asano] | Biochemical and Biophysical Research Communications | 12 February 2010 | |
| sciencedirectS002751070900373X | Temporal gene expression changes induced by a low concentration of benzo[a]pyrene diol epoxide in a normal human cell line | (±)-anti-Benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE), which causes bulky-adduct DNA damage, is well-characterized as the ultimate carcinogen of benzo[a]pyrene (BaP). In this study, we have employed Affymetrix HG-U133 Plus 2.0 microarray and quantitative real-time RT-PCR methods to investigate a temporal transcriptomic response triggered by a low concentration (0.05 ?M) of BPDE at 1, 10, and 22 h after exposure in normal human cells. The differential gene expression profiles at the three time points varied greatly, and generally reflected a cellular responsive process from initiation to progression and to recovery after the BPDE-caused damage. The dynamic regulation of the genes related with cell cycle progression and cell fate exhibited a tendency from inhibition to survival, which was accordant with the cell cycle arrest and cytotoxicity data induced by the low-dose BPDE exposure. In silico comparison of the genomic data revealed that BPDE and ultraviolet induced a panel of common transcriptional responses, which might be related with a series of similar molecular processes elicited by these two DNA-damaging agents. In conclusion, this whole-genome time-course study has identified a dynamically regulated transcriptional signature after low-dose BPDE exposure, which may help to understand the complex mechanisms of mutagenesis and carcinogenesis induced by BPDE. | [Xiangyun Lu1, Jimin Shao1, Hongjuan Li2, Yingnian Yu] | Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis | 3 February 2010 | |
| sciencedirectS0735109709037620 | Rac1-Induced Connective Tissue Growth Factor Regulates Connexin 43 and N-Cadherin Expression in Atrial Fibrillation | ObjectivesWe studied the signal transduction of atrial structural remodeling that contributes to the pathogenesis of atrial fibrillation (AF).BackgroundFibrosis is a hallmark of arrhythmogenic structural remodeling, but the underlying molecular mechanisms are incompletely understood.MethodsWe performed transcriptional profiling of left atrial myocardium from patients with AF and sinus rhythm and applied cultured primary cardiac cells and transgenic mice with overexpression of constitutively active V12Rac1 (RacET) in which AF develops at old age to characterize mediators of the signal transduction of atrial remodeling.ResultsLeft atrial myocardium from patients with AF showed a marked up-regulation of connective tissue growth factor (CTGF) expression compared with sinus rhythm patients. This was associated with increased fibrosis, nicotinamide adenine dinucleotide phosphate oxidase, Rac1 and RhoA activity, up-regulation of N-cadherin and connexin 43 (Cx43) expression, and increased angiotensin II tissue concentration. In neonatal rat cardiomyocytes and fibroblasts, a specific small molecule inhibitor of Rac1 or simvastatin completely prevented the angiotensin II–induced up-regulation of CTGF, Cx43, and N-cadherin expression. Transfection with small-inhibiting CTGF ribonucleic acid blocked Cx43 and N-cadherin expression. RacET mice showed up-regulation of CTGF, Cx43, and N-cadherin protein expression. Inhibition of Rac1 by oral statin treatment prevented these effects, identifying Rac1 as a key regulator of CTGF in vivo.ConclusionsThe data identify CTGF as an important mediator of atrial structural remodeling during AF. Angiotensin II activates CTGF via activation of Rac1 and nicotinamide adenine dinucleotide phosphate oxidase, leading to up-regulation of Cx43, N-cadherin, and interstitial fibrosis and therefore contributing to the signal transduction of atrial structural remodeling. | [Oliver Adam MD?, Daniel Lavall MS?, Katharina Theobald MS?, Mathias Hohl PhD?, Markus Grube PhD‡, Sabine Ameling MS§, Mark A. Sussman PhD?, Stephan Rosenkranz MD PhD¶, Heyo K. Kroemer PhD‡, Hans-Joachim Schäfers MD†, Michael Böhm MD?, Ulrich Laufs MD?] | Journal of the American College of Cardiology | 2 February 2010 | |
| sciencedirectS0094576509003440 | Low-shear modelled microgravity alters expression of virulence determinants of Staphylococcus aureus | Microbiological monitoring of air and surfaces within the ISS indicate that bacteria of the genus Staphylococcus are found with high frequency. Staphylococcus aureus, an opportunistic pathogen with the capacity to cause severe debilitating infection, constitutes a significant proportion of these isolates. Experiments conducted during short-term flight suggest that growth in microgravity leads to increases in bacterial antibiotic resistance and to cell wall changes. Growth under low-shear modelled microgravity (LSMMG) indicated that a reduced gravitational field acts as an environmental signal for expression of enhanced bacterial virulence in gram-negative pathogens. We therefore examined the effect of simulated microgravity on parameters of antibiotic susceptibility and virulence in methicillin-susceptible S. aureus isolates RF1, RF6 and RF11; these strains were grown in a high aspect ratio vessel under LSMMG and compared with cells grown under normal gravity (NG). There were no significant differences in antibiotic susceptibility of staphylococci grown under LSMMG compared to NG. LSMMG-induced reductions in synthesis of the pigment staphyloxanthin and the major virulence determinant ?-toxin were noted. Significant changes in global gene expression were identified by DNA microarray analysis; with isolate RF6, the expression of hla and genes of the regulatory system saeR/saeS were reduced approximately two-fold. These data provide strong evidence that growth of S. aureus under modelled microgravity leads to a reduction in expression of virulence determinants. | [Helena Rosadoa, Marie Doylea, Jason Hindsb, Peter W. Taylora] | Acta Astronautica | February–March 2010 | |
| sciencedirectS000527280900293X | Mitochondrial Complex I decrease is responsible for bioenergetic dysfunction in K-ras transformed cells | Many cancer cells are characterized by high rate of glycolysis and reduced rate of aerobic respiration, whose mechanism is still elusive. Here we investigate the down-regulation of oxidative phosphorylation (OXPHOS) in K-ras transformed mouse fibroblasts as compared to a control counterpart. Transcriptional analysis showed different expression levels of several OXPHOS nuclear genes in the two cell lines. In particular, during the exponential growth phase most genes encoding proteins of Complex I were expressed at lower levels in transformed cells. Consistently, a significant decrease of Complex I content was found in transformed cells. Moreover, analysis of NAD-dependent respiration and ATP synthesis indicated a strong decrease of Complex I activity in the mitochondria from neoplastic cells, that was confirmed by direct assay of the enzyme redox activity. At variance, succinate-dependent respiration and ATP synthesis were not significantly affected. Taken together, our results provide the new insight that the reduction of respiration observed in K-ras transformed cells is specifically due to a Complex I activity decrease. | [Alessandra Baraccaa, Ferdinando Chiaradonnab, Gianluca Sgarbia, Giancarlo Solainia, Lilia Alberghinab, Giorgio Lenaza] | Biochimica et Biophysica Acta (BBA) - Bioenergetics | February 2010 | |
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| sciencedirectS0014480009001609 | The effect of propranolol on gene expression during the blood alcohol cycle of rats fed ethanol intragastrically | Propranolol, a beta adrenergic blocker prevents the blood alcohol (BAL) cycle in rats fed ethanol intragastrically at a constant rate by preventing the cyclic changes in the metabolic rate caused by fluctuating levels of norepinephrine released into the blood. The change in the rate of metabolism changes the rate of alcohol elimination in the blood which causes the BAL to cycle. Microarray analysis of the livers from the rats fed ethanol and propranolol showed similar changes in clusters of functionally related gene expressions. The controls and the trough of the cycle differed dramatically from the cluster pattern seen in the rats at the peaks of the blood alcohol cycle. The changes in gene expression induced by ethanol were similar when propranolol was fed without ethanol especially with the changes in the kinases and phosphatases, Toll-like receptor signaling and cytokine–cytokine receptor interaction were also changed.The changes in gene expression caused by ethanol and propranolol feeding are alike probably because both drugs induce ? adrenergic receptor desensitization. | [J. Li, F. Bardag-Gorce, J. Oliva, B.A. French, J. Dedes, S.W. French] | Experimental and Molecular Pathology | February 2010 | |
| sciencedirectS0981942809002253 | Isolation and characterization of osmotic stress-induced genes in poplar cells by suppression subtractive hybridization and cDNA microarray analysis | Osmotic stress induces changes in the expression of various genes including those associated with drought tolerance, cell wall metabolism and defense. We isolated 852 cDNA clones, the expression of which is induced by osmotic stress, from cells of a hybrid poplar (Populus alba × Populus tremula var. glandulosa) by suppression subtractive hybridization after mannitol treatment. We examined how stress affected their expression using cDNA microarray analysis, which identified 104 genes significantly up-regulated by osmotic stress. These include genes with functions related to transcription, signal transduction, cell wall metabolism and defense. Other gene transcripts encoding cysteine protease and aquaporin are also up-regulated during osmotic stress. The function of about one-third of the genes in poplar cells that were significantly up-regulated by stress is not known, suggesting that the cell suspension may offer an opportunity of finding novel genes otherwise never expressed and that we still need more information at the molecular level. | [Eun-Kyung Bae, Hyoshin Lee, Jae-Soon Lee, Eun-Woon Noh] | Plant Physiology and Biochemistry | February–March 2010 | |
| sciencedirectS0278584609003765 | Prednisolone causes anxiety- and depression-like behaviors and altered expression of apoptotic genes in mice hippocampus | Glucocorticoids are known to cause psychiatric disorders including depression. Prednisolone (PSL) is one of the most widely used synthetic glucocorticoids to treat various medical diseases; however, little is known about PSL-induced behavioral changes and its molecular basis in the brain. Growing evidence has implicated that hippocampal remodeling or damage play a role in the pathogenic effect of glucocorticoids. In this study, mice were administered PSL (50 or 100 mg/kg) or vehicle for 6 or 7 days and subjected to a series of behavioral tests, i.e., open field, elevated plus maze, prepulse inhibition, forced swim, and tail suspension tests. Hippocampal tissues were subject to microarray analysis using the GeneChip Mouse Genome 430 2.0 Array (Affymetrix) containing 45,101 probes of transcripts. Increased anxiety- and depression-like behaviors assessed with open field, elevated plus maze, and tail suspension tests were observed. Microarray analysis detected 108 transcripts with a fold change of > 2.0 or < 0.5 in which many cell-death-related genes were found. The microarray data was validated by quantitative reverse transcriptase-polymerase chain reaction analysis. Our results demonstrated that PSL causes anxiety- and depression-like behaviors, and suggest that altered gene expressions related to hippocampal remodeling or damage are involved in the effect of PSL on such behaviors. | [Yu Kajiyamaa b, Yoshimi Iijimaa, Shuichi Chibaa, Miyako Furutaa, Midori Ninomiyaa b, Aiko Izumia, Shigenobu Shibatab, Hiroshi Kunugia c] | Progress in Neuro-Psychopharmacology and Biological Psychiatry | 1 February 2010 | |
| sciencedirectS0887233309002197 | Alterations in gene expression in cultured human cells after acute exposure to uranium salt: Involvement of a mineralization regulator | The risk of exposure of workers or populations to materials, such as uranium, of nuclear fuel process origins is a major concern worldwide. Our goal is to improve the knowledge of mechanisms ruling its chemical toxicity, and to search for proteins as potential indicator of effect. Such a marker of internal damage remains to be discovered in the case of uranium. This study, based on DNA microarrays, reports a comparative gene expression analysis following acute uranium exposure of several human cell lines taken from kidneys or lungs as representative targets. Among uranium altered genes, no common gene was found between cells originating from lungs and kidney. In contrast, a set of 24 altered genes was common to two kidney cell lines. Transcriptional levels of a subset of renal genes were assessed with qRT-PCR. Furthermore, we highlighted a gene (SPP1) coding for a secreted protein (osteopontin) linked to ectopic mineralization. Immunoblotting assays showed that uranyl ions affect the excretion of osteopontin in a time- and dose-dependent manner. We consider that osteopontin, described as associated with bone resorbtion and kidney mineral stones, is a worthwhile candidate to be tested in vivo as a potential indicator of uranyl mineralization effects. | [Odette Prat, Frédéric Bérenguer, Gérard Steinmetz, Sylvie Ruat, Nicole Sage, Eric Quéméneur] | Toxicology in Vitro | February 2010 | |
| sciencedirectS016817020900392X | Genome-wide analysis of host gene expression in the silkworm cells infected with Bombyx mori nucleopolyhedrovirus | The global transcriptional profile of host genes in the silkworm cell line during the early phase of Bombyx mori nucleopolyhedrovirus (BmNPV) infection was analyzed by oligonucleotide microarray. Our analysis showed 35 genes were significantly up-regulated and 17 genes were significantly down-regulated. This is the first report of changes in the expression of these genes in response to NPV infection. We further quantified the levels of mRNA expression by quantitative reverse transcriptase-polymerase chain reaction and confirmed that the expression of 13 (such as BmEts and BmToll10-3) genes significantly increased and 7 genes (such as Hsp20-1) significantly decreased after BmNPV infection. However, the expression levels of most genes were not dramatically changed except BmEts expression increased approximately 8.0-fold 12 h after BmNPV infection. | [Aki Sagisakaa, Kosuke Fujitaa, Yuki Nakamurab c, Jun Ishibashia, Hiroaki Nodab c, Shigeo Imanishid, Kazuei Mitae, Minoru Yamakawaa f, Hiromitsu Tanakaa] | Virus Research | February 2010 | |
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| sciencedirectS0006291X09024206 | Identification of candidate genes involved in endogenous protection mechanisms against acute pancreatitis in mice | We surveyed changes of the gene expression profile in caerulein-exposed pancreas using Affymetrix GeneChip system (39,000 genes). Up-regulation of genes coding for claudin 4, claudin 7, F11 receptor, cadherin 1, integrin beta 4, syndecan 1, heat shock proteins b1/90aa1, Serpinb6a, Serpinb6b, Serpinb9, Bax, Bak1, calpain 2, calpain 5, microtubule-associated protein 1 light chain 3 alpha, S100 calcium-binding proteins A4/A10 were found in mouse pancreas exposed to caerulein for 12 h. In contrast, the anti-apoptotic gene Bcl2 was down-regulated. The functions of these genes concern tight junction formation, cell–cell/cell–matrix adhesions, stress response, protease inhibition, apoptosis, autophagy, and regulation of cytoskeletal dynamics. Caerulein-exposed pancreatic acinar cells were immunohistochemically stained for claudin 4, cadherin 1, integrin beta 4, heat shock protein b1, and Serpinb6a. In conclusion, we have newly identified a set of genes that are likely to be involved in endogenous self-protection mechanisms against acute pancreatitis. | [Shinji Nakadaa, Koichi Tsuneyamab, Ichiro Katoc, Yoshiaki Tabuchid, Ichiro Takasakid, Yukihiro Furusawae, Hiroshi Kawaguchic, Makoto Fujimotoa, Hirozo Gotoa, Hiroaki Hikiamia, Takashi Kondoe, Yasuo Takanob, Yutaka Shimadaa] | Biochemical and Biophysical Research Communications | 15 January 2010 | |
| sciencedirectS0022283609013163 | Transcription Profile of Thermus thermophilus CRISPR Systems after Phage Infection | The clustered regularly interspaced short palindromic repeat (CRISPR) systems composed of DNA direct repeats designated as CRISPRs and several CRISPR-associated (cas) genes, which are present in many prokaryotic genomes, make up a host defense system against invading foreign replicons such as phages. In order to investigate the altered expression profiles of the systems after phage infection using a model organism, Thermus thermophilus HB8, which has 12 CRISPR loci, genome-wide transcription profiling of the strain infected with lytic phage ?YS40 was performed by DNA microarray analysis. Significant alteration of overall mRNA expression gradually increased during infection (i.e., from the eclipse period to the period of host cell lysis). Interestingly, the expression of most cAMP receptor protein (CRP)–regulated genes, including two CRISPR-associated (cas) operons, was most markedly up-regulated, especially around the beginning of host cell lysis, although up-regulation of the crp gene was not observed. The expression of the CRP-regulated genes was less up-regulated in a crp-deficient strain than in the wild type. Thus, it is suggested that cAMP is a signaling molecule that transmits information on phage infection to CRP to up-regulate these genes. On the other hand, the expression of several cas genes and that of CRISPRs were up-regulated independent of CRP, suggesting the involvement of unidentified regulatory factor(s) induced by phage infection. On analysis of the expression profile of the entire genome, we could speculate that upon phage infection, the signal was transmitted to the cells, with host response systems including CRISPR defense systems being activated, while the overall efficiencies of transcription, translation, and metabolism in the cells decreased. These findings will facilitate understanding of the host response mechanism following phage infection. | [Yoshihiro Agari1, Keiko Sakamoto1, Masatada Tamakoshi1 2, Tairo Oshima3, Seiki Kuramitsu1 4, Akeo Shinkai1] | Journal of Molecular Biology | 15 January 2010 | |
| sciencedirectS0304394009014530 | Differential gene expression analysis of human entorhinal cortex support a possible role of some extracellular matrix proteins in the onset of Alzheimer disease | The onset of Alzheimer's disease (AD) has been associated with the specific vulnerability of neurons in the upper layers of the entorhinal cortex. To define the molecular characteristics of those neurons, we have used microarrays to define the gene expression in that region. In this way, we identified several genes that are expressed distinctly in the upper and lower layers of the entorhinal cortex. These include the genes encoding the matrix Gla protein, collagen type 1?2, reelin, semaphorin 3C or the relaxin receptor, all related to the extracellular matrix. Thus, differences in the extracellular matrix components between the upper and lower layers of the entorhinal cortex may in part explain the vulnerability of neurons present in the upper layers of this brain region in disorders like AD. | [Ismael Santa-Mariaa b, Jesus Avilaa b, Alberto Rabanoc] | Neuroscience Letters | 14 January 2010 | |
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| sciencedirectS0027510709003376 | Nucleotide excision repair genes are expressed at low levels and are not detectably inducible in Caenorhabditis elegans somatic tissues, but their function is required for normal adult life after UVC exposure | We performed experiments to characterize the inducibility of nucleotide excision repair (NER) in Caenorhabditis elegans, and to examine global gene expression in NER-deficient and -proficient strains as well as germline vs. somatic tissues, with and without genotoxic stress. We also carried out experiments to elucidate the importance of NER in the adult life of C. elegans under genotoxin-stressed and control conditions. Adult lifespan was not detectably different between wild-type and NER-deficient xpa-1 nematodes under control conditions. However, exposure to 6 J/m2/day of ultraviolet C radiation (UVC) decreased lifespan in xpa-1 nematodes more than a dose of 100 J/m2/day in wild-type. Similar differential sensitivities were observed for adult size and feeding. Remarkably, global gene expression was nearly identical in young adult wild-type and xpa-1 nematodes, both in control conditions and 3 h after exposure to 50 J/m2 UVC. Neither NER genes nor repair activity were detectably inducible in young adults that lacked germ cells and developing embryos (glp-1 strain). However, expression levels of dozens of NER and other DNA damage response genes were much (5–30-fold) lower in adults lacking germ cells and developing embryos, suggesting that somatic and post-mitotic cells have a much lower DNA repair ability. Finally, we describe a refinement of our DNA damage assay that allows damage measurement in single nematodes. | [Windy A. Boyda, Tracey L. Crockerb, Ana M. Rodriguezd, Maxwell C.K. Leungb, D. Wade Lehmannd, Jonathan H. Freedmanc, Ben Van Houtend, Joel N. Meyerb] | Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis | 5 January 2010 | |
| sciencedirectS0024320509004573 | Nitric oxide and peroxynitrite induce gene expression of interleukin receptors increasing IL-21, IL-7, IL-1 and oncostatin M in cardiomyocytes | AimThe objective of this investigation was to determine whether nitric oxide (NO) and peroxynitrite alter the gene expression of interleukin receptors (IL-R) in cardiomyocytes.Main methodsCardiomyocytes, from neonatal mouse heart, in culture were treated with the NO donor 3-morpholinosydnonimine hydrochloride (SIN-1), which releases NO and peroxynitrite. IL-R gene expression was assessed by microarray analysis.Key findingsGene expression data show that the IL-2 receptor family showed a highly significant and 1.7-fold increase in the gamma chain component which is common to all members of the IL-2 family receptors. There was a significant and 2-fold increase in IL-21 R and an increase of 1.8-fold in IL-7 R? gene expression. In contrast there was a significant 0.7-fold decrease in IL-9 R?. The IL-1 receptor family showed a significant and 1.4-fold increase in IL-1 R1 compared to control but no change in IL-18 R1 gene expression which was similar to control. The IL-6 family showed a significant increase in oncostatin M receptor gene expression of 1.3-fold but no change in IL-6 R alpha or IL-11 R alpha.SignificanceThese data suggest that NO/peroxynitrite by increasing gene expression of certain IL-Rs may magnify the effects of specific interleukins in conditions of excess interleukin production. | [Simon W. Rabkin] | Life Sciences | 2 January 2010 | |
| sciencedirectS0006291X09022268 | IL-11 expression in retinal and corneal cells is regulated by interferon-? | Interleukin-11 (IL-11) is an anti-apoptotic, anti-inflammatory cytokine with hematopoietic potential. The expression and protective actions of IL-11 have not been explored in the eye. The expression of IL-11 in primary cultures of human retinal pigment epithelial (HRPE) and human corneal fibroblast (HCRF) cells were evaluated in these studies. Constitutive secretion of IL-11 was not observed in either HRPE or HCRF. TNF-? + IL-1 induced IL-11 secretion and this production was inhibited by NF?B pathway inhibitors. IFN-? significantly inhibited TNF-? and IL-1 induced IL-11 secretion and inhibitors of JAK-STAT pathway reversed this inhibition. TGF-? induced IL-11 secretion that was blocked by TGF-? receptor 1 inhibitor but not by IFN-?. RT-PCR analysis confirmed the effects of IL-1, TNF-?, IFN-? and TGF-? on IL-11 secretion at mRNA levels. Our results demonstrate that IL-11 is dramatically up regulated in retina and cornea cells and that IFN-? is a physiological inhibitor of IL-11 expression. | [Chandrasekharam N. Naginenia, Vijay K. Komminenia, Abitha Williama, John J. Hooksa, Barbara Detrickb] | Biochemical and Biophysical Research Communications | 1 January 2010 | |
| sciencedirectS0006291X09023468 | Effect of exercise on gene expression profile in unfractionated peripheral blood leukocytes | A 4-h bout of exercise induces immunomodulatory effects. Peripheral blood was withdrawn before, and at 4, 8 and 24 h after the start of exercise. RNA from the unfractionated white blood cells was analyzed using Agilent human 44 K microarray. The expression profiles were sorted into seven clusters based on their unique time-dependent kinetics. In a separate experiment, cell-specific markers were collected and compared among the members in each cluster. Two clusters were assigned as representing neutrophils, one as NK cells, and another mostly as T cells. Three clusters seemed to be mixtures of several cell types. Extension of this approach to other systems is discussed. | [Seiji Nakamuraa, Michie Kobayashia, Tomohiro Suginob, Osami Kajimotob, Ryo Matobaa, Kenichi Matsubaraa] | Biochemical and Biophysical Research Communications | 1 January 2010 | |
| sciencedirectS0006291X09023973 | Anti-tumor effect of small interfering RNA targeting the androgen receptor in human androgen-independent prostate cancer cells | Early phase prostate cancer is usually androgen-dependent, with the androgen/androgen receptor (AR) signaling pathway playing a central role. At this stage, the cancer responds well to androgen ablation therapy, but prostate cancers eventually acquire androgen independence and more aggressive phenotypes. Several studies, however, have shown that the majority of tumors still express functional AR, which is often amplified and mutated. To determine if the AR is a plausible therapeutic target, we investigated the anti-tumor effect of small interfering RNAs targeting the AR (siAR) in the human prostate cancer cells, LNCaP and 22Rv1, which express mutated AR. In both types of cells, transfection of siAR suppressed mutated AR expression and significantly reduced cell growth. Furthermore, atelocollagen-mediated systemic siAR administration markedly inhibited the growth of 22Rv1 cells subcutaneously xenografted in castrated nude mice. These results suggest that the AR is still a key therapeutic target even in androgen-independent prostate cancer (AIPC). Silencing of AR expression in AIPC opens promising therapeutic perspectives. | [Koji Azumaa, Koh-ichi Nakashirob c, Toyokazu Sasakia, Hiroyuki Godab, Jun Onoderad, Nozomu Tanjia c, Masayoshi Yokoyamaa, Hiroyuki Hamakawab c] | Biochemical and Biophysical Research Communications | 1 January 2010 | |
| sciencedirectS0008874910001528 | Key genes and proteins involved in CTCM-reducing microvascular endothelial cell permeability induced by SLT-IIv using gene chips and DIGE | An Affymetrix mouse genome array and differential in-gel electrophoresis (DIGE) techniques were used to investigate the pharmacological mechanisms of a mixture of herbs, designated CTCM, a compound of traditional Chinese medicine, for the treatment of increased permeability in mouse intestinal microvascular endothelial cells (MIMECs) induced by the Shiga-like toxin type II variant (SLT-IIv). MIMECs were challenged with 10 ?g/ml SLT-IIv for 12 h and then treated with CTCM at a concentration of 200 ?g/ml for 12 h. Total RNA and proteins from each treatment group were extracted from cultured MIMECs for analysis by the Affymetrix GeneChip® Mouse Genome 430 2.0 microarray and DIGE. The results obtained demonstrated that there were one genes downregulated and one genes upregulated, one protein downregulated and four proteins upregulated in the SLT-IIv group compared to the control group. In the CTCM group, four genes were upregulated, three genes were downregulated, a single protein was downregulated and a single protein was upregulated when compared to the control group. When the CTCM-treated group was compared to the SLT-IIv group, expression of one gene was found to be increased, and all other genes were decreased, with five proteins downregulated. Analysis of the data suggested that CTCM specifically and effectively reduced microvascular endothelial cell permeability to SLT-IIv in the treatment of pig edema disease. In the CTCM-treated group, hspa9 expression was increased in both gene chip and DIGE analysis, so it may be a key protein in reducing cell permeability and utilized in medical treatments. | [Pengfei Yia c, Yang Guoa b, Xin Wangd, Xiang Muc, Xubin Weia] | Cellular Immunology | 2010 | |
| sciencedirectS1521661610001646 | Imatinib Treatment of Patients with Diffuse Cutaneous Systemic Sclerosis Modifies Gene Expression in Peripheral Blood Mononuclear Cells of Clinical Responders | | [Jessica Gordon1, Robert Spiera1, Jamie Mersten1, Jacqueline Salit2, Neil Hackett2, Mary Crow1] | Clinical Immunology | 2010 | |
| sciencedirectS1521661610002251 | Imatinib Treatment of Patients with Diffuse Cutaneous Systemic Sclerosis Modifies Gene Expression in Peripheral Blood Mononuclear Cells of Clinical Responders | | [Jessica Gordon1, Robert Spiera1, Jamie Mersten1, Jacqueline Salit2, Neil Hackett2, Mary Crow1] | Clinical Immunology | 2010 | |
| sciencedirectB9780080468846015116 | 12.09 – Analysis of Altered Gene Expression in Diabetic Embryopathy | Teratogens cause developmental defects based on dose, time, length, and route of exposure. For a few teratogens, biological pathways altered by exposure have been identified through candidate gene studies. However, genome-wide expression profiling offers the advantage that new pathways may be discovered for previously uncharacterized teratogens and exposures. In this chapter, we review strategies for and outcomes from the application of genome-wide expression profiling by microarrays to a complex exposure, namely, the embryo’s response to maternal diabetes in pregnancy. | [C. Kappen, C. Kruger, J.M. Salbaum] | Comprehensive Toxicology | | |
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| sciencedirectS1087184509001728 | Genetic analysis of conidiation regulatory pathways in koji-mold Aspergillus oryzae ? | Conidia of koji-mold Aspergillus oryzae are often used as starters in the fermented food industry. However, little is known about conidiation regulation in A. oryzae. To improve the productivity of conidia in A. oryzae, it is necessary to understand conidiation regulation in the strain. Therefore, we analyzed the conidiation regulatory system in A. oryzae using 10 kinds of conidiation regulatory gene disruptants. The phenotypes of AorfluG, AorflbA, AorflbB, AorflbC, AorflbD, AorflbE, AorbrlA, AorabaA, AorwetA, and AorfadA mutants are almost identical to those of the corresponding mutants in Aspergillus nidulans. The results indicated that the functions of conidiation regulatory genes are almost conserved between A. oryzae and A. nidulans. However, the severely reduced conidiation phenotype of the AorfluG disruptant in A. oryzae differs from the phenotype of the corresponding mutant in Aspergillus fumigatus in air-exposed culture conditions. These results suggest that A. oryzae, A. nidulans, and A. fumigatus have a G-protein signaling pathway and brlA orthologs in common, and only A. fumigatus has particular brlA activation pathways that are independent of the fluG ortholog. Furthermore, the analyses of AorflbA disruptant and AorfadA dominant-active mutants implicated that AorFadA-mediated G-protein signaling suppresses vegetative growth of A. oryzae. | [Masahiro Ogawa, Masafumi Tokuoka, Feng Jie Jin, Tadashi Takahashi, Yasuji Koyama] | Fungal Genetics and Biology | January 2010 | |
| sciencedirectS1389172309003132 | The combined use of viral transcriptional and post-transcriptional regulatory elements to improve baculovirus-mediated transient gene expression in human embryonic stem cells | Transient gene expression is one possible approach to manipulate the signaling pathways that control the proliferation and differentiation of human embryonic stem (hES) cells. We tested in hES cells a range of baculoviral vectors with a human elongation factor-1? promoter and various viral regulatory elements and observed the most dramatic augmenting effect on the transient expression when the promoter was used together with the human cytomegalovirus immediate-early gene enhancer and the woodchuck hepatitis virus post-transcriptional regulatory elements. This vector provided a 1.6-fold increase in the percentage of transduced cells (up to 72%) over a vector containing the elongation factor-1? promoter alone. The effective baculoviral transduction of hES cells did not affect cell proliferation, expression of embryonic stem cell markers and teratoma formation. This new viral vector for temporary transgene expression might become a useful tool for developmental biology studies and biomedical applications of hES cells. | [Juan Du1 2 +, Jieming Zeng1 +, Ying Zhao1 2, Jerome Boulaire1, Shu Wang1 2] | Journal of Bioscience and Bioengineering | January 2010 | |
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| sciencedirectS0076687910770233 | Chapter Twenty-Three – Gene Expression Profiling of Mouse Oocytes and Preimplantation Embryos | Gene expression profiling using microarray technology is a robust, efficient, and cost-effective approach to assay a cell or tissue's transcriptome at a particular time or under a specific condition. Application of this technology to oocytes and preimplantation embryos has been limited largely because this biological material is difficult to acquire in sufficient quantities. We describe here a protocol to isolate and amplify mRNA from oocytes and preimplantation embryos that is suitable for microarray experiments. This protocol is based on a linear two-step amplification protocol using T7 RNA polymerase-based in vitro transcription and has been used to isolate more than 80 ?g of cRNA from only 20 oocytes or preimplantation embryos. Gene expression profiling has provided insight into the molecular mechanisms of meiotic maturation, fertilization, and preimplantation embryo development. It has also been used to characterize female gametes and embryos from animals harboring gene-specific knockouts or knockdowns. Finally, this technology has been useful in evaluating how various Assisted Reproductive Technologies impact global patterns of gene expression in resulting embryos. | [Francesca E. Duncan?, Richard M. Schultz†] | Methods in Enzymology | | |
| sciencedirectS0969996109002782 | Syndromic features and mild cognitive impairment in mice with genetic reduction on p300 activity: Differential contribution of p300 and CBP to Rubinstein–Taybi syndrome etiology | Rubinstein–Taybi syndrome (RSTS) is a complex autosomal-dominant disease characterized by mental and growth retardation and skeletal abnormalities. A majority of the individuals diagnosed with RSTS carry heterozygous mutation in the gene CREBBP, but a small percentage of cases are caused by mutations in EP300. To investigate the contribution of p300 to RSTS pathoetiology, we carried out a comprehensive and multidisciplinary characterization of p300+/− mice. These mice exhibited facial abnormalities and impaired growth, two traits associated to RSTS in humans. We also observed abnormal gait, reduced swimming speed, enhanced anxiety in the elevated plus maze, and mild cognitive impairment during the transfer task in the water maze. These analyses demonstrate that p300+/− mice exhibit phenotypes that are reminiscent of neurological traits observed in RSTS patients, but their comparison with previous studies on CBP deficient strains also indicates that, in agreement with the most recent findings in human patients, the activity of p300 in cognition is likely less relevant or more susceptible to compensation than the activity of CBP. | [Jose Vioscaa, Jose P. Lopez-Atalayaa, Roman Olivaresa, Richard Ecknerb, Angel Barcoa] | Neurobiology of Disease | January 2010 | |
| sciencedirectS0890623809002652 | Fetal malformations and early embryonic gene expression response in cynomolgus monkeys maternally exposed to thalidomide ? | The present study was performed to determine experimental conditions for thalidomide induction of fetal malformations and to understand the molecular mechanisms underlying thalidomide teratogenicity in cynomolgus monkeys. Cynomolgus monkeys were orally administered thalidomide at 15 or 20 mg/kg-d on days 26–28 of gestation, and fetuses were examined on day 100–102 of gestation. Limb defects such as micromelia/amelia, paw/foot hyperflexion, polydactyly, syndactyly, and brachydactyly were observed in seven of eight fetuses. Cynomolgus monkeys were orally administered thalidomide at 20 mg/kg on day 26 of gestation, and whole embryos were removed from the dams 6 h after administration. Three embryos each were obtained from the thalidomide-treated and control groups. Total RNA was isolated from individual embryos, amplified to biotinylated cRNA and hybridized to a custom Non-Human Primate (NHP) GeneChip® Array. Altered genes were clustered into genes that were up-regulated (1281 genes) and down-regulated (1081 genes) in thalidomide-exposed embryos. Functional annotation by Gene Ontology (GO) categories revealed up-regulation of actin cytoskeletal remodeling and insulin signaling, and down-regulation of pathways for vasculature development and the inflammatory response. These findings show that thalidomide exposure perturbs a general program of morphoregulatory processes in the monkey embryo. Bioinformatics analysis of the embryonic transcriptome following maternal thalidomide exposure has now identified many key pathways implicated in thalidomide embryopathy, and has also revealed some novel processes that can help unravel the mechanism of this important developmental phenotype. | [Makoto Emaa, Ryota Iseb, Hirohito Katoc, Satoru Onedad, Akihiko Hirosea, Mutsuko Hirata-Koizumia, Amar V. Singhe, Thomas B. Knudsenf, Toshio Iharac] | Reproductive Toxicology | January 2010 | |
| sciencedirectS0168170209003955 | Chemokine profiling of Japanese encephalitis virus-infected mouse neuroblastoma cells by microarray and real-time RT-PCR: Implication in neuropathogenesis | Japanese encephalitis (JE) is one of the leading causes of acute encephalopathy affecting children and adolescents in the tropics. JE virus (JEV) infection causes prominent neurological sequelae in approximately one-third of the survivors. In humans, the inflammatory response of CNS consequent to JEV induced viral encephalitis is mediated through chemokines released by various cells of CNS. In the present study, the chemokine profiles of mouse neuroblastoma cells (N2A) following JEV infection was analyzed by cDNA microarray followed by real-time RT-PCR. Eighty mRNA transcripts belonging to various functional classes exhibited significant alterations in gene expression. There was considerable induction of genes involved in apoptosis and anti-viral response. Modified levels of several transcripts involved in proinflammatory and anti-inflammatory processes exemplified the balance between opposing forces during JEV pathogenesis. Other genes displaying altered transcription included those associated with host translation, cellular metabolism, cell cycle, signal transduction, transcriptional regulation, protein trafficking, neurotransmitters, neuron maturation, protein modulators, ER stress and cytoskeletal proteins. The infection of neurons results in the synthesis of proinflammatory chemokines, which are early important mediators of leukocyte recruitment to sites of viral infection. Our results clearly suggest the implication of chemokines in neuropathogenesis of JEV infection leading to neurological sequelae. Pro- and anti-inflammatory agents targeted against chemokines such as CXCL10 may provide possible therapeutic modalities that can mitigate the morbidity associated with JEV infection of the CNS. | [Nimesh Gupta, S.R. Santhosh, J. Pradeep Babu, M.M. Parida, P.V. Lakshmana Rao] | Virus Research | January 2010 | |
| sciencedirectS0168160509003389 | Microarray-based comparative genomic indexing of the Cronobacter genus (Enterobacter sakazakii) | Cronobacter (Enterobacter sakazakii) is a recently defined genus consisting of 6 species. To extend our understanding of the genetic relationship between Cronobacter sakazakii BAA-894 and the other species of this genus, microarray-based comparative genomic indexing (CGI) was undertaken to determine the presence/absence of genes identified in the former sequenced genome and to compare 276 selected open reading frames within the different Cronobacter strains. Seventy-eight Cronobacter strains (60 C. sakazakii, 8 C. malonaticus, 5 C. dublinensis, 2 C. muytjensii, 1 C. turicensis, 1 C. genomospecies 1, and 1 Cronobacter sp.) representing clinical and environmental isolates from various geographical locations were investigated. Hierarchical clustering of the CGI data showed that the species grouped as clusters. The 5 C. dublinensis and 2 C. muytjensii strains examined formed distinct species clusters. Moreover, all of the C. sakazakii and 3 of 8 C. malonaticus strains formed a large cluster. The remaining C. malonaticus strains formed a sub-group within a larger cluster that also contained C. turicensis, C. genomospecies 1, and an unknown Cronobacter sp. Cronobacter sakazakii and 3 of 8 C. malonaticus strains could be distinguished from the others within the collection by the presence of 10 fimbrial related genes. Similarly, capsule and/or lipopolysaccharide (LPS) related glycosyltransferases differentiated several of the C. sakazakii strains from each other. | [B. Healya, S. Huynhb, N. Mullanea, S. O'Briena, C. Iversena, A. Lehnerc, R. Stephanc, C.T. Parkerb, S. Fanninga] | International Journal of Food Microbiology | 31 December 2009 | |
| sciencedirectS0006291X09019135 | RNA interference targeting against S100A4 suppresses cell growth and motility and induces apoptosis in human pancreatic cancer cells | S100A4 protein belongs to the S100 subfamily, which has grown to be one of the large subfamilies of the EF-hand Ca2+-binding proteins, and overexpression of S100A4 is suggested to associate with cell proliferation, invasion, and metastasis. We observed frequent overexpression of S100A4 in pancreatic cancer cell lines and further analyzed RNAi-mediated knockdown to address the possibility of its use as a therapeutic target for pancreatic cancer. The specific knockdown of S100A4 strongly suppressed cell growth, induced G2 arrest and eventual apoptosis, and decreased cell migration. Furthermore, microarray analyses revealed that knockdown of S100A4 induced expression of the tumor suppressor genes PRDM2 and VASH1. Our present results suggest the possibility that the inhibition of S100A4 can be utilized in antitumor applications for patients with pancreatic cancer. | [Takahiro Tabataa, Nobukazu Tsukamotoa b, Abbas Ali Imani Fooladia, Sumitaka Yamanakaa, Toru Furukawaa, Masaharu Ishidaa b, Daisuke Satoa, Zhaodi Gua, Hiroki Nagased, Shinichi Egawab, Makoto Sunamuraa b c, Akira Horiia] | Biochemical and Biophysical Research Communications | 18 December 2009 | |
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| sciencedirectS0012160609012500 | Forkhead box M1 transcriptional factor is required for smooth muscle cells during embryonic development of blood vessels and esophagus | The forkhead box m1 (Foxm1 or Foxm1b) transcription factor (previously called HFH-11B, Trident, Win, or MPP2) is expressed in a variety of tissues during embryogenesis, including vascular, airway, and intestinal smooth muscle cells (SMCs). Although global deletion of Foxm1 in Foxm1−/− mice is lethal in the embryonic period due to multiple abnormalities in the liver, heart, and lung, the specific role of Foxm1 in SMC remains unknown. In the present study, Foxm1 was deleted conditionally in the developing SMC (smFoxm1−/− mice). The majority of smFoxm1−/− mice died immediately after birth due to severe pulmonary hemorrhage and structural defects in arterial wall and esophagus. Although Foxm1 deletion did not influence SMC differentiation, decreased proliferation of SMC was found in smFoxm1−/− blood vessels and esophagus. Depletion of Foxm1 in cultured SMC caused G2 arrest and decreased numbers of cells undergoing mitosis. Foxm1-deficiency in vitro and in vivo was associated with reduced expression of cell cycle regulatory genes, including cyclin B1, Cdk1-activator Cdc25b phosphatase, Polo-like 1 and JNK1 kinases, and cMyc transcription factor. Foxm1 is critical for proliferation of smooth muscle cells and is required for proper embryonic development of blood vessels and esophagus. | [Vladimir Ustiyana, I-Ching Wanga, Xiaomeng Rena, Yufang Zhanga, Jonathan Snydera, Yan Xua, Susan E. Werta, James L. Lessardb, Tanya V. Kalina, Vladimir V. Kalinichenkoa b] | Developmental Biology | 15 December 2009 | |
| sciencedirectS0378427409013976 | Effects of ultrafine TiO2 particles on gene expression profile in human keratinocytes without illumination: Involvement of extracellular matrix and cell adhesion | Assessing in vitro cellular responses to molecular events is an effective mean to elucidate the toxicological behavior of the ultrafine nanoparticles. In this study, we utilized the DNA microarray analysis technique to determine the gene expression profiles of the human keratinocyte HaCaT cells exposed to anatase titanium dioxide (TiO2) particles of different (7 nm, 20 nm and 200 nm) average diameters without illumination. Cells were incubated for 24 h with TiO2 particles, which were dispersed in the culture medium and size-fractionated such that the concentration of titanium in all the fractionated samples was nearly equivalent. According to the cluster analysis, only genes involved in the ‘inflammatory response’ and ‘cell adhesion’, but not the genes involved in ‘oxidative stress’ and ‘apoptosis’, were over-represented among the genes that were up-regulated in HaCaT cells. After 24 h exposure to ultrafine 7 nm TiO2 particles, we observed altered expression levels of genes involved in matrix metalloproteinase activity (MMP-9 and MMP-10) and cell adhesion (fibronectin FN-1, integrin ITGB-6, and mucin MUC-4). These results suggest that the ultrafine TiO2 particles without illumination have no significant impact on ROS-associated oxidative damage, but affect the cell–matrix adhesion in keratinocytes for extracellular matrix remodeling. | [Katsuhide Fujitaa 1, Masanori Horiea 1, Haruhisa Katob, Shigehisa Endohc, Mie Suzukib, Ayako Nakamurab, Arisa Miyauchic, Kazuhiro Yamamotod, Shinichi Kinugasac, Keiko Nishioa, Yasukazu Yoshidaa, Hitoshi Iwahashia, Junko Nakanishie] | Toxicology Letters | 15 December 2009 | |
| sciencedirectS0165242709001615 | Cellular host transcriptional responses to influenza A virus in chicken tracheal organ cultures differ from responses in in vivo infected trachea | In this study a viral infection of a tissue culture model system was compared to an in vivo infection, which is of importance to gauge the utility of the model system. The aim was to characterize early immune responses induced by avian influenza virus using tracheal organ cultures (TOC) as a model system. First, the in vitro system was optimized to ensure that the host transcription responses were only influenced by virus infection and not by differences in viral load. Upper and lower trachea both could be used in the cultures because the virus load was the same. Cilia motility was not affected in non-infected TOC and only slightly in infected TOC at 24 h post-inoculation. Gene expression profiles of early immune responses were analyzed in in vitro infected TOC, and were compared to the responses found in in vivo infected trachea. The gene expression profile in infected TOC suggested the up regulation of innate anti-viral responses that were triggered by attachment, entry and uptake of virus leading to several signalling cascades including NF-?B regulation. Genes associated with IFN mediated responses were mainly type I IFN related. Overlapping gene expression profiles between non-infected and infected TOC suggested that tissue damage during excision induced wound healing responses that masked early host responses to the virus. These responses were confirmed by real-time quantitative RT-PCR showing up regulation of IL-1? and IL-6. Microarray analysis showed that gene expression profiles of infected and non-infected TOC had a large overlap. This overlap contained many immune-related genes associated with inflammatory responses, apoptosis and immune system process and development. Infected TOC and in vivo infected trachea shared few significantly differentially expressed genes. The gene expression profile of infected TOC contained fewer genes which were expressed at reduced amplitude of change. Genes that were common between TOC and trachea were associated with early immune responses likely triggered by virus attachment and entry. Most of the genes were associated with IFN-mediated responses, mainly type I IFN related. Our study implicates that although the TOC model is suitable for culturing of virus and lectin or virus binding studies, it is not suitable for measuring early immune responses upon viral infection at host transcriptional level. | [Sylvia S. Reemersa, Marian J. Groot Koerkampb, Frank C. Holstegeb, Willem van Edena, Lonneke Verveldea] | Veterinary Immunology and Immunopathology | 15 December 2009 | |
| sciencedirectS0166445X08002762 | Hypoxia alters gene expression in the gonads of zebrafish (Danio rerio) ? ?? ◊ | The objectives of this study were to characterize gene expression responses to hypoxia in gonads of mature zebrafish (Danio rerio), and to start characterizing modes of action by which hypoxia could potentially alter reproduction. Adult male and female zebrafish were maintained under normoxia (7 mg O2/L), moderate hypoxia (3 mg O2/L), and severe hypoxia (1 mg O2/L) for 4 and 14 days and changes in gene expression in gonadal tissues (n = 5 per sex per treatment) were evaluated using a commercial 21,000 gene zebrafish oligonucleotide microarray. Differentially expressed genes were determined using ANOVA (p < 0.05), and enriched gene ontology (GO) categories (p < 0.01) identified using GeneSpring GX software. Short-term (4 d) exposure to hypoxia affected expression of genes associated with the initial adaptive responses such as: metabolism of carbohydrates and proteins, nucleotide metabolism, haemoglobin synthesis, reactive oxygen species metabolism, and locomotion. Prolonged (14 d) hypoxia affected a suite of genes belonging to different GO categories: lipid metabolism, reproduction (e.g., steroid hormone synthesis), and immune responses. Results of the present study demonstrate that reproduction likely would be affected by hypoxia via multiple modes of action. These include previously hypothesized mechanisms such as modulation of expression of steroidogenic genes, and downregulation of serotonergic pathway. In addition, we propose that there are multiple other points of disruption of reproductive system function linked, for example, to reorganization of lipid transport and other mechanisms involved in responding to hypoxia (e.g., hydroxysteroid dehydrogenase alterations, downregulation of contractile elements, etc.). | [Dalma Martinovic, Daniel L. Villeneuve, Michael D. Kahl, Lindsey S. Blake, Jeffrey D. Brodin, Gerald T. Ankley] | Aquatic Toxicology | 13 December 2009 | |
| sciencedirectS0009279709003548 | Synergistic increases of metabolism and oxidation–reduction genes on their expression after combined treatment with a CYP1A inducer and andrographolide | We previously reported that andrographolide greatly enhanced the expression of CYP1A1. Since andrographolide is a major constituent of Andrographis paniculata, which has been employed for centuries in Asia and Europe as a folk remedy, we further analyzed genes whose expression was modified by andrographolide using primary-cultured mouse hepatocytes in a microarray assay. With the threshold for modification set at 2-fold, andrographolide up-regulated 18 genes among 28,853 genes, most of them related to metabolism/oxidation/reduction. Meanwhile, 5 genes, related to protein binding or calcium ion binding, were down-regulated. A combination of ?-naphthoflavone (?-NF), a CYP1A inducer, and andrographolide modified the expression of 45 genes (27 up-regulated and 18 down-regulated), although ?-NF single treatment up-regulated 4 genes. The affected genes were again mostly related to metabolism and oxidation–reduction. Among P450 isoforms, andrographolide by itself induced CYP1A1, CYP2A4, CYP2B9, and CYP2B10 expression. Synergistic expression of CYP1A1 and CYP1B1 mRNA was confirmed by quantitative RT-PCR. These observations suggest that drug interaction and risk assessment with the use of andrographolide or A. paniculata should be elucidated. | [Waranya Chatuphonpraserta b, Kanokwan Jarukamjornb, Sachiko Kondoa, Nobuo Nemotoa] | Chemico-Biological Interactions | 10 December 2009 | |
| sciencedirectS0303720709004699 | Progesterone regulation of primordial follicle assembly in bovine fetal ovaries | Fertility in mammals is dependant on females having an adequate primordial follicle pool to supply oocytes for fertilization. The formation of primordial follicles is called ovarian follicular assembly. In rats and mice progesterone and estradiol have been shown to inhibit follicle assembly with assembly occurring after birth when the pups are removed from the high-steroid maternal environment. In contrast, primordial follicle assembly in other species, such as cattle and humans, occurs during fetal development before birth. The objective of the current study is to determine if progesterone levels regulate primordial follicle assembly in fetal bovine ovaries. Ovaries and blood were collected from bovine fetuses. Interestingly, ovarian progesterone and estradiol concentrations were found to decrease with increasing fetal age and correlated to increased primordial follicle assembly. Microarray analysis of fetal ovary RNA suggests that progesterone membrane receptor and estrogen nuclear receptor are expressed. Treatment of fetal bovine ovary cultures with a higher progesterone concentration significantly decreased primordial follicle assembly. Observations indicate that progesterone affects ovarian primordial follicle assembly in cattle, as it does in rats and mice. | [Eric E. Nilsson, Michael K. Skinner] | Molecular and Cellular Endocrinology | 10 December 2009 | |
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| sciencedirectS0022283609011590 | CARM1 but not Its Enzymatic Activity Is Required for Transcriptional Coactivation of NF-?B-Dependent Gene Expression | Coactivator-associated arginine methyltransferase 1 (CARM1) belongs to the protein arginine methyltransferase family. It was reported to methylate histone as well as non-histone proteins and thus to be involved in transcriptional activation and mRNA degradation/stability. Here we report the genetic complementation of carm1−/− cells with wild-type CARM1 or an enzymatic inactive mutant of CARM1 to investigate the requirement of CARM1 and its enzymatic activity for nuclear factor ?B (NF-?B)-dependent gene expression. Using custom microarray and quantitative reverse transcription PCR, we could define a subset of NF-?B target genes that required CARM1 for their proper expression. Although several tumor necrosis factor-?- and phorbol-12-myristate-13-acetate/ionomycin-induced NF-?B target genes are CARM1 dependent, CARM1 enzymatic activity was dispensable for gene expression. Interestingly, CARM1 was not required for the stimulus-dependent recruitment of RelA/p65 to chromatin, suggesting that CARM1 is rather contributing in protein complex stabilization. Together, our results confirm the importance of CARM1 as transcriptional cofactor without the involvement of its catalytic activity. | [Sandrine Jayne, Karin M. Rothgiesser, Michael O. Hottiger] | Journal of Molecular Biology | 4 December 2009 | |
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| sciencedirectS106569950900225X | Gene networks involved in apoptosis induced by hyperthermia in human lymphoma U937 cells | To define the molecular mechanisms that mediate hyperthermia-induced apoptosis, we performed microarray and computational gene expression analyses. U937 cells, a human myelomonocytic lymphoma cell line, were treated with hyperthermia at 42 °C for 90 min and cultured at 37 °C. Apoptotic cells (∼15%) were seen 6 h after hyperthermic treatment, and elevated expression of heat shock proteins (HSPs) including Hsp27, Hsp40, and Hsp70 was detected, following the activation of heat shock factor-1. Of the 54,675 probe sets analyzed, 1334 were upregulated and 4214 were downregulated by >2.0-fold in the cells treated with hyperthermia. A non-hierarchical gene clustering algorithm, K-means clustering, demonstrated 10 gene clusters. The gene network U1 or U2 that was obtained from up-regulated genes in cluster I or IX contained HSPA1B, DNAJB1, HSPH1, and TXN or PML, LYN, and DUSP1, and were mainly associated with cellular compromise, and cellular function and maintenance or death, and cancer, respectively. In the decreased gene cluster II, the gene network D1 including CCNE1 and CEBPE was associated with the cell cycle and cellular growth and proliferation. These findings will provide a basis for understanding the detailed molecular mechanisms of apoptosis induced by hyperthermia at 42 °C in cells. | [Yukihiro Furusawab 1, Yoshiaki Tabuchia 1, Ichiro Takasakia, Shigehito Wadac, Kenzo Ohtsukad, Takashi Kondob] | Cell Biology International | December 2009 | |
| sciencedirectS1521661609008006 | Estradiol targets T cell signaling pathways in human systemic lupus | The major risk factor for developing systemic lupus erythematosus (SLE) is being female. The present study utilized gene profiles of activated T cells from females with SLE and healthy controls to identify signaling pathways uniquely regulated by estradiol that could contribute to SLE pathogenesis. Selected downstream pathway genes (+/− estradiol) were measured by real time polymerase chain amplification. Estradiol uniquely upregulated six pathways in SLE T cells that control T cell function including interferon-? signaling. Measurement of interferon-? pathway target gene expression revealed significant differences (p = 0.043) in DRIP150 (+/− estradiol) in SLE T cell samples while IFIT1 expression was bimodal and correlated moderately (r = 0.55) with disease activity. The results indicate that estradiol alters signaling pathways in activated SLE T cells that control T cell function. Differential expression of transcriptional coactivators could influence estrogen-dependent gene regulation in T cell signaling and contribute to SLE onset and disease pathogenesis. | [Emily Waltersa 1, Virginia Ridera 1, Nabih I. Abdoub, Cindy Greenwellb, Stan Svojanovskyc, Peter Smithc, Bruce F. Kimlerd] | Clinical Immunology | December 2009 | |
| sciencedirectS0301468109000796 | Desmoglein 4 is regulated by transcription factors implicated in hair shaft differentiation | The hair fiber is made of specialized keratinocytes, known as trichocytes, that primarily express hair keratins, which are cemented by a multitude of keratin-associated proteins (KAPs). The hair keratins form the intermediate filament cytoskeleton of the trichocytes, which are linked to abundant cell–cell adhesion junctions, called desmosomes. Desmoglein 4 (DSG4) is the major desmosomal cadherin expressed in the hair shaft cortex where the hair keratins are highly expressed. In humans, mutations affecting either the hair keratins or DSG4 lead to beaded hair phenotypes with features of monilethrix. In this work, we postulated that the regulatory pathways governing the expression of hair shaft components, such as hair keratins and DSG4, are shared. Therefore, we studied the transcriptional regulation of DSG4 by transcription factors/pathways that are known regulators of hair keratin or KAP expression. We show that HOXC13, LEF1 and FOXN1 repress DSG4 transcription and provide in vitro and in vivo evidence correlating the Notch pathway with the activation and/or maintenance of DSG4 expression in the hair follicle. | [Hisham Bazzia b 1, Shadmehr Demehric, Christopher S. Potterd, Alison G. Barbera, Alexander Awgulewitschd, Raphael Kopanc, Angela M. Christianoa b] | Differentiation | December 2009 | |
| sciencedirectS0098847209000719 | Transcriptional profiling of Arabidopsis seedlings in response to heavy metal lead (Pb) | Lead (Pb) is one of the main sources of pollution in the environment, and is severely toxic to plants and animals. Using a DNA microarray, the transcriptional profiles of Arabidopsis thaliana genes in response to Pb treatment were investigated under different concentrations of Pb(NO3)2 solution from low (1 ?M, 10 ?M) to high (100 ?M) during the early stages of toxicity (3 h and 24 h). At each time point, Pb content was measured to confirm that the extensive heavy metal accumulation in Arabidopsis seedlings was caused by Pb treatment. Furthermore, eighteen selected genes with either moderate or high differential expression values from the microarray analysis were independently analyzed by quantitative real-time RT-PCR to confirm the reliability of the data. In our microarray analysis, the expressions of over 1310 genes were identified in response to Pb treatment. Extensive hierarchical clustering analysis of these responses indicated that the major consistently activated genes were also involved in common stress-induced responses. Especially, those that have been previously reported to be heavy metal inducible genes were significantly induced by lead treatment. Moreover, some important genes encoding enzymes or proteins involved in sulfur assimilation, GSH metabolism, indole-3-acedic acid (IAA) and jasmonic acid (JA) biosynthesis were activated, and these pathways were linked, directly or indirectly through signaling pathways, to biosynthesis of metal transports and detoxification molecules. Taken together, our results provided a new insight into the molecular mechanism of lead detoxification in Arabidopsis, and facilitated an understanding of the general lead/heavy metal-adaptive mechanism undertaken by plants. | [Tie Liua 1, Shuiying Liub 1, Hua Guanb, Ligeng Maa c, Zhangliang Chena b, Hongya Gua, Li-Jia Qua] | Environmental and Experimental Botany | December 2009 | |
| sciencedirectS001448350900253X | Hypoxia-inducible factor-1 (HIF-1) pathway activation by quercetin in human lens epithelial cells | Quercetin is a dietary bioflavonoid which has been shown to inhibit lens opacification in a number of models of cataract. The objectives of this study were to determine gene expression changes in human lens epithelial cells in response to quercetin and to investigate in detail the mechanisms underlying the responses. FHL-124 cells were treated with quercetin (10 ?M) and changes in gene expression were measured by microarray. It was found that 65% of the genes with increased expression were regulated by the hypoxia-inducible factor-1 (HIF-1) pathway. Quercetin (10 and 30 ?M) induced a time-dependent increase in HIF-1? protein levels. Quercetin (30 ?M) was also responsible for a rapid and long-lasting translocation of HIF-1? from the cytoplasm to the nucleus. Activation of HIF-1 signaling by quercetin was confirmed by qRT–PCR which showed upregulation of the HIF-1 regulated genes EPO, VEGF, PGK1 and BNIP3. Analysis of medium taken from FHL-124 cells showed a sustained dose-dependent increase in VEGF secretion following quercetin treatment. The quercetin-induced increase and nuclear translocation of HIF-1? was reversed by addition of excess iron (100 ?M). These results demonstrate that quercetin activates the HIF-1 signaling pathway in human lens epithelial cells. | [Pauline Radreaua, Jeremy D. Rhodesb, Richard F. Mithenc, Paul A. Kroonc, Julie Sandersona] | Experimental Eye Research | December 2009 | |
| sciencedirectS1087184509001662 | Aspergillus oryzae atfA controls conidial germination and stress tolerance | We compared atfA and atfB, the genes encoding the respective ATF/CREB-type transcription factors in Aspergillus oryzae. The germination ratio of ?atfA conidia was low without any stress, unlike that of ?atfB conidia. The ?atfA conidia were more sensitive to oxidative stress than the ?atfB conidia, which are also sensitive to oxidative stress. We compared the gene expressions of these strains by using a DNA microarray, GeneChip. Almost all the genes regulated by atfB were also regulated by atfA, but atfA also regulated many genes that were not regulated by atfB, including some genes putatively involved in oxidative stress resistance. The level of glutamate, the major amino acid in A. oryzae conidia, was significantly low only in the ?atfA conidia, and the glycerol accumulation during germination was not observed only in the ?atfA strain. We therefore concluded that atfA is involved in germination via carbon and nitrogen source metabolism. | [Kazutoshi Sakamotoa c, Kazuhiro Iwashitaa, Osamu Yamadaa, Ken Kobayashia, Akihiro Mizunoa, Osamu Akitab, Shigeaki Mikamia, Hitoshi Shimoia, Katsuya Gomic] | Fungal Genetics and Biology | December 2009 | |
| sciencedirectS002075190900280X | Transcriptional profiles of adult male and female Schistosoma japonicum in response to insulin reveal increased expression of genes involved in growth and development | Microarray analysis was used to investigate differential gene regulation in adult male and female Schistosoma japonicum cultured in the presence or absence of insulin in vitro. A total of 1,101 genes were up- or down-regulated in response to insulin, the majority of differential expression occurring 24 h after the addition of insulin to the cultures. Genes differentially expressed in male or female worms were predominantly involved in growth and development, with significant sex-specific differences in transcriptional profiles evident. Insulin appeared to promote protein synthesis and control protein degradation more prominently in male parasites. The study also indicated that insulin plays a more pronounced role in the uptake of glucose in unpaired female parasites, as reflected in the increased stimulation of gene expression of the phosphatidylinositol 3-kinase sub-pathway of insulin signalling. Insulin may also impact on the sexual differentiation and fecundity of female schistosomes by activation of the mitogenic-activated protein kinase sub-pathway. | [Hong Youa b, Wenbao Zhanga, Luke Moertela, Donald P. McManusa, Geoffrey N. Goberta] | International Journal for Parasitology | December 2009 | |
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| sciencedirectS0928098709002437 | Role of MicroRNA-214 in ginsenoside-Rg1-induced angiogenesis | MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional gene modulators. Ginsenoside-Rg1, one of the active components of ginseng, has been confirmed as an angiogenesis inducer. Using miRNA microarray analysis, a total of 17 (including miR-214) and 5 miRNAs were found to be down- or up-regulated by Rg1 in human umbilical vein endothelial cells (HUVECs), respectively. Since miR-214 is closely related to endothelial nitric oxide synthase (eNOS) and hence angiogenesis, its expression was further validated by qRT-PCR. We also investigated the role of miR-214 on eNOS expression and in tubulogenesis and motility of HUVEC by transfection of specific miRNA inhibitor or precursor. Our results suggested that Rg1 can down-regulate miR-214 expression in HUVEC, leading to an increase in eNOS expression, and in vitro cell migration and tube formation which can possibly promote angiogenesis. These results signify a new understanding towards how a simple natural compound can affect physiological changes through modulation of miRNA expression. | [Lai-Sheung Chan, Patrick Ying-Kit Yue, Nai-Ki Mak, Ricky Ngok-Shun Wong] | European Journal of Pharmaceutical Sciences | 5 November 2009 | |
| sciencedirectS0168365909004805 | Interactions between octaarginine and U-937 human macrophages: Global gene expression profiling, superoxide anion content, and cytokine production | Cell penetrating peptides such as octaarginine (R8) have been widely used as intracellular delivery vectors to import biologically active membrane-impermeable molecules. However, before using these peptides clinically, human immune responses to them must be fully understood. Because macrophages are important for immune responses, we evaluated the interactions between R8 and a human U-937 cell line. Cytotoxicity, binding, internalization, genome-wide profiling of gene expression, intracellular superoxide anion content, and cytokine release were assessed after U-937 cells had been incubated with different amounts of R8. Cytotoxicity was limited for up to 40 ?M of R8 and 24 h of incubation. Kinetic analysis of the binding and uptake of cells treated with fluorescein-5-isothiocynate-R8 showed time- and concentration-dependent increases. Microarray analysis identified 4386 genes time-dependently regulated when U-937 macrophages were exposed to 10 ?M of R8 for 0.5 h and 4 h; the majority of these genes were upregulated for each time point. Thirty-five upregulated genes responded to the stimuli with immune functions, and, using real-time quantitative reverse transcriptase-polymerase chain reaction analysis, five genes – FOS, OSM, C1R, TNF, IL1R1 – were confirmed. R8 induced superoxide anion production after 0.5 h, but not after longer incubations. Incubating U-937 cells with R8 for up to 24 h did not release the proinflammatory cytokines TNF-?, IL-1?, and IL-6. In summary, exposing U-937 macrophages to R8 did not induce proinflammatory cytokine release; however, it generated superoxide anion and affected gene expression. | [Jung-hua Steven Kuoa, Ming-shiou Janb, Yi-Lin Lina, Clay Linc] | Journal of Controlled Release | 3 November 2009 | |
| sciencedirectS0734975009001074 | Global gene expression in recombinant and non-recombinant yeast Saccharomyces cerevisiae in three different metabolic states | Global gene expression of two strains of Saccharomyces cerevisiae, one recombinant (P+), accumulating large amounts of an intracellular protein Superoxide Dismutase (SOD) and one non-recombinant (P−) which does not contain the recombinant plasmid, were compared in batch culture during diauxic growth when cells were growing exponentially on glucose, when they were growing exponentially on ethanol, and in the early stationary phase when glycerol was being utilized.When comparing the gene expression for P− (and P+) during growth on ethanol to that on glucose (Eth/Gluc), overexpression is related to an increase in consumption of glycerol, activation of the TCA cycle, degradation of glycogen and metabolism of ethanol. Furthermore, 97.6% of genes (80 genes) involved in the central metabolic pathway are overexpressed. This is similar to that observed by DeRisi et al. [DeRisi, J.L., Iyer, V.R. & Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680–686.] but very different from was observed for Metabolic Flux Analysis (MFA), where the specific growth rate is lowered to ca. 40%, the fluxes in the TCA cycle are reduced to ca. 40% (to 30% in P+), glycolysis is reduced to virtually 0 and protein synthesis to ca. 50% (to 40% in P+). Clearly it is not possible to correlate in a simple or direct way, quantitative mRNA expression levels with cell function which is shown by the Metabolic Flux Analysis (MFA).When comparing the two strains in the 3 growth stages, 4 genes were found to be under or overexpressed in all cases. The products of all of these genes are expressed at the plasma membrane or cell wall of the yeast. While comparing the strains (P+/P−) when growing on glucose, ethanol and in the early stationary phase, many of the genes of the central metabolic pathways are underexpressed in P+, which is similar to the behaviour of the metabolic fluxes of both strains (MFA). Comparing the gene expression for P− (and to some extent P+) during the early stationary phase to growth on ethanol (Stat/Eth), underexpression is generalized. This shows that the switch in metabolism between ethanol and early stationary phases has an almost instantaneous effect on gene expression but a much more retarded effect on metabolic fluxes and that the “early stationary” phase represents a “late ethanol” phase from the metabolic analysis point of view since ethanol is still present and being consumed although at a much slower rate. | [H. Díaza c, B.A. Andrewsa, A. Hayesd, J. Castrillob, S.G. Oliverb, J.A. Asenjoa] | Biotechnology Advances | November–December 2009 | |
| sciencedirectS0898656809001739 | Rho GTPase activity modulates Wnt3a/?-catenin signaling ? | Wnt proteins constitute a family of secreted signaling molecules that regulate highly conserved pathways essential for development and, when aberrantly activated, drive oncogenesis in a number of human cancers. A key feature of the most widely studied Wnt signaling cascade is the stabilization of cytosolic ?-catenin, resulting in ?-catenin nuclear translocation and transcriptional activation of multiple target genes. In addition to this canonical, ?-catenin-dependent pathway, Wnt3A has also been shown to stimulate RhoA GTPase. While the importance of activated Rho to non-canonical Wnt signaling is well appreciated, the potential contribution of Wnt3A-stimulated RhoA to canonical ?-catenin-dependent transcription has not been examined and is the focus of this study. We find that activated Rho is required for Wnt3A-stimulated osteoblastic differentiation in C3H10T1/2 mesenchymal stem cells, a biological phenomenon mediated by stabilized ?-catenin. Using expression microarrays and real-time RT-PCR analysis, we show that Wnt3A-stimulated transcription of a subset of target genes is Rho-dependent, indicating that full induction of these Wnt targets requires both ?-catenin and Rho activation. Significantly, neither ?-catenin stabilization nor nuclear translocation stimulated by Wnt3A is affected by inhibition or activation of RhoA. These findings identify Rho activation as a critical element of the canonical Wnt3A-stimulated, ?-catenin-dependent transcriptional program. | [Jessica Rossol-Allisona c e 1, Laura N. Stemmlea 1, Katherine I. Swenson-Fieldsd e, Patrick Kellyb, Patrick E. Fieldsc, Shannon J. McCalla, Patrick J. Caseyb, Timothy A. Fieldsa c e] | Cellular Signalling | November 2009 | |
| sciencedirectS0145305X09001116 | Gene expression patterns associated with chicken jejunal development | Jejunal development occurs in a spatio-temporal pattern and is characterized by morphological and functional changes. To investigate jejunal development at the transcriptomic level, we performed microarray studies in 1–21-day-old chickens. Nine gene clusters were identified, each with a specific gene expression pattern. Subsequently, groups of genes with similar functions could be identified. Genes involved in morphological and functional development were highly expressed immediately after hatch with declining expression patterns afterwards. Immunological development can be roughly divided based on expression patterns into three processes over time; first innate response and immigration of immune cells, secondly differentiation and specialization, and thirdly maturation and immune regulation. We conclude that specific gene expression patterns coincide with the immunological, morphological, and functional development as measured by other methods. Our data show that transcriptomic approaches provide more detailed information on the biological processes underlying jejunal development. | [Dirkjan Schokkera, Arjan J.W. Hoekmana, Mari A. Smitsa, Johanna M.J. Rebelb] | Developmental & Comparative Immunology | November 2009 | |
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| sciencedirectS0162013409001159 | Characterization of an NF-?B-regulated, miRNA-146a-mediated down-regulation of complement factor H (CFH) in metal-sulfate-stressed human brain cells | Micro RNAs (miRNAs) represent a family of small ribonucleic acids (RNAs) that are post-transcriptional regulators of messenger RNA (mRNA) complexity. Brain cells maintain distinct populations of miRNAs that support physiologically normal patterns of expression, however, certain miRNA abundances are significantly altered in neurodegenerative disorders such as Alzheimer’s disease (AD). Here we provide evidence in human neural (HN) cells of an aluminum-sulfate- and reactive oxygen species (ROS)-mediated up-regulation of an NF-?B-sensitive miRNA-146a that down-regulates the expression of complement factor H (CFH), an important repressor of inflammation. This NF-?B-miRNA-146a-CFH signaling circuit is known to be similarly affected by A?42 peptides and in AD brain. These aluminum-sulfate-inducible events were not observed in parallel experiments using iron-, magnesium-, or zinc-sulfate-stressed HN cells. An NF-?B-containing miRNA-146a-promoter-luciferase reporter construct transfected into HN cells showed significant up-regulation of miRNA-146a after aluminum-sulfate treatment that corresponded to decreased CFH gene expression. These data suggest that (1) as in AD brain, NF-?B-sensitive, miRNA-146a-mediated, modulation of CFH gene expression may contribute to inflammatory responses in aluminum-stressed HN cells, and (2) underscores the potential of nanomolar aluminum to drive genotoxic mechanisms characteristic of neurodegenerative disease processes. | [Aileen I. Poguea, Yuan Yuan Lia, Jian-Guo Cuia, Yuhai Zhaoa, Theodore P.A. Kruckb, Maire E. Percyb c, Matthew A. Tarrd, Walter J. Lukiwa] | Journal of Inorganic Biochemistry | November 2009 | |
| sciencedirectS0047637409001304 | Alterations in microRNA expression in stress-induced cellular senescence ? | We investigated miRNA expression changes associated with stress-induced premature senescence (SIPS) in primary cultures of human diploid fibroblast (HDF) and human trabecular meshwork (HTM) cells. Twenty-five miRNAs were identified by miRNA microarray analysis and their changes in expression were validated by TaqMan real-time RT-PCR in three independent cell lines of HTM and HDF. SIPS in both HTM and HDF cell types was associated with significant down-regulation of four members of the miR-15 family and five miRNAs of the miR-106b family located in the oncogenic clusters miR-17-92, miR-106a-363, and miR-106b-25. SIPS was also associated with up-regulation of two miRNAs (182 and 183) from the miR-183-96-182 cluster. Transfection with miR-106a agomir inhibited the up-regulation of p21CDKN1A associated with SIPS while transfection with miR-106a antagomir led to increased p21CDKN1A expression in senescent cells. In addition, we identified retinoic acid receptor gamma (RARG) as a target of miR-182 and showed that this protein was down-regulated during SIPS in HDF and HTM cells. These results suggest that changes in miRNA expression might contribute to phenotypic alterations of senescent cells by modulating the expression of key regulatory proteins such as p21CDKN1A as well as by targeting genes that are down-regulated in senescent cells such as RARG. | [Guorong Li, Coralia Luna, Jianming Qiu, David L. Epstein, Pedro Gonzalez] | Mechanisms of Ageing and Development | November–December 2009 | |
| sciencedirectS0168945209002143 | Transcriptional profiling of Arabidopsis thaliana plants’ response to low relative humidity suggests a shoot–root communication | The creation of a water-stress environment usually starts with a reduction in air relative humidity (RH) while soil water potential still reflects favorable conditions. Arabidopsis plants subjected to low RH (17%) exhibited a significant increase in leaf specific hydraulic conductance, reducing the water potential. However, no detectable effects on stomatal performance or osmotic leaf adjustment were noted relative to plants exposed to high RH. In the present study, we profiled gene expression in roots 2.5 and 5 h after shoot exposure to low RH. Multiple genes with various putative biological roles were identified as differentially expressed under these conditions; among them were aquaporins, some of whose expression was induced under low RH. Transcription of two aquaporin was localized to the roots, especially to cells around the vascular system and to cells of the differentiation zone, and to leaf trichomes. Our results suggest that plant roots perceive the low RH stimulus from shoots through a sensing mechanism(s), leading to distinct plant transcriptional responses, potentially reflecting activation of various biological processes. This activation might be a prelude to the expected forthcoming drought conditions, providing the plant with enhanced resistance to future water-stress situations. | [Michal Levina, Nathalie Resnickb, Yogev Rosianskeyb, Igor Kolotilinb, Smadar Winingera, Jorge Hugo Lemcoffc, Shabtai Cohenc, Gadi Galilid, Hinanit Koltaib, Yoram Kapulnika] | Plant Science | November 2009 | |
| sciencedirectS0041008X09002956 | Long-term estrogen exposure promotes carcinogen bioactivation, induces persistent changes in gene expression, and enhances the tumorigenicity of MCF-7 human breast cancer cells | The cumulative exposure to estrogens is an important determinant in the risk of breast cancer, yet the full range of mechanisms involving estrogens in the genesis and progression of breast cancer remains a subject of debate. Interactions of estrogens and environmental toxicants have received attention as putative factors contributing to carcinogenesis. Mechanistic studies have demonstrated interactions between estrogen receptor ? (ER?) and the aryl hydrocarbon receptor (AhR), with consequences on the genes that they regulate. Many studies of ER? and AhR-mediated effects and crosstalk between them have focused on the initial molecular events. In this study, we investigated ER?- and AhR-mediated effects in long-term estrogen exposed (LTEE) MCF-7 human breast cancer cells, which were obtained by continuous culturing for at least 12 weeks in medium supplemented with 1 nM of 17?-estradiol (E2). With these LTEE cells and with parallel control cells cultured without E2 supplementation, we performed an extensive study of cytochrome P450 (CYP) induction, carcinogen bioactivation, global gene expression, and tumorigenicity in immunocompromised mice. We found that LTEE cells, in comparison with control cells, had higher levels of AhR mRNA and protein, greater responsiveness for AhR-regulated CYP1A1 and CYP1B1 induction, a 6-fold higher initial level of benzo(a)pyrene-DNA adducts as determined by liquid chromatography tandem mass spectrometry, marked differences in the expression of numerous genes, and a higher rate of E2-dependent tumor growth as xenografts. These studies indicate that LTEE causes adaptive responses in MCF-7 cells, which may reflect processes that contribute to the overall carcinogenic effect of E2. | [Barbara C. Spinka, James A. Bennettb, Brian T. Pentecosta c, Nicole Lostrittob, Neal A. Englerta c, Geoffrey K. Benna, Angela K. Goodenougha, Robert J. Tureskya c, David C. Spinka c] | Toxicology and Applied Pharmacology | 1 November 2009 | |
| sciencedirectS0022175909002002 | Molecular characterization of hybridoma subclones spontaneously switching at high frequencies in vitro | The hybridoma technology allows the production of large quantities of specific antibodies of a single isotype. Since different isotypes have special effector functions and are distributed distinctively throughout the body, it is often useful to have a library of switch variants from the original monoclonal antibody. We have shown previously that forced expression of activation induced cytidine deaminase (AID) in hybridomas increased their very low frequency of class switch recombination (CSR) in vitro only ∼ 7–13 fold. Since we had previously identified rare hybridoma subclones that spontaneously switched at more than 100 times higher frequencies, we have now examined those higher switching variants to search for ways to further increase the frequency of isotype switching in vitro. AID was not responsible for the ∼ 100 fold increase in CSR, so we used whole-genome gene expression profiling to provide a platform for studying candidate molecular pathways underlying spontaneous CSR in hybridomas. | [Maria D. Iglesias-Ussela, Jiri Zavadilb, Matthew D. Scharffa] | Journal of Immunological Methods | 31 October 2009 | |
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| sciencedirectS0378427409013587 | Gene expression profiles and pathways in skin inflammation induced by three different sensitizers and an irritant | It is often difficult to discriminate between chemically induced skin irritation and sensitization due to their similar clinical, pathological, and immunological responses. More information than that currently available from local lymph node assays (LLNAs), such as data from gene expression and pathway analysis, can provide more insightful data than the assay itself for distinguishing skin sensitization from skin irritation. This study investigated the gene expression profiles and pathways in ear skins of mice topically exposed daily for three consecutive days to the known strong contact sensitizer 1-chloro-2,4-dinitrobenzene, the skin contact sensitizer 2-phenyl-4-ethoxymethylene-5-oxazolone, the skin or respiratory sensitizer toluene 2,4-diisocyanate, or to the non-sensitizing irritant croton oil. All the sensitizers induced histological changes in ear tissues similar to those induced by the croton oil. In gene expression microarrays, sensitizers up-regulated 193 genes and down-regulated 61 genes in ear skin following chemical exposure. 13 genes whose expression was affected by more than two-fold by all three of the sensitizers, but not by the irritant, were selected by microarray analysis. Microarray and real-time RT-PCR analyses revealed that, of these genes, the allergic inflammation-related genes Oasl2 and Zbp1 were up-regulated in skin inflammation by the sensitizers. In gene expression pathway analysis of all the sensitizers and the croton oil, the top functions of the 48 genes were related to cytokine and cytokine receptors interactions, and only two genes (Cxcl9 and Cxcl10) were specific to skin sensitizer-induced skin inflammation. Thus, although contact sensitizer-induced skin inflammation is similar to irritant-induced responses in terms of histological changes and gene expression profiles, the regulation of allergic inflammation-related gene transcripts, such as those of Oasl2 and Zbp1 or Cxcl9 and Cxcl10, could help to discriminate skin sensitization from chemically induced skin inflammation. | [Hyun-Ok Kua, Sang-Hee Jeonga, Hwan-Goo Kanga, Hyun-Mi Pyoa, Joon-Hyoung Choa, Seong-Wan Sona, So-Mi Yuna, Doug-Young Ryub] | Toxicology Letters | 28 October 2009 | |
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| sciencedirectS037842740901176X | Alteration of transcriptional profile in human bronchial epithelial cells induced by cigarette smoke condensate | Despite the significance of cigarette smoke for carcinogenesis, the molecular mechanisms that lead to increased susceptibility of human cancers are not well-understood. In our present study, the oncogenic transforming effects of cigarette smoke condensate (CSC) were examined using papillomavirus-immortalized human bronchial epithelial cells (BEP2D). Growth kinetics, saturation density, resistance to serum-induced terminal differentiation, anchorage-independent growth and tumorigenicity in nude mice were used to investigate the various stages of transformation in BEP2D cells. Illumina microarray platforms were used to explore the CSC-induced alteration of global mRNA expression profiles of the earlier period and the advanced stage of CSC-treated BEP2D cells. We showed here that a series of sequential steps arose among CSC-treated immortalized human bronchial epithelial cells, including altered growth kinetics, resistance to serum-induced terminal differentiation, and anchorage-independence growth. In the earlier period of CSC treatment, 265 genes were down-regulated and 63 genes were up-regulated, respectively, and in the advanced stage of CSC treatment, 313 genes were down-regulated and 145 genes were up-regulated, respectively. Notably, among those genes, the expression of some of imprinted genes such as IGF2, NDN, H19 and MEG3 were all silenced or down-regulated in CSC-treated cells. These genes reactivated after 5 ?M 5-aza-2-deoxycytidine (5-aza-dC) treatment. These results demonstrated that long-term treatment of human bronchial epithelial cells with CSC may adversely affect their genetic and epigenetic integrity and lead to further transformation. | [Ying-Chun Hua, Zhi-Hua Yanga, Ke-Jun Zhongb, Li-Jing Niuc, Xiu-Jie Pana, De-Chang Wua, Xian-Jun Sunb, Ping-Kun Zhoua, Mao-Xiang Zhua, Yan-Ying Huoa] | Toxicology Letters | 8 October 2009 | |
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| sciencedirectS0011224009001035 | Enhancing prostate cancer cryotherapy using tumour necrosis factor related apoptosis-inducing ligand (TRAIL) sensitisation in an in vitro cryotherapy model ? | Cryotherapy is a minimally invasive treatment for prostate cancer. Complete ablation of cancer tissue some times fails and results in disease recurrence. In this study we investigate the effect of TRAIL as a sensitising agent to enhance the effects of cryotherapy on prostate cancer cells. Prostate cancer cells were cooled using Endocare cryo-system to mimic temperatures achieved during clinical cryotherapy. The effects of TRAIL, cryotherapy or combination of both treatment on DU-145 and PC-3 were evaluated. Viability and mode of cell death was assessed following treatment. Cryotherapy did not result in complete cell death at temperature −40 °C. Cells died by both necrosis and apoptosis. Cells which survived freeze–thaw cycle became more sensitive to a second freezing injury. TRAIL resulted in minimal cell death. Concomitant treatment of the tumour cells with TRAIL and cryotherapy resulted in complete loss of viability at −10 and −20 °C. Cell death was mainly due to marked increase in necrosis.Our finding demonstrates that combined treatment of TRAIL and cryotherapy represent a novel approach to increase the sensitivity to cryotherapy. This combined approach may be feasible for locally advanced prostate cancer. | [Mohamed Ismaila b, Richard Morgana, Kevin Harringtonc, John Daviesa b, Hardev Pandhaa b] | Cryobiology | October 2009 | |
| sciencedirectS0014482709002602 | Astrocytoma derived short-term cell cultures retain molecular signatures characteristic of the tumour in situ | The heterogeneity of tumours and uncertainties surrounding derived short-term cell cultures and established cell lines fundamentally challenge the research and understanding of tumour growth and development. When tumour cells are cultured, changes are inevitably induced due to the artificial growth conditions. Several recent studies have questioned how representative established cell lines or derived short-term cell cultures are of the tumour in situ. We have characterised gene expression changes induced by short-term culture in astrocytoma in order to determine whether derived short-term cell cultures are representative of the tumour in situ. In comparison to the majority of studies, paired biopsies and derived short-term cultures were investigated to reduce the effects of long-term culture and inter-tumour variability when comparing biopsies and derived cultures from tumours with the same histology from different individuals. We have used the Affymetrix GeneChip® U133A to generate gene expression profiles of 6 paediatric pilocytic astrocytoma (PA) biopsies and derived short-term cell cultures and 3 adult glioblastoma multiforme (GBM) biopsies and derived short-term cultures. Significant differential gene expression is induced by short-term culture. However, when the biopsy and derived short-term cell culture samples were grouped according to tumour type (PA and GBM) a molecular signature of 608 genes showed significant differential expression between the groups. This gene cohort can distinguish PA and GBM tumours, regardless of the sample source, suggesting that astrocytoma derived short-term cultures do retain key aspects of the global tumour expression profile and are representative of the tumour in situ. Furthermore, these genes are involved in pathways and functions characteristic of adult GBM including VEGF signalling, hypoxia and TP53 signalling. | [Nicola E. Pottera, K. Phippsb, W. Harknessb, R. Haywardb, D. Thompsonb, T.S. Jacquesc d, B. Hardingd, D.G.T. Thomase, J. Reesa, J.L. Darlingf, T.J. Warra] | Experimental Cell Research | 1 October 2009 | |
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| sciencedirectS1567576909002306 | Polysaccharides derived from Yamoa™ (Funtumia elastica) prime ?? T cells in vitro and enhance innate immune responses in vivo | Yamoa™ (ground bark of Funtumia elastica tree) is marketed and sold as a dietary supplement with anecdotal therapeutic effects in the treatment of asthma and hay fever. We determined that Yamoa™ and Yamoa™-derived polysaccharides affected innate immunity, in part, by priming ?? T cells. Gene expression patterns in purified bovine ?? T cells and monocytes induced by Yamoa™ were similar to those induced by ultrapure lipopolysaccharide (uLPS). In the presence of accessory cells, Yamoa™ had priming effects that were similar to those of LPS on bovine and murine ?? T cells, but much more potent than LPS on human ?? T cells. The bioactive component of Yamoa™ was delineated to a complex polysaccharide fraction (Yam-I). Intraperitoneal injection of Yamoa™ and Yam-I in mice induced rapid increases in peritoneal neutrophils directed by changes in chemokine expression. In support of a unique agonist found in Yam-I, similar peritonitis responses were also observed in TLR4- and MyD88-deficient mice. Therapeutic treatment with Yam-I resulted in decreased bacterial counts in feces from mice with Salmonella enterica serotype typhimurium (ST)-induced enterocolitis. This characterization of the immune stimulatory properties of polysaccharides derived from Yamoa™ suggests mechanisms for the anecdotal positive effects of its ingestion and that these polysaccharides show potential for application in innate protection from disease. | [Jill C. Graff, Emily M. Kimmel, Brett Freedman, Igor A. Schepetkin, Jeff Holderness, Mark T. Quinn, Mark A. Jutila, Jodi F. Hedges] | International Immunopharmacology | October 2009 | |
| sciencedirectS0161589009006245 | Interleukin-8 and RANTES are signature cytokines made by HOZOT, a new type of regulatory T cells | Distinct cytokine production profiles define the effector functions of both helper and regulatory T cells. Recently, we established novel cytotoxic regulatory T (Treg) cell lines, HOZOT, which have been characterized as IL-10-producing T cells. In this study, we further characterized HOZOT by performing comprehensive analyses of cytokines produced by HOZOTs in order to identify a signature cytokine profile. Using DNA microarrays, we compared the gene expression profiles of HOZOT-4, a representative HOZOT cell line, under three different conditions. Seven genes, including IL-8, IL-10, IL-13, MIP-1?, and MIP-1?, were identified as inducible cytokines when stimulated with stromal cells or anti-CD3/CD28 antibodies. Twelve genes, including IL-2, IL-3, IL-4, IL-22, CCL1, and lymphotactin, were categorized as antibody stimulation–responsive but stromal cell-non-responsive. Three genes, IL-32, RANTES, and CCL23, were constitutively expressed irrespective of stimulation condition. Among these cytokines, we focused on two chemokines, IL-8 and RANTES for further studies, and found that only HOZOT produced both of them at considerable levels whereas other T cell subsets, including Tregs and helper T cells, did not. Kinetic and inhibition experiments revealed contrasting properties for the two chemokines. IL-8 was induced only after stimulation, whereas RANTES mRNA and protein accumulated to high levels even before stimulation. Interestingly, IL-8 mRNA was induced by cycloheximide treatment and RANTES showed reduced mRNA but increased protein expression by antibody stimulation. As a whole, the unique cytokine signature profile consisting of Th1, Th2, and cytolytic T cell cytokines as well as Treg cytokines reflect the multifunctional nature of HOZOT. In particular, the dual production of IL-8 and RANTES by distinct mechanisms is a hallmark of HOZOT. | [Akira Harashimaa, Terumasa Torayaa, Ayumi Okochia, Mayuko Yamamotoa, Motoyuki Suzukia, Takeshi Otania, Toshiya Inouea, Kazue Tsuji-Takayamaa, Akira Sugimotoa, Makoto Takeuchia, Fumiyuki Yamasakib, Shuji Nakamuraa, Masayoshi Kibataa] | Molecular Immunology | October 2009 | |
| sciencedirectS0300483X09004314 | Inflammatory gene expression in response to sub-lethal ricin exposure in Balb/c mice | The toxin ricin has been shown to cause inflammatory lung damage, leading to pulmonary oedema and, at higher doses, mortality. In order to understand the genetic basis of this inflammatory cascade a custom microarray platform (1509 genes) directed towards immune and inflammatory markers was used to investigate the temporal expression profiles of genes in a Balb/c mouse model of inhalational ricin exposure. To facilitate examination of those genes involved in both inflammatory cascades and wound repair the dose which was investigated was sub-lethal across a 96-h time course. Histopathology of the lung was mapped across the time course and genetic responses considered in the context of overall lung pathology. Six hundred and eighty-five genes were found to be statistically significantly different compared to controls, across the time course and these genes have been investigated in the context of their biological function in ricin poisoning. As well as confirming key inflammatory markers associated with ricin intoxication (TNF? and IL1?) several pathways that are altered in expression were identified following pulmonary exposure to ricin. These genes included those involved in cytokine–cytokine signalling cascades (IL1, IL1r, IL1r2, Ccl 4, 6, 10), focal adhesion (Fn1, ICAM1) and tissue remodelling (VEGF, Pim1). Furthermore, the observed alteration in expression of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) indicates a key role in membrane integrity and cellular adhesion in ricin poisoning. Data captured using this transcriptomic approach could be used to develop a specific approach to the treatment of inhalational ricin exposure. This work was conducted as part of a wider programme of work to compare a number of militarily relevant lung damaging agents, with a view to establishing a rational basis for the identification of more generic medical countermeasures. | [Jonathan David, Lucy J. Wilkinson, Gareth D. Griffiths] | Toxicology | 1 October 2009 | |
| sciencedirectS0006899309014309 | Genomic analysis of ischemic preconditioning in adult rat hippocampal slice cultures | Understanding endogenous mechanisms of neuroprotection may have important clinical applications. It is well established that brain tissue becomes more resistant to ischemic injury following a sublethal ischemic insult. This process, called ischemic preconditioning (IPC), can be induced in adult rat hippocampal slice cultures by a brief oxygen–glucose deprivation (OGD) [Hassen, G.W., Tian, D., Ding, D., Bergold, P.J., 2004. A new model of ischemic preconditioning using young adult hippocampal slice cultures. Brain Res. Brain Res. Protoc. 13, 135–143]. We have analyzed the changes in gene expression brought about by IPC in this model in order to understand the mechanisms involved. Total RNA was isolated at different time points following a brief OGD (3, 6 and 12 h) and used to probe genome-wide expression microarrays. Genes were identified that were significantly up- or down-regulated relative to controls. We placed genes that were differentially expressed into statistically significant groups based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene ontology (GO) terms. Genes involved in signal transduction, transcription, and oxidative phosphorylation are differentially expressed at each time point. The analysis demonstrates that alterations in signaling pathways (TGF-?, Wnt, MAPK, ErbB, Toll-like receptor, JAK-STAT, VEGF) consistently accompany IPC. RT-PCR was used to confirm that members of these signaling pathways are regulated as predicted by the microarray analysis. We verified that protein translation following OGD is necessary for IPC. We also found that blocking the NMDA receptor during OGD does not significantly inhibit IPC in this model or produce large changes in gene expression. Our data thus suggests that changes in signaling pathways and their down-stream targets play an important role in triggering endogenous neuroprotection. | [Ethan A. Benardetea, Peter J. Bergolda b] | Brain Research | | |
| sciencedirectS0165242709001287 | Gene expression in the lamellar dermis–epidermis during the developmental phase of carbohydrate overload-induced laminitis in the horse | ObjectiveGene expression in the lamellar dermis and epidermis was compared between healthy horses and horses in the developmental phase of carbohydrate overload-induced laminitis, in order to better understand the local biochemical and cellular events involved in the pathogenesis of laminitis.AnimalsSix healthy adult horses, with no history or clinical evidence of laminitis.ProceduresHorses were randomly divided into two groups: control (n = 3) and laminitis (n = 3). Control horses received no treatment and were humanely euthanatized at the same time as the laminitis group. Horses in the laminitis group were given oligofructose (10 g/kg bwt by nasogastric tube) and humanely euthanatized 24–30 h later, before any clinical signs of laminitis were apparent. Sections of lamellar dermis and epidermis were harvested from the dorsal hoof wall of each horse immediately after death and cryopreserved until analysis. A bovine microarray chip, comprising approximately 15,000 genes, was used to compare gene expression between laminitis and control groups.ResultsA total of 155 genes were up-regulated in the laminitis group. No genes were down-regulated. Genes coding for the production of pro-inflammatory biochemical or cellular processes and those involved in protein degradation/turnover predominated. Several regulatory or anti-inflammatory genes were also up-regulated.Conclusions and clinical relevanceGeneration of inflammatory mediators within the lamellar tissues occurred before the development of substantial dermal–epidermal separation, inflammatory infiltrate, or vascular changes, and before the horses began showing signs of foot pain. While further studies are needed, early and targeted anti-inflammatory therapy may halt or prevent the development of laminitis in at-risk individuals. | [Murat T. Budaka, James A. Orsinib, Christopher C. Pollittc, Neal A. Rubinsteind] | Veterinary Immunology and Immunopathology | 15 September 2009 | |
| sciencedirectS0014482709002262 | Modulation of DNA glycosylase activities in mesenchymal stem cells | Adipose-tissue derived mesenchymal stem cells (AT-MSCs) are a promising tool for use in cell-based therapies. However, in vitro expansion is required to obtain clinically relevant cell numbers, and this might increase the chance of genomic instability. DNA repair is crucial for maintaining DNA integrity. Here we have compared the initial step of base excision repair in uncultured and cultured AT-MSCs by analysis of base removal activities and expression levels of relevant DNA glycosylases. Uracil, 5-hydroxyuracil and ethenoadenine removal activities were upregulated in cultured cells compared to uncultured cells. In contrast, both the 8-oxo-7,8-dihydroguanine (8-oxoG) removal activity and the concentration of 8-oxoG bases in the DNA were reduced in the cultured cells. Gene expression analysis showed no substantial changes in mRNA expression. The glycosylase activities remained stable through at least 12 passages, suggesting that DNA repair is proficient through the period required for in vitro expansion of AT-MSCs to clinically relevant numbers. | [Gunn A. Hildrestranda 1, Shivali Duggalb 1, Magnar Bjøråsa, Luisa Lunaa, Jan E. Brinchmannb] | Experimental Cell Research | 10 September 2009 | |
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| sciencedirectS0888754309001281 | Candidate Agtr2 influenced genes and pathways identified by expression profiling in the developing brain of Agtr2−/y mice | Intellectual disability (ID) is a common developmental disability observed in 1 to 3% of the human population. A possible role for the Angiotensin II type 2 receptor (AGTR2) in brain function, affecting learning, memory, and behavior, has been suggested in humans and rodents. Mice lacking the Agtr2 gene (Agtr2−/y) showed significant impairment in their spatial memory and exhibited abnormal dendritic spine morphology. To identify Agtr2 influenced genes and pathways, we performed whole genome microarray analysis on RNA isolated from brains of Agtr2−/y and control male mice at embryonic day 15 (E15) and postnatal day one (P1). The gene expression profiles of the Agtr2−/y brain samples were significantly different when compared to profiles of the age-matched control brains. We identified 62 differently expressed genes (p ≤ 0.005) at E15 and in P1 brains of the Agtr2−/y mice. We verified the differential expression of several of these genes in brain samples using quantitative RT-PCR. Differentially expressed genes encode molecules involved in multiple cellular processes including microtubule functions associated with dendritic spine morphology. This study provides insight into Agtr2 influenced candidate genes and suggests that expression dysregulation of these genes may modulate Agtr2 actions in the brain that influences learning and memory. | [Traci L. Pawlowskia b 1, Silvia Heringer-Waltherc 2, Chun-Huai Chengb, John G. Archiea 3, Chin-Fu Chenb, Thomas Waltherc 4, Anand K. Srivastavaa b] | Genomics | September 2009 | |
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| sciencedirectS0047637409001079 | Transcriptional profiling of the age-related response to genotoxic stress points to differential DNA damage response with age | The p53 DNA damage response attenuated with age and we have evaluated downstream factors in the DNA damage response. In old animals p21 protein accumulates in the whole cell fraction but significantly declines in the nucleus, which may alter cell cycle and apoptotic programs in response to DNA damage. We evaluated the transcriptional response to DNA damage in young and old and find 2692 genes are differentially regulated in old compared to young in response to oxidative stress (p < 0.005). As anticipated, the transcriptional profile of young mice is consistent with DNA damage induced cell cycle arrest while the profile of old mice is consistent with cell cycle progression in the presence of DNA damage, suggesting the potential for catastrophic accumulation of DNA damage at the replication fork. Unique sets of DNA repair genes are induced in response to damage in old and young, suggesting the types of damage accumulating differs between young and old. The DNA repair genes upregulated in old animals point to accumulation of replication-dependent DNA double strand breaks (DSB). Expression data is consistent with loss of apoptosis following DNA damage in old animals. These data suggest DNA damage responses differ greatly in young and old animals. | [Kirk Simona, Anju Mukundanb, Samantha Dewundarac, Holly Van Remmend e, Alan A. Dombkowskib, Diane C. Cabelofa] | Mechanisms of Ageing and Development | September 2009 | |
| sciencedirectS0161589009005835 | Infectious salmon anaemia virus (ISAV) isolates induce distinct gene expression responses in the Atlantic salmon (Salmo salar) macrophage/dendritic-like cell line TO, assessed using genomic techniques | Infectious salmon anaemia virus (ISAV) is a marine orthomyxovirus of significant interest not only as a cause of a fatal disease of farmed Atlantic salmon resulting in severe economic losses to the aquaculture industry, but also as the only poikilothermic orthomyxovirus. ISAV targets vascular endothelial cells and macrophages, and is known to influence the expression of both innate and adaptive immune response relevant genes. ISAV isolates from different geographic regions have been shown to vary considerably in their pathogenicity for Atlantic salmon. This study aimed to characterize the Atlantic salmon TO macrophage/dendritic-like cell responses to infection with a selection of ISAV isolates of different genotypes and pathogenicity phenotypes. The first TO infection trial used ISAV isolates NBISA01 and RPC/NB-04-085-1 of high and low pathogenicity, respectively, and global gene expression analyses were carried out using ∼16,000 gene (16K) salmonid cDNA microarrays to compare RNA samples extracted from TO cells harvested 24 and 72 h post-infection versus time-matched uninfected controls. Overall, the microarray experiment showed that RPC/NB-04-085-1-infected cells had a higher total number of reproducibly dysregulated genes (88 genes: the sum of genes greater than 2-fold up- or down-regulated in all four replicate microarrays of a given comparison) than the NBISA01-infected cells (10 genes) for the combined sampling points (i.e. 24 and 72 h). This microarray experiment identified several salmon genes that were differentially regulated by NBISA01 and RPC/NB-04-085-1, and which may be useful as molecular biomarkers of ISAV infection. An initial quantitative reverse transcription-polymerase chain reaction (QRT-PCR) study involving 25 microarray-identified genes confirmed the differences in the level of dysregulation of host transcripts between the two ISAV isolates (i.e. NBISA01 and RPC/NB-04-085-1). A second TO infection trial was run using a selection of four clinical ISAV isolates (Norway-810/9/99, a high pathogenicity isolate of European genotype; RPC/NB-04-085-1, a low pathogenicity isolate of European genotype; NBISA01, a high pathogenicity isolate of North American genotype; and RPC/NB-01-0593-1, an intermediate pathogenicity isolate of North American genotype), and UV-inactivated RPC/NB-04-085-1, with sampling at 24, 36, 48, 72, 96, and 120 h post-infection. The microarray-identified, QRT-PCR validated suite of 24 molecular biomarkers of response to ISAV were used in a second QRT-PCR experiment to assess the TO cell gene expression responses to the four ISAV isolates at all six time points in the infection. The QRT-PCR data showed that RPC/NB-04-085-1 caused the highest fold changes of most immune-relevant genes [such as interferon-inducible protein Gig1, Mx1 protein, interferon-induced protein with tetratricopeptide repeats 5, Radical S-adenosyl methionine domain-containing protein (viperin), and several genes involved in the ISGylation pathway], followed by Norway-810/9/99. NBISA01 and RPC/NB-01-0593-01 (both of North American genotype) showed low fold up-regulation of transcripts that were highly induced by RPC/NB-04-085-1 isolate. These findings show that ISAV isolates have strain-specific variations in their ability to induce immune response genes. | [Samuel T. Workenhea, Tiago S. Horib, Matthew L. Riseb, Molly J.T. Kibengea, Frederick S.B. Kibengea] | Molecular Immunology | September 2009 | |
| sciencedirectS0168010209001643 | Valproic acid induces up- or down-regulation of gene expression responsible for the neuronal excitation and inhibition in rat cortical neurons through its epigenetic actions | Valproic acid (VPA), a drug used to treat epilepsy and bipolar mood disorder, inhibits histone deacetylase (HDAC), which is associated with the epigenetic regulation of gene expression. Using a microarray, we comprehensively examined which genes are affected by stimulating cultured rat cortical neurons with VPA, and found that the VPA-treatment markedly altered gene expression (up-regulated; 726 genes, down-regulated; 577 genes). The mRNA expression for brain-derived neurotrophic factor (BDNF) and the ?4 subunit of the GABAA receptor (GABAAR?4), known to be involved in epileptogenesis, was up-regulated, with the increase in BDNF exon I–IX mRNA expression being remarkable, whereas that for GABAAR?2, GAD65 and 67, and the K+/Cl− co-transporter KCC2, which are responsible for the development of GABAergic inhibitory neurons, was down-regulated. The number of GAD67-positive neurons decreased upon VPA-treatment. Similar changes of up- and down-regulation were obtained by trichostatin A. VPA did not affect the intracellular Ca2+ concentration and the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2), suggesting its direct action on HDAC. The acetylation of histones H3 and H4 was increased in the promoters of up-regulated but not down-regulated genes. Thus, VPA may disrupt a balance between excitatory and inhibitory neuronal activities through its epigenetic effect. | [Mamoru Fukuchia, Takuya Niia, Naoki Ishimarua, Aya Minaminoa, Daichi Haraa, Ichiro Takasakib, Akiko Tabuchia, Masaaki Tsudaa] | Neuroscience Research | September 2009 | |
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| sciencedirectS0981942809001223 | Heat shock factor gene family in rice: Genomic organization and transcript expression profiling in response to high temperature, low temperature and oxidative stresses | Binding of heat shock factors (HSFs) with heat shock element sequence is critical for the transcriptional induction of heat shock genes. Rice genome sequence shows 26 OsHsf genes out of which 25 possess various important domains noted in HSFs i.e. DNA binding domain (DBD), oligomerization domain (OD), nuclear localization signal (NLS), nuclear export signal (NES) and AHA type activation domain. OsHsf entry LOC_Os06g226100 has the oligomerization domain but lacks the above other domains. Also, there are no ESTs or full-length cDNA noted for this entry in database. Expression profiling showed that 22 OsHsf genes are induced by high temperature. Induction of 10 and 14 OsHsf genes was also noted against low temperature stress and oxidative stress, respectively. All OsHsf genes induced by oxidative stress were also induced by high temperature. On the other hand, induction of 6 and 1 OsHsf genes was noted to be exclusive to high and low temperature stresses, respectively. Seven OsHsf genes showed induced expression in response to all the three stresses examined. While in silico promoter analysis showed that OsHsf genes contain upstream regulatory elements corresponding to different abiotic stresses, there was lack of correlation noted between the in silico profiling of the elements and their corresponding transcript expression patterns. Apart from stress inducibility, EST database suggests that various OsHsf genes are developmentally regulated in diverse tissue types. | [Dheeraj Mittal, Sveta Chakrabarti, Anshuk Sarkar, Amanjot Singh, Anil Grover] | Plant Physiology and Biochemistry | September 2009 | |
| sciencedirectS1873506109000841 | BMP inhibition stimulates WNT-dependent generation of chondrogenic mesoderm from embryonic stem cells | WNT and bone morphogenetic protein (BMP) signaling are known to stimulate hemogenesis from pluripotent embryonic stem (ES) cells. However, osteochondrogenic mesoderm was generated effectively when BMP signaling is kept to a low level, while WNT signaling was strongly activated. When mesoderm specification from ES cells was exogenous factor dependent, WNT3a addition supported the generation of cardiomyogenic cells expressing lateral plate/extraembryonic mesoderm genes, and this process involved endogenous BMP activities. Exogenous BMP4 showed a similar effect that depended on endogenous WNT activities. However, neither factor induced robust chondrogenic activity. In support, ES cell differentiation in the presence of either WNT3a or BMP4 was associated with elevated levels of both Bmp and Wnt mRNAs, which appeared to provide sufficient levels of active BMPs and WNTs to promote the nonchondrogenic mesoderm specification. The osteochondrogenic mesoderm expressed PDGFR?, which also expressed genes that mark somite and rostral presomitic mesoderm. A strong WNT signaling was required for generating the mesodermal progeny, while approximately 50- to 100-fold lower concentration of WNT3a was sufficient for specifying axial mes(end)oderm. Thus, depending on the dose and cofactor (BMP), WNT signaling stimulates the generation of different biological activities and specification of different types of mesodermal progeny from ES cells. | [Makoto Tanakaa b 1, Vanta Jokubaitisb 2, Colin Wooda, Yi Wanga b, Nathalie Brouarda 3, Martin Perab 4, Milton Hearnd, Paul Simmonsa 3, Naoki Nakayamaa b c 3] | Stem Cell Research | September–November 2009 | |
| sciencedirectS0042682209003572 | Transcriptome analysis of Frog virus 3, the type species of the genus Ranavirus, family Iridoviridae | Frog virus 3 is the best characterized species within the genus Ranavirus, family Iridoviridae. FV3's large (∼ 105 kbp) dsDNA genome encodes 98 putative open reading frames (ORFs) that are expressed in a coordinated fashion leading to the sequential appearance of immediate early (IE), delayed early (DE) and late (L) viral transcripts. As a step toward elucidating molecular events in FV3 replication, we sought to identify the temporal class of viral messages. To accomplish this objective an oligonucleotide microarray containing 70-mer probes corresponding to each of the 98 FV3 ORFs was designed and used to examine viral gene expression. Viral transcription was initially monitored during the course of a productive replication cycle at 2, 4 and 9 h after infection. To confirm results of the time course assay, viral gene expression was also monitored in the presence of cycloheximide (CHX), which limits expression to only IE genes, and following infection with a temperature-sensitive (ts) mutant which at non-permissive temperatures is defective in viral DNA synthesis and blocked in late gene expression. Subsequently, microarray analyses were validated by RT-PCR and qRT-PCR. Using these approaches we identified 33 IE genes, 22 DE genes and 36 L viral genes. The temporal class of the 7 remaining genes could not be determined. Comparison of protein function with temporal class indicated that, in general, genes encoding putative regulatory factors, or proteins that played a part in nucleic acid metabolism and immune evasion, were classified as IE and DE genes, whereas those involved in DNA packaging and virion assembly were considered L genes. Information on temporal class will provide the basis for determining whether members of the same temporal class contain common upstream regulatory regions and perhaps allow us to identify virion-associated and virus-induced proteins that control viral gene expression. | [S. Majjia, V. Thodimab 1, R. Samplea, D. Whitleya, Y. Dengb, J. Maoc, V.G. Chinchara] | Virology | 1 September 2009 | |
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| sciencedirectS0012160609009105 | Analysis of early nephron patterning reveals a role for distal RV proliferation in fusion to the ureteric tip via a cap mesenchyme-derived connecting segment | While nephron formation is known to be initiated by a mesenchyme-to-epithelial transition of the cap mesenchyme to form a renal vesicle (RV), the subsequent patterning of the nephron and fusion with the ureteric component of the kidney to form a patent contiguous uriniferous tubule has not been fully characterized. Using dual section in situ hybridization (SISH)/immunohistochemistry (IHC) we have revealed distinct distal/proximal patterning of Notch, BMP and Wnt pathway components within the RV stage nephron. Quantitation of mitoses and Cyclin D1 expression indicated that cell proliferation was higher in the distal RV, reflecting the differential developmental programs of the proximal and distal populations. A small number of RV genes were also expressed in the early connecting segment of the nephron. Dual ISH/IHC combined with serial section immunofluorescence and 3D reconstruction revealed that fusion occurs between the late RV and adjacent ureteric tip via a process that involves loss of the intervening ureteric epithelial basement membrane and insertion of cells expressing RV markers into the ureteric tip. Using Six2-eGFPCre × R26R-lacZ mice, we demonstrate that these cells are derived from the cap mesenchyme and not the ureteric epithelium. Hence, both nephron patterning and patency are evident at the late renal vesicle stage. | [Kylie Georgasa, Bree Rumballea, M. Todd Valeriusb, Han Sheng Chiua, Rathi D. Thiagarajana, Emmanuelle Lesieura, Bruce J. Aronowc, Eric W. Brunskilld, Alexander N. Combesa, Dave Tanga, Darrin Taylora, Sean M. Grimmonda, S. Steven Potterd, Andrew P. McMahonb, Melissa H. Littlea] | Developmental Biology | 15 August 2009 | |
| sciencedirectS030439400900559X | Micro-RNA abundance and stability in human brain: Specific alterations in Alzheimer's disease temporal lobe neocortex | Micro-RNA (miRNA) mediated regulation of messenger RNA (mRNA) complexity in the central nervous system (CNS) is emerging as a critical factor in the control of CNS-specific gene expression during development, plasticity, aging and disease. In these studies, miRNA array and Northern blot based tracking of specific miRNA abundances and decay kinetics in human neural (HN) cells in primary culture and in short post-mortem interval (PMI, ∼1 h) human brain tissues showed a limited stability and relatively short half-life (∼1–3.5 h) for specific brain-enriched miRNAs. In short PMI Alzheimer's disease (AD)-affected temporal lobe neocortex, miRNA-9, miRNA-125b and miRNA-146a were found to be significantly up-regulated, an effect that was not seen in several related neurological disorders. The results suggest (a) that unless specifically stabilized, certain brain-enriched miRNAs represent a rapidly executed signaling system employing highly transient effectors of CNS gene expression, and (b) that in AD temporal lobe neocortex specific brain miRNAs are significantly up-regulated in abundance and strongly correlate with the presence of AD-type neuropatholgical change. | [Prerna Sethia, Walter J. Lukiwb] | Neuroscience Letters | 7 August 2009 | |
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| sciencedirectS0009308409001728 | Microarray analysis of RAW 264.7 macrophages silenced for ORP8 | | [Olivier Beaslas, Terhi Vihervaara, Vesa M. Olkkonen] | Chemistry and Physics of Lipids | August 2009 | |
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| sciencedirectS0014483509000736 | IGF-II and collagen expression by keratocytes during postnatal development ? | Keratocytes produce the extensive stromal matrix of the cornea during the late embryonic and neonatal time periods. We propose to test the hypothesis that their biosynthetic activity declines during this process. Keratocytes were isolated from corneas of 6–8-week-old rabbits and corneas of 1–2-year-old cows and their ability to proliferate and synthesize collagen in serum-free media was determined. Rabbit keratocyte cultures increased 38% in DNA content after one week and deposited collagen type I and IGF-II in the media. Bovine keratocyte cultures, in contrast, did not increase in DNA or produce detectable collagen and IGF-II. Bovine keratocytes cultured in media previously conditioned by rabbit keratocytes, however, increased 56% in DNA content, and deposited collagen type I into the media. Microarray analysis of mRNA from neonatal and adult mouse keratocytes was used to confirm these differences. Compared to adult mouse keratocytes, neonatal keratocytes showed high expression levels of IGF-I, IGF-II and collagen types III and V. Since previous studies showed that IGFs stimulate bovine keratocytes to proliferate and to synthesize procollagen type I, we therefore propose that the results of this study suggests that the IGFs may play an important role in regulating early corneal growth in vivo. | [Bradley P. Kanea, James V. Jesterb, Jiying Huangc, Andrew Wahlertb, John R. Hassella] | Experimental Eye Research | August 2009 | |
| sciencedirectS1096719209001334 | Phenotypic expression of maternally inherited deafness is affected by RNA modification and cytoplasmic ribosomal proteins | The homoplasmic mitochondrial A1555G mutation in the 12S rRNA gene leads to a mitochondrial translation disorder associated with deafness. The absence of disease in non-cochlear tissues in all patients, and in the cochlea in some patients, is not well understood. We used a system-based approach, including whole genome expression and biological function analysis, to elucidate the pathways underlying tissue specificity and clinical severity of this condition. Levels of over 48K RNA transcripts from EBV-transformed lymphoblasts of deaf and hearing individuals with the A1555G mutation and controls were obtained. Differentially expressed transcripts were functionally grouped using gene set enrichment analysis. Over 50 RNA binding proteins were differentially expressed between deaf and hearing individuals with the A1555G mutation (P-value of 2.56E-7), confirming previous genetic data implicating this pathway in the determination of the severity of hearing loss. Unexpectedly, the majority of cytoplasmic ribosomal genes were up-regulated in a coordinated fashion in individuals with the A1555G mutation versus controls (P-value of 3.91E-135). This finding was verified through real time RT-PCR, and through measuring of protein levels by flow cytometry. Analysis of expression levels of other differentially expressed genes suggests that this coordinated over-expression of cytoplasmic ribosomal proteins might occur through the Myc/Max pathway. We propose that expression levels of RNA binding proteins help determine the severity of the cochlear phenotype, and that coordinated up-regulation of the cytoplasmic translation apparatus operates as a compensation mechanism in unaffected tissues of patients with maternal deafness associated with the A1555G mutation. | [Yelena Bykhovskaya, Emebet Mengesha, Nathan Fischel-Ghodsian] | Molecular Genetics and Metabolism | August 2009 | |
| sciencedirectS016801020900145X | Effects of lithium chloride on the gene expression profiles in Drosophila heads | To gain insight into the basic neurobiological processes regulated by lithium—an effective drug for bipolar disorder—we used Affymetrix Genome Arrays to examine lithium-induced changes in genome-wide gene expression profiles of head mRNA from the genetic model organism Drosophila melanogaster. First, to identify the individual genes whose transcript levels are most significantly altered by lithium, we analyzed the microarray data with stringent criteria (fold change > 2; p < 0.001) and evaluated the results by RT-PCR. This analysis identified 12 genes that encode proteins with various biological functions, including an enzyme responsible for amino acid metabolism and a putative amino acid transporter. Second, to uncover the biological pathways involved in lithium's action in the nervous system, we used less stringent criteria (fold change > 1.2; FDR < 0.05) and assigned the identified 66 lithium-responsive genes to biological pathways using DAVID (Database for Annotation, Visualization and Integrated Discovery). The gene ontology categories most significantly affected by lithium were amino acid metabolic processes. Taken together, these data suggest that amino acid metabolism is important for lithium's actions in the nervous system, and lay a foundation for future functional studies of lithium-responsive neurobiological processes using the versatile molecular and genetic tools that are available in Drosophila. | [Junko Kasuyaa, Garrett Kaasb, Toshihiro Kitamotoa b c] | Neuroscience Research | August 2009 | |
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| sciencedirectS0960076009001447 | Exocrine pancreas trans-differentiation to hepatocytes—A physiological response to elevated glucocorticoid in vivo | Damage or ectopic expression of some growth factors can lead to the appearance of hepatocyte-like cells within the pancreas. Since glucocorticoids promote liver hepatocyte phenotype in vitro, the effect of glucocorticoid on pancreatic differentiation in vivo was examined. Treatment of rats with glucocorticoid for 25 days at levels that significantly inhibited weight gain resulted in the appearance of acinar cells expressing cytokeratin 7 and hepatocyte markers glutamine synthetase, carbamoyl phosphate synthetase and cytochrome P450 2E (the nomenclature employed is that given at http://drnelson.utmem.edu/CytochromeP450.html). Using a plastic pancreatic acinar cell line, this response was shown to be associated with changes in the regulation of WNT signalling-related gene expression and a repression of WNT signalling activity. These data suggest that a pathological response of the pancreas in vivo to elevated glucocorticoid is a differentiation of exocrine pancreatic cells or pancreatic progenitor cells to an hepatocyte-like phenotype. | [Karen Wallacea, Carylyn J. Mareka, Richard A. Currieb, Matthew C. Wrighta] | The Journal of Steroid Biochemistry and Molecular Biology | August 2009 | |
| sciencedirectS0887233309000940 | Global transcriptional characterization of a mouse pulmonary epithelial cell line for use in genetic toxicology | Prior to its application for in vitro toxicological assays, thorough characterization of a cell line is essential. The present study uses global transcriptional profiling to characterize a lung epithelial cell line (FE1) derived from Muta™Mouse [White, P.A., Douglas, G.R., Gingerich, J., Parfett, C., Shwed, P., Seligy, V., Soper, L., Berndt, L., Bayley, J., Wagner, S., Pound, K., Blakey, D., 2003. Development and characterization of a stable epithelial cell line from Muta Mouse lung. Environmental and Molecular Mutagenesis 42, 166–184]. Results presented here demonstrate the origin of the FE1 lung cell line as epithelial, presenting both type I and type II alveolar phenotype. An assessment of toxicologically-relevant genes, including those involved in the response to stress and stimuli, DNA repair, cellular metabolism, and programmed cell death, revealed changes in expression of 22–27% of genes in one or more culture type (proliferating and static FE1 cultures, primary epithelial cultures) compared with whole lung isolates. Gene expression analysis at 4 and 24 h following benzo(a)pyrene exposure revealed the induction of cyp1a1, cyp1a2, and cyp1b1 in FE1 cells and lung isolates. The use of DNA microarrays for gene expression profiling allows an improved understanding of global, coordinated cellular events arising in cells under different physiological conditions. Taken together, these data indicate that the FE1 cell line is derived from a cell type relevant to toxic responses in vivo, and shows some similarity in response to chemical insult as the original tissue. | [M. Lynn Berndt-Weis, Lisa M. Kauri, Andrew Williams, Paul White, George Douglas, Carole Yauk] | Toxicology in Vitro | August 2009 | |
| sciencedirectS0006291X0900967X | Aldehyde dehydrogenase 1 is a putative marker for cancer stem cells in head and neck squamous cancer | Aldehyde dehydrogenase 1 (ALDH1) has been considered to be a marker for cancer stem cells. However, the role of ALDH1 in head and neck squamous cell carcinoma (HNSCC) has yet to be determined. In this study, we isolated ALDH1-positive cells from HNSCC patients and showed that these HNSCC-ALDH1+ cells displayed radioresistance and represented a reservoir for generating tumors. Based on microarray findings, the results of Western blotting and immunofluorescent assays further confirmed that ALDH1+-lineage cells showed evidence of having epithelial-mesenchymal transition (EMT) shifting and endogenously co-expressed Snail. Furthermore, the knockdown of Snail expression significantly decreased the expression of ALDH1, inhibited cancer stem-like properties, and blocked the tumorigenic abilities of CD44+CD24−ALDH1+ cells. Finally, in a xenotransplanted tumorigenicity study, we confirmed that the treatment effect of chemoradiotherapy for ALDH1+ could be improved by Snail siRNA. In summary, it is likely that ALDH1 is a specific marker for the cancer stem-like cells of HNSCC. | [Yu-Chih Chena 1, Yi-Wei Chena d 1, Han-Shui Hsua e 1, Ling-Ming Tsenga e 1, Pin-I Huanga d, Kai-Hsi Lub f, Dow-Tien Chena f, Lung-Kuo Taib f, Ming-Chi Yunga h, Shih-Ching Changa e, Hung-Hai Kub h, Shih-Hwa Chioua c f, Wen-Liang Loc g] | Biochemical and Biophysical Research Communications | 31 July 2009 | |
| sciencedirectS0273117709001999 | Transcriptome profiling in Arabidopsis inflorescence stems grown under hypergravity in terms of cell walls and plant hormones | Land plants rely on lignified secondary cell walls in supporting their body weight on the Earth. Although gravity influences the formation of the secondary cell walls, the regulatory mechanism of their formation by gravity is not yet understood. We carried out a comprehensive analysis of gene expression in inflorescence stems of Arabidopsis thaliana L. using microarray (22 K) to identify genes whose expression is modulated under hypergravity condition (300 g). Total RNA was isolated from the basal region of inflorescence stems of plants grown for 24 h at 300 g or 1 g. Microarray analysis showed that hypergravity up-regulated the expression of 403 genes to more than 2-fold. Hypergravity up-regulated the genes responsible for the biosynthesis or modification of cell wall components such as lignin, xyloglucan, pectin and structural proteins. In addition, hypergravity altered the expression of genes related to the biosynthesis of plant hormones such as auxin and ethylene and that of genes encoding hormone-responsive proteins. Our transcriptome profiling indicates that hypergravity influences the formation of secondary cell walls by modulating the pattern of gene expression, and that auxin and/or ethylene play an important role in signaling hypergravity stimulus. | [D. Tamaokia, I. Karaharaa, T. Nishiuchib, S. De Oliveirac, L. Schreiberc, T. Wakasugia, K. Yamadaa, K. Yamaguchib, S. Kamisakaa] | Advances in Space Research | 15 July 2009 | |
| sciencedirectS0012160609006721 | Comprehensive analysis of molecular signals operating at the medial fusion site of mouse palatal shelves | | [Yuji Taya, Kazuya Fujita, Yuuichi Soeno, Kaori Sato, Takaaki Aoba] | Developmental Biology | 15 July 2009 | |
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| sciencedirectS0167701209001316 | MALDI-TOF mass spectrometry for quantitative gene expression analysis of acid responses in Staphylococcus aureus | Microorganisms are constantly exposed to new and altered growth conditions, and respond by changing gene expression patterns. Several methods for studying gene expression exist. During the last decade, the analysis of microarrays has been one of the most common approaches applied for large scale gene expression studies. A relatively new method for gene expression analysis is MassARRAY, which combines real competitive-PCR and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. In contrast to microarray methods, MassARRAY technology is suitable for analysing a larger number of samples, though for a smaller set of genes. In this study we compare the results from MassARRAY with microarrays on gene expression responses of Staphylococcus aureus exposed to acid stress at pH 4.5. RNA isolated from the same stress experiments was analysed using both the MassARRAY and the microarray methods. The MassARRAY and microarray methods showed good correlation. Both MassARRAY and microarray estimated somewhat lower fold changes compared with quantitative real-time PCR (qRT-PCR). The results confirmed the up-regulation of the urease genes in acidic environments, and also indicated the importance of metal ion regulation. This study shows that the MassARRAY technology is suitable for gene expression analysis in prokaryotes, and has advantages when a set of genes is being analysed for an organism exposed to many different environmental conditions. | [Tone Mari Rodea b, Ingunn Bergetc d, Solveig Langsruda, Trond Møretrøa, Askild Holcka] | Journal of Microbiological Methods | July 2009 | |
| sciencedirectS0925477309000380 | Juvenile hormone regulation of male accessory gland activity in the red flour beetle, Tribolium castaneum | Male accessory gland proteins (Acps) act as key modulators of reproductive success in insects by influencing the female reproductive physiology and behavior. We used custom microarrays and identified 112 genes that were highly expressed in male accessory glands (MAG) in the red flour beetle, Tribolium castaneum. Out of these 112 identified genes, 59 of them contained sequences coding for signal peptide and cleavage site and the remaining 53 contained transmembrane domains. The expression of 14 of these genes in the MAG but not in other tissues of male or female was confirmed by quantitative real-time PCR. In virgin males, juvenile hormone (JH) levels increased from second day post adult emergence (PAE), remained high on third day PAE and declined on fourth day PAE. The ecdysteroid titers were high soon after adult emergence but declined to minimal levels from 1 to 5 days PAE. Feeding of juvenile hormone analog, hydroprene, but not the ecdysteroid analog, RH-2485, showed an increase in size of MAGs, as well as an increase in total RNA and protein content of MAG. Hydroprene treatment also increased the expression of Acp genes in the MAG. RNAi-mediated knock-down in the expression of JHAMT gene decreased the size of MAGs and expression of Acps. JH deficiency influenced male reproductive fitness as evidenced by a less vigor in mating behavior, poor sperm transfer, low egg and the progeny production by females mated with the JH deficient males. These data suggest a critical role for JH in the regulation of male reproduction especially through MAG secretions. | [R. Parthasarathya, A. Tana, Z. Suna, Z. Chenb, M. Rankinb, S.R. Pallia] | Mechanisms of Development | July 2009 | |
| sciencedirectS0890623809000616 | Effect of chronic exposure to the aryl hydrocarbon receptor agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin in female rats on ovarian gene expression ? | The aryl hydrocarbon receptor (AHR) mediates the effects of many endocrine disruptors and contributes to the loss of fertility in polluted environments. Female rats exposed chronically to environmentally relevant doses of the AHR agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) across their lifespan experience accelerated reproductive senescence preceded by ovarian endocrine disruption. The purpose of this study was to determine the changes in ovarian gene expression that accompany the loss of ovarian function caused by chronic exposure to TCDD. Beginning in utero, female Sprague–Dawley rats received TCDD (1, 5, 50, or 200 ng/kg-week; n = 4 per group) or vehicle weekly throughout their lifespan, and were sacrificed on diestrus just prior to loss of reproductive cyclicity at 11 months of age. Microarray analysis was used to determine differences in ovarian gene expression between control and TCDD-treated (200 ng/kg-week) animals. To confirm microarray results, real-time PCR was used to assess changes in gene expression among treatment groups. TCDD treatment decreased (p < 0.05) proestrus serum estradiol concentrations with no effect on serum progesterone. In ovaries from rats treated with 200 ng/kg-week TCDD compared to controls, 19 genes of known function were found to be up-regulated, while 31 ovarian genes were found to be down-regulated ≥1.5-fold (p ≤ 0.05). Gene expression of 17?-hydroxylase decreased following chronic TCDD treatment, suggesting the decrease in estradiol biosynthesis may be a consequence of decreased substrate. Taken together with past studies indicating a lack of effect on hypothalamus or pituitary function, the apparent regulation of key ovarian genes support the hypothesis that chronic TCDD exposure directly affects ovarian function. | [Kelli E. Valdeza b, Zhanquan Shib, Alison Y. Tinga c, Brian K. Petroffa b c] | Reproductive Toxicology | July 2009 | |
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| sciencedirectS1567568809708797 | Abstract: P711 MICROARRAY ANALYSIS OF RAW 264.7 MACROPHAGES SILENCED FOR ORP8 | | [O Beaslas, T Vihervaara, V Olkkonen] | Atherosclerosis Supplements | June 2009 | |
| sciencedirectS0012160609001730 | Estrogen receptor subtype ?2 is involved in neuromast development in zebrafish (Danio rerio) larvae | Estrogens are known to play a role in both reproductive and non-reproductive functions in mammals. Estrogens and their receptors are involved in the development of the central nervous system (brain development, neuronal survival and differentiation) as well as in the development of the peripheral nervous system (sensory-motor behaviors). In order to decipher possible functions of estrogens in early development of the zebrafish sensory system, we investigated the role of estrogen receptor ?2 (ER?2) by using a morpholino (MO) approach blocking er?2 RNA translation. We further investigated the development of lateral line organs by cell-specific labeling, which revealed a disrupted development of neuromasts in morphants. The supporting cells developed and migrated normally. Sensory hair cells, however, were absent in morphants' neuromasts. Microarray analysis and subsequent in situ hybridizations indicated an aberrant activation of the Notch signaling pathway in ER?2 morphants. We conclude that signaling via ER?2 is essential for hair cell development and may involve an interaction with the Notch signaling pathway during cell fate decision in the neuromast maturation process. | [Mirjam Froehlichera, Anja Liedtkea, Ksenia Groha, Hernán López-Schierb, Stephan C.F. Neuhaussc, Helmut Segnerd, Rik I.L. Eggena] | Developmental Biology | 1 June 2009 | |
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| sciencedirectS1567133X09000143 | Effect of fluid flow-induced shear stress on human mesenchymal stem cells: Differential gene expression of IL1B and MAP3K8 in MAPK signaling | Human bone marrow-derived mesenchymal stem cells (MSCs) can differentiate into numerous cell lineages, making them ideal for tissue engineering. Mechanical forces and mechanotransduction are important factors influencing cell responses, although such data are limited for MSCs. We investigated the effect of different profiles of fluid flow-induced shear stress on mitogen-activated protein kinase (MAPK) signaling pathway gene expression in MSCs using DNA microarray and quantitative real-time reverse transcription-PCR analysis. In response to different magnitudes and durations of fluid flow-induced shear stress, we observed significant differential gene expression for various genes in the MAPK signaling pathway. Independent of magnitude and duration, shear stress induced consistent and marked up-regulation of MAP kinase kinase kinase 8 (MAP3K8) and interleukin-1 beta (IL1B) [2-fold to >35-fold, and 4-fold to >50-fold, respectively]. We also observed consistent up-regulation of dual specificity phosphatase 5 and 6, growth arrest and DNA-damage-inducible alpha and beta, nuclear factor kappa-B subunit 1, Jun oncogene, fibroblast growth factor 1, and platelet-derived growth factor alpha. Our data support MAP3K8-induced activation of different MAPK signaling pathways in response to different profiles of shear stress, possibly as a consequence of shear-induced IL1B expression. Thus, MAP3K8 may be an important mediator of intracellular mechanotransduction in human MSCs. | [John R. Glossop, Sarah H. Cartmell] | Gene Expression Patterns | June 2009 | |
| sciencedirectS1672022908600303 | Comparative Analysis of Protein-Protein Interactions in Cancer-Associated Genes | Protein-protein interactions (PPIs) have been widely studied to understand the biological processes or molecular functions associated with different disease systems like cancer. While focused studies on individual cancers have generated valuable information, global and comparative analysis of datasets from different cancer types has not been done. In this work, we carried out bioinformatic analysis of PPIs corresponding to differentially expressed genes from microarrays of various tumor tissues (belonging to bladder, colon, kidney and thyroid cancers) and compared their associated biological processes and molecular functions (based on Gene Ontology terms). We identified a set of processes or functions that are common to all these cancers, as well as those that are specific to only one or partial cancer types. Similarly, protein interaction networks in nucleic acid metabolism were compared to identify the common/specific clusters of proteins across different cancer types. Our results provide a basis for further experimental investigations to study protein interaction networks associated with cancer. The methodology developed in this work can also be applied to study similar disease systems. | [Purnima Gudaa, Sridar V. Chitturb, Chittibabu Gudaa] | Genomics, Proteomics & Bioinformatics | June 2009 | |
| sciencedirectS0047637409000372 | Increased age reduces DAF-16 and SKN-1 signaling and the hormetic response of Caenorhabditis elegans to the xenobiotic juglone | Cells adapt to stressors by activating mechanisms that repair damage and protect them from further injury. Stress-induced damage accumulates with age and contributes to age associated diseases. Increased age attenuates the ability to mount a stress response, but little is known about the mechanisms by which this occurs. To begin addressing this problem, we studied hormesis in the nematode Caenorhabditis elegans. When exposed to a low concentration of the xenobiotic juglone, young worms mount a robust hormetic stress response and survive a subsequent exposure to a higher concentration of juglone that is normally lethal to naïve animals. Old worms are unable to mount this adaptive response. Microarray and RNAi analyses demonstrate that an altered transcriptional response to juglone is responsible in part for the reduced adaptation of old worms. Many genes differentially regulated in young versus old animals are known or postulated to be regulated by the FOXO homologue DAF-16 and the Nrf2 homologue SKN-1. Activation of these pathways is greatly reduced in juglone stressed old worms. DAF-16- and SKN-1-like transcription factors play highly conserved roles in regulating stress resistance and longevity genes. Our studies provide a foundation for developing a molecular understanding of how age affects cytoprotective transcriptional pathways. | [Aaron J. Przybyszb 1, Keith P. Choea c 1, L. Jackson Robertsb 2, Kevin Strangea c 2] | Mechanisms of Ageing and Development | June 2009 | |
| sciencedirectS1567724909000361 | Transcriptional response to mitochondrial NADH kinase deficiency in Saccharomyces cerevisiae | Yeast cells lacking the mitochondrial NADH kinase encoded by POS5 display increased sensitivity to hydrogen peroxide, a slow-growth phenotype, reduced mitochondrial function and increased levels of mitochondrial protein oxidation and mtDNA mutations. Here we examined gene expression in pos5? cells, comparing these data to those from cells containing deletions of superoxide dismutase-encoding genes SOD1 or SOD2. Surprisingly, stress–response genes were down-regulated in pos5?, sod1? and sod2? cells, implying that cells infer stress levels from mitochondrial activity rather than sensing reactive oxygen species directly. Additionally, pos5?, but not sod1 or sod2, cells displayed an anaerobic expression profile, indicating a defect in oxygen sensing that is specific to pos5, and is not a general stress–response. Finally, the pos5? expression profile is quite similar to the hap1? expression profile previously reported, which may indicate a shared mechanism. | [Gregory R. Stuarta, Margaret M. Humblea, Micheline K. Stranda b, William C. Copelanda] | Mitochondrion | June 2009 | |
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| sciencedirectS0361923009000574 | HSP90B1, a thyroid hormone-responsive heat shock protein gene involved in photoperiodic signaling | In order to further advance the understanding of genes involved in avian photoperiodic signaling, a chicken hypothalamic cDNA microarray was made to identify changes in gene expression in the whole hypothalamus of juvenile male domestic chickens after 4 days’ photostimulation. The most robust change was a depression in heat shock protein 90B1 (HSP90B1) expression. This observation was confirmed using quantitative PCR, and it was subsequently demonstrated that the depression in HSP90B1 expression first occurs in the anterior hypothalamus after 1 day's photostimulation, and was also depressed in the anterior and basal hypothalamus after 4 days’ photostimulation. Four days after an intravenous injection of thyroxine (T4), an avian photomimetic, in short day birds, HSP90B1 expression was depressed in the anterior, but not in the basal hypothalamus. Depressed HSP901 expression after photostimulation or T4 treatment was associated with increased GnRH-I mRNA and plasma LH. HSP90B1 is abundant throughout the brain where it occurs in glial cells, and is involved in regulating white matter plasticity. It is suggested that photoperiodically depressed hypothalamic HSP90B1 may affect glial function in photoperiodic signaling pathways in the neuroendocrine system. This is the first report of a thyroid hormone-responsive gene involved in photoperiodic signaling. | [Gemma Graham1, Peter J. Sharp, Qiushi Li3, Peter W. Wilson, Richard T. Talbot, Alison Downing, Timothy Boswell2] | Brain Research Bulletin | 29 May 2009 | |
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| sciencedirectS0012160609001602 | Rasip1 is required for endothelial cell motility, angiogenesis and vessel formation | Ras proteins are small GTPases that regulate cellular growth and differentiation. Components of the Ras signaling pathway have been shown to be important during embryonic vasculogenesis and angiogenesis. Here, we report that Rasip1, which encodes a novel Ras-interacting protein, is strongly expressed in vascular endothelial cells throughout development, in both mouse and frog. Similar to the well-characterized vascular markers VEGFR2 and PECAM, Rasip1 is specifically expressed in angioblasts prior to vessel formation, in the initial embryonic vascular plexus, in the growing blood vessels during angiogenesis and in the endothelium of mature blood vessels into the postnatal period. Rasip1 expression is undetectable in VEGFR2 null embryos, which lack endothelial cells, suggesting that Rasip1 is endothelial specific. siRNA-mediated reduction of Rasip1 severely impairs angiogenesis and motility in endothelial cell cultures, and morpholino knockdown experiments in frog embryos demonstrate that Rasip1 is required for embryonic vessel formation in vivo. Together, these data identify Rasip1 as a novel endothelial factor that plays an essential role in vascular development. | [Ke Xua, Diana C. Chonga, Scott A. Rankinb, Aaron M. Zornb, Ondine Cleavera] | Developmental Biology | 15 May 2009 | |
| sciencedirectS0012160609001535 | Cyclical expression of the Notch/Wnt regulator Nrarp requires modulation by Dll3 in somitogenesis | Delta-like 3 (Dll3) is a divergent ligand and modulator of the Notch signaling pathway only identified so far in mammals. Null mutations of Dll3 disrupt cycling expression of Notch targets Hes1, Hes5, and Lfng, but not of Hes7. Compared with Dll1 or Notch1, the effects of Dll3 mutations are less severe for gene expression in the presomitic mesoderm, yet severe segmentation phenotypes and vertebral defects result in both human and mouse. Reasoning that Dll3 specifically disrupts key regulators of somite cycling, we carried out functional analysis to identify targets accounting for the segmental phenotype. Using microdissected embryonic tissue from somitic and presomitic mesodermal tissue, we identified new genes enriched in these tissues, including Limch1, Rhpn2, and A130022J15Rik. Surprisingly, we only identified a small number of genes disrupted by the Dll3 mutation. These include Uncx, a somite gene required for rib and vertebral patterning, and Nrarp, a regulator of Notch/Wnt signaling in zebrafish and a cycling gene in mouse. To determine the effects of Dll3 mutation on Nrarp, we characterized the cycling expression of this gene from early (8.5 dpc) to late (10.5 dpc) somitogenesis. Nrarp displays a distinct pattern of cycling phases when compared to Lfng and Axin2 (a Wnt pathway gene) at 9.5 dpc but appears to be in phase with Lfng by 10.5 dpc. Nrarp cycling appears to require Dll3 but not Lfng modulation. In Dll3 null embryos, Nrarp displayed static patterns. However, in Lfng null embryos, Nrarp appeared static at 8.5 dpc but resumed cycling expression by 9.5 and dynamic expression at 10.5 dpc stages. By contrast, in Wnt3a null embryos, Nrarp expression was completely absent in the presomitic mesoderm. Towards identifying the role of Dll3 in regulating somitogenesis, Nrarp emerges as a potentially important regulator that requires Dll3 but not Lfng for normal function. | [William Sewella 1, Duncan B. Sparrowb c 1, Allanceson J. Smitha, Dorian M. Gonzalezd, Eric F. Rappaportd, Sally L. Dunwoodieb c e, Kenro Kusumia d f] | Developmental Biology | 15 May 2009 | |
| sciencedirectS0304394009003620 | Ventromedial hypothalamic lesions change the expression of neuron-related genes and immune-related genes in rat liver ? | There are no reports that hypothalamus can directly affect the expression of neuron-related genes and immune-related genes in liver. We identified genes of which expression profiles showed significant modulation in rat liver after ventromedial hypothalamic (VMH) lesions. Total RNA was extracted, and differences in the gene expression profiles between rats at day 3 after VMH lesioning and sham-VMH lesioned rats were investigated using DNA microarray analysis. The result revealed that VMH lesions regulated the genes that were involved in functions related to neuronal development and immunofunction in the liver. Real-time PCR also confirmed that gene expression of SULT4A1 was upregulated, but expression of ACSL1 and CISH were downregulated at day 3 after VMH lesions. VMH lesions may change the expression of neuron-related genes and immune-related genes in rat liver. | [Takayoshi Kibaa, Yuri Kintakaa, Yoko Suzukia, Eiko Nakataa, Yasuhito Ishigakib, Shuji Inouea] | Neuroscience Letters | 8 May 2009 | |
| sciencedirectS1590865808006324 | Inhibition of cell proliferation and invasion in a human colon cancer cell line by 5-aminosalicylic acid | Background5-Aminosalicylic acid lacks the well-known side effects associated with the long-term use of non-steroidal anti-inflammatory drugs. We investigated anti-carcinogenic mechanisms of 5-aminosalicylic acid on a colon cancer cell line.MethodsMTT analysis was performed for various colon cancer cell lines. The expression of NF-?B and metalloproteinases was examined in either HT-29 cells treated with IL-1? and/or 5-aminosalicylic acid. Matrigel assay was used to evaluate invasive potential of HT-29 cells. Analysis of a cDNA microarray containing 8700 genes was performed to identify the alteration of gene expression in response to treatment to 5-aminosalicylic acid.ResultsThe use of MTT analysis showed that 5-aminosalicylic acid suppressed the growth of HT-29 cells. The activity of NF-?B was also decreased by combined-treatment with IL-1? and 5-aminosalicylic acid. The use of an ELISA and zymography demonstrated that MMP-2 and MMP-9 enzyme activity were decreased in HT-29 cells by treatment with various concentration of 5-aminosalicylic acid. A matrigel analysis demonstrated that 5-aminosalicylic acid treatment on HT-29 significantly inhibited the invasiveness of the cells. In cDNA microarray, 163 genes following 5-aminosalicylic acid exposure showed altered expression.ConclusionsThis study indicated that 5-aminosalicylic acid suppresses the growth of human colon cancer cells and is able to inhibit MMPs expression via NF-?B mediated cell signals and invasiveness. | [Y.-H. Kim1, M.H. Kim1, B.J. Kim, J.J. Kim, D.K. Chang, H.J. Son, P.-L. Rhee, J.C. Rhee] | Digestive and Liver Disease | May 2009 | |
| sciencedirectS0013935109000176 | Chronic exposure to high levels of atrazine alters expression of genes that regulate immune and growth-related functions in developing Xenopus laevis tadpoles ? | Atrazine is the most commonly detected pesticide in ground and surface waters, with seasonal spikes that often exceed the Environmental Protection Agency's “Recommended Water Quality Criterion” of 350 parts per billion (ppb). Although numerous studies have shown atrazine produces adverse effects on growth, development, immune and endocrine system functions in a wide range of species, few describe gene expression changes concurrent with atrazine-induced changes in phenotype during development. In this report, developing Xenopus laevis tadpoles were chronically exposed to 400 ppb atrazine, an environmentally relevant concentration. Affymetrix microarrays and Taqman qRT-PCR were used to define gene expression changes that underlie atrazine-induced phenotypic alterations. Atrazine significantly reduced survival and growth (weight, length and fat body size) in male and female tadpoles. Microarray analysis showed atrazine altered expression of 44 genes in male tadpoles (18 upregulated, 26 downregulated) and 77 genes in female tadpoles (23 upregulated, 54 downregulated). Classification of the genes into functional groups showed the majority of genes were associated with the following biological functions: growth and metabolism, proteolysis, fibrinogen complex formation and immune regulation. Seven genes associated with immune system function, specifically defense molecules present in the skin (e.g. magainin II, levitide A, preprocarulein, skin granule protein), were significantly downregulated in female tadpoles. These results support the idea that environmental contaminants such as atrazine compromise important gene pathways during frog development that may, ultimately, be relevant to global amphibian decline. | [Anna Jelaso Langervelda, Ronald Celestinea, Renee Zayaa, Daniel Mihalkob, Charles F. Idea] | Environmental Research | May 2009 | |
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| sciencedirectS1050464809000655 | Immune- and stress-related transcriptomic responses of Solea senegalensis stimulated with lipopolysaccharide and copper sulphate using heterologous cDNA microarrays | The sole, Solea senegalensis, is a common flatfish of Atlantic and Mediterranean waters with a high potential for aquaculture. However, its cultivation is hampered by high sensitivity to different stresses and several infectious diseases. Improving protection from pathogens and stressors is thus a key step in reaching a standardized production. Fish were exposed to lipopolysaccharide (LPS), a mimetic of bacterial infections, and copper sulphate (CuSO4), used in aquaculture to control algae and outbreaks of infectious diseases. We employed a European flounder cDNA microarray to determine the transcriptomic responses of Senegalese sole to these exposures. Microarray analyses showed that many genes were altered in expression following both LPS and copper treatments in comparison to vehicle controls. Gene ontology analysis highlighted copper-specific induction of genes related to cellular adhesion and cell signalling, LPS-specific induction of genes related to the immune response, and a common induction of genes related to unfolded protein binding, intracellular transport/secretion and proteasome. Additionally transcripts for glutathione-S-transferases were down-regulated by LPS, and those for digestive enzymes were down-regulated by both treatments. We selected nine changing genes for absolute quantification of transcript copy numbers by real-time RT-PCR to validate microarray differential expression and to assess inter-individual variability in individual fishes. The quantitative RT-PCR data correlated highly with the microarray results. Overall, data reported provide novel insights into the molecular pathways that could mediate the immune and heavy metal stress responses in Senegalese sole and thus might have biotechnological applications in the culture of this important fish species. | [Inmaculada Osuna-Jiméneza 1, Timothy D. Williamsb 1, María-José Prieto-Álamoa, Nieves Abrila, J. Kevin Chipmanb 2, Carmen Pueyoa 2] | Fish & Shellfish Immunology | May 2009 | |
| sciencedirectS1050464809000837 | Identification and expression analyses of poly [I:C]-stimulated genes in channel catfish (Ictalurus punctatus) | Channel catfish (Ictalurus punctatus) have proven to be an excellent model with which to study immune responses of lower vertebrates. Identification of anti-viral antibodies and cytotoxic cells, as well as both type I and II interferon (IFN), demonstrates that catfish likely mount a vigorous anti-viral immune response. In this report, we focus on other elements of the anti-viral response, and identify more than two dozen genes that are induced following treatment of catfish cells with poly [I:C]. We showed that poly [I:C] induced type I interferon within 2 h of treatment, and that characteristic interferon stimulated genes (ISGs) appeared 6–12 h after exposure. Among the ISGs detected by RT-PCR assay were homologs of ISG15, Mx1, IFN regulatory factor 1 (IRF-1), inhibitor of apoptosis protein-1 (IAP-1) and the chemokine CXCL10. Microarray analyses showed that 13 and 24 cellular genes, respectively, were upregulated in poly [I:C]-treated B cell and fibroblast cultures. Although many of these genes were novel and did not fit the profile of mammalian ISGs, there were several (ISG-15, ubiquitin-conjugating enzyme E2G1, integrin-linked kinase, and clathrin-associated protein 47) that were identified as ISGs in mammalian systems. Taken together, these results suggest that dsRNA, either directly or through the prior induction of IFN, upregulates catfish gene products that function individually and/or collectively to inhibit virus replication. | [Ivanka Milev-Milovanovica, Sai Majjia, Venkata Thodimab, Youping Dengb, Larry Hansonc, Ana Arnizautc, Geoffrey Waldbieserd, V. Gregory Chinchara] | Fish & Shellfish Immunology | May 2009 | |
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| sciencedirectS0198885909000214 | Dendritic cell tolerogenicity: a key mechanism in immunomodulation by vitamin D receptor agonists | Dendritic cells (DC) induce or tolerize T cells, and tolerogenic DCs can promote the development of regulatory T cells (Treg) with suppressive activity. Thus, the possibility of manipulating DCs and enhancing their tolerogenic properties using different pharmacologic or biologic agents could be exploited to control a variety of chronic immuno-mediated inflammatory conditions. Among agents able to promote induction of tolerogenic DCs, vitamin D receptor (VDR) agonists have attracted considerable attention, also because of their potential in clinical translation. DCs are key targets for the immunomodulatory effects of VDR agonists, which shape DC phenotype and function, enhancing their tolerogenicity in adaptive immune responses. Tolerogenic DCs induced by a short treatment with VDR agonists promote CD4+CD25+Foxp3+ Treg cells that are able to mediate transplantation tolerance and to arrest the development of autoimmune diseases. VDR agonists not only favor induction of CD4+CD25+ Treg cells, but can also enhance their recruitment at inflammatory sites. The tolerogenic properties induced by VDR agonists in DCs, leading to enhanced Treg cell development, likely contribute to the beneficial activity of these hormone-like molecules in autoimmune disease and graft rejection models, highlighting their applicability to the treatment of chronic inflammatory conditions sustained by autoreactive or alloreactive immune responses. | [Luciano Adorini, Giuseppe Penna] | Human Immunology | May 2009 | |
| sciencedirectS1570023208008015 | Technical, bioinformatical and statistical aspects of liquid chromatography–mass spectrometry (LC–MS) and capillary electrophoresis-mass spectrometry (CE-MS) based clinical proteomics: A critical assessment ? | The search for biomarkers in biological fluids that can be used for disease diagnosis and prognosis using mass spectrometry has emerged to become a state-of-the-art methodology for clinical proteomics. Poor cross platform comparison of the findings, however, makes the need for comparison studies probably as urgent as the need for new ones. It is now increasingly recognized that standardized statistical and bioinformatics approaches during data processing are of utmost importance for such comparisons. This paper reviews two of the currently most promising methods, namely LC–MS and CE-MS techniques, and software tools used to analyze the huge amount of data they generate. We further review the statistical issues of feature selection and sample classification. | [Mohammed Daknaa, Zengyou Heb, Wei Chuan Yub, Harald Mischaka, Walter Kolchc] | Journal of Chromatography B | 1 May 2009 | |
| sciencedirectS1570023208008842 | Cross-platform Q-TOF validation of global exo-metabolomic analysis: Application to human glioblastoma cells treated with the standard PI 3-Kinase inhibitor LY294002 ? | The reproducibility of a metabolomics method has been assessed to identify changes in tumour cell metabolites. Tissue culture media extracts were analyzed by reverse phase chromatography on a Waters Acquity T3 column with a 13 min 0.1% formic acid: acetonitrile gradient on Agilent and Waters LC-Q-TOF instruments. Features (m/z, RT) were extracted by MarkerLynx™ (Waters) and Molecular Feature Extractor (Agilent) in positive and negative ionization modes. The number of features were similar on both instruments and the reproducibility of ten replicates was <35% signal variability for ∼50% and 40% of all ions detected in positive and negative ionization modes, respectively. External standards spiked to the matrix showed CVs <25% in peak areas within and between days. U87MG glioblastoma cells exposed to the PI 3-Kinase inhibitor LY294002 showed significant alterations of several confirmed features. These included glycerophosphocholine, already shown by NMR to be modulated by LY294002, highlighting the power of this technology for biomarker discovery. | [R. Pandher1, C. Ducruix1, S.A. Eccles, F.I. Raynaud] | Journal of Chromatography B | 1 May 2009 | |
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| sciencedirectS0022282809000522 | Thymosin ?4 mediated PKC activation is essential to initiate the embryonic coronary developmental program and epicardial progenitor cell activation in adult mice in vivo | Hypoxic heart disease is a predominant cause of disability and death worldwide. Since adult mammalian hearts are incapable of regeneration after hypoxia, attempts to modify this deficiency are critical. As demonstrated in zebrafish, recall of the embryonic developmental program may be the key to success. Because thymosin ?4 (TB4) is beneficial for myocardial cell survival and essential for coronary development in embryos, we hypothesized that it reactivates the embryonic developmental program and initiates epicardial progenitor mobilization in adult mammals. We found that TB4 stimulates capillary-like tube formation of adult coronary endothelial cells and increases embryonic endothelial cell migration and proliferation in vitro. The increase of blood vessel/epicardial substance (Bves) expressing cells accompanied by elevated VEGF, Flk-1, TGF-?, Fgfr-2, Fgfr-4, Fgf-17 and ?-Catenin expression and increase of Tbx-18 and Wt-1 positive myocardial progenitors suggested organ-wide recall of the embryonic program in the adult epicardium. TB4 also positively regulated the expression and phosphorylation of myristoylated alanine-rich C-kinase substrate (Marcks), a direct substrate and indicator of protein kinase C (PKC) activity in vitro and in vivo. PKC inhibition significantly reduced TB4 initiated epicardial thickening, capillary growth and the number of myocardial progenitors. Our results demonstrate that TB4 is the first known molecule capable of organ-wide activation of the embryonic coronary developmental program in the adult mammalian heart after systemic administration and that PKC plays a significant role in the process. | [Ildiko Bock-Marquettea b f, Santwana Shrivastavaa, G.C. Teg Pipesb, Jeffrey E. Thatchera, Allissa Blystonea, John M. Sheltonc, Cristi L. Galindod, Bela Meleghf, Deepak Srivastavae, Eric N. Olsonb 1, J. Michael DiMaioa 1] | Journal of Molecular and Cellular Cardiology | May 2009 | |
| sciencedirectS0026286209000041 | Copper chelator ATN-224 inhibits endothelial function by multiple mechanisms | Copper is required for the proliferation of endothelial cells and copper-lowering therapy reduces tumour growth in animal models. It has been reported that ATN-224, a novel copper chelator, potently inhibits the activity of the copper-dependent enzyme superoxide dismutase 1 (SOD1) in endothelial cells. We performed microarray analysis of gene expression in endothelial cells exposed to ATN-224 which revealed upregulation of stress response genes including heme-oxygenase 1 (HO-1) and differential regulation of several genes previously implicated in angiogenesis including CXCR4, ANGP2, PGES2, RHAMM, ITB4 and AQP1 (p < 0.01). These changes were confirmed on qPCR. Treatment of HUVEC with ATN-224 caused increased superoxide levels, phospho-ERK signalling, nuclear NRF1 expression, HO-1 expression and induction of the anti-apoptotic proteins P21, BCL2 and BCLXL. There was also nuclear translocation of SOD1. SOD1 RNA interference replicated the effects of ATN-224 on endothelial cell function but did not cause upregulation of HO-1 or PGES2, suggesting additional mechanisms of action of ATN-224. Downregulation of AQP1, which has been shown to have a role in angiogenesis, was seen with both ATN-224 and SOD1 siRNA. AQP1 expression could be rescued after ATN-224 by added copper. RNA interference to AQP1 inhibited endothelial proliferation and migration, confirming the role of AQP1 in endothelial cell function. Therefore regulation of AQP1 may represent an important action of copper chelation therapy. | [Sarah A. Lowndesa, Helen V. Sheldona, Shijie Caib, Jennifer M. Taylorb, Adrian L. Harrisa] | Microvascular Research | May 2009 | |
| sciencedirectS0168010209000418 | Identification of biomarkers associated with migraine with aura | The diagnosis of migraine can sometimes be difficult because some patients do not fulfill the International Headache Society's criteria for migraine. Hence, an accurate and reliable diagnostic marker for migraine is required. In this study, lymphocytes were used to establish Epstein-Barr virus (EBV)-immortalized lymphoblast cell lines, which were then analyzed using a differential cRNA microarray analysis. The gene expression results were validated using real-time polymerase chain reaction. Gene expression profiling identified 15 genes as being differentially expressed in lymphoblasts originating from patients diagnosed as having migraine with aura (MA). One-fifth of these genes were associated with cytoskeletal proteins. The expressions of seven genes increased significantly by more than 50% of the value in the controls, while the expressions of eight genes decreased significantly by more than 50% of the value in the controls. We also verified that the expression of ?-fodrin, which was 1 of the 15 genes that were differentially expressed in lymphoblasts originating from patients with MA, increased after cortical spreading depression in an animal model. Thus, ?-fodrin might play an important role in the pathophysiology of migraine, possibly serving as a migraine biomarker. | [Eiichiro Nagataa, Hidenori Hattorib, Mamoru Katoc, Saiko Ogasawarad, Shigeaki Suzukib, Mamoru Shibatab, Toshihiko Shimizub, Junichi Hamadae, Takashi Osadab, Rie Takaokab, Masataka Kuwanaf, Tatsuhiko Tsunodac, Sadakazu Aisod, Shunya Takizawaa, Norihiro Suzukib, Shigeharu Takagia] | Neuroscience Research | May 2009 | |
| sciencedirectS0031942209002118 | Effect of tomato pleiotropic ripening mutations on flavour volatile biosynthesis | Ripening is a tightly controlled and developmentally regulated process involving networks of genes, and metabolites that result in dramatic changes in fruit colour, texture and flavour. Molecular and genetic analysis in tomato has revealed a series of regulatory genes involved in fruit development and ripening, including MADS box and SPB box transcription factors and genes involved in ethylene synthesis, signalling and response. Volatile metabolites represent a significant part of the plant metabolome, playing an important role in plant signalling, defence strategies and probably in regulatory mechanisms. They also play an important role in fruit quality. In order to acquire a better insight into the biochemical and genetic control of flavour compound generation and links between these metabolites and the central regulators of ripening, five pleiotropic mutant tomato lines were subjected to volatile metabolite profiling in comparison with wild-type Ailsa Craig. One hundred and seventeen volatile compounds were identified and quantified using SPME (Solid Phase Microextraction) headspace extraction followed by Gas Chromatography–Mass Spectrometry (GC–MS) and the data were subjected to multivariate comparative analysis. We find that the different mutants each produce distinct volatile profiles during ripening. Through principal component analysis the volatiles most dramatically affected are those derived from fatty-acids. The results are consistent with the suggestion that specific isoforms of lipoxygenase located in the plastids and the enzymes that provide precursors and downstream metabolites play a key role in determining volatile composition. | [Katalin Kovácsa, Rupert G. Fraya, Yury Tikunovb, Neil Grahama, Glyn Bradleya, Graham B. Seymoura, Arnaud G. Bovyb, Donald Griersona] | Phytochemistry | May 2009 | |
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| sciencedirectS0006291X09003477 | TRAIL inhibited the cyclic AMP responsible element mediated gene expression | Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) not only causes apoptotic cell death in tumor cells, but also activates some transcription factors and affects several other cellular functions. In this study, we observed the effect of administration of TRAIL on gene expression downstream of the cyclic AMP responsive element (CRE) enhancer by using the signal transduction reporter cis-element plasmid pCRE-d2EGFP. Western blotting showed that after administration of TRAIL, the expression level of reporter protein d2EGFP was down-regulated in NIH3T3 cells. To confirm the TRAIL-induced down-regulation of CRE enhancer controlled gene expression, DNA Chip time series analysis of the intrinsic genes expressed in NIH3T3 cells was carried out. As a result, the expression levels of six genes, which have CRE sequence in their promoter region, were slightly down-regulated within three hours after administration of TRAIL. | [Yasuhito Tokumotoa, Katsuhisa Horimotob, Jun Miyakea c] | Biochemical and Biophysical Research Communications | 17 April 2009 | |
| sciencedirectS0006295209000045 | Gene expression profiling of leukemia T-cells resistant to methotrexate and 7-hydroxymethotrexate reveals alterations that preserve intracellular levels of folate and nucleotide biosynthesis ? | In vitro treatment of human T-cell leukemia cells with 7-hydroxymethotrexate, the major metabolite of methotrexate resulted in acquired resistance as a result of the complete loss of folypolyglutamate synthetase (FPGS) activity. This was in contradistinction to the major modality of antifolate resistance of impaired drug transport in leukemia cells exposed to methotrexate. To identify the genes associated with methotrexate and 7-hydroxymethotrexate resistance, we herein explored the patterns of genome-wide expression profiles in these antifolte-resistant leukemia sublines. mRNA levels of the reduced folate carrier, the primary influx transporter of folates and antifolates, were down-regulated more than two-fold in methotrexate-resistant cells. The dramatic loss of FPGS activity in 7-hydroxymethotrexate-resistant cells was associated with alterations in the expression of various genes aimed at preserving reduced folates and/or enhancing purine nucleotide biosynthesis, e.g. methylene tetrahydrofolate reductase, glycinamide ribonucleotide formyltransferase, adenosine deaminase, cystathionine ? synthase, as well as the ATP-dependent folate exporters BCRP/ABCG2 and MRP1/ABCC1. The observed changes in gene expression were generally not paralleled by acquired DNA copy numbers alterations, suggesting transcriptional regulatory mechanisms. Interestingly, gene expression of DNA/RNA metabolism and transport genes were more profoundly altered in methotrexate-resistant subline, whereas in 7-hydroxymethotrexate-resistant cells, the most profoundly affected groups of genes were those encoding for proteins involved in metabolism and cellular proliferation. Thus, the present investigation provides evidence that 7-hydroxymethotrexate induces gene expression alterations and an antifolate resistance modality that are distinct from its parent drug methotrexate. | [Alan Kambiz Fotoohia 1, Yehuda G. Assarafb 1, Ali Moshfegha 1, Jamileh Hashemic 1, Gerrit Jansend, Godefridus J. Petersd, Catharina Larssonc, Freidoun Albertionia] | Biochemical Pharmacology | 15 April 2009 | |
| sciencedirectS0300483X09000262 | Gene expression profiles in rat lung after inhalation exposure to C60 fullerene particles | Concern over the influence of nanoparticles on human health has risen due to advances in the development of nanotechnology. We are interested in the influence of nanoparticles on the pulmonary system at a molecular level. In this study, gene expression profiling of the rat lung after whole-body inhalation exposure to C60 fullerene (0.12 mg/m3; 4.1 × 104 particles/cm3, 96 nm diameter) and ultrafine nickel oxide (Uf-NiO) particles (0.2 mg/m3; 9.2 × 104 particles/cm3, 59 nm diameter) as a positive control were employed to gain insights into these molecular events. In response to C60 fullerene exposure for 6 h a day, for 4 weeks (5 days a week), C60 fullerene particles were located in alveolar epithelial cells at 3 days post-exposure and engulfed by macrophages at both 3 days and 1 month post-exposures. Gene expression profiles revealed that few genes involved in the inflammatory response, oxidative stress, apoptosis, and metalloendopeptidase activity were up-regulated at both 3 days and 1 month post-exposure. Only some genes associated with the immune system process, including major histocompatibility complex (MHC)-mediated immunity were up-regulated. These results were significantly different from those of Uf-NiO particles which induced high expression of genes associated with chemokines, oxidative stress, and matrix metalloproteinase 12 (Mmp12), suggesting that Uf-NiO particles lead to acute inflammation for the inhalation exposure period, and the damaged tissues were repaired in the post-exposure period. We suggest that C60 fullerene might not have a severe pulmonary toxicity under the inhalation exposure condition. | [Katsuhide Fujitaa, Yasuo Morimotob, Akira Ogamib, Toshihiko Myojyob, Isamu Tanakab, Manabu Shimadac, Wei-Ning Wangc, Shigehisa Endohd, Kunio Uchidad, Tetsuya Nakazatod, Kazuhiro Yamamotoe, Hiroko Fukuia, Masanori Horiea, Yasukazu Yoshidaa, Hitoshi Iwahashia, Junko Nakanishif] | Toxicology | 5 April 2009 | |
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| sciencedirectS0014480008001251 | Betaine prevents Mallory-Denk body formation in drug-primed mice by epigenetic mechanisms | Previous studies showed that S-Adenosylmethionine (SAMe) prevented MDB formation and the hypomethylation of histones induced by DDC feeding. These results suggest that formation of MDBs is an epigenetic phenomenon. To further test this theory, drug-primed mice were fed the methyl donor, betaine, together with DDC, which was refed for 7 days. Betaine significantly reduced MDB formation, decreased the liver/body weight ratio and decreased the number of FAT10 positive liver cells when they proliferate in response to DDC refeeding. Betaine also significantly prevented the decreased expression of BHMT, AHCY, MAT1a and GNMT and the increased expression of MTHFR, caused by DDC refeeding. S-Adenosylhomocysteine (SAH) levels were reduced by DDC refeeding and this was prevented by betaine. The results support the concept that betaine donates methyl groups, increasing methionine available in the cell. SAMe metabolism was reduced by the decrease in GNMT expression, which prevented the conversion of SAMe to SAH. As a consequence, betaine prevented MDB formation and FAT10 positive cell proliferation by blocking the epigenetic memory expressed by hepatocytes. The results further support the concept that MDB formation is the result of an epigenetic phenomenon, where a change in methionine metabolism causes global gene expression changes in hepatocytes. | [Joan Olivaa, Fawzia Bardag-Gorcea, Jun Lia, Barbara A. Frencha, Sheila K. Nguyena, Shelly C. Lub, Samuel W. Frencha] | Experimental and Molecular Pathology | April 2009 | |
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| sciencedirectS0047637408002832 | Whole-genome microarray analysis identifies up-regulation of Nr4a nuclear receptors in muscle and liver from diet-restricted rats | One of the most conserved methods to significantly increase lifespan in animals is through dietary restriction (DR). The mechanisms by which DR increases survival are controversial but are thought to include improvements in mitochondrial function concomitant with reductions in reactive oxygen species production and alterations in the insulin signalling pathway, resulting in global metabolic adaptation. In order to identify novel genes that may be important for lifespan extension of Brown Norway rats, we compared gene expression profiles from skeletal muscle of 28-month-old animals fed ad libitum or DR diets using whole-genome arrays. Following DR, 426 transcripts were significantly down-regulated whilst only 52 were up-regulated. Included in the up-regulated transcripts were three functionally related previously unidentified DR-regulated genes: Nr4a1, Nr4a2, and Nr4a3. Up-regulation of all three Nr4a receptors was also observed in liver – but not brain – of DR-fed animals. Furthermore, RT-PCR revealed up-regulation of several NR4A transcriptional targets (Ucp-3, Ampk-?3, Pgc-1? and Pgc-1?) in skeletal muscle of DR animals. Due to the proposed roles of the NR4A nuclear receptors in sensing and responding to changes in the nutritional environment and in regulating glucose and lipid metabolism and insulin sensitivity, we hypothesise that these proteins may contribute to DR-induced metabolic adaptation. | [Radu C. Oitaa 1, Dawn J. Mazzattia 1, Fei Ling Lima, Jonathan R. Powella, Brian J. Merryb] | Mechanisms of Ageing and Development | April 2009 | |
| sciencedirectS0882401008001678 | Transcriptional responses of Mycobacterium tuberculosis to lung surfactant | This study uses microarray analyses to examine gene expression profiles for Mycobacterium tuberculosis (Mtb) induced by exposure in vitro to bovine lung surfactant preparations that vary in apoprotein content: (i) whole lung surfactant (WLS) containing the complete mixture of endogenous lipids and surfactant proteins (SP)-A, -B, -C, and -D; (ii) extracted lung surfactant (CLSE) containing lipids plus SP-B and -C; (iii) column-purified surfactant lipids (PPL) containing no apoproteins, and (iv) purified human SP-A. Exposure to WLS evoked a multitude of transcriptional responses in Mtb, with 52 genes up-regulated and 23 genes down-regulated at 30 min exposure, plus 146 genes up-regulated and 27 genes down-regulated at 2 h. Notably, WLS rapidly induced several membrane-associated lipases that presumptively act on surfactant lipids as substrates, and a large number of genes involved in the synthesis of phthiocerol dimycocerosate (PDIM), a cell wall component known to be important in macrophage interactions and Mtb virulence. Exposure of Mtb to CLSE, PPL, or purified SP-A caused a substantially weaker transcriptional response (≤20 genes were induced) suggesting that interactions among multiple lipid–protein components of WLS may contribute to its effects on Mtb transcription. | [Ute Schwaba, Kyle H. Rohdea, Zhengdong Wangb, Patricia R. Chessb, Robert H. Notterb c, David G. Russella] | Microbial Pathogenesis | April 2009 | |
| sciencedirectS0161589008008079 | Enhanced transcription of complement and coagulation genes in the absence of adaptive immunity | A recessive nonsense mutation in the zebrafish recombination activating gene 1 (rag1) gene results in defective V(D)J recombination; however, animals homozygous for this mutation (rag1−/−) are reportedly viable and fertile in standard, nonsterile aquarium conditions but display increased mortality after intraperitoneal injection with mycobacteria. Based on their survival in nonsterile environments, we hypothesized that the rag1−/− zebrafish may possess an “enhanced” innate immune response to compensate for the lack of an adaptive immune system. To test this hypothesis, microarray analyses were used to compare the expression profiles of the intestines and hematopoietic kidneys of rag1 deficient zebrafish to the expression profiles of control (heterozygous) siblings. The expression levels of 12 genes were significantly altered in the rag1−/− kidney including the up regulation of a putative interferon stimulated gene, and the down regulation of genes encoding fatty acid binding protein 10, keratin 5 and multiple heat shock proteins. The expression levels of 87 genes were shown to be significantly altered in the rag1−/− intestine; the majority of these differences reflect increased expression of innate immune genes, including those of the coagulation and complement pathways. Subsequent analyses of orthologous coagulation and complement genes in Rag1−/− mice indicate increased transcription of the complement C4 gene in the Rag1−/− intestine. | [Dereje D. Jimaa 1, Radhika N. Shaha b, Timothy M. Orcutta, Deepa Joshic, J. McHugh Lawb d, Gary W. Litmane f g, Nikolaus S. Tredec, Jeffrey A. Yodera b] | Molecular Immunology | April 2009 | |
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| sciencedirectS0969996109000096 | Dopamine depletion induced up-regulation of HCN3 enhances rebound excitability of basal ganglia output neurons | Motor symptoms in Parkinson's disease (PD) are associated with complex changes of firing properties in basal ganglia output neurons (BGON). The abnormalities are generally attributed to altered synaptic input and potential post-synaptic mechanisms are currently unknown. Our cell-type selective transcriptome analyses of BGON in the rat 6-hydroxydopamine (6-OHDA) model of PD identified the ion channel HCN3 as a likely contributor to altered neuronal excitability. Quantitative PCR experiments confirmed the HCN3 upregulation in the rat and mouse 6-OHDA models and also demonstrated selectivity of the effect for HCN3. In accordance with the mRNA expression data, in vitro whole cell patch-clamp recordings in BGON showed increased HCN3 current amplitudes and increased rebound excitability in BGON of 6-OHDA treated rats. These data establish HCN3 up-regulation as a novel candidate mechanism that might contribute to the in vivo changes of electrical activity in basal ganglia output neurons of the parkinsonian brain. | [Bernhard H. Meurersa b, Gustavo Dziewczapolskic 1, Anton Bittnerb, Tao Shib, Fredrik Kammeb, Clifford W. Shultsc 2] | Neurobiology of Disease | April 2009 | |
| sciencedirectS0890623809000239 | Teratogen responsive signaling pathways in organogenesis stage mouse limbs | Teratogen exposure activates damage response pathways during organogenesis that determine the fate of the embryo. Cyclophosphamide, an alkylating agent, induces growth reduction defects in organogenesis stage mouse limbs. Here we identify components of the signaling network triggered by in vitro exposure of CD-1 murine limbs to 4-hydroperoxycyclophosphamide (4-OOHCPA), a preactivated analog of cyclophosphamide. The predominant response was downregulation of gene expression; many of the affected genes were transcription factors, transcription regulators, or oncogenes. Pathway analysis of the genes regulated by 4-OOHCPA exposure revealed a novel damage response pathway in limbs comprised of basic transcription factors, Hif1a, Ndn, Hes1 and Myog, transcription activators and repressors, Egr1 and E2f1, intracellular transducers, effectors and modulators, Bmpr1b and Pea15, and oncogenes and tumor suppressors, Hras1, Abl1, Smad1, and Ttf1. Thus, teratogen exposure triggers both developmentally specific signaling pathways and a general damage response. We hypothesize that hypoxia signaling plays a central role in integrating these responses. | [Chunwei Huang, Barbara F. Hales] | Reproductive Toxicology | April 2009 | |
| sciencedirectS0035378709000241 | Resumes des communications affichees - vendredi 3 avril 2009 | | [] | Revue Neurologique | April 2009 | |
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| sciencedirectS0887233308003111 | Reproducible chemical-induced changes in gene expression profiles in human hepatoma HepaRG cells under various experimental conditions | The use of in vitro human liver cell models is an attractive approach in toxicogenomic studies designed to analyze gene expression changes induced by a toxic chemical. However, in such studies, reliability, reproducibility and interlaboratory concordance of microarrays, as well as the choice of the most suitable cell model, remain a matter of debate. This work was aimed at evaluating the robustness of microarray technologies and the suitability of the highly differentiated human HepaRG cell line in the investigation of gene expression changes induced by a toxic compound in human liver. The influence of various experimental conditions including cell cultures grown at different test sites, different generations of microarrays, RNA analysis platforms and softwares, was tested on gene expression profiles induced by a 20 h treatment with an 8 mM concentration of phenobarbital as the toxic compound. As many as 1099 genes (p-value < 0.01 and 1.5-fold-change), representing 74% and 30% of the signature genes detected with Agilent 22 and 44K pangenomic microarrays, respectively, were shown to be modulated in common in six independently performed experiments. The most modulated genes included both those known to be regulated by phenobarbital, such as cytochromes P450 and membrane transporters, and those involved in oxidative stress, inflammation and apoptosis, typifying a toxic insult. These data provide strong support for the use of a toxicogenomic approach for the in vitro prediction of chemical toxicity, and for the choice of human HepaRG cells as a promising model system for human hepatotoxicity testing. | [Carine B. Lamberta b, Catherine Spirea, Marie-Pierre Renauda, Nancy Claudea, Andre Guillouzob] | Toxicology in Vitro | April 2009 | |
| sciencedirectS004268220800799X | Evidence that selective changes in the lipid composition of raft-membranes occur during respiratory syncytial virus infection | We examined the structure of lipid-raft membranes in respiratory syncytial virus infected cells. Cholesterol depletion studies using methyl-?-cyclodextrin suggested that membrane cholesterol was required for virus filament formation, but not inclusion bodies. In addition, virus filament formation coincided with elevated 3-hydroxy-3-methylglutaryl-coenzyme A reductase expression, suggesting an increase in requirement for endogenous cholesterol synthesis during virus assembly. Lipid raft membranes were examined by mass spectrometry, which suggested that virus infection induced subtle changes in the lipid composition of these membrane structures. This analysis revealed increased levels of raft-associated phosphatidylinositol (PI) and phosphorylated PI during RSV infection, which correlated with the appearance of phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-triphosphate (PIP3) within virus inclusion bodies, and inhibiting the synthesis of PIP3 impaired the formation of progeny virus. Collectively, our analysis suggests that RSV infection induces specific changes in the composition of raft-associated lipids, and that these changes play an important role in virus maturation. | [Dawn Su-Yin Yeoa, Robin Chanb, Gaie Brownc, Li Yinga, Richard Sutejoa, Jim Aitkenc, Boon-Huan Tand, Markus R. Wenkb, Richard J. Sugruea] | Virology | 30 March 2009 | |
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| sciencedirectS0003269708008336 | Stripping custom microRNA microarrays and the lessons learned about probe–slide interactions | Microarrays have been used extensively in gene expression profiling and genotyping studies. To reduce the high cost and enhance the consistency of microarray experiments, it is often desirable to strip and reuse microarray slides. Our genome-wide analysis of microRNA expression involves the hybridization of fluorescently labeled nucleic acids to custom-made, spotted DNA microarrays based on GAPSII-coated slides. We describe here a simple and effective method to regenerate such custom microarrays that uses a very low-salt buffer to remove labeled nucleic acids from microarrays. Slides can be stripped and reused multiple times without significantly compromising data quality. Moreover, our analyses of the performance of regenerated slides identifies parameters that influence the attachment of oligonucleotide probes to GAPSII slides, shedding light on the interactions between DNA and the microarray surface and suggesting ways in which to improve the design of oligonucleotide probes. | [Xiaoxiao Zhanga, Wayne Xub, Jiankang Tana, Yan Zenga c] | Analytical Biochemistry | 15 March 2009 | |
| sciencedirectS0012160608013560 | ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult | Starting with SAGE-libraries prepared from C. elegans FAC-sorted embryonic intestine cells (8E–16E cell stage), from total embryos and from purified oocytes, and taking advantage of the NextDB in situ hybridization data base, we define sets of genes highly expressed from the zygotic genome, and expressed either exclusively or preferentially in the embryonic intestine or in the intestine of newly hatched larvae; we had previously defined a similarly expressed set of genes from the adult intestine. We show that an extended TGATAA-like sequence is essentially the only candidate for a cis-acting regulatory motif common to intestine genes expressed at all stages. This sequence is a strong ELT-2 binding site and matches the sequence of GATA-like sites found to be important for the expression of every intestinal gene so far analyzed experimentally. We show that the majority of these three sets of highly expressed intestinal-specific/intestinal-enriched genes respond strongly to ectopic expression of ELT-2 within the embryo. By flow-sorting elt-2(null) larvae from elt-2(+) larvae and then preparing Solexa/Illumina-SAGE libraries, we show that the majority of these genes also respond strongly to loss-of-function of ELT-2. To test the consequences of loss of other transcription factors identified in the embryonic intestine, we develop a strain of worms that is RNAi-sensitive only in the intestine; however, we are unable (with one possible exception) to identify any other transcription factor whose intestinal loss-of-function causes a phenotype of comparable severity to the phenotype caused by loss of ELT-2. Overall, our results support a model in which ELT-2 is the predominant transcription factor in the post-specification C. elegans intestine and participates directly in the transcriptional regulation of the majority (> 80%) of intestinal genes. We present evidence that ELT-2 plays a central role in most aspects of C. elegans intestinal physiology: establishing the structure of the enterocyte, regulating enzymes and transporters involved in digestion and nutrition, responding to environmental toxins and pathogenic infections, and regulating the downstream intestinal components of the daf-2/daf-16 pathway influencing aging and longevity. | [James D. McGheea, Tetsunari Fukushigeb, Michael W. Krauseb, Stephanie E. Minnemaa, Barbara Goszczynskia, Jeb Gaudeta, Yuji Koharac, Olaf Bossingerd, Yongjun Zhaoe, Jaswinder Khattrae, Martin Hirste, Steven J.M. Jonese, Marco A. Marrae, Peter Ruzanovf, Adam Warnerg, Richard Zapfg, Donald G. Moermang, John M. Kalba 1] | Developmental Biology | 15 March 2009 | |
| sciencedirectS0735109709002423 | Vascular Disease | | [] | Journal of the American College of Cardiology | Supplement | |
| sciencedirectS0303720708005108 | G protein-coupled receptor expression in the adult and fetal adrenal glands | Hormonal regulation of adrenal function occurs primarily through G protein-coupled receptors (GPCR), which may play different roles in fetal vs. adult adrenal glands. In this study, we compared the transcript levels of GPCR between fetal and adult adrenal and found that gonadotropin-releasing hormone receptor (GnRHR), latrophilin 3 receptor, G protein-coupled receptor 37, angiotensin II receptor type 2, latrophilin 2 receptor and melanocortin receptor were expressed at significantly higher levels in fetal adrenal. High GnRHR protein expression was also detected in fetal adrenal using immunohistochemical analysis. To define potential ligand sources for fetal adrenal GnRHR, we demonstrated that GnRH1 mRNA was expressed at high levels in the placenta, while fetal adrenal had high expression of GnRH2. In summary, certain GPCR particularly GnRHR were highly expressed in fetal adrenal and the expression of GnRH mRNA in the placenta and the fetal adrenal raises the possibility of endocrine and/or paracrine/autocrine influences on fetal adrenal function. However, the exact function of GnRHR in fetal adrenal remains to be determined. | [Yewei Xing, Yasuhiro Nakamura, William E. Rainey] | Molecular and Cellular Endocrinology | 5 March 2009 | |
| sciencedirectS0300483X08005763 | Gene expression signatures in peripheral blood cells from Japanese women exposed to environmental cadmium | The objective of this study was to examine the effects of environmental cadmium (Cd) exposure on the gene expression profile of peripheral blood cells, using an original oligoDNA microarray. The study population consisted of 20 female residents in a Cd-polluted area (Cd-exposed group) and 20 female residents in a non-Cd-polluted area individually matched for age (control group). The mRNA levels in Cd-exposed subjects were compared with those in respective controls, using a microarray containing oligoDNA probes for 1867 genes. Median Cd concentrations in blood (3.55 ?g/l) and urine (8.25 ?g/g creatinine) from the Cd-exposed group were 2.4- and 1.9-times higher than those of the control group, respectively. Microarray analysis revealed that the Cd-exposed group significantly up-regulated 137 genes and down-regulated 80 genes, compared with the control group. The Ingenuity Pathway Analysis Application (IPA) revealed that differentially expressed genes were likely to modify oxidative stress and mitochondria-dependent apoptosis pathways. Among differentially expressed genes, the expression of five genes was positively correlated with Cd concentrations in blood or urine. Quantitative real-time PCR (RT-PCR) analysis validated the significant up-regulation of CASP9, TNFRSF1B, GPX3, HYOU1, SLC3A2, SLC19A1, SLC35A4 and ITGAL, and down-regulation of BCL2A1 and COX7B. After adjustment for differences in the background characteristics of the two groups, we finally identified seven Cd-responsive genes (CASP9, TNFRSF1B, GPX3, SLC3A2, ITGAL, BCL2A1, and COX7B), all of which constituted a network that controls oxidative stress response by IPA. These seven genes may be marker genes useful for the health risk assessment of chronic low level exposure to Cd. | [Satoru Dakeshitaa, Tomoko Kawaib, Hirokazu Uemuraa, Mineyoshi Hiyoshia, Etsuko Ogumac, Hyogo Horiguchic, Fujio Kayamac, Keiko Aoshimad, Satoshi Shirahamae, Kazuhito Rokutanb, Kokichi Arisawaa] | Toxicology | 4 March 2009 | |
| sciencedirectS1011134408002297 | Effects of linear polarized infrared light irradiation on the transcriptional regulation of IL-8 expression in IL-1?-stimulated human rheumatoid synoviocytes involves phosphorylation of the NF-?B RelA subunit | Although recent clinical studies have shown that laser therapy acts as an anti-inflammatory effector in the treatment of some diseases, little is known about the mechanism by which it acts in rheumatoid arthritis (RA) patients. The purpose of our work was to examine how irradiation with linear polarized infrared light (LPIL) suppresses inflammatory responses in the MH7A rheumatoid fibroblast-like synoviocyte cell line. We initially confirmed the effects of two disease-modifying anti-rheumatic treatments, LPIL irradiation and dexamethasone (Dex) administration, under experimental inflammatory conditions using gene chip technology. We found that LPIL exerted a smaller effect on gene transcription than Dex; however, IL-1?-inducible target genes such as the CXCL type chemokines IL-8, IL-1? and IL-6 were all clearly suppressed by LPIL to the same degree as by Dex. We also found that IL-1?-induced release of IL-8 from MH7A cells was completely blocked by pretreatment with the (IL-8) inhibitor Bay11-7085, indicating that activation of NF-?B signaling plays an important role in the secretion of IL-8. Although the levels of NFKB1 and RELA transcription were unaffected by IL-1? stimulation, phosphorylation of RelA S276 was suppressed by both LPIL and Dex. Thus LPIL likely exerts its anti-inflammatory effects by inhibiting the release of the inflammatory chemokine IL-8. A fuller understanding of the anti-inflammatory mechanism of LPIL in rheumatoid synoviocytes could serve as the basis for improved treatment of RA patients in the future. | [Yasuko Shibataa, Hidefumi Arakia, Toshiyuki Oshitania, Asayo Imaokaa b, Masaru Matsuib, Keiji Miyazawac, Yoshimitsu Abikoa] | Journal of Photochemistry and Photobiology B: Biology | 3 March 2009 | |
| sciencedirectS0306452208017582 | Cognitive performance and age-related changes in the hippocampal proteome | Declining cognitive performance is associated with increasing age, even in the absence of overt pathological processes. We and others have reported that declining cognitive performance is associated with age-related changes in brain glucose utilization, long-term potentiation and paired-pulse facilitation, protein expression, neurotransmitter levels, and trophic factors. However, it is unclear whether these changes are causes or symptoms of the underlying alterations in dendritic and synaptic morphology that occur with age. In this study, we examined the hippocampal proteome for age- and cognition-associated changes in behaviorally stratified young and old rats, using two-dimensional in-gel electrophoresis and MS/MS. Comparison of old cognitively intact with old cognitively impaired animals revealed additional changes that would not have been detected otherwise. Interestingly, not all age-related changes in protein expression were associated with cognitive decline, and distinct differences in protein expression were found when comparing old cognitively intact with old cognitively impaired rats. A large number of protein changes with age were related to the glycolysis/gluconeogenesis pathway. In total, the proteomic changes suggest that age-related alterations act synergistically with other perturbations to result in cognitive decline. This study also demonstrates the importance of examining behaviorally-defined animals in proteomic studies, as comparison of young to old animals regardless of behavioral performance would have failed to detect many cognitive impairment–specific protein expression changes evident when behavioral stratification data were used. | [W.M. Freemana, H.D. VanGuildera, C. Bennettb, W.E. Sonntagc] | Neuroscience | 3 March 2009 | |
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| sciencedirectS1087184508001552 | Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics | The saprobic fungus Aspergillus niger is an efficient producer of a suite of extracellular enzymes involved in carbohydrate modification and degradation. Genome mining has resulted in the prediction of at least 39 genes encoding enzymes involved in the depolymerisation of the backbone of pectin. Additional genes, encoding enzymatic activities required for the degradation of the arabinan and arabinogalactan side chains were predicted as well. DNA microarray analysis was used to study the condition-dependent expression of these genes, and to generate insights in possible synergistic interactions between the individual members of the pectin degrading enzyme network. For this purpose, A. niger was grown on sugar-beet pectin and on galacturonic acid, rhamnose and xylose, the main monomeric sugar constituents of pectin. An analysis of the corresponding transcriptomes revealed expression of 46 genes encoding pectinolytic enzymes. Their transcriptional profiles are discussed in detail and a cascade model of pectin degradation is proposed. | [Elena S. Martens-Uzunova, Peter J. Schaap] | Fungal Genetics and Biology | Supplement | |
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| sciencedirectS1074742708001834 | The effects of acute 17?-estradiol treatment on gene expression in the young female mouse hippocampus | Previous studies have demonstrated that treatment with 17?-estradiol (E2) improves both spatial and nonspatial memory in young female mice. Still unclear, however, are the molecular mechanisms underlying the beneficial effects of E2 on memory. We have previously demonstrated that a single post-training intraperitoneal (i.p.) injection of 0.2 mg/kg E2 can enhance hippocampal-dependent spatial and object memory consolidation (e.g., Gresack & Frick, 2006b). Therefore, in the present study, we performed a microarray analysis on the dorsal hippocampi of 4-month-old female mice injected i.p. with vehicle or 0.2 mg/kg E2. Genes were considered differentially expressed following E2 treatment if they showed a greater than 2-fold change in RNA expression levels compared to controls. Overall, out of a total of approximately 25,000 genes represented on the array, 204 genes showed altered mRNA expression levels upon E2 treatment, with 111 up-regulated and 93 down-regulated. Of these, 17 of the up-regulated and 6 of the down-regulated genes are known to be involved in learning and memory. mRNA expression changes in 5 of the genes were confirmed by real-time quantitative PCR analysis, and protein changes in these same genes were confirmed by Western blot analysis: Hsp70, a heat shock protein known to be estrogen responsive; Igfbp2, an IGF-I binding protein; Actn4, an actin binding protein involved in protein trafficking; Tubb2a, the major component of microtubules; and Snap25, a synaptosome-specific protein required for neurotransmitter release. The types of genes altered indicate that E2 may induce changes in the structural mechanics of cells within the dorsal hippocampus that could be conducive to promoting memory consolidation. | [Angela S. Pecheninoa, Karyn M. Fricka b] | Neurobiology of Learning and Memory | March 2009 | |
| sciencedirectS0168010208002964 | Impaired neurogenesis in embryonic spinal cord of Phgdh knockout mice, a serine deficiency disorder model | Mutations in the d-3-phosphoglycerate dehydrogenase (PHGDH; EC 1.1.1.95) gene, which encodes an enzyme involved in de novol-serine biosynthesis, are shown to cause human serine deficiency disorder. This disorder has been characterized by severe neurological symptoms including congenital microcephaly and psychomotor retardation. Our previous work demonstrated that targeted disruption of mouse Phgdh leads to a marked decrease in serine and glycine, severe growth retardation of the central nervous system, and lethality after embryonic day 13.5. To clarify how a serine deficiency causes neurodevelopmental defects, we characterized changes in metabolites, gene expression and morphological alterations in the spinal cord of Phgdh knockout mice. BeadChip microarray analysis revealed significant dysregulation of genes involved in the cell cycle. Ingenuity Pathway Analysis also revealed a significant perturbation of regulatory networks that operate in the cell cycle progression. Moreover, morphological examinations of the knockout spinal cord demonstrated a marked deficit in dorsal horn neurons. Radial glia cells, native neural stem/progenitor cells, accumulated in the dorsal ventricular zone, but they did not proceed to a G0-like quiescent state. The present integrative study provides in vivo evidence that normal cell cycle progression and subsequent neurogenesis of radial glia cells are severely impaired by serine deficiency. | [Yuriko Kawakamia c, Kazuyuki Yoshidae g, Jung Hoon Yanga c, Takeshi Suzukia d, Norihiro Azumae, Kazuhisa Sakaih, Tsutomu Hashikawah, Masahiko Watanabef, Kaori Yasudad i, Satoru Kuharab d, Yoshio Hirabayashig j, Shigeki Furuyaa c g] | Neuroscience Research | March 2009 | |
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| sciencedirectS0960076009000065 | Use of global gene expression patterns in mechanistic studies of oestrogen action in MCF7 human breast cancer cells ? | Over the years, the MCF7 human breast cancer cell line has provided a model system for the study of cellular and molecular mechanisms in oestrogen regulation of cell proliferation and in progression to oestrogen and antioestrogen independent growth. Global gene expression profiling has shown that oestrogen action in MCF7 cells involves the coordinated regulation of hundreds of genes across a wide range of functional groupings and that more genes are downregulated than upregulated. Adaptation to long-term oestrogen deprivation, which results in loss of oestrogen-responsive growth, involves alterations to gene patterns not only at early time points (0–4 weeks) but continuing through to later times (20–55 weeks), and even involves alterations to patterns of oestrogen-regulated gene expression. Only 48% of the genes which were regulated ≥2-fold by oestradiol in oestrogen-responsive cells retained this responsiveness after long-term oestrogen deprivation but other genes developed de novo oestrogen regulation. Long-term exposure to fulvestrant, which resulted in loss of growth inhibition by the antioestrogen, resulted in some very large fold changes in gene expression up to 10,000-fold. Comparison of gene profiles produced by environmental chemicals with oestrogenic properties showed that each ligand gave its own unique expression profile which suggests that environmental oestrogens entering the human breast may give rise to a more complex web of interference in cell function than simply mimicking oestrogen action at inappropriate times. | [A.J. Sadler, D. Pugazhendhi, P.D. Darbre] | The Journal of Steroid Biochemistry and Molecular Biology | March 2009 | |
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| sciencedirectS004268220800723X | Differential HIV-1 integration targets more actively transcribed host genes in neonatal than adult blood mononuclear cells | We have recently shown an increased HIV-1 replication and gene expression in neonatal (cord) blood mononuclear cells compared with adult cells, which could be due to HIV-1 integration as it targets active host genes. Here we have characterized 468 HIV-1 integration sites within cord and adult blood T-lymphocytes and monocyte-derived macrophages (MDM) from five donors. Several functional classes of genes were identified by gene ontology to be over represented, including genes for cellular components, maintenance of intracellular environment, enzyme regulation, cellular metabolism, catalytic activity and cation transport. Numerous potential transcription factor binding sites at the sites of integration were identified. Furthermore, the genes at the site of integration, transcription factors which potentially bind upstream of the HIV-1 promoter and factors that assist HIV-1 integration were found to be expressed at higher levels in cord than adult cells. Taken together, these results suggest HIV-1 integration occurred in a more actively transcribed genes in neonatal cells compared with adult cells, which may help explain a higher level of HIV-1 gene expression and replication in neonatal compared with adult cells. | [Brian P. Wellensiek1, Rajesh Ramakrishnan2, Vasudha Sundaravaradan3, Roshni Mehta4, David T. Harris, Nafees Ahmad] | Virology | 1 March 2009 | |
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| sciencedirectS0303720708005273 | The farnesoid X receptor regulates transcription of 3?-hydroxysteroid dehydrogenase type 2 in human adrenal cells | Recent studies have shown that the adrenal cortex expresses high levels of farnesoid X receptor (FXR), but its function remains unknown. Herein, using microarray technology, we tried to identify candidate FXR targeting genes in the adrenal glands, and showed that FXR regulated 3?-hydroxysteroid dehydrogenase type 2 (HSD3B2) expression in human adrenocortical cells. We further demonstrated that FXR stimulated HSD3B2 promoter activity and have defined the cis-element responsible for FXR regulation of HSD3B2 transcription. Transfection of H295R adrenocortical cells with FXR expression vector effectively increased FXR expression levels and additional treatment with chenodeoxycholic acid (CDCA) caused a 25-fold increase in the mRNA for organic solute transporter alpha (OST?), a known FXR target gene. HSD3B2 mRNA levels also increased following CDCA treatment in a concentration-dependent manner. Cells transfected with a HSD3B2 promoter construct and FXR expression vector responded to CDCA with a 20-fold increase in reporter activity compared to control. Analysis of constructs containing sequential deletions of the HSD3B2 promoter suggested a putative regulatory element between −166 and −101. Mutation of an inverted repeat between −137 and −124 completely blocked CDCA/FXR induced reporter activity. Chromatin immunoprecipitation assays further confirmed the presence of a FXR response element in the HSD3B2 promoter. In view of the emerging role of FXR agonists as therapeutic treatment of diabetes and certain liver diseases, the effects of such agonists on other FXR expressing tissues should be considered. Our findings suggest that in human adrenal cells, FXR increases transcription and expression of HSD3B2. Alterations in this enzyme would influence the capacity of the adrenal gland to produce corticosteroids. | [Yewei Xinga 1, Karla Saner-Amighb 1, Yasuhiro Nakamuraa, Margaret M. Hinshelwoodb, Bruce R. Carrb, J. Ian Masonc, William E. Raineya] | Molecular and Cellular Endocrinology | 27 February 2009 | |
| sciencedirectS0006899308029995 | Hippocampal gene expression changes during age-related cognitive decline | As humans age, cognitive performance decreases differentially across individuals. This age-related decline in otherwise healthy individuals is likely due to the interaction of multiple factors including genetics and environment. We hypothesized that altered spatial memory performance in genetically similar mice could be in part due to differential gene expression patterns in the hippocampus. To investigate this we utilized Morris water maze (MWM) testing in a group of young (3 months) and aged (24 months) C57BL/J male mice. Two sub-groups were identified in the aged animals; one in which MWM performance was not significantly different when compared to the young animals (aged-unimpaired; “AU”) and one in which performance was significantly different by 1.5 standard deviations from the mean (aged-impaired; “AI”). One week after testing was completed the entire hippocampus was collected from six each of AU, AI and young mice and their gene expression profiles were compared using Affymetrix microarrays. Benjamini and Hochberg FDR correction at p < 0.05 identified 18 genes differentially expressed between the AI and AU mice. The correlation between behavioral deficits and gene expression patterning allows a better understanding of how altered gene expression in the hippocampus contributes to accelerated age-related cognitive decline and delineates between gene expression changes associated with normal aging vs. memory performance. | [Traci L. Pawlowskia, Linda L. Bellushb, Amy W. Wrightb, Jon P. Walkerb, Robert A. Colvinb, Matthew J. Huentelmana] | Brain Research | | |
| sciencedirectS0165027008005773 | Gene expression profiling of individual hypothalamic nuclei from single animals using laser capture microdissection and microarrays | In order to identify novel genes involved in appetite and body weight regulation we have developed a microarray based method suitable for detecting small changes in gene expression in discrete groups of hypothalamic neurons. The method is based on a combination of stereological sampling, laser capture microdissection (LCM), PCR based amplification (SuperAmp™), and one-color cDNA microarray analysis.To validate the method we assessed and compared fasting induced changes in mRNA levels of Neuropeptide Y (NPY) and proopiomelanocortin (POMC) in the hypothalamic arcuate nucleus (ARC) of diet-induced obese rats using cDNA microarrays, quantitative PCR and in situ hybridization. All methods revealed statistically significant fasting-induced changes in NPY and POMC expression. An additional 3480 differentially expressed probes (fold change >1.22, t-test p = 0.05) were identified in the microarray analysis.Our findings demonstrate a consistent gene expression pattern across three different gene expression detection methods and strongly suggest that LCM coupled microarray analysis combined with SuperAmp™ can be used as a semi-quantitative mRNA profiling tool. Importantly, the sensitivity of the method greatly improves the usefulness of the microarray technology for gene expression profiling in non-homogeneous tissues such as the brain. | [Sarah Juel Paulsena b, Leif Kongskov Larsena, Jacob Jelsinga, Uwe Janßenc, Bernhard Gerstmayerc, Niels Vranga] | Journal of Neuroscience Methods | 15 February 2009 | |
| sciencedirectS0009279708005759 | Gene expression profiles in HPV-immortalized human cervical cells treated with the nicotine-derived carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone | Human papillomavirus (HPV) infection is an established etiological factor for cervical cancer. Epidemiological studies suggest that smoking in combination with HPV infection plays a significant role in the etiology of this disease. We have previously shown that the tobacco carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), is present in human cervical mucus. Here, we hypothesized that treatment of HPV-16-immortalized human ectocervical cells (Ecto1/E6E7) with NNK would alter the expression of genes involved in cellular transformation. Ecto1/E6E7 cells were treated with water (vehicle control) alone or with 1 ?M, 10 ?M, and 100 ?M of NNK in water for 12 weeks. The colony-forming efficiency increased following NNK treatment; the maximum effect was observed after 12 weeks with 100 ?M NNK. Microarray analysis revealed that, independent of the dose of NNK, expression of 30 genes was significantly altered; 22 of these genes showed a dose–response pattern. Genes identified are categorized as immune response (LTB4R), RNA surveillance pathway (SMG1), metabolism (ALDH7A1), genes frequently expressed in later stages of neoplastic development (MT1F), DNA binding (HIST3H3 and CHD1L), and protein biosynthesis (UBA52). Selected genes were confirmed by qRT-PCR. Western blot analysis indicates that phosphorylation of histone 3 at serine 10, a marker of cellular transformation, was up-regulated in cells treated with NNK. This is the first study showing that NNK can alter gene expression that may, in part, account for transformation of HPV-immortalized human cervical cells. The results support previous epidemiological observations that, in addition to HPV, tobacco smoking also plays an important role in the development of cervical cancer. | [Bogdan Prokopczyka, Indu Sinhab, Neil Trushina, Willard M. Freemana, Karam El-Bayoumyb] | Chemico-Biological Interactions | 12 February 2009 | |
| sciencedirectS1002007108003390 | A novel methodology for finding the regulation on gene expression data | DNA microarray technology is a high throughput and parallel technique for genomic investigation due to its advantages of simultaneously surveying features of large scales complex data in biology. This paper aims to find feature subset to build the classifier for gene expression data analysis. At first, K-means clustering algorithm was carried out on the dataset of yeast cell cycle. Based on Rand calculation, a statistical method was used to pick out the data points (genes) for classifier design. Meanwhile, the principal component analysis was applied to help to construct the classifier. For the validation of classifier built and prediction of a target subset of genes, discriminant analysis in terms of partial least square regression and artificial neural network were also performed. | [Wei Liua, Bo Wanga, Jarka Glasseyb, Elaine Martinb, Jian Zhaoa] | Progress in Natural Science | 10 February 2009 | |
| sciencedirectS0378427408013362 | Contribution of methylmercury, polychlorinated biphenyls and organochlorine pesticides to the toxicity of a contaminant mixture based on Canadian Arctic population blood profiles | Human populations are simultaneously exposed to a variety of anthropogenic contaminants. However, despite extensive literature on animal exposure to single compounds, data on the toxicity of complex mixtures are scarce. The Northern Contaminant Mixture (NCM) was formulated to contain the 27 most abundant contaminants in the same relative proportions found in the blood of Canadian Arctic populations. Sprague–Dawley rat dams were dosed from the first day of gestation until weaning with methylmercury (MeHg), polychlorinated biphenyls (PCBs) or organochlorines pesticides (OCs) administered either separately or together in the NCM. An additional control group for hypothyroxinemia was included by dosing dams with the goitrogen 6-propyl-2-thiouracil (PTU). Offspring growth, survival, serum thyroxine and Thyroid Stimulating Hormone (TSH) levels, thyroid gland morphology, brain taurine content and cerebellum and hippocampus protein expression patterns resulting from such exposures were monitored. Pups’ increased mortality rate and impaired growth observed in the NCM treatment group were attributed to MeHg, while decreased circulating thyroxine levels and perturbations of thyroid gland morphology were mostly attributable to PCBs. Interestingly, despite comparable reduction in serum thyroxine levels, PCBs and PTU exposures produced markedly different effects on pup's growth, serum TSH level and brain taurine content. Analysis of cerebellum and hippocampus protein expression patterns corroborated previous cerebellum gene expression data, as contaminant co-exposure in the NCM significantly masked the effects of individual components on protein two-dimensional electrophoresis patterns. Identification by MALDI-TOF/TOF MS of differentially expressed proteins involved notably in neuronal and mitochondrial functions provided clues on the cellular and molecular processes affected by these contaminant mixtures. | [Guillaume Pelletiera, Sheila Massona, Mike J. Wadea, Jamie Nakaia, Ramona Alwisa, Susantha Mohottalageb, Premkumari Kumarathasanb, Paleah Blacka, Wayne J. Bowersa, Ih Chua, Renaud Vincenta] | Toxicology Letters | 10 February 2009 | |
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| sciencedirectS0006899308025560 | Genomic response of the rat brain to global ischemia and reperfusion | To identify genes that are involved in ischemia response of the brain, we have evaluated changes of gene expression in rat cerebrum after 15 min complete global ischemia, followed by reperfusion for 1 h, 6 h or 24 h. The expression profiles of ∼ 30,000 transcripts from three subjects in each group (including sham-operated controls) were monitored employing oligonucleotide microarrays. About 20,000 transcripts were detectable in rat brains. The levels of 576 transcripts (∼ 2.9%) were significantly altered in response to experimental ischemia. 419 transcripts were up- and 157 downregulated; 39 transcripts changed after 1 h reperfusion, 174 after 6 h and 462 after 24 h. Results from quantitative real-time reverse transcription PCR of 18 selected genes showed excellent agreement with the microarray data. There is surprisingly little overlap between gene regulation patterns at different reperfusion times (only seven genes displayed significant changes in transcript levels at all reperfusion times. Several genes that were previously unknown to be involved in ischemia-response have been identified. Analyses of gene ontology patterns and the most strongly regulated transcripts showed that the immediate response to an ischemia/reperfusion is mediated by the induction of specific transcription factors and stress genes. Delayed gene expression response is characterised by inflammation and immune-related genes. These results support the hypothesis that the brain's response to ischemia is an active, specific and coordinated process. | [Fabian Büttnera 1, Christian Cordesb 1, Frank Gerlachc 1, Axel Heimannb, Beat Alessandrib, Ulrich Luxemburgerd, Özlem Türecid, Thomas Hankelne, Oliver Kempskib, Thorsten Burmesterc] | Brain Research | | |
| sciencedirectS1874939908002526 | Stable Argonaute2 overexpression differentially regulates microRNA production | microRNAs are a class of small RNA molecules that associate with Argonaute proteins to regulate gene expression. Argonaute proteins not only mediate the functions of microRNAs, but also play an essential role in the biogenesis of microRNAs. Here, we report that stable, long-term overexpression of Argonaute2, an Argonaute isoform, induces the production of a number of microRNAs, such as the let-7 family of microRNAs, in 293T cells. On the other hand, the expression of many microRNAs is insensitive to elevated Argonaute levels, and microRNAs in the miR-17-92 and homologous clusters are even down-regulated. The down-regulation may result from the let-7-mediated inhibition of the expression of Myc, which positively controls the transcription of the microRNAs clusters. Our data suggest that human cells have a mechanism for microRNA homeostasis, and that overexpression of a general microRNA processing factor can differentially regulate the expression of specific microRNAs. | [Xiaoxiao Zhanga, Paul R. Gravesb, Yan Zenga c] | Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms | February 2009 | |
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| sciencedirectS1521661608008127 | Hyperexpression of NOD2 in intestinal mast cells of Crohn's disease patients: Preferential expression of inflammatory cell-recruiting molecules via NOD2 in mast cells | NOD2, an intracellular sensor of bacteria-derived muramyl dipeptide (MDP) has been implicated as a key player in intestinal immune health and disease. Mast cells (MCs) have been reported to be increased in the gut of patients with inflammatory bowel disease. However, NOD2 expression and its role in human primary MCs are unknown. The number of NOD2+ intestinal MCs was significantly increased in the Crohn's disease (CD) specimens compared to Ulcerative colitis (UC) specimens and controls. IFN-? upregulated NOD2 expression in MCs. CXCL10 and urokinase-type plasminogen activator (uPA) upregulation was specific to MCs activated by MDP compared to MCs activated by LPS and IgE/anti-IgE. MDP-induced upregulation of ICAM-1, VCAM-1, and uPA was specific to MCs compared to mononuclear cells. The number of CXCL10+NOD2+ intestinal MCs was significantly increased in the CD patients. Our results suggest that NOD2+ MCs have specific pathogenic roles that involve the recruitment of inflammatory cells in CD. | [Shigeru Okumurab 1 2, Keisuke Yukia 1, Ryota Kobayashic, Shinichi Okamurac, Kazumitsu Ohmorid, Hirohisa Saitoe, Chisei Raa, Yoshimichi Okayamaa] | Clinical Immunology | February 2009 | |
| sciencedirectS0145305X08002000 | Expression profiles of cloned channel catfish (Ictalurus punctatus) lymphoid cell lines and mixed lymphocyte cultures | Clonal channel catfish lymphoid cell lines and mixed lymphocyte cultures (MLCs) have proven extremely useful in examining immune responses at the cellular and molecular levels. To date clonal catfish cell lines and MLCs have been biologically and phenotypically characterized using a variety of techniques including reverse transcription polymerase chain reaction (RT-PCR), as well as Northern and Southern blotting. To expand the molecular characterization of these cultures, microarray analysis was employed. Clonal B (3B11), macrophage (42TA), and cytotoxic T cell (TS32.15 and TS32.17) lines and MLCs were examined using a cDNA array containing ∼2500 probes derived from EST libraries prepared from the 42TA macrophage cell line, a MLC, and 5–14-day-old catfish fry. Analysis showed that each cell line displayed a unique RNA expression profile that included a variety of immune-related genes. Pearson correlation analysis indicated that one cytotoxic T cell line (TS32.15) clustered with the MLC, whereas a second cytotoxic T cell line (TS32.17) was more closely associated with a second cluster containing B cells and macrophages. This study illustrates the utility of microarray analyses in profiling RNA expression patterns in catfish lymphoid cell lines and will serve as a platform for examining catfish immune responses following virus infection or poly [I:C] treatment. | [S. Majjia, V. Thodimab, A. Arnizautc, Y. Dengb, W. Mayd, D. Sittmane, G.C. Waldbieserf, L. Hansonc, M.A. Cuchensa, E. Bengtena, V.G. Chinchara] | Developmental & Comparative Immunology | February 2009 | |
| sciencedirectS0301468108000169 | Developmental pathways during in vitro progression of human islet neogenesis | Islet neogenesis, or the differentiation of islet cells from precursor cells, is seen in vitro and in vivo both embryonically and after birth. However, little is known about the differentiation pathways during embryonic development for human pancreas. Our previously reported in vitro generation of islets from human pancreatic tissue provides a unique system to identify potential markers of neogenesis and to determine the molecular mechanisms underlying this process. To this end, we analyzed the gene expression profiles of three different stages during in vitro islet generation: the Initially Adherent, Expanded, and Differentiated stages. Samples from four human pancreases were hybridized to Affymetrix U95A GeneChips, and data analyzed using GeneSpring 7.0/9.0 software. Using scatter plots we selected genes with a 2-fold or greater differential expression. Of the 12,000 genes/ESTs present on these arrays, 295 genes including 38 acinar-enriched genes were selectively lost during the progression from the Initially Adherent stage to the Expanded stage; 468 genes were increased in this progression to Expanded tissue; and 529 genes had a two-fold greater expression in the Differentiated stage than in the Expanded tissue. Besides the expected increases in insulin, glucagon, and duct markers (mucin 6, aquaporin 1 and 5), the beta cell auto-antigen IA-2/phogrin was increased 5-fold in Differentiated. In addition, developmentally important pathways, including notch/jagged, Wnt/frizzled, TGF? superfamily (follistatin, BMPs, and SMADs), and retinoic acid (COUP-TFI, CRABP1, 2, and RAIG1) were differentially regulated during the expansion/differentiation. Two putative markers for islet precursor cells, UCHL1/PGP9.5 and DMBT1, were enhanced during the progression to differentiated cells, but only the latter could be a marker of islet precursor cells. We suggest that appropriate manipulation of these differentiation-associated pathways will enhance the efficiency of differentiation of insulin-producing ?-cells in this in vitro model. | [Rikke Dodge, Cindy Loomans, Arun Sharma, Susan Bonner-Weir] | Differentiation | February 2009 | |
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| sciencedirectS1087184508002466 | Loss of heterozygosity in commensal isolates of the asexual diploid yeast Candida albicans | Candida albicans is a commensal and the most frequent fungal pathogen of humans. One mechanism of genetic variation in this diploid asexual yeast involves loss of heterozygosity (LOH). LOH events occur upon infection and contribute to the acquisition of antifungal resistance in patients. In contrast, little is known about the nature and extent of LOH events during commensalism. Using a combination of single nucleotide polymorphism typing, positional transcript profiling and karyotyping, we have characterized related C. albicans commensal isolates that differ by LOH events. Most of these LOH events encompassed the entirety of the chromosome or a large region extending to the telomere, suggesting chromosome loss or mitotic recombination/break-induced replication events, respectively. They were frequently accompanied by karyotype alterations such as chromosome length polymorphism and copy number variations at other chromosomes. These results demonstrate the high plasticity of the C. albicans genome during commensalism. | [Dorothée Diogoa, Christiane Bouchierb, Christophe d’Enferta, Marie-Elisabeth Bougnouxa c] | Fungal Genetics and Biology | February 2009 | |
| sciencedirectS1087184508002296 | Genome-wide analysis of Candida albicans gene expression patterns during infection of the mammalian kidney | Global analysis of the molecular responses of microbial pathogens to their mammalian hosts represents a major challenge. To date few microarray studies have been performed on Candida albicans cells derived from infected tissues. In this study we examined the C. albicans SC5314 transcriptome from renal infections in the rabbit. Genes involved in adhesion, stress adaptation and the assimilation of alternative carbon sources were up-regulated in these cells compared with control cells grown in RPMI 1640, whereas genes involved in morphogenesis, fermentation and translation were down-regulated. When we compared the congenic virulent C. albicans strains NGY152 and SC5314, there was minimal overlap between their transcriptomes during kidney infections. This suggests that much of the gene regulation observed during infections is not essential for virulence. Indeed, we observed a poor correlation between the transcriptome and phenome for those genes that were regulated during kidney infection and that have been virulence tested. | [Louise A. Walker, Donna M. MacCallum, Gwyneth Bertram, Neil A.R. Gow, Frank C. Odds, Alistair J.P. Brown] | Fungal Genetics and Biology | February 2009 | |
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| sciencedirectS0887233308002518 | Endothelial effects of emission source particles: Acute toxic response gene expression profiles | Air pollution epidemiology has established a strong association between exposure to ambient particulate matter (PM) and cardiovascular outcomes. Experimental studies in both humans and laboratory animals support varied biological mechanisms including endothelial dysfunction as potentially a central step to the elicitation of cardiovascular events. We therefore hypothesized that relevant early molecular alterations on endothelial cells should be assessable in vitro upon acute exposure to PM components previously shown to be involved in health outcomes. Using a model emission PM, residual oil fly ash and one of its predominant constituents (vanadium–V), we focused on the development of gene expression profiles to fingerprint that particle and its constituents to explore potential biomarkers for PM-induced endothelial dysfunction. Here we present differential gene expression and transcription factor activation profiles in human vascular endothelial cells exposed to a non-cytotoxic dose of fly ash or V following semi-global gene expression profiling of ∼8000 genes. Both fly ash and it’s prime constituent, V, induced alterations in genes involved in passive and active transport of solutes across the membrane; voltage-dependent ion pumps; induction of extracellular matrix proteins and adhesion molecules; and activation of numerous kinases involved in signal transduction pathways. These preliminary data suggest that cardiovascular effects associated with exposure to PM may be mediated by perturbations in endothelial cell permeability, membrane integrity; and ultimately endothelial dysfunction. | [Srikanth S. Nadadura, Najwa Haykal-Coatesa, Anuradha Mudipallib, Daniel L. Costaa] | Toxicology in Vitro | February 2009 | |
| sciencedirectS088723330800266X | Identification of tumor promotion marker genes for predicting tumor promoting potential of chemicals in BALB/c 3T3 cells | Tumor promoters can cause development of tumors in initiated cells and the majority of them are non-genotoxic carcinogens. The detection of tumor promoters is important for the prevention of cancer. The in vitro two-stage transformation assay, using BALB/c 3T3 cells, is a useful system, and benefits from a convenient protocol and high predictability of mammalian carcinogenicity. But these assays are time-consuming and often require expertise for microscopic observation. To construct an in vitro tumor promoting activity test system, we performed large-scale gene expression analyses, using DNA microarrays, of BALB/c 3T3 cells following treatment with nine chemicals that are known to induce tumor promotion: TPA, zinc chloride, sodium orthovanadate, okadaic acid, insulin, lithocolic acid, phenobarbital sodium, sodium saccharide, sodium arsenite. As a result of DNA microarray and real time PCR analyses, 22 marker genes were identified. These consisted of genes related to cell cycle, regulation of transcription, anti-apoptosis, and positive regulation of cell proliferation. There was a correlation between these 22 marker genes and the cell transformation assay results in BALB/c 3T3 cells. These results suggest that this tumor promoting activity test system, based on 22 marker genes, can become a valuable tool for screening potential tumor promoters. | [Hideki Maeshima, Katsutoshi Ohno, Yukimasa Tanaka-Azuma, Shigeru Nakano, Toshihiro Yamada] | Toxicology in Vitro | February 2009 | |
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| sciencedirectS089158490800614X | MicroRNA expression changes during human leukemic HL-60 cell differentiation induced by 4-hydroxynonenal, a product of lipid peroxidation | 4-Hydroxynonenal (HNE) is one of several lipid oxidation products that may have an impact on human pathophysiology. It is an important second messenger involved in the regulation of various cellular processes and exhibits antiproliferative and differentiative properties in various tumor cell lines. The mechanisms by which HNE affects cell growth and differentiation are only partially clarified. Because microRNAs (miRNAs) have the ability to regulate several cellular processes, we hypothesized that HNE, in addition to other mechanisms, could affect miRNA expression. Here, we present the results of a genome-wide miRNA expression profiling of HNE-treated HL-60 leukemic cells. Among 470 human miRNAs, 10 were found to be differentially expressed between control and HNE-treated cells (at p < 0.05). Six miRNAs were down-regulated (miR-181a*, miR-199b, miR-202, miR-378, miR-454-3p, miR-575) and 4 were up-regulated (miR-125a, miR-339, miR-663, miR-660). Three of these regulated miRNAs (miR-202, miR-339, miR-378) were further assayed and validated by quantitative real-time RT-PCR. Moreover, consistent with the down-regulation of miR-378, HNE also induced the expression of the SUFU protein, a tumor suppressor recently identified as a target of miR-378. The finding that HNE could regulate the expression of miRNAs and their targets opens new perspectives on the understanding of HNE-controlled pathways. A functional analysis of 191 putative gene targets of miRNAs modulated by HNE is discussed. | [Stefania Pizzimentia, Manuela Ferracinb, Silvia Sabbionib, Cristina Toaldoa, Piergiorgio Pettazzonia, Mario Umberto Dianzania, Massimo Negrinib, Giuseppina Barreraa] | Free Radical Biology and Medicine | 15 January 2009 | |
| sciencedirectS0027510708002303 | Bypass of hexavalent chromium-induced growth arrest by a protein tyrosine phosphatase inhibitor: Enhanced survival and mutagenesis | Although the consequences of genotoxic injury include cell cycle arrest and apoptosis, cell survival responses after genotoxic injury can produce intrinsic death-resistance and contribute to the development of a transformed phenotype. Protein tyrosine phosphatases (PTPs) are integral components of key survival pathways, and are responsible for their inactivation, while PTP inhibition is often associated with enhanced cell proliferation. Our aim was to elucidate signaling events that modulate cell survival after genotoxin exposure. Diploid human lung fibroblasts (HLF) were treated with Cr(VI) (as Na2CrO4), the soluble oxyanionic dissolution product of certain particulate chromates, which are well-documented human respiratory carcinogens. In vitro soluble Cr(VI) induces a wide spectrum of DNA damage, in both the presence and absence of a broad-range PTP inhibitor, sodium orthovanadate (SOV). Notably, SOV abrogated Cr(VI)-induced clonogenic lethality. The enhanced survival of Cr(VI)-exposed cells after SOV treatment was predominantly due to a bypass of cell cycle arrest, as there was no effect of the PTP inhibitor on Cr-induced apoptosis. Moreover, the SOV effect was not due to decreased Cr uptake as evidenced by unchanged Cr-DNA adduct burden. Additionally, the bypass of Cr-induced growth arrest by SOV was accompanied by a decrease in Cr(VI)-induced expression of cell cycle inhibiting genes, and an increase in Cr(VI)-induced expression of cell cycle promoting genes. Importantly, SOV resulted in an increase in forward mutations at the HPRT locus, supporting the hypothesis that PTP inhibition in the presence of certain types of DNA damage may lead to increased genomic instability, via bypass of cell cycle checkpoints. | [Dongsoon Baea, Tura C. Camillia, Gina Chuna c, Madhu Lala c, Kristen Wrighta c, Travis J. O’Briena c d, Steven R. Patiernoa b c d, Susan Ceryaka b c d] | Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis | 15 January 2009 | |
| sciencedirectS0378113508002770 | Gene expression profiling and antigen mining of the tuberculin production strain Mycobacterium bovis AN5 | Control of bovine tuberculosis (bTB) relies on regular testing of cattle with a crude preparation of mycobacterial antigens termed purified protein derivative (PPD). Worldwide production of bovine PPD uses the Mycobacterium bovis AN5, a strain that was originally isolated circa 1948 in Great Britain (GB). Despite its worldwide use, the AN5 strain is poorly characterised. AN5 was adapted to grow on glycerol in a process similar to that used for the derivation of the BCG vaccine strains; during this process, it is known that BCG deleted the genes for some potent antigens. Our previous analysis of the genome of M. bovis AN5 showed that it had not suffered extensive gene deletion events during in vitro adaptation. However, glycerol adaptation of AN5 strain may have caused differences in its global gene expression profile that could affect antigen expression. To assess this, we determined the transcriptome profile of AN5 and compared it to expression data for two endemic GB strains of M. bovis that account for ∼61% of all GB bTB cases. Genes expressed at lower levels in AN5 compared to M. bovis field isolates were then screened for antigenicity in naturally infected animals. Using this approach a number of genes were found to be expressed at lower levels in AN5, including those for known antigens. Our results show that field strains of M. bovis show some significant differences in gene expression to AN5, and that this differential gene expression may impact on the antigen profiles expressed by AN5 during in vitro culture. | [M. Carmen Garcia Pelayo, Javier Nunez Garcia, Paul Golby, Christopher Pirson, Katie Ewer, Martin Vordermeier, R. Glyn Hewinson, Stephen V. Gordon] | Veterinary Microbiology | 13 January 2009 | |
| sciencedirectS1044743108001541 | Expanded CAG repeats in the murine Huntington's disease gene increases neuronal differentiation of embryonic and neural stem cells | Huntington's disease is an uncommon autosomal dominant neurodegenerative disorder caused by expanded polyglutamine repeats. Increased neurogenesis was demonstrated recently in Huntington's disease post-mortem samples. In this manuscript, neuronally differentiated embryonic stem cells with expanded CAG repeats in the murine Huntington's disease homologue and neural progenitors isolated from the subventricular zone of an accurate mouse Huntington's disease were examined for increased neurogenesis. Embryonic stem cells with expanded CAG repeats in the murine Huntington's disease homologue were demonstrated to undergo facilitated differentiation first into neural progenitors, then into more mature neurons. Neural progenitor cells isolated from the subventricular zone of a Huntington's disease knock-in animal displayed increased production of neural progenitors and increased neurogenesis. These findings suggested that neuronally differentiating embryonic stem cells with expanded CAG repeats is a reasonable system to identify factors responsible for increased neurogenesis in Huntington's disease. Expression profiling analysis comparing neuronally differentiating embryonic stem cells with expanded CAG repeats to neuronally differentiating embryonic stem cells without expanded CAG repeats identified transcripts involved in development and transcriptional regulation as factors possibly mediating increased neurogenesis in response to expanded CAG repeats. | [Matthew T. Lorincz, Virginia A. Zawistowski] | Molecular and Cellular Neuroscience | 5 January 2009 | |
| sciencedirectS0889159108003176 | Altered gene expression and function of peripheral blood natural killer cells in children with autism | Immune related abnormalities have repeatedly been reported in autism spectrum disorders (ASD), including evidence of immune dysregulation and autoimmune phenomena. NK cells may play an important role in neurodevelopmental disorders such as ASD. Here we performed a gene expression screen and cellular functional analysis on peripheral blood obtained from 52 children with ASD and 27 typically developing control children enrolled in the case-control CHARGE study. RNA expression of NK cell receptors and effector molecules were significantly upregulated in ASD. Flow cytometric analysis of NK cells demonstrated increased production of perforin, granzyme B, and interferon gamma (IFN?) under resting conditions in children with ASD (p < 0.01). Following NK cell stimulation in the presence of K562 target cells, the cytotoxicity of NK cells was significantly reduced in ASD compared with controls (p < 0.02). Furthermore, under similar stimulation conditions the presence of perforin, granzyme B, and IFN? in NK cells from ASD children was significantly lower compared with controls (p < 0.001). These findings suggest possible dysfunction of NK cells in children with ASD. Abnormalities in NK cells may represent a susceptibility factor in ASD and may predispose to the development of autoimmunity and/or adverse neuroimmune interactions during critical periods of development. | [Amanda M. Enstroma h, Lisa Litb h, Charity E. Onorea h, Jeff P. Greggc h i, Robin L. Hansend h i, Isaac N. Pessahe h i, Irva Hertz-Picciottof h i, Judy A. Van de Waterg h i, Frank R. Sharpb h i, Paul Ashwooda h i] | Brain, Behavior, and Immunity | January 2009 | |
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| sciencedirectS0008874909000240 | Study on the antiendotoxin action of Pulsatillae Decoction using an Affymetrix rat genome array | A high-throughput and efficient Affymetrix rat genome array was used to investigate the pharmacological mechanism of the traditional Chinese medicine, Pulsatillae Decoction (PD), used for the treatment of diseases induced by lipopolysaccharide (LPS). Rat intestinal microvascular endothelial cells (RIMECs) were challenged with 1 ?g/ml LPS for 3 h, and then treated with PD at a concentration of 1 mg/ml for 24 h. Total RNA from each treatment group was extracted from cultured RIMECs for detection by the Affymetrix Rat Genome 230 2.0 Array. The results showed that 36 genes were upregulated and 33 genes were downregulated in the LPS group vs. the blank control group; 566 genes were upregulated and 12 genes were downregulated in the PD-treated group vs. the LPS group; and 93 genes were upregulated and 29 genes were downregulated in the PD-treated group vs. the blank control group. The analysis of these data suggested that PD specifically and effectively reduce damage induced by LPS, and improved physiological and biochemical responses to counteract the effects of LPS. | [Yiyi Hua, Xi Chenb, Hong Linc, Yuanliang Hua, Xiang Muc] | Cellular Immunology | 2009 | |
| sciencedirectS0008874909000252 | The distinct response of ?? T cells to the Nod2 agonist muramyl dipeptide | Purified ?? T cells are primed directly in response to pathogen associated molecular patterns (PAMPs) to better respond to secondary signals and increase expression of chemokine and activation-related genes. Transcripts encoding the innate receptor Nod2 were detected in bovine and human ?? T cells. Nod2 is the intracellular receptor for muramyl dipeptide (MDP), functions in regulating innate activities, and was thought to be expressed primarily in APCs. The response of ?? T cells to MDP was analyzed by microarray, Q-PCR, proteome array and functional priming assays. MDP had a consistent priming effect on ?? T cells, characterized by changes in transcripts and enhanced proliferation response to secondary signaling. Knockdown experiments implicated Nod2 as the receptor for MDP in ?? T cell-enriched bovine PBLs. The results indicate priming of ?? T cells by MDP, and offer definitive evidence of the expression of functional Nod2 in ?? T cells. | [Hannah M.M. Kerns, Mark A. Jutila, Jodi F. Hedges] | Cellular Immunology | 2009 | |
| sciencedirectS1521661608008061 | A locus on chromosome 1 promotes susceptibility of experimental autoimmune myocarditis and lymphocyte cell death ? | We previously identified by linkage analysis a region on chromosome 1 (Eam1) that confers susceptibility to experimental autoimmune myocarditis (EAM). To evaluate the role of Eam1, we created a congenic mouse strain, carrying the susceptible Eam1 locus of A.SW on the resistant B10.S background (B10.A-Eam1 congenic) and analyzed three outcomes: 1) the incidence and severity of EAM, 2) the susceptibility of lymph node cells (LNCs) to Cy-enhanced cell death, and 3) susceptibility of lymphoctyes to antigen-induced cell death. Incidence of myocarditis in B10.A-Eam1 congenic mice was comparable to A.SW mice, confirming that Eam1 plays an important role in disease development. Caspase 3, 8 and 9 activation in LNCs following Cy treatment and in CD4+ T cells after immunization with myosin/CFA was significantly lower in A.SW than B10.S mice whereas B10.A-Eam1 congenic mice exhibited an intermediate phenotype. Our results show that Eam1 reduces lymphocyte apoptosis and increases susceptibility to EAM. | [Davinna L. Ligonsa, Mehmet L. Gulera, Haiyan S. Lia, Noel R. Rosea b] | Clinical Immunology | January 2009 | |
| sciencedirectS1525730411700808 | Exosomal MicroRNA: A Diagnostic Marker for Lung Cancer | PurposeTo date, there is no screening test for lung cancer shown to affect overall mortality. MicroRNAs (miRNAs) are a class of small noncoding RNA genes found to be abnormally expressed in several types of cancer, suggesting a role in the pathogenesis of human cancer.Patients and MethodsWe evaluated the circulating levels of tumor exosomes, exosomal small RNA, and specific exosomal miRNAs in patients with and without lung adenocarcinoma, correlating the levels with the American Joint Committee on Cancer (AJCC) disease stage to validate it as an acceptable marker for diagnosis and prognosis in patients with adenocarcinoma of the lung.ResultsTo date, 27 patients with lung adenocarcinoma AJCC stages I-IV and 9 controls, all aged 21-80 years, were enrolled in the study. Small RNA was detected in the circulating exosomes. The mean exosome concentration was 2.85 mg/mL (95% CI, 1.94–3.76) for the lung adenocarcinoma group versus 0.77 mg/mL (95% CI, 0.68–0.86) for the control group (P < .001). The mean miRNA concentration was 158.6 ng/mL (95% CI, 145.7–171.5) for the lung adenocarcinoma group versus 68.1 ng/mL (95% CI, 57.2–78.9) for the control group (P < .001). Comparisons between peripheral circulation miRNA-derived exosomes and miRNA-derived tumors indicated that the miRNA signatures were not significantly different.ConclusionThe significant difference in total exosome and miRNA levels between lung cancer patients and controls, and the similarity between the circulating exosomal miRNA and the tumor-derived miRNA patterns, suggest that circulating exosomal miRNA might be useful as a screening test for lung adenocarcinoma. No correlation between the exosomal miRNA levels and the stage of disease can be made at this point. | [Guilherme Rabinowits1, Cicek Gerçel-Taylor1, Jamie M. Day, Douglas D. Taylor, Goetz H. Kloecker] | Clinical Lung Cancer | January 2009 | |
| sciencedirectB9780123739612001065 | EPILEPTOGENESIS | Gene Expression in Immature and Mature Hippocampus After Status Epilepticus | Effective therapy is currently limited for childhood epilepsy because little is known about the cellular and molecular changes caused by seizures in the developing brain. This situation is different for the adult epilepsies, where works on numerous animal models have led to important insights about underlying bases of the seizure condition. For example, kainic acid (KA)-induced seizures have been studied as an animal model for status epilepticus (SE) and temporal lobe epilepsy for more than three decades. KA injections in mature rats result in the development of spontaneous seizures and a distinctive pattern of neurodegeneration resembling hippocampal sclerosis in human patients. In younger rats, however, KA-induced SE does not cause spontaneous seizures or cell death. Indeed, the impact of seizures has been less well-studied in younger rats than in adult rats. Recently available microarray technology enables us to look at the complex molecular changes in a genome-wide survey. With this tool, we have investigated age-specific, time-dependent changes in gene expression after KA-induced seizures, and compared the brain transcriptomes in mature and immature rats. Understanding how differently the immature and mature nervous systems respond to seizures could ultimately lead to new interventions to prevent seizure-induced neuronal loss and/or subsequent cognitive dysfunction. | [H. Chung, S. Koh] | Encyclopedia of Basic Epilepsy Research | | |
| sciencedirectB9780123694201000482 | Chapter 48 – Viral Chip Technology in Genomic Medicine | | [Zeno Földes-Papp] | Genomic and Personalized Medicine — Volume I & II | | |
| sciencedirectB9780123694201001062 | Chapter 106 – Bipolar Disorder in the Era of Genomic Psychiatry | | [Ayman H. Fanous, Frank Middleton, Carlos N. Pato, Michele T. Pato] | Genomic and Personalized Medicine — Volume I & II | | |
| sciencedirectB9780123694201001153 | Index | | [] | Genomic and Personalized Medicine — Volume I & II | | |
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| sciencedirectS0041008X08004201 | Estrogenic status modulates the effect of soy on hepatic responses to 7,12-dimethylbenz(a)anthracene (DMBA) | We examined the influence of estradiol (E2) status and soy protein isolate (SPI) intake on the hepatic responses altered by 7,12-dimethylbenz(a)anthracene (DMBA, a polycyclic aromatic hydrocarbon [PAH]). Sprague–Dawley rats were ovariectomized (OVX) at PND50 and infused with E2 or vehicle for 14 d and gavaged with 50 mg/kg DMBA or vehicle 24 h before sacrifice at PND64. Rats were fed an AIN-93G diet made with SPI or casein as sole protein source throughout the study. Basal AhR protein levels were reduced (P < 0.05) by SPI feeding irrespective of the E2 status. However, DMBA increased (P < 0.05) AhR-induced CYP1A1 gene expression in OVX, SPI-fed rats, but reduced (P < 0.05) CYP1A1 in OVX + E2, SPI-fed rats. Chromatin-immunoprecipitation demonstrated lower (P < 0.05) DMBA-mediated recruitment of estrogen receptor alpha to the CYP1A1 promoter by SPI feeding in the presence of E2, suggesting an estrogen-like action of SPI on DMBA-mediated signaling in the absence of E2. Further, microarray analysis (Rat 230-2.0 Affymetrix-GeneChip™) revealed 231 genes common to SPI + DMBA and SPI + E2 + DMBA (normalized to E2) treatments. AhR-activated genes (CYP1A1, CYP1A2, and NQO1) were down-regulated by SPI + E2 + DMBA compared to SPI + DMBA. Unique interactions among SPI, DMBA and E2 altered the expression profile of 316 genes, not observed by either treatment alone. Our data suggest that although E2 status does not effect soy-mediated AhR degradation, it modulates the effects of soy on many genes, including CYP1A1. | [Rohit Singhala, Thomas M. Badgerb c, Martin J. Ronisa c] | Toxicology and Applied Pharmacology | 1 January 2009 | |
| sciencedirectS0168170208003316 | Human immunodeficiency virus type 1 chronic infection is associated with different gene expression in MT-4, H9 and U937 cell lines | To investigate cellular factors involved in HIV-1 chronic infection, three cell lines chronically infected with the same HIV-1 viral isolate (s61) were studied by cDNA microarray analysis. Two T cell lines, H61 and M61, showed the characteristics of a persistent infection whereas U61 cell line displayed a latent infection pattern. Analysis of genes with altered expression in the three cell lines revealed evidence of apoptosis control by up-regulation of anti-apoptotic genes and down-regulation of pro-apoptotic genes. In addition, cell cycle control was affected in the two persistent T cell lines particularly through the down-regulation of cyclin-dependent kinase inhibitor 1A (CDKN1A/p21). Moreover, each cell line showed specific characteristics, like in M61 cells, genes related with cellular activation and with cell migration and motility. In U61 cells, genes associated with immune response were activated. Genes with altered expression in our experiments, and not previously related with HIV such as ANXA 1 or CFLAR were detected and validated. This work revealed that different cell mechanism such as control of apoptosis and cell cycle are important for “in vitro” HIV-1 chronic infections, and discovered new genes previously not related with HIV-1 replication. | [Isabel Olivaresa, Alicia Ballestera, Luis Lombardiab, Orlando Dominguezb, Cecilio López-Galíndeza] | Virus Research | January 2009 | |
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| sciencedirectS0006291X08020172 | Oxidative stress modulates theophylline effects on steroid responsiveness | Oxidative stress is a central factor in many chronic inflammatory diseases such as severe asthma and chronic obstructive pulmonary disease (COPD). Oxidative stress reduces the anti-inflammatory corticosteroid action and may therefore contribute to the relative corticosteroid insensitivity seen in these diseases. Low concentrations of theophylline can restore the anti-inflammatory action of corticosteroids in oxidant exposed cells, however the mechanism remains unknown. Here, we demonstrate that a low concentration of theophylline restores corticosteroid repression of pro-inflammatory mediator release and histone acetylation in oxidant exposed cells. Global gene expression analysis shows that theophylline regulates distinct pathways in naïve and oxidant exposed cells and reverses oxidant mediated modulated of pathways. Furthermore, quantitative chemoproteomics revealed that theophylline has few high affinity targets in naive cells but an elevated affinity in oxidant stressed cells. In conclusion, oxidative stress alters theophylline binding profile and gene expression which may result in restoration of corticosteroid function. | [John A. Marwicka b, Gillian Wallisa, Koremu Mejaa, Bernhard Kusterc, Tewis Bouwmeesterc, Probir Chakravartya, Danielle Fletchera, Paul A. Whittakera, Peter J. Barnesb, Kazuhiro Itob, Ian M. Adcockb, Paul A. Kirkhama b] | Biochemical and Biophysical Research Communications | 19 December 2008 | |
| sciencedirectS0006291X08019797 | Analysis of transcriptional profiles and functional clustering of global cerebellar gene expression in PCD3J mice | The Purkinje cell degeneration (PCD) mutant mouse is characterized by a degeneration of cerebellar Purkinje cells and progressive ataxia. To identify the molecular mechanisms that lead to the death of Purkinje neurons in PCD mice, we used Affymetrix microarray technology to compare cerebellar gene expression profiles in pcd3J mutant mice 14 days of age (prior to Purkinje cell loss) to unaffected littermates. Microarray analysis, Ingenuity Pathway Analysis (IPA) and expression analysis systematic explorer (EASE) software were used to identify biological and molecular pathways implicated in the progression of Purkinje cell degeneration. IPA analysis indicated that mutant pcd3J mice showed dysregulation of specific processes that may lead to Purkinje cell death, including several molecules known to control neuronal apoptosis such as Bad, CDK5 and PTEN. These findings demonstrate the usefulness of these powerful microarray analysis tools and have important implications for understanding the mechanisms of selective neuronal death and for developing therapeutic strategies to treat neurodegenerative disorders. | [Gregory D. Forda b 1, Byron D. Fordb 1, Ernest C. Steele Jr.b, Alicia Gatesb, Darryl Hooda, Mika A.B. Matthewsb, Sophia Mirzab, Peter R. MacLeishb] | Biochemical and Biophysical Research Communications | 12 December 2008 | |
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| sciencedirectS0014482708003972 | Regulation of CRABP-II expression by MycN in Wilms tumor | Cellular retinoic acid binding protein II (CRABP-II) is overexpressed in a wide variety of cancers. Previously we have shown that CRABP-II expression levels are also elevated in neuroblastoma and Wilms tumors. To elucidate the molecular mechanisms underlying the abnormal expression of CRABP-II in Wilms tumor, we studied the expression of MycN and CRABP-II in these tumor samples. Our data revealed that CRABP-II is overexpressed in Wilms tumor compared to normal adjacent non-neoplastic tissue and its levels are even higher in late stage tumors. Its expression correlates with MycN expression in tumors. The tumors that do not express MycN have no CRABP-II expression. The expression of CRABP-II is also regulated by methylation and its promoter is unmethylated in tumors. Knockdown of MycN by small interfering RNA leads to downregulation of CRABP-II. Thus our results suggest that both MycN and DNA methylation are responsible for CRABP-II expression in pediatric tumors and demethylation of CRABP-II may be an early event in tumor development. | [Anu Guptaa, Patricia Kesslerb, Jawhar Rawwasc, Bryan R.G. Williamsd] | Experimental Cell Research | 10 December 2008 | |
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| sciencedirectS0965174808001616 | A genome-wide analysis of genes and gene families involved in innate immunity of Bombyx mori | A genome-wide analysis of innate immunity-related genes and gene families was conducted using the silkworm, Bombyx mori. We identified orthologs for a large number of genes involved in insect immunity that have been reported from Drosophila melanogaster (Diptera), Anopheles gambiae (Diptera), Apis mellifera (Hymenoptera) and Tribolium castaneum (Coleoptera). B. mori has a unique recognition gene and antimicrobial peptide genes that are not present in the Drosophila, Anopheles, Apis and Tribolium genomes, suggesting a lineage-specific gene evolution for lepidopteran insects. The comparative analysis of the insect immune repertoires indicated a dynamic and flexible gene expansion in recognition, modulation and effector mechanisms due to different selection pressures. Differential gene regulation by different bacterial species was found in PGRP and Serpin genes, suggesting that Bombyx has a highly selective gene regulation system depending on bacterial species. | [Hiromitsu Tanakaa 1, Jun Ishibashia 1, Kosuke Fujitaa, Yoshiro Nakajimaa, Aki Sagisakaa, Kazuya Tomimotoa, Noriko Suzukia, Mikio Yoshiyamaa, Yoichi Kanekob, Takashi Iwasakib, Tomoya Sunagawab, Kayoko Yamajib, Ai Asaokaa, Kazuei Mitac, Minoru Yamakawaa b] | Insect Biochemistry and Molecular Biology | December 2008 | |
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| sciencedirectS0168945208002136 | Expression profiling of the genes induced by Na2CO3 and NaCl stresses in leaves and roots of Leymus chinensis | Alkaline soil is more challenging factor to grow plants than saline soil based on the size of its affected area. To reveal genetic expression changes by alkaline and saline soil, Leymus chinensis (Trin.) Tzvel. was examined response to Na2CO3 and NaCl stresses by using microarray chips comprising 1642 cDNA clones, previously reported by us. A total of 536 genes were responsive to Na2CO3 and NaCl stresses by up-regulation or down-regulation. We observed transcriptional changes arose more to Na2CO3 stress, or leaves than to NaCl stress or roots, respectively, in L. chinensis genome. Overall, 99 and 59 genes were up-regulated, while 365 and 176 genes were down-regulated in leaves and roots, respectively; demonstrating down-regulation occurs more as the response to the Na2CO3 and NaCl stress. The majority of the down-regulated genes (30.1%) were classified to photosynthesis related proteins while that of the up-regulated genes were categorized into metabolism proteins or noble proteins. Only 37 genes in the stressed leaves and 6 genes in the stressed roots were showed the same expression changing patterns between Na2CO3 and NaCl stresses during three time points of detections. Among those genes, 70% were constantly up-regulated or down-regulated during our detection presenting difference in the gene regulation systems against two difference stress, the saline-alkali stress (Na2CO3) and saline stress (NaCl). In addition, a total of 87 genes detected in this study were characterized to the unclassified proteins, whereas 72 had no similarity to the current GenBank databases which were considered as novel proteins detected in the alkali and saline stressed L. chinensis genome. The four important genes to abiotic stress tolerance, ACC, GDP, hsp70, and elF1 were detected constantly for all of three time points of stressed which are the grand candidates for establishing stress tolerance plants by developing transgenic. | [H. Jina b 1, H.R. Kima 1, P. Plahaa c, S.K. Liud, J.Y. Parka, Y.Z. Piaob, Z.H. Yanga, G.B. Jiangb, S.S. Kwake, G. Anf, M. Sonf, Y.H. Jina, J.H. Sohne, Y.P. Lima] | Plant Science | December 2008 | |
| sciencedirectS0168945208002380 | Differential LongSAGE tag abundance analysis in a barley seed germination time course and validation with relative real-time RT-PCR | A Long Serial Analysis of Gene Expression (LongSAGE) approach was employed to identify changes in mRNA transcript abundance in a time course of malting barley (Hordeum vulgare L.). Statistical analyses confidently identified 57 LongSAGE sequence tags as having significant changes in abundance between points in the time course. Eight of the genes which correspond to these tags were targeted for validation by relative real-time reverse transcriptase PCR (RT-PCR) analysis. Each gene was analysed by SYBR® Green detection in grain sampled at each of four time points from dry seed to grain germinated to 120 h post-steeping. Among the genes examined are alpha-amylase type B, a key starch degrading enzyme involved in germination (1-3,1-4)-beta-d-glucanase, the major cell wall degrading enzyme, and cysteine proteinase EP-B, an important enzyme of proteolysis in barley seed germination. These three transcripts show significant up-regulation at 48 h post-steeping and remain significantly elevated throughout malting. These results provide transcriptional data to support the understanding of how the relative rates of protein and carbohydrate modification contribute to malting and brewing. mRNA abundance levels observed using real-time RT-PCR show good correlation with the data obtained from the LongSAGE study. This confirms the sensitivity of detection obtainable with SAGE technology and validates the patterns of change of transcript abundance exhibited by some key genes for barley seed germination. | [Jessica White, Toni Pacey-Miller, Peter Bundock, Robert Henry] | Plant Science | December 2008 | |
| sciencedirectS0960076008002380 | Pangenomic changes induced by DHEA in the skin of postmenopausal women | The objective of this study was to explore, for the first time, the changes in the pangenomic profile induced in human skin in women treated with dehydroepiandrosterone (DHEA) applied locally.Sixty postmenopausal women participated in this phase II prospective, randomized, double-blind and placebo-controlled study. Women were randomized to the twice daily local application of 0% (placebo), 0.3%, 1% or 2% DHEA cream. Changes in the pangenomic expression profile were studied using Affymetrix Genechips.Significant changes (p < 0.05) in sixty-six DHEA-responsive probe sets corresponding to 52 well-characterized genes and 9 unknown gene sequences were identified. A dose-dependent increase in the expression of several members of the collagen family was observed, namely COL1, COL3 and COL5 as well as the concomitant modulation of SPARC, a gene required for the normal deposition and maturation of collagen fibrils in the dermis. Several genes involved in the proliferation and differentiation of keratinocytes were also modulated. In addition, topical DHEA reduced the expression of genes associated with the terminal differentiation and cornification of keratinocytes.Our results strongly suggest the possibility that DHEA could exert an anti-aging effect in the skin through stimulation of collagen biosynthesis, improved structural organization of the dermis while modulating keratinocyte metabolism. | [E. Calvoa, V. Luu-Thea, J. Morissettea, C. Martela, C. Labriea, B. Bernardb, F. Bernerdb, C. Delocheb, V. Chaussadeb, J. Leclaireb, F. Labriea] | The Journal of Steroid Biochemistry and Molecular Biology | December 2008 | |
| sciencedirectS1003632609600042 | Development and application of functional gene arrays for microbial community analysis | Functional gene markers can provide important information about functional gene diversity and potential activity of microbial communities. Although microarray technology has been successfully applied to study gene expression for pure cultures, simple, and artificial microbial communities, adapting such a technology to analyze complex microbial communities still presents a lot of challenges in terms of design, sample preparation, and data analysis. This work is focused on the development and application of functional gene arrays (FGAs) to target key functional gene markers for microbial community studies. A few key issues specifically related to FGAs, such as oligonucleotide probe design, nucleic acid extraction and purification, data analysis, specificity, sensitivity, and quantitative capability are discussed in detail. Recent studies have demonstrated that FGAs can provide specific, sensitive, and potentially quantitative information about microbial communities from a variety of natural environments and controlled ecosystems. This technology is expected to revolutionize the analysis of microbial communities, and link microbial structure to ecosystem functioning. | [Z.L. HE, J.D. VAN NOSTRAND, L.Y. WU, J.Z. ZHOU] | Transactions of Nonferrous Metals Society of China | December 2008 | |
| sciencedirectS0006291X08018299 | Attenuated BDNF-induced upregulation of GABAergic markers in neurons lacking Xbp1 | XBP1 is a transcription factor induced by unconventional splicing associated with endoplasmic reticulum stress and plays a role in development. Brain-derived neurotrophic factor (BDNF) causes splicing of Xbp1 mRNA in neurites, and Xbp1 is required for BDNF-induced neurite extension and branching. To search for the molecular mechanisms of how Xbp1 plays a role in neural development, comprehensive gene expression analysis was performed in primary telencephalic neurons obtained from Xbp1 knockout mice at embryonic day 12.5. By searching for the genes induced by BDNF in wild type neurons but not in Xbp1 knockout mice, we found that upregulation of three GABAergic markers, somatostatin (Sst), neuropeptide Y (Npy), and calbindin (Calb1), were compromised in Xbp1 knockout neurons. Attenuated upregulation of Npy and Calb1 in Xbp1 knockout neurons was confirmed by quantitative RT-PCR. This finding may be relevant to impaired BDNF-induced neurite extension in Xbp1 knockout neurons. | [Akiko Hayashi, Takaoki Kasahara, Mizue Kametani, Tadafumi Kato] | Biochemical and Biophysical Research Communications | 28 November 2008 | |
| sciencedirectS0303720708003353 | NeuroD1 and Mash1 temporally regulate GnRH receptor gene expression in immortalized mouse gonadotrope cells | Accurate spatial and temporal expression of gonadotrope-specific genes, such as the gonadotropin-releasing hormone receptor (GnRHR) gene, is critical for gonadotrope maturation. Herein, we show that a specific E-box in the mouse GnRHR promoter binds two group A basic-helix-loop-helix (bHLH) transcription factors. Mutation of this E-box decreases expression in mouse gonadotrope-derived ?T3-1 and L?T2 cell lines. Microarray and western blots show that the bHLH transcription factor NeuroD1 is strongly expressed in the gonadotrope progenitor, ?T3-1, whereas Mash1 is strongly expressed in the more mature gonadotrope, L?T2. Over-expression of NeuroD1 or Mash1 increases expression of the GnRHR gene or a multimer of the E-box and this increase is lost upon mutation of the E-box. Electrophoretic mobility shift assays reveal that the GnRHR E-box binds NeuroD1 from ?T3-1 cells, but binds Mash1 from L?T2 cells. The sequential binding of different members of the group A bHLH transcription factor family to mouse GnRHR E-box 3 as the gonadotrope differentiates may represent a mechanism necessary for proper spatial and temporal expression of the GnRHR during gonadotrope development. | [Brian D. Cherrington1 2, Janice S. Bailey1 3, Alejandro L. Diaz, Pamela L. Mellon] | Molecular and Cellular Endocrinology | 25 November 2008 | |
| sciencedirectS0891584908004930 | Induction of adaptive response and enhancement of PC12 cell tolerance by lipopolysaccharide primarily through the upregulation of glutathione S-transferase A3 via Nrf2 activation | Increasing evidence indicates that reactive oxygen species and other physiologically existing oxidative stimuli upregulate the antioxidant system, thereby triggering the adaptive response. In this study, we focused on adaptive cytoprotection induced by lipopolysaccharide (LPS), which induces oxidative stress and inflammatory cytokines, in PC12 cells, a model of the neuronal cell. After treating PC12 cells with LPS at sublethal concentrations, we found that they developed resistance to subsequent oxidative stress induced by 13S-hydroperoxy-9Z,11E-octadecadienoic acid and 5-amino-3-(4-morpholinyl)-1,2,3-oxadiazolium. To determine the underlying molecular mechanisms responsible for an adaptive response induced by LPS, we studied the changes in the antioxidant system. LPS treatment resulted in an increase in the gene expression of glutathione S-transferase A3 (GST-A3) by up to 60-fold as well as in GST enzyme activity. A GST inhibitor and GST A3 small interfering RNA effectively attenuated the adaptive response. The nuclear factor erythroid 2 p45-related factor 2 (Nrf2) was transcriptionally activated by LPS. Nrf2 small interfering RNA effectively attenuated the increase in GST A3 mRNA level as well as the adaptive response induced by LPS. In addition, peripheral injection of LPS at sublethal concentrations increased GST enzyme activity in mouse brain. These findings, taken together, indicate that stimulation with LPS at sublethal concentrations induces an adaptive response and enhances PC12 cell tolerance, primarily through the induction of GST A3 via the transcriptional activation of the Nrf2 signaling pathway. | [Yo Omataa, Yoshiro Saitoa b, Katsuhide Fujitaa, Yoko Ogawaa, Keiko Nishioa, Yasukazu Yoshidaa, Etsuo Nikia] | Free Radical Biology and Medicine | 15 November 2008 | |
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| sciencedirectS0378427408012344 | Gene expression analysis of bromine-induced burns in porcine skin ? | Bromine is an industrial chemical that is irritating to the skin and causes cutaneous burns. An important factor in selecting or developing an effective treatment is to understand the underlying molecular mechanisms of tissue damage and wound healing. This study used a weanling swine burn model and microarray analysis to evaluate the effect of exposure length and sampling times on the transcriptional changes in response to cutaneous bromine injury. Ventral abdominal sites (N = 4/treatment group) were exposed to 600 ?L undiluted bromine for 45 s or 8 min. At 24 h and 7 d post-exposure, total RNA from skin samples was isolated, processed, and hybridized to Affymetrix GeneChip® Porcine Genome Arrays. Expression analysis revealed that bromine exposure duration appeared to have less effect on the transcript changes than the sampling time. The percent transcripts changed at 24 h were similar (30%) whether having a 45 s or 8 min bromine exposure; percent transcripts changed at 7 d were also similar (62%) regardless of exposure length. However, only 13–14% of the transcripts were similar when comparing samples analyzed at 24 h and 7 d. Ingenuity Pathways Analysis (IPA) revealed six common biological functions among the top 10 functions of each experimental group, while canonical pathway analysis revealed 11 genes that were commonly shared among 24 significantly altered signaling pathways. Additionally, there were 11 signaling pathways in which there were no commonly shared transcripts. The present study is an initial assessment of the transcriptional responses to cutaneous bromine exposure identifying molecular networks and genes that could serve as targets for developing therapeutics for bromine-induced skin injury. | [Jennifer A. Pricea, James V. Rogersa, James N. McDougalb, Morgan Q. Shawa, Frances M. Reida, Robyn C. Kisera, John S. Grahamc] | Toxicology Letters | 10 November 2008 | |
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| sciencedirectS1742706108001414 | Human coronary artery smooth muscle cell response to a novel PLA textile/fibrin gel composite scaffold | Previous studies have demonstrated the potential of fibrin as a cell carrier for cardiovascular tissue engineering applications. Unfortunately, fibrin exhibits poor mechanical properties. One method of addressing this issue is to incorporate a textile in fibrin to provide structural support. However, it is first necessary to develop a deeper understanding of the effect of the textile on cell response. In this study, the cytotoxicity of a polylactic acid (PLA) warp-knit textile was assessed with human coronary artery smooth muscle cells (HCASMC). Subsequently, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) was employed to examine the gene expression of HCASMC embedded in fibrin with and without the textile. Five genes were examined over a 3-week period: smooth muscle ?-actin (SM??), myosin heavy chain 11 smooth muscle (SM1/SM2), calponin, myosin heavy chain 10 non-muscle (SMemb) and collagen. Additionally, a microarray analysis was performed to examine a wider range of genes. The knitting process did not adversely affect the cell response; there was no dramatic change in cell number or metabolic rate compared to the negative control. After 3 weeks, there was no significant difference in gene expression, except for a slight decrease of 10% in SMemb in the fibrin with textile. After 3 weeks, there were no obvious cytotoxic effects observed as a result of the knitting process and the gene expression profile did not appear to be altered in the presence of the mesh in the fibrin gel. | [Sarah Gundya, Grainne Manninga, Enda O’Connella, Ville Elläb, Marvi Sri Harwokoc, Yuri Rocheva, Terry Smitha, Valerie Barrona] | Acta Biomaterialia | November 2008 | |
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| sciencedirectS1065699508005143 | Establishment and functional characterization of a tracheal epithelial cell line RTEC11 from transgenic rats harboring temperature-sensitive simian virus 40 large T-antigen | A tracheal epithelial cell line RTEC11 was established from transgenic rats harboring temperature-sensitive simian virus 40 large T-antigen. The cells grew continuously at a permissive temperature of 33 °C but not at a non-permissive temperature of 39 °C. Morphological and functional investigations demonstrated that the cells were polarized epithelial cells maintaining a regulated permeability barrier function. Interestingly, the expression levels of Muc1 (mucin 1) and Scgb1a1 (uteroglobin), non-ciliated secretory cell markers, and Tubb4 (tubulin beta 4), a ciliated cell marker, were significantly increased under the cell growth-restricted condition. Global gene expression and computational network analyses demonstrated a significant genetic network associated with cellular development and differentiation in cells cultured at the non-permissive temperature. The tracheal epithelial cell line RTEC11 with unique characteristics should be useful as an in vitro model for studies of the physiological functions and gene expression of tracheal epithelial cells. | [Yoshiaki Tabuchia, Takeshi Doia, Ichiro Takasakia, Ri-ichi Takahashib, Masatsugu Uedab, Yoshihisa Suzukic, Masuo Obinatac] | Cell Biology International | November 2008 | |
| sciencedirectS0301468109600335 | Chemically defined medium supporting cardiomyocyte differentiation of human embryonic stem cells | Many applications of human embryonic stem cells (hESCs) will require fully defined growth and differentiation conditions including media devoid of fetal calf serum. To identify factors that control lineage differentiation we have analyzed a serum-free (SF) medium conditioned by the cell line END2, which efficiently induces hESCs to form cardiomyocytes. Firstly, we noted that insulin, a commonly used medium supplement, acted as a potent inhibitor of cardiomyogenesis in multiple hESC lines and was rapidly cleared by medium conditioning. In the presence of insulin or IGF-1, which also suppressed cardiomyocyte differentiation, the PI3/Akt pathway was activated in undifferentiated hESC, suggesting that insulin/IGF-1 effects were mediated by this signaling cascade. Time course analysis and quantitative RT-PCR revealed impaired expression of endoderm and mesoderm markers in the presence of insulin, particularly if added during early stages of hESC differentiation. Relatively high levels of the neural ectoderm marker Sox1 were expressed under these conditions. Secondly, comparative gene expression showed that two key enzymes in the prostaglandin I2 (PGI2) synthesis pathway were highly up-regulated in END2 cells compared with a related, but non-cardiogenic, cell line. Biochemical analysis confirmed 6–10-fold higher PGI2 levels in END2 cell-conditioned medium (END2-CM) vs. controls. Optimized concentrations of PGI2 in a fully synthetic, insulin-free medium resulted in a cardiogenic activity equivalent to END2-CM. Addition of the p38 mitogen-activated protein kinase-inhibitor SB203580, which we have shown previously to enhance hESC cardiomyogenesis, to these insulin-free and serum-free conditions resulted in a cardiomyocyte content of >10% in differentiated cultures without any preselection. This study represents a significant step toward developing scalable production for cardiomyocytes from hESC using clinically compliant reagents compatible with Good Manufacturing Practice. | [Xiu Qin Xu1 2, Ralph Graichen1, Set Yen Soo1 2, Thavamalar Balakrishnan1 2, Siti Norfiza Bte Rahmat1 2, Shirly Sieh1, Su Chin Tham1, Christian Freund3, Jennifer Moore3, Christine Mummery3, Alan Colman1 2, Robert Zweigerdt1 2, Bruce P. Davidson1] | Differentiation | November 2008 | |
| sciencedirectS0301468109600372 | Phylogenetic and expression analysis of the basic helix-loop-helix transcription factor gene family: genomic approach to cellular differentiation | A phylogenetic analysis of seven different species (human, mouse, rat, worm, fly, yeast, and plant) utilizing all (541) basic helix-loop-helix (bHLH) genes identified, including expressed sequence tags (EST), was performed. A super-tree involving six clades and a structural categorization involving the entire coding sequence was established. A nomenclature was developed based on clade distribution to discuss the functional and ancestral relationships of all the genes. The position/location of specific genes on the phylogenetic tree in relation to known bHLH factors allows for predictions of the potential functions of uncharacterized bHLH factors, including EST's. A genomic analysis using microarrays for four different mouse cell types (i.e. Sertoli, Schwann, thymic, and muscle) was performed and considered all known bHLH family members on the microarray for comparison. Cell-specific groups of bHLH genes helped clarify those bHLH genes potentially involved in cell specific differentiation. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique aspects of the evolution and functional relationships of the different genes in the bHLH gene family. | [Jeffrey D. Stevens1, Eric H. Roalson2, Michael K. Skinner1] | Differentiation | November 2008 | |
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| sciencedirectS1087184508001576 | An evolutionary conserved d-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation | Transcriptome analysis of Aspergillus niger transfer cultures grown on galacturonic acid media identified a highly correlating cluster of four strongly induced hypothetical genes linked with a subset set of genes encoding pectin degrading enzymes. Three of the encoded hypothetical proteins now designated GAAA to GAAC are directly involved in further galacturonic acid catabolism. Functional and biochemical analysis revealed that GAAA is a novel d-galacturonic acid reductase. Two non-allelic Aspergillus nidulans strains unable to utilize galacturonic acid are mutated in orthologs of gaaA and gaaB, respectively. The A. niger gaaA and gaaC genes share a common promoter region. This feature appears to be strictly conserved in the genomes of plant cell wall degrading fungi from subphylum Pezizomycotina. Combined with the presence of homologs of the gaaB gene in the same set of fungi, these strongly suggest that a common d-galacturonic acid utilization pathway is operative in these species. | [Elena S. Martens-Uzunova, Peter J. Schaap] | Fungal Genetics and Biology | November 2008 | |
| sciencedirectS0378111908003284 | Functional identification of an anti-?E factor from Thermus thermophilus HB8 | The TTHB212 gene from extremely thermophilic bacterium Thermus thermophilus HB8 forms an operon with the upstream sigE gene encoding an extracytoplasmic function ? factor, ?E, the sole alternative ? factor of this strain, on megaplasmid pTT27. The TTHB212 gene encodes a poorly conserved protein, which has been predicted to be a transmembrane one with N-terminal intracellular and C-terminal extracytoplasmic domains. The N-terminal domain of TTHB212 protein (TTHB212N) prevented ?E from binding to RNA polymerase (RNAP) core enzyme in vitro, and TTHB212N bound ?E in a molar ratio of 1:1 when both proteins were co-expressed in Escherichia coli. Furthermore, TTHB212N inhibited the transcription activity of RNAP-?E holoenzyme, but not that of the RNAP-?A one, in vitro. The expression of several genes that are under the control of ?E was increased in a TTHB212 gene-disruptant strain. Thus, TTHB212 protein was identified as an anti-?E factor. These findings indicate that T. thermophilus HB8 has a regulatory system involving ?E and anti-?E factors. | [Keiko Sakamotoa 1, Yoshihiro Agaria 1, Shigeyuki Yokoyamaa b c, Seiki Kuramitsua d, Akeo Shinkaia] | Gene | 1 November 2008 | |
| sciencedirectS0888754308001432 | Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation | While there have been significant advances in understanding the genetic etiology of human hair loss over the previous decade, there remain a number of hereditary disorders for which a causative gene has yet to be identified. We studied a large, consanguineous Brazilian family that presented with woolly hair at birth that progressed to severe hypotrichosis by the age of 5, in which 6 of the 14 offspring were affected. After exclusion of known candidate genes, a genome-wide scan was performed to identify the disease locus. Autozygosity mapping revealed a highly significant region of extended homozygosity (lod score of 10.41) that contained a haplotype with a linkage lod score of 3.28. Results of these two methods defined a 9-Mb region on chromosome 13q14.11–q14.2. The interval contains the P2RY5 gene, in which we recently identified pathogenic mutations in several families of Pakistani origin affected with autosomal recessive woolly and sparse hair. After the exclusion of several other candidate genes, we sequenced the P2RY5 gene and identified a homozygous mutation (C278Y) in all affected individuals in this family. Our findings show that mutations in P2RY5 display variable expressivity, underlying both hypotrichosis and woolly hair, and underscore the essential role of P2RY5 in the tissue integrity and maintenance of the hair follicle. | [Lynn Petukhovaa, Edilson C. Sousa Jr.b, Amalia Martinez-Mira 1, Anna Vitebskya, Lina G. dos Santosc, Lawrence Shapirod, Chad Haynese, Derek Gordonf, Yutaka Shimomuraa, Angela M. Christianoa g] | Genomics | November 2008 | |
| sciencedirectS0198885908004370 | Human leukocyte antigen class I-restricted immunosuppression by human CD8+ regulatory T cells requires CTLA-4-mediated interaction with dendritic cells | We previously reported autoreactive CD8+ regulatory T cells (Tregs) that were expanded and cloned from human peripheral blood by coculture with autologous dendritic cells (DC). Here we demonstrate that these CD8+ Tregs require human leukocyte antigen (HLA)-class I restricted activation and then mediate cell-contact-dependent suppression of CD4+ T cells. CD8+ Tregs interacted with DC to suppress T-cell responses but DC were not irreversibly altered by this interaction because they could subsequently stimulate CD4+ T cells normally. The ability of DC to form conjugates with CD4+ T cells was reduced in the presence of CD8+ Tregs. Suppression was blocked by Abs to CD80 and CTLA-4, implicating CTLA-4:CD80 interactions in the function of CD8+ Tregs. CD8+ Tregs rapidly express very high levels of surface CTLA-4 following activation compared with conventional T cells. Related to this, the expression of TRAT1 mRNA (T-cell receptor interacting molecule, or TRIM) was highly upregulated in microarray analysis of CD8+ Tregs compared with conventional cytotoxic or nonregulatory CD8+ T cells. TRIM acts to chaperone CTLA-4 transport to the cell surface; this function would be required to account for the phenotypic and functional properties of CD8+ Tregs. | [Lorna B. Jarvis, Jane C. Goodall, J.S. Hill Gaston] | Human Immunology | November 2008 | |
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| sciencedirectS0733521008000714 | Identification and genetic mapping of variant forms of puroindoline b expressed in developing wheat grain | Transcripts encoding three novel variant forms of puroindoline b have been identified in developing seeds of wheat. These show 57–60% sequence identity with the wild type form of Pin b but all lack one of the three tryptophan residues present in the “tryptophan loop” region of the wild type protein. Counts of ESTs and array analysis indicate that the transcripts encoding variant forms of Pin b are about an order of magnitude less abundant than those encoding wild type Pin b while array analysis also shows that expression of the variant form 1 declines more rapidly than that of the wild type form during the later stages of grain development. The gene(s) encoding variant form 1, named Pinb-A2, were mapped to the long arm of chromosome 7A of bread wheat where they show linkage to novel QTLs for hardness which have been identified in two doubled haploid populations derived from crosses between hard parental cultivars (Shamrock × Shango, Malacca × Charger). | [Mark Wilkinsona, Yongfang Wana, Paola Tosia, Michelle Leveringtonb, John Snapeb, Rowan A.C. Mitchella, Peter R. Shewrya] | Journal of Cereal Science | November 2008 | |
| sciencedirectS0946672X08000667 | Effects of long-term zinc supplementation and deprivation on gene expression in human THP-1 mononuclear cells | Zinc is an essential trace element that is critical for cellular function and structural integrity. It has an important regulatory role in the immune system, in particular in monocytes. To identify the diverse cellular targets and mechanisms of action of zinc in this cell type, we used microarray technology to assess the effects of zinc supplementation and depletion on global gene expression. mRNA expression in the human monocytic cell line THP-1 was analyzed and compared in response to 40 h supplementation with 50 ?mol/L zinc, or zinc deprivation by 2.5 ?mol/L of the membrane-permeant zinc chelator TPEN [N,N,N′,N′-tetrakis-(2-pyridyl-methyl)ethylenediamine]. Analysis of microarrays consisting of approximately 19,000 unique oligonucleotides identified over 1400 genes, or approximately 7%, as zinc-sensitive. Notably, this yielded several sets of structurally or functionally related genes. Among those groups, which were mainly affected by zinc deprivation, were histones, S100 calcium and zinc binding proteins, and chemokines and their receptors. These groups of genes may mediate zinc-effects on chromatin regulation, zinc homeostasis, and chemotaxis, respectively. In addition, functional networks were analyzed, showing that the well known effect of zinc on pro-inflammatory cytokines is not limited to these genes; it acts on a number of functionally connected genes, as well. These results provide novel molecular targets and pathways that may aid in explaining the role of zinc in monocyte function. | [Dawn J. Mazzattia, Peter Uciechowskib, Silke Hebelb, Gabriela Engelhardtb, Andrew J. Whitec, Jonathan R. Powella, Lothar Rinkb, Hajo Haaseb] | Journal of Trace Elements in Medicine and Biology | November 2008 | |
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| sciencedirectS0956566308001504 | Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics | In order to design a method for the accurate detection and identification of food-borne pathogens, we used comparative genomics to select 70-mer oligonucleotide probes specific for 11 major food-borne pathogens (10 overlapping probes per pathogen) for use in microarray analysis. We analyzed the hybridization pattern of this constructed microarray with the Cy3-labeled genomic DNA of various food-borne pathogens and other bacteria. Our microarray showed a highly specific hybridization pattern with the genomic DNA of each food-borne pathogen; little unexpected cross-hybridization was observed. Microarray data were analyzed and clustered using the GenePix Pro 6.0 and GeneSpring GX 7.3.1 programs. The analyzed dendrogram revealed the discriminating power of constructed microarray. Each food-borne pathogen clustered according to its hybridization specificity and non-pathogenic species were discriminated from pathogenic species. Our method can be applied to the rapid and accurate detection and identification of food-borne pathogens in the food industry. In addition, this study demonstrates that genome sequence comparison and DNA microarray analysis have a powerful application in epidemiologic and taxonomic studies, as well as in the food safety and biodefense fields. | [Hyun-Joong Kima, Si-Hong Parka, Tae-Ho Leeb, Baek-Hie Nahmb, Young-Rok Kima, Hae-Yeong Kima] | Biosensors and Bioelectronics | 15 October 2008 | |
| sciencedirectS0041008X08002949 | The crucial protective role of glutathione against tienilic acid hepatotoxicity in rats | To investigate the hepatotoxic potential of tienilic acid in vivo, we administered a single oral dose of tienilic acid to Sprague–Dawley rats and performed general clinicopathological examinations and hepatic gene expression analysis using Affymetrix microarrays. No change in the serum transaminases was noted at up to 1000 mg/kg, although slight elevation of the serum bile acid and bilirubin, and very mild hepatotoxic changes in morphology were observed. In contrast to the marginal clinicopathological changes, marked upregulation of the genes involved in glutathione biosynthesis [glutathione synthetase and glutamate-cysteine ligase (Gcl)], oxidative stress response [heme oxygenase-1 and NAD(P)H dehydrogenase quinone 1] and phase II drug metabolism (glutathione S-transferase and UDP glycosyltransferase 1A6) were noted after 3 or 6 h post-dosing. The hepatic reduced glutathione level decreased at 3–6 h, and then increased at 24 or 48 h, indicating that the upregulation of NF-E2-related factor 2 (Nrf2)-regulated gene and the late increase in hepatic glutathione are protective responses against the oxidative and/or electrophilic stresses caused by tienilic acid. In a subsequent experiment, tienilic acid in combination with l-buthionine-(S,R)-sulfoximine (BSO), an inhibitor of Gcl caused marked elevation of serum alanine aminotransferase (ALT) with extensive centrilobular hepatocyte necrosis, whereas BSO alone showed no hepatotoxicity. The elevation of ALT by this combination was observed at the same dose levels of tienilic acid as the upregulation of the Nrf2-regulated genes by tienilic acid alone. In conclusion, these results suggest that the impairment of glutathione biosynthesis may play a critical role in the development of tienilic acid hepatotoxicity through extensive oxidative and/or electrophilic stresses. | [Takayoshi Nishiyaa, Kazuhiko Moria, Chiharu Hattoria, Kiyonori Kaia, Hiroko Kataokaa, Noriko Masubuchib, Toshimasa Jindoa, Sunao Manabea] | Toxicology and Applied Pharmacology | 15 October 2008 | |
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| sciencedirectS0378427408006061 | Differences in jet fuel-induced gene expression in human and rat epidermis after the same brief in vivo exposures | | [James N. McDougal, Richard Simman, Carol Garrett] | Toxicology Letters | 5 October 2008 | |
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| sciencedirectS0929139308000917 | The impact of burning and Calluna removal on below-ground methanotroph diversity and activity in a peatland soil | Methanotroph community structure and activity was investigated in a peat soil in which the above-ground vegetation was burned repeatedly during the last 50 years, and in soil unburned since 1954. Regular burning (every 10 years) was found to have no obvious impact on the potential methane-uptake capacity; however, a lower abundance of type I methanotrophs relative to type II methanotrophs in the frequently burned soils was observed using pmoA (encoding a key polypeptide of particulate methane monooxygenase) microarray analyses. Denaturing gradient gel electrophoresis of bacterial 16S rRNA genes indicated that the total bacterial community, and not just the methanotrophs, was affected by the burning. The regular burning also resulted in a decreased abundance of Calluna vegetation relative to mixed grasses in the peatland plots. In a separate mesocosm experiment, Calluna plants and their roots were removed from the peat soils for a growing season (from February 2006 to November 2006). It was shown that removal of Calluna from the soil greatly decreased the methane-uptake capacity of the soils, although no obvious impact on the methanotroph population structure was observed. Real-time PCR quantification of pmoA genes showed that the abundance of methanotrophs in barren soil (without Calluna vegetation) was about fivefold less than in the control soil (with Calluna vegetation). These findings indicate that the methanotroph community is strongly influenced by the above-ground vegetation cover. Burning of Calluna seemed to favour the type II methanotrophs, whereas the removal of the Calluna cover did not appear to affect the relative abundance of methanotroph genera but caused a uniform decrease in the size of methanotroph populations. | [Yin Chena, Niall P. McNamarab, Marc G. Dumonta, Levente Bodrossyc, Nancy Stralis-Pavesec, J. Colin Murrella] | Applied Soil Ecology | October 2008 | |
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| sciencedirectS1389172308702032 | Changes in Gene Expression of Commercial Baker's Yeast during an Air-Drying Process that Simulates Dried Yeast Production | Changes in the gene expression of commercial baker's yeast during an air-drying process, which simulated dried yeast production, were analyzed. K-means clustering suggested that the genes involved in protein folding were transiently up-regulated at early stages, and that the genes involved in fatty acid metabolism were continuously up-regulated. | [Toshihide Nakamuraa, Satomi Mizukami-Murataa, Akira Andoa, Yoshinori Murataa, Hiroshi Takagib, Jun Shimaa] | Journal of Bioscience and Bioengineering | October 2008 | |
| sciencedirectS0168165608007268 | Genomic mechanisms of inhibitor-detoxification for low-cost lignocellulosic bioethanol conversion | | [Zonglin Lewis Liu1, Jaewoong Moon1, Mingzhou Joe Song2] | Journal of Biotechnology | October 2008 | |
| sciencedirectS1000194808600507 | Oligomicroarray-based primary study of gene expression profile changes in Barrett's esophagus | ObjectiveTo analyze the differential expression genes (DEGs) between Barrett's esophagus (BE) and normal esophagus mucosa and explore the target genes related to the development and progression of BE.MethodsThe total RNAs of matched BE and normal esophagus mucosa of BE patients were isolated using one step Trizol method. Matched RNAs were qualified using 10 g/L agarose gel electrophoresis. cRNAs were synthesized, fluorescence labeled and purified after total RNAs were purified. The RNAs of BE and normal esophagus mucosa were hybridized with Agilent oligomicroarray (30 968 probes). The fluorescence intensity features were detected by Agilent scanner and quantified by feature extraction software.Results(1) The total RNA, reverse transcription product and fluorescence labeled cRNA were all of high quality; (2) There were 142 up-regulated genes and 284 down-regulated genes among 2-fold DEGs.ConclusionMicroarray-based studies are feasible in endoscopically obtained tissues. Many BE-associated genes are screened by the high-throughput gene chip. The development and progression of BE is a complicated process involving multiple genes and multiple procedures, and functional study of these genes may help to identify the key genes or pathways involved in the pathogenesis and development of BE. | [Wang Xingweia, Sun Yongganga, Xu Meia, Fang Dianchuna, Gao Hengjunb, Xu Jiangtaob] | Journal of Medical Colleges of PLA | October 2008 | |
| sciencedirectS0885576508001045 | Gene expression analysis of the wheat response to infection by Fusarium pseudograminearum | Crown rot (CR) of wheat, caused by Fusarium pseudograminearum (Fp) and other Fusarium species, is an important disease globally. To understand the host response to challenge by Fp, we examined gene expression changes in the wheat stem base following inoculation with macroconidia using the Affymetrix GeneChip Wheat Genome Array. Induced genes included mainly those with defensive functions such as genes encoding anti-microbial proteins as well as oxidative stress-related proteins, signalling molecules, and proteins involved in both primary and secondary metabolism. Comparison of genes induced by Fp and the biotrophic rust pathogen Puccinia triticina revealed substantial overlap in most functional classes of induced genes, except for oxidative stress-related genes which were specifically induced by the necrotroph, Fp. Differential expression of selected Fp-induced genes was confirmed and further analysed using real-time quantitative RT-PCR on an inoculation time-course of wheat cultivars Kennedy and Sunco. Interestingly, several genes were induced earlier, and to higher levels, in the partially CR-resistant cultivar Sunco than in susceptible Kennedy. Many Fp-induced genes were also activated by methyl jasmonate and benzothiadiazole, an analogue of salicylic acid, suggesting that these signalling molecules may be involved in activating defences during crown rot. Most of the genes identified here that were induced by Fp were also induced by deoxynivalenol (DON), a toxin produced by Fp during CR. In particular, DON induced several genes encoding glucosyltransferases that may be involved in DON detoxification. To initiate functional characterisation, one of these wheat glucosyltransferase genes was over-expressed in Arabidopsis thaliana, however this did not result in improved tolerance to DON. This study is the first comprehensive analysis of the wheat transcriptome during CR and provides new insights into the host processes potentially involved in plant defence against this pathogen. | [Olivia J. Desmonda b c, John M. Mannersa, Peer M. Schenkb, Donald J. Macleanc, Kemal Kazana] | Physiological and Molecular Plant Pathology | October 2008 | |
| sciencedirectS1359511308001980 | Growth phase-dependent expression of Kluyveromyces lactis genes and involvement of 3′-UTR elements | The analysis of Kluyveromyces lactis gene expression by heterologous microarray hybridization and the study of individual genes from K. lactis relative to the growth phase are presented. A total of 248 open reading frames (ORFs) showed preferential expression at early or late logarithmic phases. Some individual genes were also analyzed by Northern blot in a comparative study between K. lactis and Saccharomyces cerevisiae for a more complete view of this regulatory mechanism in yeast. Taking into account the important role of 3′-untranslated regions (3′-UTR) elements in gene expression, the data obtained were used to analyze the 3′-UTR of these genes, searching for regulatory elements. As a result, two potential 3′-UTR cis-elements, MYC and GYC, involved in K. lactis growth phase-dependent regulation of mRNA levels were found in a specific set of genes of early and late logarithmic phases, respectively. The MYC consensus was proved to be functional on KlCYC1 as an element regulating early logarithmic mRNA abundance of its short transcript. | [S. Seoane Rosende, M. Becerra, M.T. Salgado, M. Lamas-Maceiras, M. González, M.A. Freire Picos] | Process Biochemistry | October 2008 | |
| sciencedirectS0041008X08002512 | Gene expression profiles modulated by the human carcinogen aristolochic acid I in human cancer cells and their dependence on TP53 | Aristolochic acid (AA) is the causative agent of urothelial tumours associated with aristolochic acid nephropathy. These tumours contain TP53 mutations and over-express TP53. We compared transcriptional and translational responses of two isogenic HCT116 cell lines, one expressing TP53 (p53-WT) and the other with this gene knocked out (p53-null), to treatment with aristolochic acid I (AAI) (50−100 ?M) for 6−48 h. Modulation of 118 genes was observed in p53-WT cells and 123 genes in p53-null cells. Some genes, including INSIG1, EGR1, CAV1, LCN2 and CCNG1, were differentially expressed in the two cell lines. CDKN1A was selectively up-regulated in p53-WT cells, leading to accumulation of TP53 and CDKN1A. Apoptotic signalling, measured by caspase-3 and -7 activity, was TP53-dependent. Both cell types accumulated in S phase, suggesting that AAI-DNA adducts interfere with DNA replication, independently of TP53 status. The oncogene MYC, frequently over-expressed in urothelial tumours, was up-regulated by AAI, whereas FOS was down-regulated. Observed modulation of genes involved in endocytosis, e.g. RAB5A, may be relevant to the known inhibition of receptor-mediated endocytosis, an early sign of AA-mediated proximal tubule injury. AAI-DNA adduct formation was significantly greater in p53-WT cells than in p53-null cells. Collectively, phenotypic anchoring of the AAI-induced expression profiles to DNA adduct formation, cell-cycle parameters, TP53 expression and apoptosis identified several genes linked to these biological outcomes, some of which are TP53-dependent. These results strengthen the importance of TP53 in AA-induced cancer, and indicate that other alterations, e.g. to MYC oncogenic pathways, may also contribute. | [Maria L. Simõesa, Sarah L. Hockleya 1, Tanja Schwerdtleb 2, Gonçalo Gamboa da Costaa 3, Heinz H. Schmeiserc, David H. Phillipsa, Volker M. Arlta] | Toxicology and Applied Pharmacology | 1 October 2008 | |
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| sciencedirectS0168365908002605 | A peptide-based carrier for intracellular delivery of proteins into malignant glial cells in vitro | Aiming at identification of novel peptides that can be employed for effective targeting of malignant gliomas, we used a 12-mer peptide phage display library and cultured human malignant glioma cells for phage selection. Several common phage clones emerged after 4 rounds of biopanning against the U87MG glioblastoma cell line. The most abundant phage clone VTW, expressing a sequence of VTWTPQAWFQWV, bound to U87MG cells 700-fold more efficiently than the original unselected library. The VTW phage also bound strongly to other human glioma cell lines, including H4, SW1088 and SW1783, but very weakly to normal human astrocytes and SV40-immortalized human astroglial cells. When compared to other non-glial tumor cells, the phage showed 400- to 1400-fold higher binding efficiency for U87MG cells. After linked to positively charged lysine peptides, the VTW peptide became water soluble and was able to deliver biologically active, hydrophilic beta-galactosidase into U87MG cells, with up to 90% of the cells being stained intensively blue. This peptide carrier did not show obvious protein delivery activities in the human astrocytes. Our results provide a proof of principle to the concept that peptides identified through phage display technology can be used to develop protein carriers that are capable of mediating intracellular delivery of hydrophilic macromolecules in a tumor cell-specific manner. | [Chunxiao Wua, Seong Loong Loa, Jerome Boulairea, Michelle Li Wen Hongb, Hui Min Behb, Doreen Siu Yi Leunga, Shu Wanga b] | Journal of Controlled Release | 10 September 2008 | |
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| sciencedirectS1095643308009355 | Time series analyses of sea bream (Sparus aurata L.) stress response after confinement exposure | | [J.A. Calduch-Ginera, A. Saera-Vilaa, M. Cairnsb, G. Daveyb, P. Prunetc, J. Pérez-Sánchezd] | Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology | Supplement | |
| sciencedirectS1568786408001894 | Altered gene expression profiles and higher frequency of spontaneous DNA strand breaks in APEX2-null thymus | A second class II AP endonuclease, APEX2, possesses strong 3′–5′ exonuclease and 3′-phosphodiesterase activities but only very weak AP-endonuclease activity. APEX2 associates with proliferating cell nuclear antigen (PCNA), and the progression of S phase of the cell cycle is accompanied by its expression. APEX2-null mice exhibit severe dyslymphopoiesis in thymus as well as moderate dyshematopoiesis and growth retardation. Comparative gene expression profiling of wild-type and APEX2-null mice using an oligonucleotide microarray revealed that APEX2-null thymus has significantly altered gene expression profiles, reflecting its altered populations of thymocytes. Beyond these altered populations, APEX2-null thymus exhibits significant alterations in expression of genes involved in DNA replication, recombination and repair, including Apex1, Exo1 and Fen1 as well as master genes for the DNA damage response, such as E2f1, Chek1, and proapoptotic genes. We therefore examined the extent of DNA strand breakage, and found that both of single-strand breaks detected as comets and double-strand breaks detected as ?H2AX foci were significantly higher in frequency in most APEX2-null thymocytes compared to wild-type thymocytes. This higher frequency of DNA breaks was accompanied by increased expression of PCNA and increased phosphorylation of p53 at Ser23 and to a lesser extent, at Ser18. The present study clearly demonstrates that APEX2-null lymphocytes have a higher frequency of DNA breaks, indicating that APEX2 may play an important role(s) during their generation and/or repair. | [Yukihiko Dana, Yutaka Ohtab, Daisuke Tsuchimotoa, Mizuki Ohnoa, Yasuhito Idea, Manabu Samib, Tomomasa Kandab, Kunihiko Sakumia, Yusaku Nakabeppua] | DNA Repair | 1 September 2008 | |
| sciencedirectS0012160608010026 | Identification of unique molecular subdomains in the perichondrium and periosteum and their role in regulating gene expression in the underlying chondrocytes | Developing cartilaginous and ossified skeletal anlagen is encapsulated within a membranous sheath of flattened, elongated cells called, respectively, the perichondrium and the periosteum. These periskeletal tissues are organized in distinct morphological layers that have been proposed to support distinct functions. Classical experiments, particularly those using an in vitro organ culture system, demonstrated that these tissues play important roles in regulating the differentiation of the subjacent skeletal elements. However, there has been a lack of molecular markers that would allow analysis of these interactions. To understand the molecular bases for the roles played by the periskeletal tissues, we generated microarrays from perichondrium and periosteum cDNA libraries and used them to compare the gene expression profiles of these two tissues. In situ hybridization analysis of genes identified on the microarrays revealed many unique markers for these tissues and demonstrated that the histologically distinct layers of the perichondrium and periosteum are associated with distinct molecular expression domains. Moreover our marker analysis identified new domains that had not been previously recognized as distinct within these tissues as well as a previously uncharacterized molecular domain along the lateral edges of the adjacent developing cartilage that experimental analysis showed to be dependent upon the perichondrium. | [Amitabha Bandyopadhyaya 1 2, James K. Kubilusb 1, Marsha L. Crochiereb 1, Thomas F. Linsenmayerb, Clifford J. Tabina] | Developmental Biology | 1 September 2008 | |
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| sciencedirectS1087184508001023 | Impact of the unfolded protein response upon genome-wide expression patterns, and the role of Hac1 in the polarized growth, of Candida albicans | The unfolded protein response (UPR) regulates the expression of genes involved in the protein secretory pathway and in endoplasmic reticulum (ER) stress in yeasts and filamentous fungi. We have characterized the global transcriptional response of Candida albicans to ER stresses (dithiothreitol and tunicamycin) and established the impact of the transcription factor Hac1 upon this response. Expression of C. albicans Hac1, which is the functional homologue of Saccharomyces cerevisiae Hac1p, is predicted to be translationally regulated via an atypical mRNA splicing event during ER stress. C. albicans genes involved in secretion, vesicle trafficking, stress responses and cell wall biogenesis are up-regulated in response to ER stress, and translation and ribosome biogenesis genes are down-regulated. Hac1 is not essential for C. albicans viability, but plays a major role in this stress-related transcriptional response and is required for resistance to ER stress. In addition, we show that Hac1 plays an important role in regulating the morphology of C. albicans and in the expression of genes encoding cell surface proteins during ER stress, factors that are important in virulence of this fungal pathogen. | [Tithira T. Wimalasenaa, Brice Enjalbertb 1, Thomas Guillemettea 2, Andrew Plumridgea 3, Susan Budgeb, Z. Yinb, Alistair J.P. Brownb, David B. Archera] | Fungal Genetics and Biology | September 2008 | |
| sciencedirectS1567133X08000690 | A microarray analysis of the XX Wnt4 mutant gonad targeted at the identification of genes involved in testis vascular differentiation | One of the earliest morphological changes during testicular differentiation is the establishment of an XY specific vasculature. The testis vascular system is derived from mesonephric endothelial cells that migrate into the gonad. In the XX gonad, mesonephric cell migration and testis vascular development are inhibited by WNT4 signaling. In Wnt4 mutant XX gonads, endothelial cells migrate from the mesonephros and form a male-like coelomic vessel. Interestingly, this process occurs in the absence of other obvious features of testis differentiation, suggesting that Wnt4 specifically inhibits XY vascular development. Consequently, the XX Wnt4 mutant mice presented an opportunity to focus a gene expression screen on the processes of mesonephric cell migration and testicular vascular development. We compared differences in gene expression between XY Wnt4+/+ and XX Wnt4+/+ gonads and between XX Wnt4−/− and XX Wnt4+/+ gonads to identify sets of genes similarly upregulated in wildtype XY gonads and XX mutant gonads or upregulated in XX gonads as compared to XY gonads and XX mutant gonads. We show that several genes identified in the first set are expressed in vascular domains, and have predicted functions related to cell migration or vascular development. However, the expression patterns and known functions of other genes are not consistent with roles in these processes. This screen has identified candidates for regulation of sex specific vascular development, and has implicated a role for WNT4 signaling in the development of Sertoli and germ cell lineages not immediately obvious from previous phenotypic analyses. | [Douglas Coveney1, Andrea J. Ross1, Jesse D. Slone, Blanche Capel] | Gene Expression Patterns | September 2008 | |
| sciencedirectS1567576908000714 | Induction of high expression of CCR7 and high production of IL-12 in human monocyte-derived dendritic cells by a new bacterial component: LCOS 1013 | Dendritic cells (DCs) are the most potent antigen presenting cells of the immune system as they can act as initiators, stimulators and regulators of the immune response. Human DCs are most commonly generated for clinical use by in vitro differentiation of monocytes with exogenous cytokines. Here, we investigate the effect of LCOS 1013 on the production of mature Mo-DCs. LCOS 1013 is a new bacterial component from walls of gram+Klebsellia pneumoniae bacteria that contain some OmpA glycoproteins. Purified peripheral blood monocytes were cultured for 6 days with IL-4 and GM-CSF in order to obtain immature dendritic cells (Im-MoDCs). On day six, Im-MoDCs were matured with either LCOS 1013, TNF alpha, LPS or CD40-Ligand. LCOS 1013 matured Mo-DCs (LCO-DCs) showed a higher expression of DC-LAMP, CD80, CD83, CD54 and CD40 than TNF alpha, LPS and CD40L matured Mo-DCs. Interestingly, LCO-DCs exhibited high expression of full competent CCR7 and high secretion of IL-12 during their maturation. Functionally, LCO-DCs have equivalent potency to trigger mixed leukocyte reaction and antigen-specific reaction and polarize immune response towards Th1 way. Moreover, we found that LCOS 1013 activates DCs through TLR2. LCOS 1013 represents an attractive therapeutic maturation agent of DCs allowing the production of Mo-DCs with high capacity to migrate and to induced Th1 immune responses. | [Stéphanie Gillet-Hladkya, Karine Duperriera, Stéphanie Picandeta, Virginie Mathiasa, Miranda Camila de Carvalhoa, Janine Bernauda, Daniel Masseaub, Jacques Bienvenuc, Dominique Rigala] | International Immunopharmacology | September 2008 | |
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| sciencedirectS0300483X08002424 | A toxicogenomics approach for early assessment of potential non-genotoxic hepatocarcinogenicity of chemicals in rats | For assessing carcinogenicity in animals, it is difficult and costly, an alternative strategy has been desired. We explored the possibility of applying a toxicogenomics approach by using comprehensive gene expression data in rat liver treated with various compounds. As prototypic non-genotoxic hepatocarcinogens, thioacetamide (TAA) and methapyrilene (MP) were selected and 349 commonly changed genes were extracted by statistical analysis. Taking both compounds as positive with six compounds, acetaminophen, aspirin, phenylbutazone, rifampicin, alpha-naphthylisothiocyanate, and amiodarone as negative, prediction analysis of microarray (PAM) was performed. By training and 10-fold cross validation, a classifier containing 112 probe sets that gave an overall success rate of 95% was obtained. The validity of the present discriminator was checked for 30 chemicals. The PAM score showed characteristic time-dependent increases by treatment with several non-genotoxic hepatocarcinogens, including TAA, MP, coumarin, ethionine and WY-14643, while almost all of the non-carcinogenic samples were correctly predicted. Measurement of hepatic glutathione content suggested that MP and TAA cause glutathione depletion followed by a protective increase, but the protective response is exhausted during repeated administration. Therefore, the presently obtained PAM classifier could predict potential non-genotoxic hepatocarcinogenesis within 24 h after single dose and the inevitable pseudo-positives could be eliminated by checking data of repeated administrations up to 28 days. Tests for carcinogenicity using rats takes at least 2 years, while the present work suggests the possibility of lowering the time to 28 days with high precision, at least for a category of non-genotoxic hepatocarcinogens causing oxidative stress. | [Takeki Ueharaa, Mitsuhiro Hirodea, Atsushi Onoa, Naoki Kiyosawaa, Ko Omuraa, Toshinobu Shimizua, Yumiko Mizukawaa b, Toshikazu Miyagishimaa, Taku Nagaoa c, Tetsuro Urushidania b] | Toxicology | 19 August 2008 | |
| sciencedirectS1570023208002912 | GC–MS methods for metabolic profiling of microbial fermentation products of dietary polyphenols in human and in vitro intervention studies ? | Flavonoids, a subclass of polyphenols, are major constituents of many plant-based foods and beverages, including tea, wine and chocolate. Epidemiological studies have shown that a flavonoid-rich diet is associated with reduced risk of cardiovascular diseases. The majority of the flavonoids survive intact until they reach the colon where they are then extensively metabolized into smaller fragments. Here, we describe the development of GC–MS-based methods for the profiling of phenolic microbial fermentation products in urine, plasma, and fecal water. Furthermore, the methods are applicable for profiling products obtained from in vitro batch culture fermentation models. The methods incorporate enzymatic deconjugation, liquid–liquid extraction, derivatization, and subsequent analysis by GC–MS. At the level of individual compounds, the methods gave recoveries better than 80% with inter-day precision being better than 20%, depending on the matrix. Limits of detection were below 0.1 ?g/ml for most phenolic acids. The newly developed methods were successfully applied to samples from human and in-vitro intervention trials, studying the metabolic impact of flavonoid intake. In conclusion, the methods presented are robust and generally applicable to diverse biological fluids. Its profiling character is useful to investigate on a large scale the gut microbiome-mediated bioavailability of flavonoids. | [Christian H. Grüna, Ferdi A. van Dorstena, Doris M. Jacobsa, Marie Le Belleguica, Ewoud J.J. van Velzena, Max O. Binghama, Hans-Gerd Janssena b, John P.M. van Duynhovena] | Journal of Chromatography B | 15 August 2008 | |
| sciencedirectS157002320800189X | Metabolic profiling of serum using Ultra Performance Liquid Chromatography and the LTQ-Orbitrap mass spectrometry system | Advances in analytical instrumentation can provide significant advantages to the volume and quality of biological knowledge acquired in metabolomic investigations. The interfacing of sub-2 ?m liquid chromatography (UPLC ACQUITY®) and LTQ-Orbitrap mass spectrometry systems provides many theoretical advantages. The applicability of the interfaced systems was investigated using a simple 11-component metabolite mix and a complex mammalian biofluid, serum. Metabolites were detected in the metabolite mix with signals that were linear with their concentration over 2.5–3.5 orders of magnitude, with correlation coefficients greater than 0.993 and limits of detection less than 1 ?mol L−1. Reproducibility of retention time (RSD < 3%) and chromatographic peak area (RSD < 15%) and a high mass accuracy (<2 ppm) were observed for 14 QC serum samples interdispersed with other serum samples, analysed over a period of 40 h. The evaluation of a single deconvolution software package (XCMS) was performed and showed that two parameters (snthresh and bw) provided significant changes to the number of peaks detected and the peak area reproducibility for the dataset used. The data were used to indicate possible biomarkers of pre-eclampsia and showed both the instruments and XCMS to be applicable to the reproducible and valid detection of disease biomarkers present in serum. | [Warwick B. Dunna 1, David Broadhurstb 1, Marie Brownb 1, Philip N. Bakerc, Christopher W.G. Redmand, Louise C. Kennyc e, Douglas B. Kella b] | Journal of Chromatography B | 15 August 2008 | |
| sciencedirectS157002320800250X | A sample extraction and chromatographic strategy for increasing LC/MS detection coverage of the erythrocyte metabolome ? | Reproducible and comprehensive sample extraction and detection of metabolites with a broad range of physico-chemical properties from biological matrices can be a highly challenging process. A single LC/MS separation method was developed for a 2.1 mm × 100 mm, 1.8 ?m ZORBAX SB-Aq column that was used to separate human erythrocyte metabolites extracted under sample extraction solvent conditions where the pH was neutral or had been adjusted to either, pH 2, 6 or 9. Internal standards were included and evaluated for tracking sample extraction efficiency. Through the combination of electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) techniques in both positive (+) and negative (−) ion modes, a total of 2370 features (compounds and associated compound related components: isotopes, adducts and dimers) were detected across all pHs. Broader coverage of the detected metabolome was achieved by observing that (1) performing extractions at pH 2 and 9, leads to a combined 92% increase in detected features over pH 7 alone; and (2) including APCI in the analysis results in a 34% increase in detected features, across all pHs, than the total number detected by ESI. A significant dependency of extraction solvent pH on the recovery of heme and other compounds was observed in erythrocytes and underscores the need for a comprehensive sample extraction strategy and LC/MS analysis in metabolomics profiling experiments. | [Theodore R. Sana, Keith Waddell, Steven M. Fischer] | Journal of Chromatography B | 15 August 2008 | |
| sciencedirectS0165242708001694 | Construction and application of an avian intestinal intraepithelial lymphocyte cDNA microarray (AVIELA) for gene expression profiling during Eimeria maxima infection | Intestinal intraepithelial lymphocytes (IELs) are the primary immune effector cells in the gut and play a critical role in eliciting protective immunity to enteric pathogens such as Eimeria, the etiologic agent of avian coccidiosis. In this study, a microarray of genes expressed by intestinal IELs from Eimeria-infected chickens was constructed using the expressed sequence tag (EST) strategy. The avian intestinal IEL cDNA microarray (AVIELA) contained duplicates of 9668 individual ESTs (6654 known genes and 3014 unique singletons of unknown identity) and was used to analyze gene expression profiles during primary and secondary Eimeria maxima infections. Following primary inoculation with E. maxima, the expression levels of 74 genes were significantly altered more than two-fold over the 3-day infection period (51 up-regulated, 23 down-regulated). Following secondary infection, the expression levels of 308 genes were significantly altered (62 up-regulated, 246 down-regulated). Pathway gene analysis indicated that many of the modulated genes were related to apoptosis, JAK/STAT, MAPK, interleukin, and TLR signaling pathways, and involving innate and adaptive immune responses. This chicken IEL microarray will provide a valuable resource for future transcriptional profiling of the genes involved in protective immunity to chicken enteric pathogens. | [Chul Hong Kima, Hyun S. Lillehoja, Travis W. Blissb, Calvin L. Keeler Jr.b, Yeong Ho Honga, Dong Woon Parka, Mat Yamagea 1, Wongi Mina 2, Erik P. Lillehojc] | Veterinary Immunology and Immunopathology | 15 August 2008 | |
| sciencedirectS0006291X08010164 | Differential display of grouper iridovirus-infected grouper cells by immunostaining | Grouper iridovirus (GIV) is one of the most devastating infectious pathogens of aquaculture fish. When infecting a susceptible cell line, such as GK-2, GIV causes antigenic changes in host cellular proteins. To understand the host gene expression characteristics after viral infection, we developed an immunostaining method to screen differentially expressed genes of fish cells in response to GIV infection using phage display complementary DNA libraries. In total, 66 genes were identified from grouper kidney and brain cell lines. These genes are related to replication, transcription, translation, immunity, apoptosis, structure proteins, metabolism, energy, protein modification, and homeostasis. Four dynamic antigenic patterns were observed among these immunocloned genes upon GIV infection. Microarray analysis further confirmed the transcriptional patterns of 80% of the identified genes. This immunostaining screening method provides insights into a host’s cellular protein response to viral infection on a translational basis. | [Chiao-Hwa Yeha b, Yao-Sheng Chenb, Ming-Shan Wub, Chien-Wen Chenb, Chung-Hsiang Yuanb, Kuo-Wen Panb, Ya-Nan Changb, Nin-Nin Chuangb, Chi-Yao Changb] | Biochemical and Biophysical Research Communications | 8 August 2008 | |
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| sciencedirectS1568786408001857 | Transcriptional changes in trichothiodystrophy cells | Mutations in three of the genes encoding the XPB, XPD and TTDA components of transcription factor TFIIH can result in the clinical phenotype of trichothiodystrophy (TTD). Different mutations in XPB and XPD can instead cause xeroderma pigmentosum (XP). The completely different features of these disorders have been attributed to TTD being a transcription syndrome. In order to detect transcriptional differences between TTD and XP cells from the XP-D complementation group, we have compared gene expression profiles in cultured fibroblasts from normal, XP and TTD donors. Although we detected transcriptional differences between individual cell strains, using an algorithm of moderate stringency, we did not identify any genes whose expression was reproducibly different in proliferating fibroblasts from each type of donor. Following UV-irradiation, many genes were up- and down-regulated in all three cell types. The microarray analysis indicated some apparent differences between the different donor types, but on more detailed inspection, these turned out to be false positives. We conclude that there are minimal differences in gene expression in proliferating fibroblasts from TTD, XP-D and normal donors. | [Judith Offmana, Nipurna Jinab, Therina Therona 1, Jacky Pallasc, Mike Hubankb, Alan Lehmanna] | DNA Repair | 2 August 2008 | |
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| sciencedirectS036192300800141X | Changes in brain gene expression during migration in the white-crowned sparrow | Long-term recordings of seasonal sleep patterns in captive white-crowned sparrows (Zonotrichia leucophrys gambelii) have shown that these birds markedly reduce sleep time during the migratory period relative to the non-migratory period. It was also found that, despite this sleep reduction, sparrows showed no evidence of neurobehavioral deficits in a standard operant task used to assess the effects of sleep loss. In this study, we performed an extensive microarray analysis of gene expression in the sparrow telencephalon during the migratory season (M), relative to a 78-h period of enforced sleep restriction during the non-migratory season (SR), and a 6-h period of normal wakefulness during the non-migratory season (W). Of the estimated 17,100 transcripts that were reliably detected, only 0.17% changed expression as a function of M (relative to both SR and W), and 0.11% as a function of SR (relative to both M and W). Brain transcripts whose expression increased during M include the facilitated glucose transporter GLUT1, the presenilin associated rhomboid-like protein PARL, and several members of the heat shock protein family, such as HSP70, HSP90, GRP78 and BiP. These data suggest that migration is associated with brain cellular stress and enhanced energetic demands. | [Stephany Jonesa b, Martha Pfister-Genskowb, Chiara Cirellib, Ruth M. Bencab] | Brain Research Bulletin | 30 July 2008 | |
| sciencedirectS0300483X08002163 | Gene expression profiles in the articular cartilage of juvenile rats receiving the quinolone antibacterial agent ofloxacin | Quinolone antibacterial agents are extensively utilized in antimicrobial chemotherapy. However, they have been reported to induce arthropathy in juvenile animals, and the mechanism has not been clarified. In the present study, to investigate the molecular details of the chondrotoxicity of the quinolone ofloxacin (OFLX), it was orally administered by gavage at a dose level of 900 mg/kg once to male juvenile Sprague–Dawley rats, 3 weeks of age. Then gene expression profiles in the articular cartilage of the distal femur were analyzed at 2, 4, 8 and 24 h post-dose. In the GeneChip analysis, the expression of 134 gene probes in the OFLX-treated group showed statistically significant differences with at least 1.5-fold difference from the control. Among them, intracellular signaling cascade- and stress response-related genes changed at 2 h post-dose; cell death- and inflammatory response-related genes at 4 and 8 h post-dose; basic-leucine zipper transcription factor and stress response-related genes at 8 and 24 h post-dose; stress response-, proteolysis- and glycoprotein-related genes at 24 h post-dose. In a quantitative real-time reverse transcription-polymerase chain reaction analysis, up-regulated Dusp1 (intracellular signaling cascade-related gene), Tnfrsf12a (cell death-related gene), Ptgs2, Fos (inflammatory response-related genes), Mt1a, Plaur (stress response-related genes) and Mmp3 (proteolysis-related gene) and down-regulated Sstr1 and Has2 (glycoprotein-related genes) were observed with dose dependency in the articular cartilage of juvenile rats treated with OFLX at 100, 300 and 900 mg/kg. The expression of Tnfrsf12a, Ptgs2, Plaur and Mmp3 was also noted in chondrocytes around the cartilage lesions by in situ hybridization. In conclusion, our results suggest that cytokines, chemokines and/or proteases produced by up-regulation of cell death-, inflammatory response-, stress response- and proteolysis-related genes play a important role in the onset of OFLX-induced chondrotoxicity in juvenile rats. | [Koichi Goto, Koichi Yabe, Takami Suzuki, Kiyoshi Takasuna, Toshimasa Jindo, Sunao Manabe] | Toxicology | 30 July 2008 | |
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| sciencedirectS0306452208006386 | Network-based gene expression analysis of intracranial aneurysm tissue reveals role of antigen presenting cells | Little is known about the pathology and pathogenesis of the rupture of intracranial aneurysms. For a better understanding of the molecular processes involved in intracranial aneurysm (IA) formation we performed a gene expression analysis comparing ruptured and unruptured aneurysm tissue to a control artery.Tissue samples of six ruptured and four unruptured aneurysms, and four cerebral arteries serving as controls, were profiled using oligonucleotide microarrays. Gene ontology classification of the differentially expressed genes was analyzed and regulatory functional networks and canonical pathways were identified with a network-based computational pathway analysis tool.Real time reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemical staining were performed as confirmation.Analysis of aneurysmal and control tissue revealed 521 differentially expressed genes. The most significantly associated gene ontology term was antigen processing (P=1.64E-16).Further network-based analysis showed the top scoring regulatory functional network to be built around overexpressed major histocompatibility class (MHC) I and II complex related genes and confirmed the canonical pathway “Antigen Presentation” to have the highest upregulation in IA tissue (P=7.3E-10).Real time RT-PCR showed significant overexpression of MHC class II genes. Immunohistochemical staining showed strong positivity for MHC II molecule specific antibody (HLA II), for CD68 (macrophages, monocytes), for CD45RO (T-cells) and HLA I antibody.Our results offer strong evidence for MHC class II gene overexpression in human IA tissue and that antigen presenting cells (macrophages, monocytes) play a key role in IA formation. | [B. Krischeka b, H. Kasuyab c, A. Tajimad, H. Akagawab, T. Sasakib, T. Yoneyamab, H. Ujiieb, O. Kubob, M. Bonine, K. Takakurac, T. Horib, I. Inoued] | Neuroscience | 17 July 2008 | |
| sciencedirectS0944501308000153 | Transcript profiling of a MAP kinase pathway in C. albicans | SummaryIn Candida albicans, a MAP kinase pathway has been implicated in aspects of controlling hyphal development. We have examined the transcription profile of cells deleted for the transcription factor Cph1p as well as Cst20p, Hst7p, and Cek1p, three upstream kinases potentially involved in Cph1p regulation. Deletion of any of these four elements does not block filament induction by serum and does not dramatically affect the transcription profile of the yeast–hyphal transition, but deletion of CPH1 delays filamentation. Over-expression of Cph1p by ADH1pt-CPH1 significantly enhances filamentation, suggesting that Cph1p is helpful but not essential for filament induction. Interestingly, the transcription profile of ADH1pt-CPH1 expressing cells under yeast conditions is similar to that of wild-type strains undergoing the yeast–hyphal transition. Finally, it appears that Cek1 and its regulators Hst7p and Cst20p may control the repression of genes such as CHT2 through a process independent of the Cph1p transcription factor. | [Hao Huanga, Doreen Harcusa, Malcolm Whitewaya b] | Microbiological Research | 15 July 2008 | |
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| sciencedirectS0361923008000038 | Targeting of neurotrophic factors, their receptors, and signaling pathways in the developmental neurotoxicity of organophosphates in vivo and in vitro ? | Neurotrophic factors control neural cell differentiation and assembly of neural circuits. We previously showed that organophosphate pesticides differentially regulate members of the fibroblast growth factor (fgf) gene family. We administered chlorpyrifos and diazinon to neonatal rats on postnatal days 1–4 at doses devoid of systemic toxicity or growth impairment, and spanning the threshold for barely-detectable cholinesterase inhibition. We evaluated the impact on gene families for different classes of neurotrophic factors. Using microarrays, we examined the regional expression of mRNAs encoding the neurotrophins (ntfs), brain-derived neurotrophic factor (bdnf), nerve growth factor (ngf), the wnt and fzd gene families and the corresponding receptors. Chlorpyrifos and diazinon both had widespread effects on the fgf, ntf, wnt and fzd families but much less on the bdnf and ngf groups. However, the two organophosphates showed disparate effects on a number of key neurotrophic factors. To determine if the actions were mediated directly on differentiating neurons, we tested chlorpyrifos in PC12 cells, an in vitro model of neural cell development. Effects in PC12 cells mirrored many of those for members of the fgf, ntf and wnt families, as well as the receptors for the ntfs, especially during early differentiation, the stage known to be most susceptible to disruption by organophosphates. Our results suggest that actions on neurotrophic factors provide a mechanism for the developmental neurotoxicity of low doses of organophosphates, and, since effects on expression of the affected genes differed with test agent, may help explain regional disparities in effects and critical periods of vulnerability. | [Theodore A. Slotkina, Frederic J. Seidlera, Fabio Fumagallib] | Brain Research Bulletin | 1 July 2008 | |
| sciencedirectS0012160608002820 | UNC-85, a C. elegans homolog of the histone chaperone Asf1, functions in post-embryonic neuroblast replication | Normal animal development requires accurate cell divisions, not only in the early stages of rapid embryonic cleavages, but also in later developmental stages. The Caenorhabditis elegans unc-85 gene is implicated only in cell divisions that occur post-embryonically, primarily in terminal neuronal lineages. Variable post-embryonic cell division failures in ventral cord motoneuron precursors result in uncoordinated locomotion of unc-85 mutant larvae by the second larval stage. These neuroblast cell division failures often result in unequally sized daughter nuclei, and sometimes in nuclear fusions. Using a combination of conventional mapping techniques and microarray analysis, we cloned the unc-85 gene, and find that it encodes one of two C. elegans homologs of the yeast Anti-silencing function 1 (Asf1) histone chaperone. The unc-85 gene is expressed in replicating cells throughout development, and the protein is localized in nuclei. Examination of null mutants confirms that embryonic neuroblast cell divisions occur normally, but post-embryonic neuroblast cell divisions fail. Analysis of the DNA content of the mutant neurons indicates that defective replication in post-embryonic neuroblasts gives rise to ventral cord neurons with an average DNA content of approximately 2.5 n. We conclude that UNC-85 functions in post-embryonic DNA replication in ventral cord motor neuron precursors. | [Iwen F. Grigsby1, Fern P. Finger] | Developmental Biology | 1 July 2008 | |
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| sciencedirectS0090825808003430 | MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer | ObjectivesMost ovarian cancer patients are diagnosed at an advanced stage (67%) and prospects for significant improvement in survival reside in early diagnosis. While expression patterns of a recently identified biomarker family, microRNA, appear to be characteristic of tumor type and developmental origin, microRNA profiling has been limited to tissue specimens. Tumors actively release exosomes into the peripheral circulation and we now demonstrate the association of microRNAs with circulating tumor-derived exosomes.MethodsCirculating tumor exosomes were isolated using a modified MACS procedure with anti-EpCAM. Initially, microRNA profiles of ovarian tumors were compared to those of tumor exosomes isolated from the same patients. Levels of 8 microRNAs (miR-21, miR-141, miR-200a, miR-200c, miR-200b, miR-203, miR-205 and miR-214) previously demonstrated as diagnostic, were compared in exosomes isolated from sera specimens of women with benign disease and various stages of ovarian cancer.ResultsMicroRNA from ovarian tumor cells and exosomes from the same patients were positive for 218 of 467 mature microRNAs analyzed. The levels of the 8 specific microRNAs were similar between cellular and exosomal microRNAs (exhibiting correlations from 0.71 to 0.90). While EpCAM-positive exosomes were detectable in both patients with benign ovarian disease and ovarian cancer, exosomal microRNA from ovarian cancer patients exhibited similar profiles, which were significantly distinct from profiles observed in benign disease. Exosomal microRNA could not be detected in normal controls.ConclusionsThese results suggest that microRNA profiling of circulating tumor exosomes could potentially be used as surrogate diagnostic markers for biopsy profiling, extending its utility to screening asymptomatic populations. | [Douglas D. Taylor, Cicek Gercel-Taylor] | Gynecologic Oncology | July 2008 | |
| sciencedirectS0141113608000639 | Abstracts from Fourteenth International Symposium on Pollutant Responses in Marine Organisms (PRIMO 14) - Environmental Genomics | | [] | Marine Environmental Research | July 2008 | |
| sciencedirectS0141113608000652 | Intersexuality in crustaceans: Genetic, individual and population level effects | Scientists investigating toxicants such as endocrine disrupting chemicals (EDCs) at the cellular at the sub-cellular level are often faced with criticisms as to how these effects can be extrapolated to the level of individuals and their populations. This report aims to provide an overview of the studies undertaken on crustacean model, Echinogammarus marinus LEACH (AMPHIPODA), and intersex phenotypes, at the individual and population levels, and provide additional emergent data at the genomic level. These, normal and intersex, males and females have been investigated by cross-hybridisation microarray analysis and specific sexually dimorphic genes and corresponding properties identified between each sexual phenotype. The morphology, physiology and histology of these intersexes have been investigated in detail and a number of reproductive costs have been identified including reduced fecundity and fertility. These costs have been incorporated into a population model and simulated over a ten-year period to ascertain how different levels of intersexuality affect the stability of populations. Based on the information gained through study of intersex models (with known endocrine dysfunction) together with the substantial quantity of historical data relating to effects of chemicals on amphipod fecundity, growth and mortality, the development of appropriate biomarkers is nearer to being assessed from the level of genes to that of the population. | [Alex T. Forda, Christine Samblesb, Peter Killeb] | Marine Environmental Research | July 2008 | |
| sciencedirectS1044743108000924 | Fibroblast growth factor induces a neural stem cell phenotype in foetal forebrain progenitors and during embryonic stem cell differentiation | Neural stem (NS) cell lines may be derived via differentiation of pluripotent embryonic stem (ES) cells or from foetal forebrain. However, because NS cells arise in vitro from heterogeneous populations their immediate cellular origin remains unclear. We used microarray-based expression profiling to identify a set of markers expressed by mouse NS cells but not ES cells. One differentially expressed gene encodes the cell surface protein, CD44. CD44 expression is activated by FGF-2 in a subset of cells in both differentiating ES cells and foetal forebrain cultures. Following isolation by flow cytometry the CD44+ population was found to be highly enriched for NS cell founders. We found that other NS cell marker genes are also induced by FGF in culture, including: Adam12, Cadherin20, Cx3cl1, EGFR, Frizzled9, Kitl, Olig1, Olig2 and Vav3. We speculate that the self-renewing NS cell state may be generated in vitro following transcriptional resetting induced by FGF. | [Steven M. Pollarda b, Richard Wallbankc, Simon Tomlinsonc, Lars Grotewoldc, Austin Smitha b] | Molecular and Cellular Neuroscience | July 2008 | |
| sciencedirectS0003497508005195 | Lipopolysaccharide Stimulation of Human Aortic Valve Interstitial Cells Activates Inflammation and Osteogenesis | BackgroundCalcific aortic stenosis may be an inflammatory disease with active bone formation in the valve leaflets rather than a disease of passive calcium deposition. Epidemiologic data demonstrating correlation of poor dental hygiene to atherosclerotic pathologies suggests that circulating bacterial products could be involved in the pathogenesis of aortic valve stenosis. We hypothesized that lipopolysaccharide (LPS) stimulation of human aortic valve interstitial cells (HAVICs) would induce inflammatory and osteogenic gene expression.MethodsThe HAVICs were isolated from normal aortic valves obtained from explanted hearts during transplantation (n = 5) and grown in culture. Cells underwent 4 and 24 hours of LPS stimulation (LPS, 200 ng/mL) or ?-glycerol phosphate treatment (BGP) (osteogenic media as positive control). Media was removed for interleukin (IL)-6 and IL-8 immunoassay. Ribonucleic acid was extracted for microarray analysis. Statistics were by analysis of variance with post-hoc analysis (p < 0.05).ResultsThe LPS stimulation induced the gene expression of proinflammatory cytokines, chemokines, and adhesion molecules. Protein level confirmation by immunoassay demonstrated 3.4-fold (± 0.35, p < 0.01) and 9.5-fold (± 1.5 p < 0.01) increase over control of IL-6 and IL-8, respectively. The LPS and BGP both induced critical mediators of osteogenesis including bone morphogenetic protein 2 and platelet-derived growth factor alpha.ConclusionsThe LPS stimulation of HAVICs not only induces inflammatory mediators but also induces gene expression of osteogenic factors, similar to that induced by osteogenic media. Bacterial products stimulation, likely by toll-like receptor 4 and the innate immune system, may contribute to the pathogenesis of aortic valve stenosis. | [Ashok N. Babu MD, Xianzhong Meng MD PhD, Ning Zou MD, Xiaoping Yang PhD, Maorong Wang MD, Yong Song MD, Joseph C. Cleveland MD, Michael Weyant MD, Anirban Banerjee PhD, David A. Fullerton MD] | The Annals of Thoracic Surgery | July 2008 | |
| sciencedirectS0960076008001064 | Differing transcriptional responses to pulsed or continuous estradiol exposure in human umbilical vein endothelial cells | This study used human umbilical vein endothelial cells (HUVECs) that were treated with 17?-estradiol for 5 days as 1 h pulse or 24 h continuous treatment at concentrations such that the 24 h exposure (concentration × time) was identical in both conditions. Cell proliferation was studied and gene expression profiling was carried out using the Affymetrix GeneChip microarray analysis. Changes in morphology and apoptosis in HUVECs were examined with electron microscopy. Time-course studies of expression of genes vascular endothelial growth factor (VEGF), inducible nitric oxide synthase (iNOS) and endothelial nitric oxide synthase (eNOS) were performed by quantitative PCR. We observed that cell proliferation was significantly decreased over days 3–5 with pulsed estradiol treatment relative to constant exposure. Microarray results showed that after 5 days, 801 genes differed (P < 0.05) between continuous versus pulsed estradiol treatment. Functional analysis showed a significant number of genes to be associated with apoptosis and cell cycle pathways. We did not find any evidence of apoptosis from flow cytometry or electron microscopy examination. Our study highlights a large number of significantly different molecular responses to estradiol depending upon the mode of administration of estradiol. Significant changes were observed in genes involved in apoptosis and proliferation including VEGF, IGF receptors, and tumor protein p53. | [Jin Lia, Hongliang Wanga, Suzanne M. Johnsonb, Emma Horner-Glisterb, John Thompsonc, Ian N.H. Whiteb, Farook Al-Azzawia] | The Journal of Steroid Biochemistry and Molecular Biology | July 2008 | |
| sciencedirectS0041008X08000744 | An in vitro method to assess toxicity of waterborne metals to fish | The transcription of metal-responsive genes in the rainbow trout (Oncorhynchus mykiss) gill tissue can be used to detect effects of bioreactive metals in natural waters. Here we take advantage of an in vitro gill epithelium, which can be directly exposed to test water samples. The in vitro gill epithelial model mimics the molecular response of in vivo gill epithelial cells to waterborne contaminants. The same culture system can detect trace metals and organic waterborne contaminants. Furthermore, combining this epithelial model with transcriptomic profiling yields an extremely discriminatory biomonitoring tool able to detect and differentiate waterborne metal contaminants. The bioreactive fraction of metal in the water sample is detected using the cells naturally occurring metal sensor, metal-responsive transcription factor 1 (MTF1), which acts upon Metal Response Elements (MRE's) in the enhancer region of metal regulated genes. Induction of the MTF1 responsive genes, metallothionein-A (MTA), metallothionein-B (MTB), and zinc transporter 1 (ZnT-1) in the cell culture was strongly dependent of the concentrations of bioreactive zinc and silver in the test water. Importantly, gene expression in cell culture reflected animal toxicity, measured as inhibition of Ca2+ and Na+ influx, in live rainbow trout exposed to the same waters. A cDNA microarray was deployed to determine the differential profiles of transcripts characteristic of exposure to silver, copper or cadmium within this in vitro system. These experiments illustrated the potential power of combining the in vitro gill model epithelium with genetic profiling for accurate characterisation and identification of bioreactive toxicants in waterborne samples. | [Paul A. Walkera 1, Peter Killeb, Anna Hurleyb, Nic R. Burya, Christer Hogstranda] | Toxicology and Applied Pharmacology | 1 July 2008 | |
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| sciencedirectS0361923008000270 | Gene expression profile in cerebrum in the filial imprinting of domestic chicks (Gallus gallus domesticus) | In newly hatched chicks, gene expression in the brain has previously been shown to be up-regulated following filial imprinting. By applying cDNA microarrays containing 13,007 expressed sequence tags, we examined the comprehensive gene expression profiling of the intermediate medial mesopallium in the chick cerebrum, which has been shown to play a key role in filial imprinting. We found 52 up-regulated genes and 6 down-regulated genes of at least 2.0-fold changes 3 h after the training of filial imprinting, compared to the gene expression of the dark-reared chick brain. The up-regulated genes are known to be involved in a variety of pathways, including signal transduction, cytoskeletal organization, nuclear function, cell metabolism, RNA binding, endoplasmic reticulum or Golgi function, synaptic function, ion channel, and transporter. In contrast, fewer genes were down-regulated in the imprinting, coinciding with the previous data that the total RNA synthesis increased associated with filial imprinting. Our data suggests that the filial imprinting involves the modulation of multiple signaling pathways. | [Shinji Yamaguchia, Ikuko Fujii-Tairaa, Sachiko Katagiria, Ei-Ichi Izawac, Yasuyuki Fujimotoa, Hideaki Takeuchid, Tatsuya Takanoa, Toshiya Matsushimab, Koichi J. Hommaa] | Brain Research Bulletin | 15 June 2008 | |
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| sciencedirectS0014482708001304 | Growth of cancer cell lines under stem cell-like conditions has the potential to unveil therapeutic targets | Malignant tumors comprise a small proportion of cancer-initiating cells (CIC), capable of sustaining tumor formation and growth. CIC are the main potential target for anticancer therapy. However, the identification of molecular therapeutic targets in CIC isolated from primary tumors is an extremely difficult task. Here, we show that after years of passaging under differentiating conditions, glioblastoma, mammary carcinoma, and melanoma cell lines contained a fraction of cells capable of forming spheroids upon in vitro growth under stem cell-like conditions. We found an increased expression of surface markers associated with the stem cell phenotype and of oncogenes in cell lines and clones cultured as spheroids vs. adherent cultures. Also, spheroid-forming cells displayed increased tumorigenicity and an altered pattern of chemosensitivity. Interestingly, also from single retrovirally marked clones, it was possible to isolate cells able to grow as spheroids and associated with increased tumorigenicity. Our findings indicate that short-term selection and propagation of CIC as spheroid cultures from established cancer cell lines, coupled with gene expression profiling, represents a suitable tool to study and therapeutically target CIC: the notion of which genes have been down-regulated during growth under differentiating conditions will help find CIC-associated therapeutic targets. | [Germana Rappa, Javier Mercapide, Fabio Anzanello, Lina Prasmickaite, Yaguang Xi, Jingfang Ju, Oystein Fodstad, Aurelio Lorico] | Experimental Cell Research | 10 June 2008 | |
| sciencedirectS0014482708001419 | Downregulation of hepatocyte nuclear factor-4? and its role in regulation of gene expression by TGF-? in mammary epithelial cells | We found that a specific isoform of hepatocyte nuclear factor 4? (HNF-4?), HNF-4?8, was expressed in mouse mammary epithelial NMuMG cells, and that its expression was repressed by TGF-?. The repression was interfered by dominant negative forms of activin receptor-like kinase 5 (ALK5) and Smad3, and sensitive to cycloheximide, suggesting the involvement of additional protein(s) as well as ALK5 and Smad3 in the repression. Further study showed that high mobility group A2 (HMGA2), which is reported to be directly upregulated by Smads, repressed HNF-4?8 expression. Therefore, it is likely that HMGA2 mediates the downregulation of HNF-4?8 downstream of ALK5 and Smads To determine the significance of the downregulation of HNF-4?8 in TGF-? signaling, we performed DNA microarray analysis and extracted a subgroup of TGF-?1-regulated genes, including tenascin C and tissue inhibitor of metalloproteinase 3 (TIMP-3), whose regulation by TGF-?1 was attenuated by forced expression of HNF-4?8. HMGA2 has recently emerged as a transcriptional organizer of TGF-? signaling, regulating several key factors involved in epithelial–mesenchymal transition (EMT). In this study, we identified an isoform of HNF-4? as a new target downstream of HMGA2 and assigned a new role to HNF-4? in the TGF-? signaling/transcriptional cascade driven by ALK5/Smad/HMGA2 and associated with the malignant transformation of cells. | [Fumihiro Ishikawa, Kiyoshi Nose, Motoko Shibanuma] | Experimental Cell Research | 10 June 2008 | |
| sciencedirectS0006291X08006220 | Gene expression patterns in glucose-stimulated podocytes ? | To explore the mechanisms of podocyte injury under diabetic conditions, we performed an expression profile in glucose-stimulated podocytes. Differential gene expression profiles between conditionally immortalized mouse podocytes cultured in medium containing 5.6 and 30 mM glucose were measured with oligonucleotide microarrays. Of the genes identified, heme oxygenase-1, vascular endothelial growth factor-A, and thrombospondin-1 showed a consistently increased pattern, whereas angiotensin-converting enzyme-2 and peroxisomal proliferator activator receptor-? were down-regulated. These results were validated using real-time PCR and western blotting in podocytes, and with immunohistochemistry on renal tissues from streptozotocin-induced diabetic rats. Not only is this the first report of gene expression profiling of podocyte injury under diabetic conditions, but the identified genes are promising targets for future diabetes research. | [Seung Hyeok Hana, Sanghwa Yangc, Dong Sub Jungb, Jin Ji Lid, Jin Ju Kimb, Seung Jae Kwakb, Dong Ki Kima, Sung Jin Moona, Jung Eun Leea, Dae-Suk Hana, Shin-Wook Kanga] | Biochemical and Biophysical Research Communications | 6 June 2008 | |
| sciencedirectS0006899308005726 | Gene profiling the response to repeated cocaine self-administration in dorsal striatum: A focus on circadian genes | Alterations in gene expression in the dorsal striatum caused by chronic cocaine exposure have been implicated in the long-term behavioral changes associated with cocaine addiction. To gain further insight into the molecular alterations that occur as a result of cocaine self-administration, we conducted a microarray analysis of gene expression followed by bioinformatic gene network analysis that allowed us to identify adaptations at the level of gene expression as well as into interconnected networks. Changes in gene expression were examined in the dorsal striatum of rats 1 day after they had self-administered cocaine for 7 days under a 24-h access, discrete trial paradigm (averaging 98 mg/kg/day). Here we report the regulation of the circadian genes Clock, Bmal1, Cryptochrome1, Period2, as well as several genes that are regulated by/associated with the circadian system (i.e., early growth response 1, dynorphin). We also observed regulation of other relevant genes (i.e., Nur77, beta catenin). These changes were then linked to curated pathways and formulated networks which identified circadian rhythm processes as affected by cocaine self-administration. These data strongly suggest involvement of circadian-associated genes in the brain's response to cocaine and may contribute to an understanding of addictive behavior including disruptions in sleep and circadian rhythmicity. | [Wendy J. Lyncha, Matthew J. Girgentib, Florence J. Breslina, Samuel S. Newtonb, Jane R. Taylorb] | Brain Research | | |
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| sciencedirectS0165017308000283 | Global profiling of influence of intra-ischemic brain temperature on gene expression in rat brain | Mild to moderate differences in brain temperature are known to greatly affect the outcome of cerebral ischemia. The impact of brain temperature on ischemic disorders has been mainly evaluated through pathological analysis. However, no comprehensive analyses have been conducted at the gene expression level. Using a high-density oligonucleotide microarray, we screened 24 000 genes in the hippocampus under hypothermic (32 °C), normothermic (37 °C), and hyperthermic (39 °C) conditions in a rat ischemia-reperfusion model. When the ischemic group at each intra-ischemic brain temperature was compared to a sham-operated control group, genes whose expression levels changed more than three-fold with statistical significance could be detected. In our screening condition, thirty-three genes (some of them novel) were obtained after screening, and extensive functional surveys and literature reviews were subsequently performed. In the hypothermic condition, many neuroprotective factor genes were obtained, whereas cell death- and cell damage-associated genes were detected as the brain temperature increased. At all intra-ischemic brain temperatures, multiple molecular chaperone genes were obtained. The finding that intra-ischemic brain temperature affects the expression level of many genes related to neuroprotection or neurotoxicity coincides with the different pathological outcomes at different brain temperatures, demonstrating the utility of the genetic approach. | [Megumi Sugahara Kobayashia b, Satoshi Asaia, Koichi Ishikawab, Yayoi Nishidaa, Toshihito Nagataa, Yasuo Takahashia] | Brain Research Reviews | June 2008 | |
| sciencedirectS1087184508000455 | Aspergillus oryzae atfB encodes a transcription factor required for stress tolerance in conidia | Using an Aspergillus oryzae EST database, we identified a gene encoding a transcription factor (atfB), which is a member of the ATF/CREB family. Expression of atfB was barely detectable during vegetative growth, but was readily detected during conidiation in solid-state culture. Microarray analyses showed that expression of many other genes, including catalase (catA), were downregulated in an atfB-disruptant. The expression of most of these genes was upregulated in the wild-type strain during the conidiation phase in solid-state culture, and the expression pattern was similar to that of atfB itself. In the absence of stress, e.g. heat-shock or hydrogen peroxide, the conidial germination ratios for the ?atfB strain and the wild-type strain were similar, but the stress tolerance of conidia carrying the ?atfB deletion was less than that of the wild-type conidia. CRE-like DNA motifs, which are bound by ATF/CREB proteins, were found in the promoters of most of the downregulated genes in the ?atfB strain. Thus, atfB appears to encode a transcription factor required for stress tolerance in conidia. | [Kazutoshi Sakamotoa c, Toshi-hide Arimab, Kazuhiro Iwashitaa, Osamu Yamadaa, Katsuya Gomic, Osamu Akitaa] | Fungal Genetics and Biology | June 2008 | |
| sciencedirectS0047637408000419 | Aging-induced alterations in gene transcripts and functional activity of mitochondrial oxidative phosphorylation complexes in the heart | Aging is associated with progressive decline in energetic reserves compromising cardiac performance and tolerance to injury. Although deviations in mitochondrial functions have been documented in senescent heart, the molecular bases for the decline in energy metabolism are only partially understood. Here, high-throughput transcription profiles of genes coding for mitochondrial proteins in ventricles from adult (6-months) and aged (24-months) rats were compared using microarrays. Out of 614 genes encoding for mitochondrial proteins, 94 were differentially expressed with 95% downregulated in the aged. The majority of changes affected genes coding for proteins involved in oxidative phosphorylation (39), substrate metabolism (14) and tricarboxylic acid cycle (6). Compared to adult, gene expression changes in aged hearts translated into a reduced mitochondrial functional capacity, with decreased NADH-dehydrogenase and F0F1 ATPase complex activities and capacity for oxygen-utilization and ATP synthesis. Expression of genes coding for transcription co-activator factors involved in the regulation of mitochondrial metabolism and biogenesis were downregulated in aged ventricles without reduction in mitochondrial density. Thus, aging induces a selective decline in activities of oxidative phosphorylation complexes I and V within a broader transcriptional downregulation of mitochondrial genes, providing a substrate for reduced energetic efficiency associated with senescence. | [Claudia C. Prestona b, Andrew S. Oberlinb, Ekhson L. Holmuhamedovb, Anu Guptaa b, Sandeep Sagarb, Rashad H. Khazi Syedb, Sabeeh A. Siddiquib, Sreekumar Raghavakaimalc, Andre Terzica b, Arshad Jahangira b] | Mechanisms of Ageing and Development | June 2008 | |
| sciencedirectS0168010208000400 | Behavioral and gene expression analyses of Wfs1 knockout mice as a possible animal model of mood disorder | Wolfram disease is a rare genetic disorder frequently accompanying depression and psychosis. Non-symptomatic mutation carriers also have higher rates of depression and suicide. Because WfS1, the causative gene of Wolfram disease, is located at 4p16, a linkage locus for bipolar disorder, mutations of WfS1 were suggested to be involved in the pathophysiology of bipolar disorder. In this study, we performed behavioral and gene expression analyses of Wfs1 knockout mice to assess the validity as an animal model of mood disorder. In addition, the distribution of Wfs1 protein was examined in mouse brain. Wfs1 knockout mice did not show abnormalities in circadian rhythm and periodic fluctuation of wheel-running activity. Behavioral analysis showed that Wfs1 knockout mice had retardation in emotionally triggered behavior, decreased social interaction, and altered behavioral despair depending on experimental conditions. Wfs1-like immunoreactivity in mouse brain showed a similar distribution pattern to that in rats, including several nuclei potentially relevant to the symptoms of mood disorders. Gene expression analysis showed down-regulation of Cdc42ep5 and Rnd1, both of which are related to Rho GTPase, which plays a role in dendrite development. These findings may be relevant to the mood disorder observed in patients with Wolfram disease. | [Tadafumi Katoa, Mizuho Ishiwataa, Kazuyuki Yamadab, Takaoki Kasaharaa, Chihiro Kakiuchia, Kazuya Iwamotoa, Koki Kawamurac, Hisamitsu Ishiharad, Yoshitomo Okad] | Neuroscience Research | June 2008 | |
| sciencedirectS0304394008004199 | Novel candidate genes identified in the brain during nociception in common carp (Cyprinus carpio) and rainbow trout (Oncorhynchus mykiss) | Recent studies have demonstrated that teleost fish possess nociceptors that detect potentially painful stimuli and that the physiological properties of these fibres are markedly similar to those found in mammals. This finding led to suggestions of possible pain perception in fish, contrary to the view that the sensory response in these animals is limited to the spinal cord and hindbrain and as such is reflexive. Therefore, the aim of this study was to determine if the brain is active at the molecular level by using a microarray analysis of gene expression in the forebrain, midbrain and hindbrain of two fish species. A comparison between the two species at different time points showed that many genes were differentially regulated in response to a noxious stimulus compared with controls. A number of genes that are involved in mammalian nociception, such as brain-derived neurotrophic factor (BDNF) and the cannabinoid CB1 receptor were regulated in the fish brain after a nociceptive event. Novel candidates that showed significant regulation in both species were also identified. In particular, the Van Gogh-like 2 gene, was regulated in both carp and trout and should be pursued to establish its precise role in nociception. | [Siobhan C. Reillya, John P. Quinnb, Andrew R. Cossinsa, Lynne U. Sneddona] | Neuroscience Letters | 30 May 2008 | |
| sciencedirectS0006899308005568 | Neurobehavioral basis of the impaired nurturing in mice lacking the immediate early gene FosB | The transcription factor FosB is induced in neurons of the medial preoptic area (MPOA) during parenting, through activation of the extracellular signal-regulated kinase (ERK). FosB mutant (−/−) postpartum mice and virgin mice that are exposed to pups show defective nurturing behavior. The FosB (−/−) MPOA fails to fully up-regulate SPRY1 and Rad, the feedback regulators of ERK and calcium signaling, respectively. Here we studied FosB function by examining the gene expression profiles and the behavioral characteristics of FosB (−/−) mice. We found that FosB (−/|−) mice exhibited not only decreased parenting but also decreased infanticide compared with (+/) littermates. We then performed gene expression analysis in the MPOA of FosB (−/−) mice compared with the wild-type littermates. We found up-regulation of glial fibrillary acidic protein (GFAP), C4, and Ela1 mRNA in the MPOA of FosB (−/−) mice; all of these gene products were implicated in general neuropathological conditions. Immunohistochemical analysis showed that up-regulation of GFAP was not restricted to MPOA but extended throughout the forebrain, including the cerebral cortex and striatum. Such pervasive GFAP up-regulation suggested that FosB (−/−) mice might have other behavioral abnormalities than nurturing. Indeed, these mice showed a clear alteration in emotionality, detected by the acoustic startle, elevated plus maze, and passive avoidance tests. These results suggest that FosB (−/−) mice have broader neurobehavioral dysfunctions, with which the nurturing defect might share the common mechanism. | [Kumi O. Kurodaa b, Michael J. Meaneyc, Noriko Uetanid, Tadafumi Katob] | Brain Research | | |
| sciencedirectS0889159107002589 | Sex differences in the recognition of and innate antiviral responses to Seoul virus in Norway rats | Among rodents that carry hantaviruses, more males are infected than females. Male rats also have elevated copies of Seoul virus RNA and reduced transcription of immune-related genes in the lungs than females. To further characterize sex differences in antiviral defenses and whether these differences are mediated by gonadal hormones, we examined viral RNA in the lungs, virus shedding in saliva, and antiviral defenses among male and female rats that were intact, gonadectomized neonatally, or gonadectomized in adulthood. Following inoculation with Seoul virus, high amounts viral RNA persisted longer in lungs from intact males than intact females. Removal of the gonads in males reduced the amount of viral RNA to levels comparable with intact females at 40 days post-inoculation (p.i.). Intact males shed more virus in saliva than intact females 15 days p.i.; removal of the gonads during either the neonatal period or in adulthood increased virus shedding in females and decreased virus shedding in males. Induction of pattern recognition receptors (PRRs; Tlr7 and Rig-I), expression of antiviral genes (Myd88, Visa, Jun, Irf7, Ifn?, Ifnar1, Jak2, Stat3, and Mx2), and production of Mx protein was elevated in the lungs of intact females compared with intact males. Gonadectomy had more robust effects on the induction of PRRs than on downstream IFN? or Mx2 expression. Putative androgen and estrogen response elements are present in the promoters of several of these antiviral genes, suggesting the propensity for sex steroids to directly affect dimorphic antiviral responses against Seoul virus infection. | [Michele F. Hannaha, Vladimir B. Bajicb, Sabra L. Kleina] | Brain, Behavior, and Immunity | May 2008 | |
| sciencedirectS0531556508000387 | Effects of interleukin-6 −174C/G and metallothionein 1A +647A/C single-nucleotide polymorphisms on zinc-regulated gene expression in ageing ? | Decreased zinc ion availability in ageing is associated with altered immune response. One of the main regulators of zinc availability is metallothionein. Metallothionein induction is under the control of interleukin-6, a pro-inflammatory cytokine whose production is associated with poor ageing. The production of interleukin-6 is controlled, in part, by variability in the −174 nucleotide position. Under conditions of chronic inflammation, such as in ageing, zinc release by metallothionein is limited and may reduce zinc availability. Understanding the precise nature of the interactions between interleukin-6 and metallothioneins will aid in identifying individuals who are at risk of zinc deficiency. In the current study, we used gene arrays to investigate the effects of in vitro zinc supplementation on gene expression in elderly donors with described interleukin-6 and metallothionein 1a polymorphisms. Ingenuity Pathway Analysis™ identified several zinc-responsive genetic networks uniquely regulated only in elderly individuals with the pro-inflammatory interleukin-6 polymorphism. These include zinc-dependent decreased transcription of pro-inflammatory cytokines and alterations in metabolic regulatory pathways. The genomic effects of zinc increased in significance in the presence of the metallothionein 1a +647 C/A transition, suggesting that the interleukin-6 and metallothionein 1a genes act in a concerted manner to control zinc-regulated gene expression. | [D.J. Mazzattia, M. Malavoltab, A.J. Whitec, L. Costarellib, R. Giacconib, E. Mutib, C. Ciprianob, J.R. Powella, E. Mocchegianib] | Experimental Gerontology | May 2008 | |
| sciencedirectS1087184507002344 | Gene expression in Fusarium graminearum grown on plant cell wall | Fusarium graminearum is a phytopathogenic filamentous fungus attacking a wide range of plants including Humulus lupulus (hop). Transcriptional analysis of F. graminearum grown on minimal media containing hop cell wall or glucose as the sole carbon source was performed by applying a highly stringent method combining microarrays and a subtracted cDNA library. In addition to genes coding for various cell wall degrading enzymes (CWDE), several metabolic pathways were induced in response to the plant cell wall substrate. Many genes participating in these pathways are probably involved in cellular transport. But the most interesting was that all the genes composing the 4-aminobutyrate-shunt (GABA-shunt) were also up-regulated in the presence of plant cell wall material and were present in the cDNA library. This study provides a description of a part of the fungal gene expression profile when it is in contact with raw biological materials, and helps in understanding the plant cell wall degradation and the infection process. | [Raphaël Carapitoa, Didier Hatschb, Sonja Vorwerkc, Elizabet Petkovskid, Jean-Marc Jeltscha, Vincent Phalipa] | Fungal Genetics and Biology | May 2008 | |
| sciencedirectS0888754308000396 | ZFAT expression in B and T lymphocytes and identification of ZFAT-regulated genes | The human ZFAT gene encodes a 1243-amino-acid protein containing one AT hook and 18 C2H2 zinc finger domains, which are highly conserved among ZFAT orthologues from fish to mammalian species. Consistent with the presence of multiple predicted nuclear localization signals, endogenous ZFAT protein was found to be localized to the nucleus. In the mouse tissues examined by Western blotting, ZFAT was found to be expressed in thymus, spleen, and lymph nodes, but not in other tissues, including bone marrow. Furthermore, ZFAT protein was found to be up-regulated during the transition from CD4-CD8- to CD4+CD8+ thymocytes and to be expressed only in B and T lymphocytes in peripheral lymphoid tissues. Expression array analyses demonstrated that genes that are down-regulated upon ZFAT overexpression in mouse Ba/F3 cells are significantly enriched for those functionally related to immune responses. These results suggest that ZFAT functions as a critical transcriptional regulator in B and T lymphocytes. | [Midori Koyanagia 1, Kazuhiko Nakabayashia b 1, Takahiro Fujimotoa, Ning Gua, Iwai Babaa, Yasuo Takashimaa, Keiko Doia, Haruhito Haradac, Norihiro Katoc, Takehiko Sasazukic, Senji Shirasawaa] | Genomics | May 2008 | |
| sciencedirectS0965174808000234 | Cross-induction of detoxification genes by environmental xenobiotics and insecticides in the mosquito Aedes aegypti: Impact on larval tolerance to chemical insecticides ? | The effect of exposure of Aedes aegypti larvae to sub-lethal doses of the pyrethroid insecticide permethrin, the organophosphate temephos, the herbicide atrazine, the polycyclic aromatic hydrocarbon fluoranthene and the heavy metal copper on their subsequent tolerance to insecticides, detoxification enzyme activities and expression of detoxification genes was investigated. Bioassays revealed a moderate increase in larval tolerance to permethrin following exposure to fluoranthene and copper while larval tolerance to temephos increased moderately after exposure to atrazine, copper and permethrin. Cytochrome P450 monooxygenases activities were induced in larvae exposed to permethrin, fluoranthene and copper while glutathione S-transferase activities were induced after exposure to fluoranthene and repressed after exposure to copper. Microarray screening of the expression patterns of all detoxification genes following exposure to each xenobiotic with the Aedes Detox Chip identified multiple genes induced by xenobiotics and insecticides. Further expression studies using real-time quantitative PCR confirmed the induction of multiple CYP genes and one carboxylesterase gene by insecticides and xenobiotics. Overall, this study reveals the potential of xenobiotics found in polluted mosquito breeding sites to affect their tolerance to insecticides, possibly through the cross-induction of particular detoxification genes. Molecular mechanisms involved and impact on mosquito control strategies are discussed. | [Rodolphe Poupardina, Stéphane Reynauda, Clare Strodeb, Hilary Ransonb, John Vontasc, Jean-Philippe Davida] | Insect Biochemistry and Molecular Biology | May 2008 | |
| sciencedirectS0945053X08000085 | Fibroblast adhesion results in the induction of a matrix remodeling gene expression program | Fibrosis is believed to occur through the failure to terminate the normal tissue remodeling program. Tissue repair intimately involves the ability of fibroblasts to attach to extracellular matrix (ECM), resulting in cell migration and ECM contraction. Elevated, activated adhesive signaling is a key phenotypic hallmark of fibrotic cells. The precise contribution of adhesion to tissue remodeling and repair and fibrotic responses in fibroblasts is unclear, but involves focal adhesion kinase (FAK). FAK signals downstream of integrin-mediates attachment of fibroblasts to extracellular matrix. In this report, we show that FAK is required for the expression of a cohort of mRNAs encoding ECM and matrix remodeling genes including CCN2, ?-smooth muscle actin (SMA) and type I collagen. Adhesion of fibroblasts to fibronectin, a component of the provisional matrix deposited in the initial phases of tissue repair, also resulted in the induction of CCN2, ?-SMA and type I collagen mRNAs. Endothelin-1 (ET-1), a key inducer of pro-fibrotic gene expression, was also induced upon fibroblast attachment to ECM, and antagonism of the ET-1 receptors significantly reduced the ability of adhesion to induce expression of CCN2, ?-SMA and type I collagen mRNAs. These results suggest that adhesion of fibroblasts to matrix during the initial phases of tissue remodeling and repair may actively contribute to the tissue repair program through the induction of pro-fibrotic gene expression. | [Laura Kennedya, Xu Shi-wenb, David E. Carterc, David J. Abrahamb, Andrew Leaska] | Matrix Biology | May 2008 | |
| sciencedirectS1286457908000543 | Effect of bacterial vaginosis, Lactobacillus and Premarin estrogen replacement therapy on vaginal gene expression changes ? | The aim of the study was to investigate gene expression profiles of post-menopausal women receiving Premarin estrogen replacement therapy (ERT), compared to controls, and to examine any correlations between the bacterial vaginosis (BV) status of the subjects. Based upon an expected finding of a 50–60% difference between gene expression of host antimicrobials with alpha = 0.05 (2-sided), beta = 0.20 the calculation of 7 subjects per group, led to a sample size of 10 subjects receiving Premarin estrogen replacement therapy and 10 healthy, age-matched controls. Vaginal samples were collected at a single timepoint and processed for RNA recovery and Affymetrix array analysis, as well as Nugent scoring and denaturing gradient gel electrophoresis to identify bacteria. Lactobacillus iners was the most commonly detected species in the normal flora and this was confirmed with L. iners-specific PCR method. Vaginal swabs from 6 Premarin and 8 control vaginal samples provided a non-invasive means to analyze human gene expression. There was no significant up-regulation of cancer-associated gene expression in subject receiving Premarin ERT, but some evidence that the potentially protective innate immunity was reduced in patients with BV. Of those with a normal flora, there was a 2-fold down-regulation of carcinoma associated forkhead box A1 gene expression. BV was associated with 7-fold down-regulation of host antimicrobial colony stimulating factor, −9.83-fold for IL-1?, −8.33 for IL-1? and −3.63 for IL-6. This is the first study to use gene arrays to correlate changes in host expression response to estrogen replacement therapy and BV. | [Adam Dahna, Sheri Saundersb, Jo-Anne Hammondb c, David Carterd, Pirkka Kirjavainenb e, Kingsley Anukamb, Gregor Reida b f] | Microbes and Infection | May 2008 | |
| sciencedirectS0161589008000096 | Coordinated down-regulation of the antigen processing machinery in the gills of amoebic gill disease-affected Atlantic salmon (Salmo salar L.) | Several important cultured marine fish are highly susceptible to an ectoparasitic condition known as amoebic gill disease (AGD). In AGD-affected fish, modulation of IL-1?, p53 and p53-regulated transcripts is restricted to the (multi)focal AGD-associated gill lesions. To determine whether this lesion-restricted modulation of transcripts occurs on a transcriptome-wide scale and to identify mechanisms that underpin the susceptibility of fish to AGD, we compared the transcriptome of AGD lesions with “normal” tissue from AGD-affected and healthy individuals. Global gene expression profiling using a 16 K salmonid microarray, revealed a total of 176 significantly regulated annotated features and of those, the modulation of 99 (56%) was lesion-restricted. Annotated transcripts were classified according to functional gene ontology. Within the immune response category, transcripts were almost universally down-regulated. In AGD-affected tissue, significant, coordinated down-regulation of the major histocompatibility complex class I (MHC I) pathway-related genes occurred during the later stages of infection and appeared to be mediated by down-regulation of interferon-regulatory factor (IRF)-1, independent of interferon-?, interferon-? and IRF-2 expression. Within this micro-environment, suppression of the MHC I and possibly the MHC II pathways may inhibit the development of acquired immunity and could explain the unusually high susceptibility of Atlantic salmon to AGD. | [N.D. Younga, G.A. Cooperb, B.F. Nowaka, B.F. Koopb, R.N. Morrisona] | Molecular Immunology | May 2008 | |
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| sciencedirectS030442380800006X | Profiling gibberellin (GA3)-responsive genes in mature mandarin fruit using a citrus 22K oligoarray | Gibberellin3 (GA3)-responsive genes were investigated with a citrus 22K oligoarray1 to further the understanding of transcriptional regulation by GA3 treatment in Satsuma mandarin fruit (Citrus unshiu Marc.). 213 GA3-responsive genes were identified that showed a 3-fold or greater expression change after 72 h GA3 treatment, compared to expression after 72 h air treatment. GA3 treatment induced expression of pathogenesis-related (PR) proteins and genes that function in photosynthesis, chloroplast biogenesis, resistance, defense and stress. Also, GA3 treatment reduced the transcription of several ethylene-inducible genes, such as carotenoid metabolic genes, which are associated with fruit ripening.Contrasting effects between GA3 and ethylene were observed on photosynthesis and chloroplast biogenesis, chlorophyll metabolism, and carotenoid metabolism, indicating that the endogenous GA3 level might be important for the endogenous regulation of maturation and senescence in mature citrus fruit. It was also found that the GA response pathway was likely to take part in cross-talk with the pathogen-related pathway in mature citrus fruit. | [Hiroshi Fujiia, Takehiko Shimadaa, Aiko Sugiyamab, Tomoko Endoa, Fumie Nishikawaa, Michiharu Nakanob, Yoshinori Ikomaa, Tokuro Shimizua, Mitsuo Omurab] | Scientia Horticulturae | 1 May 2008 | |
| sciencedirectS0014299908001088 | Systemic evaluation of gene expression changes in major target organs induced by atorvastatin | Statins have been reported to protect against end-organ damage in essential hypertension; however, detailed mechanisms underlying organ-protective actions of statins remain unclear. Statins can exert pleiotropic effects aside from lowering cholesterol and blood pressure levels through several different pathways, which may lead to distinct patterns of changes in gene expression in vital end-organs. The aim of the present study was to systemically evaluate gene expression changes in three major end-organs (the brain, heart and kidney) induced by atorvastatin at a dose that altered neither blood pressure nor plasma total cholesterol levels. The stroke-prone spontaneously hypertensive (SHRSP) rats, an established model of hypertension and end-organ damage, was treated with atorvastatin (15 mg/kg/day) for 4 weeks from 12 to 16 weeks of age. DNA microarray technology was used to identify gene expression changes in three end-organs. In the current experimental setting, 4 weeks of atorvastatin treatment lowered plasma levels of non-esterified fatty acid significantly (P = 0.0012) and triglyceride modestly (P = 0.07) without altering blood pressure and plasma total cholesterol levels in male SHRSP rats. The level of expression of a number of genes was changed in an organ-specific manner after 4 weeks of drug administration to SHRSP rats. Among the end-organs studied, the most prominent alteration in gene expression was observed in the heart. The identical treatment protocol was applied to age-matched normotensive control rats, Wistar Kyoto rats, and this also caused a number of genes to be differentially expressed in an organ-specific manner. These results provide new insights into the mechanisms underlying the potential efficacy of statins in protecting against end-organ damage in essential hypertension and thus lay the foundation for future studies. | [Norihiro Kato, Yi-Qiang Liang, Yoshinori Ochiai, Subrina Jesmin] | European Journal of Pharmacology | 28 April 2008 | |
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| naturepublishinggroup10.1038/modpathol.2011.213 | Genomic analysis of marginal zone and lymphoplasmacytic lymphomas identified common and disease-specific abnormalities | Lymphoplasmacytic lymphomas and marginal zone lymphomas of nodal, extra-nodal and splenic types account for 10% of non-Hodgkin lymphomas. They are similar at the cell differentiation level, sometimes making difficult to distinguish them from other indolent non-Hodgkin lymphomas. To better characterize their genetic basis, we performed array-based comparative genomic hybridization in 101 marginal zone lymphomas (46 MALT, 35 splenic and 20 nodal marginal zone lymphomas) and 13 lymphoplasmacytic lymphomas. Overall, 90% exhibited copy-number abnormalities. Lymphoplasmacytic lymphomas demonstrated the most complex karyotype (median=7 copy-number abnormalities), followed by MALT (4), nodal (3.5) and splenic marginal zone lymphomas (3). A comparative analysis exposed a group of copy-number abnormalities shared by several or all the entities with few disease-specific abnormalities. Gain of chromosomes 3, 12 and 18 and loss of 6q23-q24 (TNFAIP3) were identified in all entities. Losses of 13q14.3 (MIRN15A-MIRN16-1) and 17p13.3-p12 (TP53) were found in lymphoplasmacytic and splenic marginal zone lymphomas; loss of 11q21-q22 (ATM) was found in nodal, splenic marginal zone and lymphoplasmacytic lymphomas and loss of 7q32.1-q33 was found in MALT, splenic and lymphoplasmacytic lymphomas. Abnormalities affecting the nuclear factor kappa B pathway were observed in 70% of MALT and lymphoplasmacytic lymphomas and 30% of splenic and nodal marginal zone lymphomas, suggesting distinct roles of this pathway in the pathogenesis/progression of these subtypes. Elucidation of the genetic alterations contributing to the pathogenesis of these lymphomas may guide to design-specific therapeutic approaches. | [Esteban Braggio, Ahmet Dogan, Jonathan J Keats, Wee J Chng, Gaofeng Huang, Julie M Matthews, Matthew J Maurer, Mark E Law, David S Bosler, Michael Barrett, Izidore S Lossos, Thomas E Witzig, Rafael Fonseca] | Modern Pathology | 2012-02-03 | |
| naturepublishinggroup10.1038/bjc.2012.6 | The association of statins and taxanes: an efficient combination trigger of cancer cell apoptosis | | [J Follet, L Corcos, G Baffet, F Ezan, F Morel, B Simon, C Le Jossic-Corcos] | British Journal of Cancer | 2012-01-31 | |
| naturepublishinggroup10.1038/onc.2011.646 | SIX1 promotes epithelial|[ndash]|mesenchymal transition in colorectal cancer through ZEB1 activation | Epithelial–mesenchymal transition (EMT) has a major role in cancer progression, as well as normal organ development and human pathology such as organ fibrosis and wound healing. Here, we performed a gene expression array specialized in EMT of colorectal cancer (CRC). From a comprehensive gene expression analysis using epithelial- and mesenchymal-like CRC cell lines, and following the ontology (GO) analysis, SIX1 gene was identified to be an EMT-related gene in CRC. Using SW480 cells stably transfected with a SIX1 expression construct and their control counterparts, we demonstrated that SIX1 overexpression represses CDH1 expression and promotes EMT in CRC. SIX1-induced CDH1 repression and EMT in CRC cells were correlated at least in part with posttranscriptional ZEB1 activation and miR-200-family transcriptional repression. In primary tumors of CRC, in accord with the functional findings, aberrant expression of SIX1 in cancer cells was observed at the disruption of the basement membrane and at the tumor invasive front, where tumor cells underwent EMT in vivo. Taken together, SIX1 overexpression is suggested to occur in carcinogenesis, and contribute to repression of CDH1 expression and promotion of EMT partly through repression of miR-200-family expression and activation of ZEB1 in CRC. | [H Ono, I Imoto, K Kozaki, H Tsuda, T Matsui, Y Kurasawa, T Muramatsu, K Sugihara, J Inazawa] | Oncogene | 2012-01-30 | |
| naturepublishinggroup10.1038/onc.2011.624 | Androgen-regulated miR-32 targets BTG2 and is overexpressed in castration-resistant prostate cancer | The androgen receptor (AR) signaling pathway is involved in the emergence of castration-resistant prostate cancer (CRPC). Here, we identified several androgen-regulated microRNAs (miRNAs) that may contribute to the development of CRPC. Seven miRNAs, miR-21, miR-32, miR-99a, miR-99b, miR-148a, miR-221 and miR-590-5p, were found to be differentially expressed in CRPC compared with benign prostate hyperplasia (BPH) according to microarray analyses. Significant growth advantage for LNCaP cells transfected with pre-miR-32 and pre-miR-148a was found. miR-32 was demonstrated to reduce apoptosis, whereas miR-148a enhanced proliferation. Androgen regulation of miR-32 and miR-148a was confirmed by androgen stimulation of the LNCaP cells followed by expression analyses. The AR-binding sites in proximity of these miRNAs were demonstrated with chromatin immunoprecipitation (ChIP). To identify target genes for the miRNAs, mRNA microarray analyses were performed with LNCaP cells transfected with pre-miR-32 and pre-miR-148a. Expression of BTG2 and PIK3IP1 was reduced in the cells transfected with pre-miR-32 and pre-miR-148a, respectively. Also, the protein expression was reduced according to western blot analysis. BTG2 and PIK3IP1 were confirmed to be targets by 3′UTR-luciferase assays. Finally, immunostainings showed a statistically significant (P<0.0001) reduction of BTG2 protein in CRPCs compared with untreated prostate cancer (PC). The lack of BTG2 staining was also associated (P<0.01) with a short progression-free time in patients who underwent prostatectomy. In conclusion, androgen-regulated miR-32 is overexpressed in CRPC, leading to reduced expression of BTG2. Thus, miR-32 is a potential marker for aggressive disease and is a putative drug target in PC. | [S E Jalava, A Urbanucci, L Latonen, K K Waltering, B Sahu, O A J|[auml]|nne, J Sepp|[auml]|l|[auml]|, H L|[auml]|hdesm|[auml]|ki, T L J Tammela, T Visakorpi] | Oncogene | 2012-01-23 | |
| naturepublishinggroup10.1038/emboj.2011.500 | Myeloid translocation gene 16 is required for maintenance of haematopoietic stem cell quiescence | The t(8;21) and t(16;21) that are associated with acute myeloid leukaemia disrupt two closely related genes termed Myeloid Translocation Genes 8 (MTG8) and 16 (MTG16), respectively. Many of the transcription factors that recruit Mtg16 regulate haematopoietic stem and progenitor cell functions and are required to maintain stem cell self-renewal potential. Accordingly, we found that Mtg16-null bone marrow (BM) failed in BM transplant assays. Moreover, when removed from the animal, Mtg16-deficient stem cells continued to show defects in stem cell self-renewal assays, suggesting a requirement for Mtg16 in this process. Gene expression analysis indicated that Mtg16 was required to suppress the expression of several key cell-cycle regulators including E2F2, and chromatin immunoprecipitation assays detected Mtg16 near an E2A binding site within the first intron of E2F2. BrdU incorporation assays indicated that in the absence of Mtg16 more long-term stem cells were in the S phase, even after competitive BM transplantation where normal stem and progenitor cells are present, suggesting that Mtg16 plays a role in the maintenance of stem cell quiescence. | [Melissa A Fischer, Isabel Moreno-Miralles, Aubrey Hunt, Brenda J Chyla, Scott W Hiebert] | The EMBO Journal | 2012-01-20 | |
| naturepublishinggroup10.1038/ismej.2011.215 | Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions | Regulatory small RNAs (sRNAs) have crucial roles in the adaptive responses of bacteria to changes in the environment. Thus far, potential regulatory RNAs have been studied mainly in marine picocyanobacteria in genetically intractable Prochlorococcus, rendering their molecular analysis difficult. Synechococcus sp. WH7803 is a model cyanobacterium, representative of the picocyanobacteria from the mesotrophic areas of the ocean. Similar to the closely related Prochlorococcus it possesses a relatively streamlined genome and a small number of genes, but is genetically tractable. Here, a comparative genome analysis was performed for this and four additional marine Synechococcus to identify the suite of possible sRNAs and other RNA elements. Based on the prediction and on complementary microarray profiling, we have identified several known as well as 32 novel sRNAs. Some sRNAs overlap adjacent coding regions, for instance for the central photosynthetic gene psbA. Several of these novel sRNAs responded specifically to environmentally relevant stress conditions. Among them are six sRNAs changing their accumulation level under cold stress, six responding to high light and two to iron limitation. Target predictions suggested genes encoding components of the light-harvesting apparatus as targets of sRNAs originating from genomic islands and that one of the iron-regulated sRNAs might be a functional homolog of RyhB. These data suggest that marine Synechococcus mount adaptive responses to these different stresses involving regulatory sRNAs. | [Gregor Gierga, Bj|[ouml]|rn Voss, Wolfgang R Hess] | The ISME Journal | 2012-01-19 | 10.0 |
| naturepublishinggroup10.1038/ismej.2011.203 | Acyl homoserine lactone-based quorum sensing in a methanogenic archaeon | Acyl homoserine lactone (AHL)-based quorum sensing commonly refers to cell density-dependent regulatory mechanisms found in bacteria. However, beyond bacteria, this cell-to-cell communication mechanism is poorly understood. Here we show that a methanogenic archaeon, Methanosaeta harundinacea 6Ac, encodes an active quorum sensing system that is used to regulate cell assembly and carbon metabolic flux. The methanogen 6Ac showed a cell density-dependent physiology transition, which was related to the AHL present in the spent culture and the filI gene-encoded AHL synthase. Through extensive chemical analyses, a new class of carboxylated AHLs synthesized by FilI protein was identified. These carboxylated AHLs facilitated the transition from a short cell to filamentous growth, with an altered carbon metabolic flux that favoured the conversion of acetate to methane and a reduced yield in cellular biomass. The transcriptomes of the filaments and the short cell forms differed with gene expression profiles consistent with the physiology. In the filaments, genes encoding the initial enzymes in the methanogenesis pathway were upregulated, whereas those for cellular carbon assimilation were downregulated. A luxI–luxR ortholog filI–filR was present in the genome of strain 6Ac. The carboxylated AHLs were also detected in other methanogen cultures and putative filI orthologs were identified in other methanogenic genomes as well. This discovery of AHL-based quorum sensing systems in methanogenic archaea implies that quorum sensing mechanisms are universal among prokaryotes. | [Guishan Zhang, Fan Zhang, Gang Ding, Jie Li, Xiaopeng Guo, Jinxing Zhu, Liguang Zhou, Shichun Cai, Xiaoli Liu, Yuanming Luo, Guifeng Zhang, Wenyuan Shi, Xiuzhu Dong] | The ISME Journal | 2012-01-12 | |
| naturepublishinggroup10.1038/bjc.2011.595 | Changes in circulating microRNA levels associated with prostate cancer | | [R J Bryant, T Pawlowski, J W F Catto, G Marsden, R L Vessella, B Rhees, C Kuslich, T Visakorpi, F C Hamdy] | British Journal of Cancer | 2012-01-12 | |
| naturepublishinggroup10.1038/emboj.2011.486 | RP58 controls neuron and astrocyte differentiation by downregulating the expression of Id1|[ndash]|4 genes in the developing cortex | Appropriate number of neurons and glial cells is generated from neural stem cells (NSCs) by the regulation of cell cycle exit and subsequent differentiation. Although the regulatory mechanism remains obscure, Id (inhibitor of differentiation) proteins are known to contribute critically to NSC proliferation by controlling cell cycle. Here, we report that a transcriptional factor, RP58, negatively regulates all four Id genes (Id1–Id4) in developing cerebral cortex. Consistently, Rp58 knockout (KO) mice demonstrated enhanced astrogenesis accompanied with an excess of NSCs. These phenotypes were mimicked by the overexpression of all Id genes in wild-type cortical progenitors. Furthermore, Rp58 KO phenotypes were rescued by the knockdown of all Id genes in mutant cortical progenitors but not by the knockdown of each single Id gene. Finally, we determined p57 as an effector gene of RP58-Id-mediated cell fate control. These findings establish RP58 as a novel key regulator that controls the self-renewal and differentiation of NSCs and restriction of astrogenesis by repressing all Id genes during corticogenesis. | [Shinobu Hirai, Akiko Miwa, Chiaki Ohtaka-Maruyama, Masataka Kasai, Shigeo Okabe, Yutaka Hata, Haruo Okado] | The EMBO Journal | 2012-01-10 | |
| naturepublishinggroup10.1038/emboj.2011.487 | A molecular mechanism that links Hippo signalling to the inhibition of Wnt/|[beta]|-catenin signalling | The Hippo signalling pathway has emerged as a key regulator of organ size, tissue homeostasis, and patterning. Recent studies have shown that two effectors in this pathway, YAP/TAZ, modulate Wnt/β-catenin signalling through their interaction with β-catenin or Dishevelled, depending on biological contexts. Here, we identify a novel mechanism through which Hippo signalling inhibits Wnt/β-catenin signalling. We show that YAP and TAZ, the transcriptional co-activators in the Hippo pathway, suppress Wnt signalling without suppressing the stability of β-catenin but through preventing its nuclear translocation. Our results show that YAP/TAZ binds to β-catenin, thereby suppressing Wnt-target gene expression, and that the Hippo pathway-stimulated phosphorylation of YAP, which induces cytoplasmic translocation of YAP, is required for the YAP-mediated inhibition of Wnt/β-catenin signalling. We also find that downregulation of Hippo signalling correlates with upregulation of β-catenin signalling in colorectal cancers. Remarkably, our analysis demonstrates that phosphorylated YAP suppresses nuclear translocation of β-catenin by directly binding to it in the cytoplasm. These results provide a novel mechanism, in which Hippo signalling antagonizes Wnt signalling by regulating nuclear translocation of β-catenin. | [Masamichi Imajo, Koichi Miyatake, Akira Iimura, Atsumu Miyamoto, Eisuke Nishida] | The EMBO Journal | 2012-01-10 | |
| naturepublishinggroup10.1038/cr.2012.4 | A human ESC model for MLL-AF4 leukemic fusion gene reveals an impaired early hematopoietic-endothelial specification | The MLL-AF4 fusion gene is a hallmark genomic aberration in high-risk acute lymphoblastic leukemia in infants. Although it is well established that MLL-AF4 arises prenatally during human development, its effects on hematopoietic development in utero remain unexplored. We have created a human-specific cellular system to study early hemato-endothelial development in MLL-AF4-expressing human embryonic stem cells (hESCs). Functional studies, clonal analysis and gene expression profiling reveal that expression of MLL-AF4 in hESCs has a phenotypic, functional and gene expression impact. MLL-AF4 acts as a global transcriptional activator and a positive regulator of homeobox gene expression in hESCs. Functionally, MLL-AF4 enhances the specification of hemogenic precursors from hESCs but strongly impairs further hematopoietic commitment in favor of an endothelial cell fate. MLL-AF4 hESCs are transcriptionally primed to differentiate towards hemogenic precursors prone to endothelial maturation, as reflected by the marked upregulation of master genes associated to vascular-endothelial functions and early hematopoiesis. Furthermore, we report that MLL-AF4 expression is not sufficient to transform hESC-derived hematopoietic cells. This work illustrates how hESCs may provide unique insights into human development and further our understanding of how leukemic fusion genes, known to arise prenatally, regulate human embryonic hematopoietic specification. | [Clara Bueno, Rosa Montes, Gustavo J Melen, Ver|[oacute]|nica Ramos-Mejia, Pedro J Real, Ver|[oacute]|nica Ayll|[oacute]|n, Laura Sanchez, Gertrudis Ligero, Iv|[aacute]|n Gutierrez-Aranda, Agust|[iacute]|n F Fern|[aacute]|ndez, Mario F Fraga, Inmaculada Moreno-Gimeno, Deborah Burks, Mar|[iacute]|a del Carmen Plaza-Calonge, Juan C Rodr|[iacute]|guez-Manzaneque, Pablo Menendez] | Cell Research | 2012-01-03 | |
| naturepublishinggroup10.1038/emboj.2011.459 | Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors | Long non-coding RNAs (lncRNAs) are a numerous class of newly discovered genes in the human genome, which have been proposed to be key regulators of biological processes, including stem cell pluripotency and neurogenesis. However, at present very little functional characterization of lncRNAs in human differentiation has been carried out. In the present study, we address this using human embryonic stem cells (hESCs) as a paradigm for pluripotency and neuronal differentiation. With a newly developed method, hESCs were robustly and efficiently differentiated into neurons, and we profiled the expression of thousands of lncRNAs using a custom-designed microarray. Some hESC-specific lncRNAs involved in pluripotency maintenance were identified, and shown to physically interact with SOX2, and PRC2 complex component, SUZ12. Using a similar approach, we identified lncRNAs required for neurogenesis. Knockdown studies indicated that loss of any of these lncRNAs blocked neurogenesis, and immunoprecipitation studies revealed physical association with REST and SUZ12. This study indicates that lncRNAs are important regulators of pluripotency and neurogenesis, and represents important evidence for an indispensable role of lncRNAs in human brain development. | [Shi-Yan Ng, Rory Johnson, Lawrence W Stanton] | The EMBO Journal | 2011-12-23 | |
| naturepublishinggroup10.1038/bjc.2011.522 | The anticancer effects of chaetocin are independent of programmed cell death and hypoxia, and are associated with inhibition of endothelial cell proliferation | | [C R Isham, J D Tibodeau, A R Bossou, J R Merchan, K C Bible] | British Journal of Cancer | 2011-12-20 | |
| naturepublishinggroup10.1038/srep00201 | Triterpenoid modulation of IL-17 and Nrf-2 expression ameliorates neuroinflammation and promotes remyelination in autoimmune encephalomyelitis | Inflammatory cytokines and endogenous anti-oxidants are variables affecting disease progression in multiple sclerosis (MS). Here we demonstrate the dual capacity of triterpenoids to simultaneously repress production of IL-17 and other pro-inflammatory mediators while exerting neuroprotective effects directly through Nrf2-dependent induction of anti-oxidant genes. Derivatives of the natural triterpene oleanolic acid, namely CDDO-trifluoroethyl-amide (CDDO-TFEA), completely suppressed disease in a murine model of MS, experimental autoimmune encephalomyelitis (EAE), by inhibiting Th1 and Th17 mRNA and cytokine production. Encephalitogenic T cells recovered from treated mice were hypo-responsive to myelin antigen and failed to adoptively transfer the disease. Microarray analyses showed significant suppression of pro-inflammatory transcripts with concomitant induction of anti-inflammatory genes including Ptgds and Hsd11b1. Finally, triterpenoids induced oligodendrocyte maturation in vitro and enhanced myelin repair in an LPC-induced non-inflammatory model of demyelination in vivo. These results demonstrate the unique potential of triterpenoid derivatives for the treatment of neuroinflammatory disorders such as MS. | [Tej K. Pareek, Abdelmadjid Belkadi, Sashi Kesavapany, Anita Zaremba, Sook L. Loh, Lianhua Bai, Mark L. Cohen, Colin Meyer, Karen T. Liby, Robert H. Miller, Michael B. Sporn, John J. Letterio] | Scientific Reports | 2011-12-19 | |
| naturepublishinggroup10.1038/emboj.2011.465 | Identification and characterization of a resident vascular stem/progenitor cell population in preexisting blood vessels | Vasculogenesis, the in-situ assembly of angioblast or endothelial progenitor cells (EPCs), may persist into adult life, contributing to new blood vessel formation. However, EPCs are scattered throughout newly developed blood vessels and cannot be solely responsible for vascularization. Here, we identify an endothelial progenitor/stem-like population located at the inner surface of preexisting blood vessels using the Hoechst method in which stem cell populations are identified as side populations. This population is dormant in the steady state but possesses colony-forming ability, produces large numbers of endothelial cells (ECs) and when transplanted into ischaemic lesions, restores blood flow completely and reconstitutes de-novo long-term surviving blood vessels. Moreover, although surface markers of this population are very similar to conventional ECs, and they reside in the capillary endothelium sub-population, the gene expression profile is completely different. Our results suggest that this heterogeneity of stem-like ECs will lead to the identification of new targets for vascular regeneration therapy. | [Hisamichi Naito, Hiroyasu Kidoya, Susumu Sakimoto, Taku Wakabayashi, Nobuyuki Takakura] | The EMBO Journal | 2011-12-16 | |
| naturepublishinggroup10.1038/gt.2011.198 | Molecular signature of the immune and tissue response to non-coding plasmid DNA in skeletal muscle after electrotransfer | Electrotransfer of plasmid DNA in skeletal muscle is a common non-viral delivery method for both therapeutic genes and DNA vaccines. Yet, despite the similar approaches, an immune response is detrimental in gene therapy, but desirable for vaccines. However, the full nature of the immune and tissue responses to nucleic acids and electrotransfer in skeletal muscle has not been addressed. Here we used microarray analysis, fluorescence-activated cell sorting and quantitative polymerase chain reaction to obtain the molecular and cellular signature of the tissue and immune response to electrotransfer of saline and non-coding plasmid DNA. Saline electrotransfer resulted in limited infiltration and induction of a moderate damage–repair gene expression pattern not involving innate immune activation. However, plasmid electrotransfer augmented expression of the same genes in addition to inducing a strong innate immune response associated with pro-inflammatory infiltration. In particular, the inflammasome, Toll-like receptor 9 and other pattern recognition receptors able to respond to cytoplasmic DNA were upregulated. Several key differences in the nature of the inflammatory infiltrate and the kinetics of gene expression were also identified when comparing electrotransfer of conventional and CpG-free plasmids. Our data provide insights into the mechanisms of DNA detection and response in muscle that has relevance for non-viral gene therapy and DNA vaccination. | [C J Mann, X M Anguela, J Montan|[eacute]|, M Obach, C Roca, A Ruzo, P Otaegui, L M Mir, F Bosch] | Gene Therapy | 2011-12-15 | |
| naturepublishinggroup10.1038/npp.2011.285 | Cerebrospinal Fluid Biomarkers for Major Depression Confirm Relevance of Associated Pathophysiology | Individual characteristics of pathophysiology and course of depressive episodes are at present not considered in diagnostics. There are no biological markers available that can assist in categorizing subtypes of depression and detecting molecular variances related to disease-causing mechanisms between depressed patients. Identification of such differences is important to create patient subgroups, which will benefit from medications that specifically target the pathophysiology underlying their clinical condition. To detect characteristic biological markers for major depression, we analyzed the cerebrospinal fluid (CSF) proteome of depressed vs control persons, using two-dimensional polyacrylamide gel electrophoresis and time-of-flight (TOF) mass spectrometry peptide profiling. Proteins of interest were identified by matrix-assisted laser desorption ionization TOF mass spectrometry (MALDI-TOF-MS). Validation of protein markers was performed by immunoblotting. We found 11 proteins and 144 peptide features that differed significantly between CSF from depressed patients and controls. In addition, we detected differences in the phosphorylation pattern of several CSF proteins. A subset of the differentially expressed proteins implicated in brain metabolism or central nervous system disease was validated by immunoblotting. The identified proteins are involved in neuroprotection and neuronal development, sleep regulation, and amyloid plaque deposition in the aging brain. This is one of the first hypothesis-free studies that identify characteristic protein expression differences in CSF of depressed patients. Proteomic approaches represent a powerful tool for the identification of disease markers for subgroups of patients with major depression. | [Claudia Ditzen, Ning Tang, Archana M Jastorff, Larysa Teplytska, Alexander Yassouridis, Giuseppina Maccarrone, Manfred Uhr, Thomas Bronisch, Christine A Miller, Florian Holsboer, Christoph W Turck] | Neuropsychopharmacology | 2011-12-14 | |
| naturepublishinggroup10.1038/nm.2574 | Focal adhesion kinase links mechanical force to skin fibrosis via inflammatory signaling | Exuberant fibroproliferation is a common complication after injury for reasons that are not well understood1. One key component of wound repair that is often overlooked is mechanical force, which regulates cell-matrix interactions through intracellular focal adhesion components, including focal adhesion kinase (FAK)1, 2. Here we report that FAK is activated after cutaneous injury and that this process is potentiated by mechanical loading. Fibroblast-specific FAK knockout mice have substantially less inflammation and fibrosis than control mice in a model of hypertrophic scar formation. We show that FAK acts through extracellular-related kinase (ERK) to mechanically trigger the secretion of monocyte chemoattractant protein-1 (MCP-1, also known as CCL2), a potent chemokine that is linked to human fibrotic disorders3, 4, 5. Similarly, MCP-1 knockout mice form minimal scars, indicating that inflammatory chemokine pathways are a major mechanism by which FAK mechanotransduction induces fibrosis. Small-molecule inhibition of FAK blocks these effects in human cells and reduces scar formation in vivo through attenuated MCP-1 signaling and inflammatory cell recruitment. These findings collectively indicate that physical force regulates fibrosis through inflammatory FAK–ERK–MCP-1 pathways and that molecular strategies targeting FAK can effectively uncouple mechanical force from pathologic scar formation. | [Victor W Wong, Kristine C Rustad, Satoshi Akaishi, Michael Sorkin, Jason P Glotzbach, Michael Januszyk, Emily R Nelson, Kemal Levi, Josemaria Paterno, Ivan N Vial, Anna A Kuang, Michael T Longaker, Geoffrey C Gurtner] | Nature Medicine | 2011-12-11 | |
| naturepublishinggroup10.1038/onc.2011.554 | Identification of novel CHD1-associated collaborative alterations of genomic structure and functional assessment of CHD1 in prostate cancer | A clearer definition of the molecular determinants that drive the development and progression of prostate cancer (PCa) is urgently needed. Efforts to map recurrent somatic deletions in the tumor genome, especially homozygous deletions (HODs), have provided important positional information in the search for cancer-causing genes. Analyzing HODs in the tumors of 244 patients from two independent cohorts and 22 PCa xenografts using high-resolution single-nucleotide polymorphism arrays, herein we report the identification of CHD1, a chromatin remodeler, as one of the most frequently homozygously deleted genes in PCa, second only to PTEN in this regard. The HODs observed in CHD1, including deletions affecting only internal exons of CHD1, were found to completely extinguish the expression of mRNA of this gene in PCa xenografts. Loss of this chromatin remodeler in clinical specimens is significantly associated with an increased number of additional chromosomal deletions, both hemi- and homozygous, especially on 2q, 5q and 6q. Together with the deletions observed in HEK293 cells stably transfected with CHD1 small hairpin RNA, these data suggest a causal relationship. Downregulation of Chd1 in mouse prostate epithelial cells caused dramatic morphological changes indicative of increased invasiveness, but did not result in transformation. Indicating a new role of CHD1, these findings collectively suggest that distinct CHD1-associated alterations of genomic structure evolve during and are required for the development of PCa. | [W Liu, J Lindberg, G Sui, J Luo, L Egevad, T Li, C Xie, M Wan, S-T Kim, Z Wang, A R Turner, Z Zhang, J Feng, Y Yan, J Sun, G S Bova, C M Ewing, G Yan, M Gielzak, S D Cramer, R L Vessella, S L Zheng, H Gr|[ouml]|nberg, W B Isaacs, J Xu] | Oncogene | 2011-12-05 | |
| naturepublishinggroup10.1038/onc.2011.558 | Inflammation-induced repression of tumor suppressor miR-7 in gastric tumor cells | Inflammation has an important role in cancer development through various mechanisms. It has been shown that dysregulation of microRNAs (miRNAs) that function as oncogenes or tumor suppressors contributes to tumorigenesis. However, the relationship between inflammation and cancer-related miRNA expression in tumorigenesis has not yet been fully understood. Using K19-C2mE and Gan mouse models that develop gastritis and gastritis-associated tumors, respectively, we found that 21 miRNAs were upregulated, and that 29 miRNAs were downregulated in gastric tumors in an inflammation-dependent manner. Among these miRNAs, the expression of miR-7, a possible tumor suppressor, significantly decreased in both gastritis and gastric tumors. Moreover, the expression of miR-7 in human gastric cancer was inversely correlated with the levels of interleukin-1β and tumor necrosis factor-α, suggesting that miR-7 downregulation is related to the severity of inflammatory responses. In the normal mouse stomach, miR-7 expression was at a basal level in undifferentiated gastric epithelial cells, and was induced during differentiation. Moreover, transfection of a miR-7 precursor into gastric cancer cells suppressed cell proliferation and soft agar colony formation. These results suggest that suppression of miR-7 expression is important for maintaining the undifferentiated status of gastric epithelial cells, and thus contributes to gastric tumorigenesis. Although epigenetic changes were not found in the CpG islands around miR-7-1 of gastritis and gastric tumor cells, we found that activated macrophage-derived small molecule(s) (<3 kDa) are responsible for miR-7 repression in gastric cancer cells. Furthermore, the miR-7 expression level significantly decreased in the inflamed gastric mucosa of Helicobacter-infected mice, whereas it increased in the stomach of germfree K19-C2mE and Gan mice wherein inflammatory responses were suppressed. Taken together, these results indicate that downregulation of tumor suppressor miR-7 is a novel mechanism by which the inflammatory response promotes gastric tumorigenesis. | [D Kong, Y-S Piao, S Yamashita, H Oshima, K Oguma, S Fushida, T Fujimura, T Minamoto, H Seno, Y Yamada, K Satou, T Ushijima, T-O Ishikawa, M Oshima] | Oncogene | 2011-12-05 | |
| naturepublishinggroup10.1038/nature10688 | FBXO11 targets BCL6 for degradation and is inactivated in diffuse large B-cell lymphomas | BCL6 is the product of a proto-oncogene implicated in the pathogenesis of human B-cell lymphomas1, 2. By binding specific DNA sequences, BCL6 controls the transcription of a variety of genes involved in B-cell development, differentiation and activation. BCL6 is overexpressed in the majority of patients with aggressive diffuse large B-cell lymphoma (DLBCL), the most common lymphoma in adulthood, and transgenic mice constitutively expressing BCL6 in B cells develop DLBCLs similar to the human disease3, 4. In many DLBCL patients, BCL6 overexpression is achieved through translocation (~40%) or hypermutation of its promoter (~15%). However, many other DLBCLs overexpress BCL6 through an unknown mechanism. Here we show that BCL6 is targeted for ubiquitylation and proteasomal degradation by a SKP1–CUL1–F-box protein (SCF) ubiquitin ligase complex that contains the orphan F-box protein FBXO11 (refs 5, 6). The gene encoding FBXO11 was found to be deleted or mutated in multiple DLBCL cell lines, and this inactivation of FBXO11 correlated with increased levels and stability of BCL6. Similarly, FBXO11 was either deleted or mutated in primary DLBCLs. Notably, tumour-derived FBXO11 mutants displayed an impaired ability to induce BCL6 degradation. Reconstitution of FBXO11 expression in FBXO11-deleted DLBCL cells promoted BCL6 ubiquitylation and degradation, inhibited cell proliferation, and induced cell death. FBXO11-deleted DLBCL cells generated tumours in immunodeficient mice, and the tumorigenicity was suppressed by FBXO11 reconstitution. We reveal a molecular mechanism controlling BCL6 stability and propose that mutations and deletions in FBXO11 contribute to lymphomagenesis through BCL6 stabilization. The deletions/mutations found in DLBCLs are largely monoallelic, indicating that FBXO11 is a haplo-insufficient tumour suppressor gene. | [Shanshan Duan, Lukas Cermak, Julia K. Pagan, Mario Rossi, Cinzia Martinengo, Paola Francia di Celle, Bjoern Chapuy, Margaret Shipp, Roberto Chiarle, Michele Pagano] | Nature | 2011-11-23 | 11.5 |
| naturepublishinggroup10.1038/ejhg.2011.212 | Case report: type 1 diabetes in monozygotic quadruplets | Type 1 diabetes (T1D) is an autoimmune disease characterized by the lack of insulin due to an autoimmune destruction of pancreatic beta cells. Here, we report a unique case of a family with naturally conceived quadruplets in which T1D was diagnosed in two quadruplets simultaneously. At the same time, the third quadruplet was diagnosed with the pre-diabetic stage. Remarkably, all four quadruplets were positive for anti-islet cell antibodies, GAD65 and IA-A2. Monozygotic status of the quadruplets was confirmed by testing 14 different short tandem repeat polymorphisms. Serological examination confirmed that all quadruplets and their father suffered from a recent enteroviral infection of EV68-71 serotype. To assess the nature of the molecular pathological processes contributing to the development of diabetes, immunocompetent cells isolated from all family members were characterized by gene expression arrays, immune-cell enumerations and cytokine-production assays. The microarray data provided evidence that viral infection, and IL-27 and IL-9 cytokine signalling contributed to the onset of T1D in two of the quadruplets. The propensity of stimulated immunocompetent cells from non-diabetic members of the family to secrete high level of IFN-α further corroborates this conclusion. The number of T regulatory cells as well as plasmacytoid and/or myeloid dendritic cells was found diminished in all family members. Thus, this unique family is a prime example for the support of the so-called ‘fertile-field’ hypothesis proposing that genetic predisposition to anti-islet autoimmunity is ‘fertilized’ and precipitated by a viral infection leading to a fully blown T1D. | [Katerina Stechova, Zbynek Halbhuber, Miluse Hubackova, Jana Kayserova, Lenka Petruzelkova, Jana Vcelakova, Stanislava Kolouskova, Tereza Ulmannova, Maria Faresj|[ouml]|, Ales Neuwirth, Radek Spisek, Anna Sediva, Dominik Filipp, Zdenek Sumnik] | European Journal of Human Genetics | 2011-11-23 | |
| naturepublishinggroup10.1038/mt.2011.257 | RNAi Targeting CXCR4 Inhibits Tumor Growth Through Inducing Cell Cycle Arrest and Apoptosis | CXC chemokine receptor 4 (CXCR4) is involved in many human malignant tumors and plays an important role in tumor growth and metastasis. To explore the effects of CXCR4 expression on the malignant cells of oral squamous cell carcinoma (OSCC), Tca8113 and SCC-9 cell lines, as well as their xenograft models, of nude mice were used to detect cancer cell proliferation alteration. This study also examined the corresponding molecular mechanism after CXCR4 knockdown using a recombinant lentiviral vector expressing small interference RNA (siRNA) for CXCR4. RNA interference-mediated knockdown of CXCR4 in highly aggressive (Tca8113 and SCC-9) tumor cells significantly inhibited the proliferation of the two cell lines in vitro and in vivo. The expression levels of >1,500 genes involved in cell cycle, apoptosis, and multiple signaling pathways were also altered. These results provide new evidence of CXCR4 as a promising tumor gene therapeutic target. | [Tao Yu, Yingying Wu, Yi Huang, Chaoran Yan, Ying Liu, Zongsheng Wang, Xiaoyi Wang, Yuming Wen, Changmei Wang, Longjiang Li] | Molecular Therapy | 2011-11-22 | |
| naturepublishinggroup10.1038/jhg.2011.126 | Tumor suppressive microRNA-133a regulates novel molecular networks in lung squamous cell carcinoma | Analysis of the microRNA (miRNA) expression signature of lung squamous cell carcinoma (lung-SCC) revealed that the expression levels of miR-133a were significantly reduced in cancer tissues compared with normal tissues. In this study, we focused on the functional significance of miR-133a in cancer cell lines derived from lung-SCC and the identification of miR-133a-regulated novel cancer networks in lung-SCC. Restoration of miR-133a expression in PC10 and H157 cell lines resulted in significant inhibition of cell proliferation, suggesting that miR-133a functions as a tumor suppressor. We used genome-wide gene expression analysis to identify the molecular targets of miR-133a regulation. Gene expression data and web-based searching revealed several candidate genes, including transgelin 2 (TAGLN2), actin-related protein2/3 complex, subunit 5, 16kDa (ARPC5), LAG1 homolog, ceramide synthase 2 (LASS2) and glutathione S-transferase pi 1 (GSTP1). ARPC5 and GSTP1 likely represent bona fide targets as their expression is elevated in lung-SCC clinical specimens. Furthermore, transient transfection of miR-133a, repressed ARPC5 and GSTP1 mRNA and protein levels. As cell proliferation was significantly inhibited in lung-SCC cells following RNAi knock down of either gene, ARPC5 and GSTP1 may function as oncogenes in the development of lung-SCC. The identification of a tumor suppressive miRNA and the novel cancer pathways it regulates could provide new insights into potential molecular mechanisms of lung-SCC carcinogenesis. | [Yasumitsu Moriya, Nijiro Nohata, Takashi Kinoshita, Muradil Mutallip, Tatsuro Okamoto, Shigetoshi Yoshida, Makoto Suzuki, Ichiro Yoshino, Naohiko Seki] | Journal of Human Genetics | 2011-11-17 | |
| naturepublishinggroup10.1038/labinvest.2011.161 | Wnt activation is implicated in glioblastoma radioresistance | Glioblastoma (GBM) patients have dismal median survival even with the most rigorous treatments currently available. Radiotherapy is the most effective non-surgical therapy for GBM patients; however, patients succumb due to tumor recurrence within a year. To develop a curative therapeutic approach, we need to better understand the underlying molecular mechanism of radiation resistance in GBM. Towards this goal, we developed an in vivo orthotopic GBM model system that mimics the radiation response of human GBM, using both established-GBM cell line and patient-derived freshly dissociated GBM specimen. In-vivo ionizing radiation (IR) treatment prolonged the survival of mice with intracranical tumor derived from U373MG, but failed to prevent tumor recurrence. U373MG and GBM578 cells isolated after in-vivo IR (U373-IR and 578-IR) were more clonogenic and enriched with stem cell-like characteristics, compared with mock-treated control tumor cells. Transcriptomic analyses and quantitative real-time reverse-transcription PCR analyses using these matched GBM cells before and after radiation treatment revealed that Wnt pathways were preferentially activated in post-IR GBM cells. U373-IR cells and 578-IR were enriched with cells positive for both active β-catenin (ABC) and Sox2 population, and this subpopulation was further increased after additional in-vitro radiation treatment, suggesting that radiation resistance of GBM is mediated due, in part, to the activation of stem cell-associated pathways including Wnt. Finally, pharmacological and siRNA inhibition of Wnt pathway significantly decreased the survival and clonogenicity of GBM cells and reduced their ABC+/Sox2+ population. Together, these data suggest that Wnt activation is a molecular mechanism to confer GBM radioresistance and an important therapeutic target. | [Yonghyun Kim, Kang Ho Kim, Jeena Lee, Young-Ae Lee, Misuk Kim, Se Jeong Lee, Kernyu Park, Heekyoung Yang, Juyoun Jin, Kyeung Min Joo, Jeongwu Lee, Do-Hyun Nam] | Laboratory Investigation | 2011-11-14 | |
| naturepublishinggroup10.1038/onc.2011.509 | Mice deficient in MIM expression are predisposed to lymphomagenesis | Missing in metastasis (MIM) is a member of newly emerged inverse Bin-Amphiphysin-Rvs (BAR) domain protein family and a putative metastasis suppressor. Although reduced MIM expression has been associated with bladder, breast and gastric cancers, evidence for the role of MIM in tumor progression remains scarce and controversial. Herein we characterized a MIM knockout mouse strain and observed that MIM-deficient mice often developed enlarged spleens. Autopsy and histological analysis revealed that nearly 78% of MIM(−/−) mice developed tumors with features similar to diffuse large B lymphoma during a period from 1 to 2 years. MIM(−/−) mice also exhibited abnormal distribution of B cells in lymphoid organs with decrease in the spleen but increase in the bone marrow and the peripheral blood. Furthermore, the bone marrow of MIM(−/−) mice contained a higher percentage of pre-B2 cells but fewer immature B-cells than wild-type mice. In response to CXCL13, a B-cell chemokine released from splenic stromal cells, MIM-deficient B-cells did not undergo chemotaxis or morphological changes in response to the chemokine and also did not internalize CXCR5, the receptor of CXCL13. Microarray analyses demonstrated that MIM is the only member of the I-BAR domain family that was highly expressed in human B cells. However, low or absent MIM expression was common in either primary B-cell malignancies or established B-cell acute lymphocytic leukemia or lymphomas. Thus, our data demonstrate for the first time an important role for MIM in B-cell development and suggest that predisposition of MIM-null mice to lymphomagenesis may involve aberrant interactions between B lineage cells and the lymphoid microenvironment. | [D Yu, X H Zhan, X F Zhao, M S Williams, G B Carey, E Smith, D Scott, J Zhu, Y Guo, S Cherukuri, C I Civin, X Zhan] | Oncogene | 2011-11-14 | |
| naturepublishinggroup10.1038/nature10630 | A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma | So far, two genes associated with familial melanoma have been identified, accounting for a minority of genetic risk in families. Mutations in CDKN2A account for approximately 40% of familial cases1, and predisposing mutations in CDK4 have been reported in a very small number of melanoma kindreds2. Here we report the whole-genome sequencing of probands from several melanoma families, which we performed in order to identify other genes associated with familial melanoma. We identify one individual carrying a novel germline variant (coding DNA sequence c.G1075A; protein sequence p.E318K; rs149617956) in the melanoma-lineage-specific oncogene microphthalmia-associated transcription factor (MITF). Although the variant co-segregated with melanoma in some but not all cases in the family, linkage analysis of 31 families subsequently identified to carry the variant generated a log of odds (lod) score of 2.7 under a dominant model, indicating E318K as a possible intermediate risk variant. Consistent with this, the E318K variant was significantly associated with melanoma in a large Australian case–control sample. Likewise, it was similarly associated in an independent case–control sample from the United Kingdom. In the Australian sample, the variant allele was significantly over-represented in cases with a family history of melanoma, multiple primary melanomas, or both. The variant allele was also associated with increased naevus count and non-blue eye colour. Functional analysis of E318K showed that MITF encoded by the variant allele had impaired sumoylation and differentially regulated several MITF targets. These data indicate that MITF is a melanoma-predisposition gene and highlight the utility of whole-genome sequencing to identify novel rare variants associated with disease susceptibility. | [Satoru Yokoyama, Susan L. Woods, Glen M. Boyle, Lauren G. Aoude, Stuart MacGregor, Victoria Zismann, Michael Gartside, Anne E. Cust, Rizwan Haq, Mark Harland, John C. Taylor, David L. Duffy, Kelly Holohan, Ken Dutton-Regester, Jane M. Palmer, Vanessa Bonazzi, Mitchell S. Stark, Judith Symmons, Matthew H. Law, Christopher Schmidt, Cathy Lanagan, Linda O’Connor, Elizabeth A. Holland, Helen Schmid, Judith A. Maskiell, Jodie Jetann, Megan Ferguson, Mark A. Jenkins, Richard F. Kefford, Graham G. Giles, Bruce K. Armstrong, Joanne F. Aitken, John L. Hopper, David C. Whiteman, Paul D. Pharoah, Douglas F. Easton, Alison M. Dunning, Julia A. Newton-Bishop, Grant W. Montgomery, Nicholas G. Martin, Graham J. Mann, D. Timothy Bishop, Hensin Tsao, Jeffrey M. Trent, David E. Fisher, Nicholas K. Hayward, Kevin M. Brown] | Nature | 2011-11-13 | |
| naturepublishinggroup10.1038/bcj.2011.39 | Analysis of genomic aberrations and gene expression profiling identifies novel lesions and pathways in myeloproliferative neoplasms | Polycythemia vera (PV), essential thrombocythemia and primary myelofibrosis, are myeloproliferative neoplasms (MPNs) with distinct clinical features and are associated with the JAK2V617F mutation. To identify genomic anomalies involved in the pathogenesis of these disorders, we profiled 87 MPN patients using Affymetrix 250K single-nucleotide polymorphism (SNP) arrays. Aberrations affecting chr9 were the most frequently observed and included 9pLOH (n=16), trisomy 9 (n=6) and amplifications of 9p13.3–23.3 (n=1), 9q33.1–34.13 (n=1) and 9q34.13 (n=6). Patients with trisomy 9 were associated with elevated JAK2V617F mutant allele burden, suggesting that gain of chr9 represents an alternative mechanism for increasing JAK2V617F dosage. Gene expression profiling of patients with and without chr9 abnormalities (+9, 9pLOH), identified genes potentially involved in disease pathogenesis including JAK2, STAT5B and MAPK14. We also observed recurrent gains of 1p36.31–36.33 (n=6), 17q21.2–q21.31 (n=5) and 17q25.1–25.3 (n=5) and deletions affecting 18p11.31–11.32 (n=8). Combined SNP and gene expression analysis identified aberrations affecting components of a non-canonical PRC2 complex (EZH1, SUZ12 and JARID2) and genes comprising a ‘HSC signature’ (MLLT3, SMARCA2 and PBX1). We show that NFIB, which is amplified in 7/87 MPN patients and upregulated in PV CD34+ cells, protects cells from apoptosis induced by cytokine withdrawal. | [K L Rice, X Lin, K Wolniak, B L Ebert, W Berkofsky-Fessler, M Buzzai, Y Sun, C Xi, P Elkin, R Levine, T Golub, D G Gilliland, J D Crispino, J D Licht, W Zhang] | Blood Cancer Journal | 2011-11-01 | 11.0.2 |
| naturepublishinggroup10.1038/gt.2011.159 | Effect of topical interferon-|[gamma]| gene therapy using gemini nanoparticles on pathophysiological markers of cutaneous scleroderma in Tsk|[sol]||[plus]| mice | Scleroderma is a chronic disorder manifested by excessive synthesis and deposition of collagen in skin and connective tissue, vascular abnormalities, and autoimmunity. Using microarray and real-time PCR data, we show that intradermally expressed interferon γ (IFN-γ), generated after intradermal injection of IFN-γ-coding plasmid, and non-invasive topical nanoparticle (TNP) treatment with IFN-γ-coding plasmid, decreased collagen synthesis (via the Jak/Stat 1 pathway), upregulated Th1 cytokine levels, and downregulated the profibrotic cytokine Transforming growth factor β and the Smad pathways in the Tsk/+ (tight-skin scleroderma) mouse model. The TNP gene delivery system was constructed from gemini surfactant 16-3-16 and IFN-γ-coding plasmid. Topical administration of IFN-γ-coding plasmid in TNPs was effective in expressing IFN-γ levels after a 20-day treatment regimen without increased TLR4, CCL2, CCL11 and CCR2 mRNA levels that were observed in injected animals, signs considered to be innate responses to injury. The more uniform transgene IFN-γ expression caused significant (70–72%) collagen reduction, as assessed by reverse transcription real-time PCR. These results demonstrate efficient in vivo transfection using a gemini surfactant-based TNP delivery system able to modulate excessive collagen synthesis in scleroderma-affected skin. | [I Badea, C Virtanen, R E Verrall, A Rosenberg, M Foldvari] | Gene Therapy | 2011-11-10 | |
| naturepublishinggroup10.1038/emboj.2011.391 | Signal-dependent incorporation of MyoD|[ndash]|BAF60c into Brg1-based SWI/SNF chromatin-remodelling complex | Tissue-specific transcriptional activators initiate differentiation towards specialized cell types by inducing chromatin modifications permissive for transcription at target loci, through the recruitment of SWItch/Sucrose NonFermentable (SWI/SNF) chromatin-remodelling complex. However, the molecular mechanism that regulates SWI/SNF nuclear distribution in response to differentiation signals is unknown. We show that the muscle determination factor MyoD and the SWI/SNF subunit BAF60c interact on the regulatory elements of MyoD-target genes in myoblasts, prior to activation of transcription. BAF60c facilitates MyoD binding to target genes and marks the chromatin for signal-dependent recruitment of the SWI/SNF core to muscle genes. BAF60c phosphorylation on a conserved threonine by differentiation-activated p38α kinase is the signal that promotes incorporation of MyoD–BAF60c into a Brg1-based SWI/SNF complex, which remodels the chromatin and activates transcription of MyoD-target genes. Our data support an unprecedented two-step model by which pre-assembled BAF60c–MyoD complex directs recruitment of SWI/SNF to muscle loci in response to differentiation cues. | [Sonia V Forcales, Sonia Albini, Lorenzo Giordani, Barbora Malecova, Luca Cignolo, Andrei Chernov, Paula Coutinho, Valentina Saccone, Silvia Consalvi, Roy Williams, Kepeng Wang, Zhenguo Wu, Svetlana Baranovskaya, Andrew Miller, F Jeffrey Dilworth, Pier Lorenzo Puri] | The EMBO Journal | 2011-11-08 | |
| naturepublishinggroup10.1038/onc.2011.486 | Transgenic IGF-IR overexpression induces mammary tumors with basal-like characteristics, whereas IGF-IR-independent mammary tumors express a claudin-low gene signature | Molecular profiling has allowed a more precise classification of human cancers. With respect to breast cancer, this approach has been used to identify five subtypes; luminal A, luminal B, HER2-enriched, basal-like and claudin-low. In addition, this approach can be used to determine the type of tumor represented by particular cell lines or transgenic animal models. Therefore, this approach was utilized to classify the mammary tumors that develop in MTB-IGFIR transgenic mice. It was determined that the primary mammary tumors, which develop due to elevated expression of the type I insulin-like growth factor receptor (IGF-IR) in mammary epithelial cells, most closely resemble murine tumors with basal-like or mixed gene expression profiles and with human basal-like breast cancers. Downregulation of IGF-IR transgene in MTB-IGFIR tumor-bearing mice leads to the regression of most of the tumors, followed by tumor reappearance in some of the mice. These tumors that reappear following IGF-IR transgene downregulation do not express the IGF-IR transgene and cluster with murine mammary tumors that express a mesenchymal gene expression profile and with human claudin-low breast cancers. Therefore, IGF-IR overexpression in murine mammary epithelial cells induces mammary tumors with primarily basal-like characteristics, whereas tumors that develop following IGF-IR downregulation express a gene signature that most closely resembles human claudin-low breast tumors. | [S E Franks, C I Campbell, E F Barnett, M D Siwicky, J Livingstone, S Cory, R A Moorehead] | Oncogene | 2011-10-24 | |
| naturepublishinggroup10.1038/nmeth.1740 | NKX2-5eGFP/w hESCs for isolation of human cardiac progenitors and cardiomyocytes | NKX2-5 is expressed in the heart throughout life. We targeted eGFP sequences to the NKX2-5 locus of human embryonic stem cells (hESCs); NKX2-5eGFP/w hESCs facilitate quantification of cardiac differentiation, purification of hESC-derived committed cardiac progenitor cells (hESC-CPCs) and cardiomyocytes (hESC-CMs) and the standardization of differentiation protocols. We used NKX2-5 eGFP+ cells to identify VCAM1 and SIRPA as cell-surface markers expressed in cardiac lineages. | [David A Elliott, Stefan R Braam, Katerina Koutsis, Elizabeth S Ng, Robert Jenny, Ebba L Lagerqvist, Christine Biben, Tanya Hatzistavrou, Claire E Hirst, Qing C Yu, Rhys J P Skelton, Dorien Ward-van Oostwaard, Sue Mei Lim, Ouda Khammy, Xueling Li, Susan M Hawes, Richard P Davis, Adam L Goulburn, Robert Passier, Owen W J Prall, John M Haynes, Colin W Pouton, David M Kaye, Christine L Mummery, Andrew G Elefanty, Edouard G Stanley] | Nature Methods | 2011-10-23 | |
| naturepublishinggroup10.1038/bjc.2011.404 | Low ANXA10 expression is associated with disease aggressiveness in bladder cancer | | [P P Munksgaard, F Mansilla, A-S Brems Eskildsen, N Fristrup, K Birkenkamp-Demtr|[ouml]|der, B P Ulh|[oslash]|i, M Borre, M Agerb|[aelig]|k, G G Hermann, T F |[Oslash]|rntoft, L Dyrskj|[oslash]|t] | British Journal of Cancer | 2011-10-06 | |
| naturepublishinggroup10.1038/onc.2011.441 | Myc, Aurora Kinase A, and mutant p53R172H co-operate in a mouse model of metastatic skin carcinoma | Clinical observations, as well as data obtained from the analysis of genetically engineered mouse models, firmly established the gain-of-function (GOF) properties of certain p53 mutations. However, little is known about the underlying mechanisms. We have used two independent microarray platforms to perform a comprehensive and global analysis of tumors arising in a model of metastatic skin cancer progression, which compares the consequences of a GOF p53R172H mutant vs p53 deficiency. DNA profiling revealed a higher level of genomic instability in GOF vs loss-of-function (LOF) p53 squamous cell carcinomas (SCCs). Moreover, GOF p53 SCCs showed preferential amplification of Myc with a corresponding increase in its expression and deregulation of Aurora Kinase A. Fluorescent in situ hybridization confirmed amplification of Myc in primary GOF p53 SCCs and its retention in metastatic tumors. We also identified by RNA profiling distinct gene expression profiles in GOF p53 tumors, which included enriched integrin and Rho signaling, independent of tumor stage. Thus, the progression of GOF p53 papillomas to carcinoma was marked by the acquisition of epithelial-to-mesenchymal transition and metastatic signatures. In contrast, LOF p53 tumors showed enrichment of genes associated with cancer proliferation and chromosomal instability. Collectively, these observations suggest that genomic instability has a prominent role in the early stages of GOF p53 tumor progression (that is, papillomas), whereas it is implicated at a later stage in LOF p53 tumors (that is, SCCs). This model will allow us to identify specific targets in mutant p53 SCCs, which may lead to the development of new therapeutic agents for the treatment of metastatic SCCs. | [E C Torchia, C Caulin, S Acin, T Terzian, B J Kubick, N F Box, D R Roop] | Oncogene | 2011-10-03 | 11 |
| naturepublishinggroup10.1038/labinvest.2011.144 | Roles of |[beta]|-catenin signaling in phenotypic expression and proliferation of articular cartilage superficial zone cells | The superficial zone (SFZ) of articular cartilage has unique structural and biomechanical features, is thought to promote self-renewal of articular cartilage, and is thus important for joint long-term function, but the mechanisms regulating its properties remain unclear. Previous studies revealed that Wnt/β-catenin signaling is continuously active in SFZ, indicating that it may be essential for SFZ function. Thus, we examined whether Wnt/β-catenin signaling regulates proliferation and phenotypic expression in SFZ cells. Using transgenic mice, we found that acute activation of Wnt/β-catenin signaling increases SFZ thickness, Proteoglycan 4 (Prg4, also called lubricin) expression and the number of slow-cell cycle cells, whereas conditional ablation of β-catenin causes the opposite. We developed a novel method to isolate SFZ cell-rich populations from the epiphyseal articular cartilage of neonatal mice, and found that the SFZ cells in culture exhibit a fibroblastic cytoarchitecture and higher Prg4 and Ets-related gene (Erg) expression and lower aggrecan expression compared with chondrocyte cultures. Gene array analyses indicated that SFZ cells have distinct gene expression profiles compared with underlying articular chondrocytes. Treatment of Wnt3a strongly stimulated SFZ cell proliferation and maintained strong expression of Prg4 and Erg, whereas ablation of β-catenin strongly impaired proliferation and phenotypic expression. When the cells were transplanted into athymic mice, they formed Prg4- and aggrecan-expressing cartilaginous masses attesting to their autonomous phenotypic capacity. Ablation of β-catenin caused a rapid loss of Prg4 gene expression and strong increases in expression of aggrecan and collagen 10, the latter being a trait of hypertrophic chondrocytes. Together, the data reveal that Wnt/β-catenin signaling is a key regulator of SFZ cell phenotype and proliferation, and may be as important for articular cartilage long-term function. | [Rika Yasuhara, Yoichi Ohta, Takahito Yuasa, Naoki Kondo, Tai Hoang, Sankar Addya, Paolo Fortina, Maurizio Pacifici, Masahiro Iwamoto, Motomi Enomoto-Iwamoto] | Laboratory Investigation | 2011-10-03 | 10.0 |
| naturepublishinggroup10.1038/msb.2011.68 | The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation | | [Etienne Caron, Krystel Vincent, Marie-H|[eacute]|l|[egrave]|ne Fortier, Jean-Philippe Laverdure, Alexandre Bramoull|[eacute]|, Marie-Pierre Hardy, Gr|[eacute]|gory Voisin, Philippe P Roux, S|[eacute]|bastien Lemieux, Pierre Thibault, Claude Perreault] | Nature a - z index | 2011-09-27 | |
| naturepublishinggroup10.1038/nature10448 | Derivation of haploid embryonic stem cells from mouse embryos | Most animals are diploid, but haploid-only and male-haploid (such as honeybee and ant) species have been described1. The diploid genomes of complex organisms limit genetic approaches in biomedical model species such as mice. To overcome this problem, experimental induction of haploidy has been used in fish2, 3. Haploid development in zebrafish has been applied for genetic screening2. Recently, haploid pluripotent cell lines from medaka fish (Oryzias latipes) have also been established3. In contrast, haploidy seems less compatible with development in mammals4, 5. Although haploid cells have been observed in egg cylinder stage parthenogenetic mouse embryos6, most cells in surviving embryos become diploid. Here we describe haploid mouse embryonic stem cells and show their application in forward genetic screening. | [Martin Leeb, Anton Wutz] | Nature | 2011-09-07 | |
| naturepublishinggroup10.1038/ni.2097 | Human cytomegalovirus microRNA miR-US4-1 inhibits CD8+ T cell responses by targeting the aminopeptidase ERAP1 | | [Sungchul Kim, Sanghyun Lee, Jinwook Shin, Youngkyun Kim, Irini Evnouchidou, Donghyun Kim, Young-Kook Kim, Young-Eui Kim, Jin-Hyun Ahn, Stanley R Riddell, Efstratios Stratikos, V Narry Kim, Kwangseog Ahn] | Nature Immunology | 2011-09-04 | |
| naturepublishinggroup10.1038/mp.2011.101 | Genome-wide association analysis of coffee drinking suggests association with CYP1A1|[sol]|CYP1A2 and NRCAM | Coffee consumption is a model for addictive behavior. We performed a meta-analysis of genome-wide association studies (GWASs) on coffee intake from 8 Caucasian cohorts (N=18 176) and sought replication of our top findings in a further 7929 individuals. We also performed a gene expression analysis treating different cell lines with caffeine. Genome-wide significant association was observed for two single-nucleotide polymorphisms (SNPs) in the 15q24 region. The two SNPs rs2470893 and rs2472297 (P-values=1.6 × 10−11 and 2.7 × 10−11), which were also in strong linkage disequilibrium (r2=0.7) with each other, lie in the 23-kb long commonly shared 5′ flanking region between CYP1A1 and CYP1A2 genes. CYP1A1 was found to be downregulated in lymphoblastoid cell lines treated with caffeine. CYP1A1 is known to metabolize polycyclic aromatic hydrocarbons, which are important constituents of coffee, whereas CYP1A2 is involved in the primary metabolism of caffeine. Significant evidence of association was also detected at rs382140 (P-value=3.9 × 10−09) near NRCAM—a gene implicated in vulnerability to addiction, and at another independent hit rs6495122 (P-value=7.1 × 10−09)—an SNP associated with blood pressure—in the 15q24 region near the gene ULK3, in the meta-analysis of discovery and replication cohorts. Our results from GWASs and expression analysis also strongly implicate CAB39L in coffee drinking. Pathway analysis of differentially expressed genes revealed significantly enriched ubiquitin proteasome (P-value=2.2 × 10−05) and Parkinson's disease pathways (P-value=3.6 × 10−05). | [N Amin, E Byrne, J Johnson, G Chenevix-Trench, S Walter, I M Nolte, J M Vink, R Rawal, M Mangino, A Teumer, J C Keers, G Verwoert, S Baumeister, R Biffar, A Petersmann, N Dahmen, A Doering, A Isaacs, L Broer, N R Wray, G W Montgomery, D Levy, B M Psaty, V Gudnason, A Chakravarti, P Sulem, D F Gudbjartsson, L A Kiemeney, U Thorsteinsdottir, K Stefansson, F J A van Rooij, Y S Aulchenko, J J Hottenga, F R Rivadeneira, A Hofman, A G Uitterlinden, C J Hammond, S-Y Shin, A Ikram, J C M Witteman, A C J W Janssens, H Snieder, H Tiemeier, B H R Wolfenbuttel, B A Oostra, A C Heath, E Wichmann, T D Spector, H J Grabe, D I Boomsma, N G Martin, C M van Duijn] | Molecular Psychiatry | 2011-08-30 | |
| naturepublishinggroup10.1038/onc.2011.378 | Introduction of SV40ER and hTERT into mammospheres generates breast cancer cells with stem cell properties | Emerging evidence suggests that cancers arise in stem/progenitor cells. Yet, the requirements for transformation of these primitive cells remains poorly understood. In this study, we have exploited the ‘mammosphere’ system that selects for primitive mammary stem/progenitor cells to explore their potential and requirements for transformation. Introduction of Simian Virus 40 Early Region and hTERT into mammosphere-derived cells led to the generation of NBLE, an immortalized mammary epithelial cell line. The NBLEs largely comprised of bi-potent progenitors with long-term self-renewal and multi-lineage differentiation potential. Clonal and karyotype analyses revealed the existence of heterogeneous population within NBLEs with varied proliferation, differentiation and sphere-forming potential. Significantly, injection of NBLEs into immunocompromised mice resulted in the generation of invasive ductal adenocarcinomas. Further, these cells harbored a sub-population of CD44+/CD24− fraction that alone had sphere- and tumor-initiating potential and resembled the breast cancer stem cell gene signature. Interestingly, prolonged in vitro culturing led to their further enrichment. The NBLE cells also showed increased expression of stemness and epithelial to mesenchymal transition markers, deregulated self-renewal pathways, activated DNA-damage response and cancer-associated chromosomal aberrations—all of which are likely to have contributed to their tumorigenic transformation. Thus, unlike previous in vitro transformation studies that used adherent, more differentiated human mammary epithelial cells our study demonstrates that the mammosphere-derived, less-differentiated cells undergo tumorigenic conversion with only two genetic elements, without requiring oncogenic Ras. Moreover, the striking phenotypic and molecular resemblance of the NBLE-generated tumors with naturally arising breast adenocarcinomas supports the notion of a primitive breast cell as the origin for this subtype of breast cancer. Finally, the NBLEs represent a heterogeneous population of cells with striking plasticity, capable of differentiation, self-renewal and tumorigenicity, thus offering a unique model system to study the molecular mechanisms involved with these processes. | [A N Paranjape, T Mandal, G Mukherjee, M V Kumar, K Sengupta, A Rangarajan] | Oncogene | 2011-08-29 | |
| naturepublishinggroup10.1038/nm.2415 | Stem cell gene expression programs influence clinical outcome in human leukemia | | [Kolja Eppert, Katsuto Takenaka, Eric R Lechman, Levi Waldron, Björn Nilsson, Peter van Galen, Klaus H Metzeler, Armando Poeppl, Vicki Ling, Joseph Beyene, Angelo J Canty, Jayne S Danska, Stefan K Bohlander, Christian Buske, Mark D Minden, Todd R Golub, Igor Jurisica, Benjamin L Ebert, John E Dick] | Nature Medicine | 2011-08-28 | |
| naturepublishinggroup10.1038/emboj.2011.301 | CAMTA1 is a novel tumour suppressor regulated by miR-9/9|[ast]| in glioblastoma stem cells | Cancer stem cells or cancer initiating cells are believed to contribute to cancer recurrence after therapy. MicroRNAs (miRNAs) are short RNA molecules with fundamental roles in gene regulation. The role of miRNAs in cancer stem cells is only poorly understood. Here, we report miRNA expression profiles of glioblastoma stem cell-containing CD133+ cell populations. We find that miR-9, miR-9* (referred to as miR-9/9*), miR-17 and miR-106b are highly abundant in CD133+ cells. Furthermore, inhibition of miR-9/9* or miR-17 leads to reduced neurosphere formation and stimulates cell differentiation. Calmodulin-binding transcription activator 1 (CAMTA1) is a putative transcription factor, which induces the expression of the anti-proliferative cardiac hormone natriuretic peptide A (NPPA). We identify CAMTA1 as an miR-9/9* and miR-17 target. CAMTA1 expression leads to reduced neurosphere formation and tumour growth in nude mice, suggesting that CAMTA1 can function as tumour suppressor. Consistently, CAMTA1 and NPPA expression correlate with patient survival. Our findings could provide a basis for novel strategies of glioblastoma therapy. | [Daniel Schraivogel, Lasse Weinmann, Dagmar Beier, Ghazaleh Tabatabai, Alexander Eichner, Jia Yun Zhu, Martina Anton, Michael Sixt, Michael Weller, Christoph P Beier, Gunter Meister] | The EMBO Journal | 2011-08-19 | |
| naturepublishinggroup10.1038/jhg.2011.93 | Remapping and mutation analysis of benign adult familial myoclonic epilepsy in a Japanese pedigree | Benign adult familial myoclonic epilepsy (BAFME), alternatively named familial adult myoclonic epilepsy 1/familial cortical myoclonic tremor with epilepsy 1 (FAME1/FCMTE1), is a hereditary epileptic syndrome characterized by autosomal dominant inheritance, adult-onset tremulous hand movement, myoclonus, infrequent epileptic seizure and non-progressive course without cerebellar ataxia and dementia. We previously reported evidence for linkage of BAFME to the region between D8S1784 and D8S1694 on chromosome 8q. Subsequently, other research groups reported mapping of the same clinical syndrome to different chromosomal loci, 2p and 5p, in Italian (FAME2/FCMTE2) and French (FAME3/FCMTE3) families, respectively. In this study, we performed a genome-wide linkage analysis using 10K single-nucleotide polymorphism arrays and additional microsatellite markers to reconfirm the BAFME-linked region. The BAFME-linked region was mapped to 7.16 Mb spanned by rs1898287 and rs2891799 on chromosomes 8q23.3–8q24.13 with a maximum two-point logarithm of odds score of 6.0 for the marker rs1021897. Sequence analysis and copy-number variant analysis of all 38 genes localized in the candidate region were performed, but no pathogenic mutation was identified. We conclude that the etiology of BAFME remains to be solved, and further genetic studies, which may require analysis in non-coding regions of a gene, introns or intergenic spacer regions, are necessary to reveal its unknown mutations. | [Satsuki Mori, Masayuki Nakamura, Takeshi Yasuda, Shu-ichi Ueno, Sunao Kaneko, Akira Sano] | Journal of Human Genetics | 2011-08-18 | |
| naturepublishinggroup10.1038/msb.2011.56 | Oncogenic K-Ras decouples glucose and glutamine metabolism to support cancer cell growth | | [Daniela Gaglio, Christian M Metallo, Paulo A Gameiro, Karsten Hiller, Lara Sala Danna, Chiara Balestrieri, Lilia Alberghina, Gregory Stephanopoulos, Ferdinando Chiaradonna] | Nature a - z index | 2011-08-16 | |
| naturepublishinggroup10.1038/emboj.2011.299 | CBP is required for environmental enrichment-induced neurogenesis and cognitive enhancement | The epigenetic changes of the chromatin represent an attractive molecular substrate for adaptation to the environment. We examined here the role of CREB-binding protein (CBP), a histone acetyltransferase involved in mental retardation, in the genesis and maintenance of long-lasting systemic and behavioural adaptations to environmental enrichment (EE). Morphological and behavioural analyses demonstrated that EE ameliorates deficits associated to CBP deficiency. However, CBP-deficient mice also showed a strong defect in environment-induced neurogenesis and impaired EE-mediated enhancement of spatial navigation and pattern separation ability. These defects correlated with an attenuation of the transcriptional programme induced in response to EE and with deficits in histone acetylation at the promoters of EE-regulated, neurogenesis-related genes. Additional experiments in CBP restricted and inducible knockout mice indicated that environment-induced adult neurogenesis is extrinsically regulated by CBP function in mature granule cells. Overall, our experiments demonstrate that the environment alters gene expression by impinging on activities involved in modifying the epigenome and identify CBP-dependent transcriptional neuroadaptation as an important mediator of EE-induced benefits, a finding with important implications for mental retardation therapeutics. | [Jose P Lopez-Atalaya, Alessandro Ciccarelli, Jose Viosca, Luis M Valor, Maria Jimenez-Minchan, Santiago Canals, Maurizio Giustetto, Angel Barco] | The EMBO Journal | 2011-08-16 | |
| naturepublishinggroup10.1038/bjc.2011.311 | Tumour suppressive microRNA-874 regulates novel cancer networks in maxillary sinus squamous cell carcinoma | | [N Nohata, T Hanazawa, N Kikkawa, D Sakurai, L Fujimura, T Chiyomaru, K Kawakami, H Yoshino, H Enokida, M Nakagawa, A Katayama, Y Harabuchi, Y Okamoto, N Seki] | British Journal of Cancer | 2011-08-16 | |
| naturepublishinggroup10.1038/cr.2011.133 | Defining the nature of human pluripotent stem cell progeny | While it is clear that human pluripotent stem cells (hPSCs) can differentiate to generate a panoply of various cell types, it is unknown how closely in vitro development mirrors that which occurs in vivo. To determine whether human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs) make equivalent progeny, and whether either makes cells that are analogous to tissue-derived cells, we performed comprehensive transcriptome profiling of purified PSC derivatives and their tissue-derived counterparts. Expression profiling demonstrated that hESCs and hiPSCs make nearly identical progeny for the neural, hepatic, and mesenchymal lineages, and an absence of re-expression from exogenous reprogramming factors in hiPSC progeny. However, when compared to a tissue-derived counterpart, the progeny of both hESCs and hiPSCs maintained expression of a subset of genes normally associated with early mammalian development, regardless of the type of cell generated. While pluripotent genes (OCT4, SOX2, REX1, and NANOG) appeared to be silenced immediately upon differentiation from hPSCs, genes normally unique to early embryos (LIN28A, LIN28B, DPPA4, and others) were not fully silenced in hPSC derivatives. These data and evidence from expression patterns in early human fetal tissue (3-16 weeks of development) suggest that the differentiated progeny of hPSCs are reflective of very early human development (< 6 weeks). These findings provide support for the idea that hPSCs can serve as useful in vitro models of early human development, but also raise important issues for disease modeling and the clinical application of hPSC derivatives. | [Michaela Patterson, David N. Chan, Iris Ha, Dana Case, Yongyan Cui, Ben Van Handel, Hanna KA Mikkola, William E Lowry] | Cell Research | 2011-08-16 | |
| naturepublishinggroup10.1038/jid.2011.227 | Modulation in Proteolytic Activity Is Identified as a Hallmark of Exogen by Transcriptional Profiling of Hair Follicles | Exogen is the process by which the hair follicle actively sheds its club fiber from the follicle. However, little is known about signals that govern the cellular mechanisms of shedding. Here, we have identified factors that are important in regulating either the retention or release of the hair club fiber from its epithelial silo within the follicle. Using the vibrissa follicle as our model, we isolated follicle segments containing club fibers and surrounding follicle tissue at different time points before their natural release from the hair follicle. We then performed microarray analysis to identify key molecular changes as the club fiber approached final release. Among the different classes of genes that were identified, we found changes in the expression pattern of protease inhibitors and proteases, suggesting that proteolysis may mediate fiber release, either through terminal differentiation or proteolytic cleavage. We validated transcriptional changes using reverse transcription-PCR, and further immunofluorescence analysis indicated that protease inhibitors surrounding the club fiber may have an important role in regulating the process of club fiber shedding. Our findings also highlighted that molecular differentiation of the innermost layer of cells immediately surrounding the club fiber, the companionCL, is likely to be important in hair shedding. | [Claire A Higgins, Gillian E Westgate, Colin A B Jahoda] | Journal of Investigative Dermatology | 2011-08-11 | |
| naturepublishinggroup10.1038/jhg.2011.84 | A nonsense mutation in the HOXD13 gene underlies synpolydactyly with incomplete penetrance | Synpolydactyly 1 (SPD1; OMIM 186000), also known as type II syndactyly, is a dominantly inherited limb malformation that is characterized by an increased number of digits. SPD1 is most commonly caused by polyalanine repeat expansions in the coding region of the HOXD13 gene, which are believed to show a dominant-negative effect. In addition, missense and out-of-frame deletion mutations in the HOXD13 gene are also known to cause SPD, and the mechanism responsible for the phenotype appears to be haploinsufficiency. Here, we analyzed a large consanguineous family from Pakistan with SPD showing a wide variation in phenotype among affected individuals. We performed genetic linkage analysis, which identified a region on chromosome 2 containing the HOXD13 gene. Haplotype analysis with microsatellite markers suggested segregation of the phenotype with HOXD13 gene with incomplete penetrance. Direct sequencing analysis of HOXD13 gene revealed a nonsense mutation, designated as Q248X. All affected individuals with the severe SPD phenotype are homozygous for the mutation, whereas those with the mild SPD phenotype are heterozygous for the mutation. Furthermore, some unaffected individuals also carry the mutation in the heterozygous state, showing incomplete penetrance. Our results show the first nonsense mutation in the HOXD13 gene underlying a severe form of SPD in the homozygous state, and a milder form of SPD with ~50% penetrance in the heterozygous state, most likely because of the production of 50% of protein compared with normal individuals. | [Mazen Kurban, Muhammad Wajid, Lynn Petukhova, Yutaka Shimomura, Angela M Christiano] | Journal of Human Genetics | 2011-08-04 | |
| naturepublishinggroup10.1038/bjc.2011.268 | Repression of KIAA1199 attenuates Wnt-signalling and decreases the proliferation of colon cancer cells | | [K Birkenkamp-Demtroder, A Maghnouj, F Mansilla, K Thorsen, C L Andersen, B |[Oslash]|ster, S Hahn, T F |[Oslash]|rntoft] | British Journal of Cancer | 2011-07-19 | |
| naturepublishinggroup10.1038/onc.2011.283 | CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute | CHEK2 encodes a serine/threonine kinase (Chk2) activated by ATM in response to DNA double-strand breaks. On the one hand, CHEK2 has been described as a tumor suppressor with proapoptotic, cell-cycle checkpoint and mitotic functions. On the other hand, Chk2 is also commonly activated (phosphorylated at T68) in cancers and precancerous lesions. Here, we report an extensive characterization of CHEK2 across the panel of 60 established cancer cell lines from the NCI Anticancer Screen (the NCI-60) using genomic and proteomic analyses, including exon-specific mRNA expression, DNA copy-number variation (CNV) by aCGH, exome sequencing, as well as western blot analyses for total and activated (pT68-Chk2) Chk2. We show that the high heterogeneity of Chk2 levels in cancer cells is primarily due to its inactivation (owing to low gene expression, alternative splicing, point mutations, copy-number alterations and premature truncation) or reduction of protein levels. Moreover, we observe that a significant percentage of cancer cells (12% of the NCI-60 and HeLa cells) show high endogenous Chk2 activation, which is always associated with p53 inactivation, and which is accompanied by downregulation of the Fanconi anemia and homologous recombination pathways. We also report the presence of activated Chk2 (pT68-Chk2) along with histone γ-H2AX in centrosomes. | [G Zoppoli, S Solier, W C Reinhold, H Liu, J W Connelly, A Monks, R H Shoemaker, O D Abaan, S R Davis, P S Meltzer, J H Doroshow, Y Pommier] | Oncogene | 2011-07-18 | |
| naturepublishinggroup10.1038/nature10228 | Control of TH17 cells occurs in the small intestine | Interleukin (IL)-17-producing T helper cells (TH17) are a recently identified CD4+ T cell subset distinct from T helper type 1 (TH1) and T helper type 2 (TH2) cells1. TH17 cells can drive antigen-specific autoimmune diseases and are considered the main population of pathogenic T cells driving experimental autoimmune encephalomyelitis (EAE)2, the mouse model for multiple sclerosis. The factors that are needed for the generation of TH17 cells have been well characterized3, 4, 5, 6. However, where and how the immune system controls TH17 cells in vivo remains unclear. Here, by using a model of tolerance induced by CD3-specific antibody, a model of sepsis and influenza A viral infection (H1N1), we show that pro-inflammatory TH17 cells can be redirected to and controlled in the small intestine. TH17-specific IL-17A secretion induced expression of the chemokine CCL20 in the small intestine, facilitating the migration of these cells specifically to the small intestine via the CCR6/CCL20 axis. Moreover, we found that TH17 cells are controlled by two different mechanisms in the small intestine: first, they are eliminated via the intestinal lumen; second, pro-inflammatory TH17 cells simultaneously acquire a regulatory phenotype with in vitro and in vivo immune-suppressive properties (rTH17). These results identify mechanisms limiting TH17 cell pathogenicity and implicate the gastrointestinal tract as a site for control of TH17 cells. | [Enric Esplugues, Samuel Huber, Nicola Gagliani, Anja E. Hauser, Terrence Town, Yisong Y. Wan, William O’Connor, Anthony Rongvaux, Nico Van Rooijen, Ann M. Haberman, Yoichiro Iwakura, Vijay K. Kuchroo, Jay K. Kolls, Jeffrey A. Bluestone, Kevan C. Herold, Richard A. Flavell] | Nature | 2011-07-17 | |
| naturepublishinggroup10.1038/jid.2011.202 | Inhibition of Transcription Factor Specificity Protein 1 Alters the Gene Expression Profile of Keratinocytes Leading to Upregulation of Kallikrein-Related Peptidases and Thymic Stromal Lymphopoietin | Transcription factor specificity protein 1 (Sp1) is involved in diverse cellular functions. We recently found that Sp1 was significantly decreased in skin biopsy samples obtained from patients with atopic dermatitis (AD) and had an even greater reduction in AD patients with a history of eczema herpeticum. In the current study, we sought to better understand the role of Sp1 in skin biological processes by using a small-interfering RNA (siRNA) technique to knock down Sp1 gene expression in normal human keratinocytes (NHKs) and investigated the genome-wide gene expression profiling of Sp1-silenced NHKs. The gene arrays revealed that 53 genes had greater than 3-fold changes in the expression in Sp1-silenced NHKs as compared with scrambled siRNA-silenced cells. Strikingly, six kallikrein (KLK)-related peptidase genes, namely KLK5, KLK6, KLK7, KLK8, KLK10, and KLK12, were upregulated in NHKs following Sp1 silencing. Functionally, protease activity was significantly enhanced in Sp1-silenced keratinocytes as compared with scrambled siRNA-silenced keratinocytes. Moreover, thymic stromal lymphopoietin (TSLP), an epithelial-derived TH2-promoting cytokine, was induced in Sp1-silenced keratinocytes because of elevated KLK activity. These results indicate that Sp1 expression deficiency leads to abnormally increased KLK protease activity in keratinocytes and may contribute to TH2 immune responses in the skin by inducing TSLP. | [Lianghua Bin, Byung E Kim, Clifton F Hall, Sonia M Leach, Donald Y M Leung] | Journal of Investigative Dermatology | 2011-07-14 | |
| naturepublishinggroup10.1038/ncomms1381 | The Wnt3a/[beta]-catenin target gene Mesogenin1 controls the segmentation clock by activating a Notch signalling program | | [Ravindra B. Chalamalasetty, William C. Dunty Jr, Kristin K. Biris, Rieko Ajima, Michelina Iacovino, Arica Beisaw, Lionel Feigenbaum, Deborah L. Chapman, Jeong Kyo Yoon, Michael Kyba, Terry P. Yamaguchi] | Nature Communications | 2011-07-12 | x10 |
| naturepublishinggroup10.1038/onc.2011.280 | miR-221|[sol]|222 overexpession in human glioblastoma increases invasiveness by targeting the protein phosphate PTP|[mu]| | Glioblastoma is the most frequent brain tumor in adults and is the most lethal form of human cancer. Despite the improvements in treatments, survival of patients remains poor. In order to identify microRNAs (miRs) involved in glioma tumorigenesis, we evaluated, by a miRarray, differential expression of miRs in the tumorigenic glioma LN-18, LN-229 and U87MG cells compared with the non-tumorigenic T98G cells. Among different miRs we focused our attention on miR-221 and -222. We demonstrated the presence of a binding site for these two miRs in the 3′ untranslated region of the protein tyrosine phosphatase μ (PTPμ). Previous studies indicated that PTPμ suppresses cell migration and is downregulated in glioblastoma. Significantly, we found that miR-221 and -222 overexpression induced a downregulation of PTPμ as analyzed by both western blot and real-time PCR. Furthermore, miR-222 and -221 induced an increase in cell migration and growth in soft agar in glioma cells. Interestingly, the re-expression of PTPμ gene was able to revert the miR-222 and -221 effects on cell migration. Furthermore, we found an inverse correlation between miR-221 and -222 and PTPμ in human glioma cancer samples. In conclusion, our results suggest that miR-221 and -222 regulate glioma tumorigenesis at least in part through the control of PTPμ protein expression. | [C Quintavalle, M Garofalo, C Zanca, G Romano, M Iaboni, M del Basso De Caro, J C Martinez-Montero, M Incoronato, G Nuovo, C M Croce, G Condorelli] | Oncogene | 2011-07-11 | |
| naturepublishinggroup10.1038/nature10263 | Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors | The location and timing of cellular differentiation must be stringently controlled for proper organ formation. Normally, hepatocytes differentiate from hepatic progenitor cells to form the liver during development1, 2. However, previous studies have shown that the hepatic program can also be activated in non-hepatic lineage cells after exposure to particular stimuli or fusion with hepatocytes3, 4, 5, 6, 7, 8, 9. These unexpected findings suggest that factors critical to hepatocyte differentiation exist and become activated to induce hepatocyte-specific properties in different cell types. Here, by screening the effects of twelve candidate factors, we identify three specific combinations of two transcription factors, comprising Hnf4α plus Foxa1, Foxa2 or Foxa3, that can convert mouse embryonic and adult fibroblasts into cells that closely resemble hepatocytes in vitro. The induced hepatocyte-like (iHep) cells have multiple hepatocyte-specific features and reconstitute damaged hepatic tissues after transplantation. The generation of iHep cells may provide insights into the molecular nature of hepatocyte differentiation and potential therapies for liver diseases. | [Sayaka Sekiya, Atsushi Suzuki] | Nature | 2011-06-29 | |
| naturepublishinggroup10.1038/cr.2011.107 | Reprogramming fibroblasts into induced pluripotent stem cells with Bmi1 | Somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by the transcription factors Oct4, Sox2, and Klf4 in combination with c-Myc. Recently, Sox2 plus Oct4 was shown to reprogram fibroblasts and Oct4 alone was able to reprogram mouse and human neural stem cells (NSCs) into iPS cells. Here, we report that Bmi1 leads to the transdifferentiation of mouse fibroblasts into NSC-like cells, and, in combination with Oct4, can replace Sox2, Klf4 and c-Myc during the reprogramming of fibroblasts into iPS cells. Furthermore, activation of sonic hedgehog signaling (by Shh, purmorphamine, or oxysterol) compensates for the effects of Bmi1, and, in combination with Oct4, reprograms mouse embryonic and adult fibroblasts into iPS cells. One- and two-factor iPS cells are similar to mouse embryonic stem cells in their global gene expression profile, epigenetic status, and in vitro and in vivo differentiation into all three germ layers, as well as teratoma formation and germline transmission in vivo. These data support that converting fibroblasts with Bmi1 or activation of the sonic hedgehog pathway to an intermediate cell type that expresses Sox2, Klf4, and N-Myc allows iPS generation via the addition of Oct4. | [Jai-Hee Moon, June Seok Heo, Jun Sung Kim, Eun Kyoung Jun, Jung Han Lee, Aeree Kim, Jonggun Kim, Kwang Youn Whang, Yong-Kook Kang, Seungeun Yeo, Hee-Joung Lim, Dong Wook Han, Dong-Wook Kim, Sejong Oh, Byung Sun Yoon, Hans R Sch|[ouml]|ler, Seungkwon You] | Cell Research | 2011-06-28 | |
| naturepublishinggroup10.1038/modpathol.2011.99 | THBS4, a novel stromal molecule of diffuse-type gastric adenocarcinomas, identified by transcriptome-wide expression profiling | Gastric adenocarcinomas can be divided into two major histological types, the diffuse and intestinal type (Laurén classification). Since they diverge in many clinical and molecular characteristics, it is widely accepted that they represent distinct disease entities that may benefit from different therapeutic approaches. Gene expression profiling studies have identified numerous genes that are differentially expressed between them. However, none of these studies covered the whole transcriptome and the published gene lists reveal little overlap, raising the need for further, more comprehensive analyses. Here, we present the first transcriptome-wide expression profiling study comparing the two types (diffuse n=19, intestinal n=24), which identified >1000 genes that are differentially expressed. Among them, thrombospondin 4 (THBS4) showed the strongest correlation to histological type, with vast overexpression in the diffuse type. Quantitative real-time PCR validated this strong overexpression and revealed that intestinal tumors generally lack THBS4 expression. Immunohistochemistry demonstrated THBS4 overexpression on the protein level (n=10) and localized THBS4 to the stromal aspect. Its expression was primarily observed within the extracellular matrix surrounding the tumor cells, with the highest intensities found in regions of high tumor cell density and invasion. Intestinal tumors and matched non-neoplastic gastric epithelium and stroma did not feature any relevant THBS4 expression in a preliminary selection of analyzed cases (n=5). Immunohistochemical colocalization and in vitro studies revealed that THBS4 is expressed and secreted by cancer-associated fibroblasts. Furthermore, we show that THBS4 transcription in fibroblasts is stimulated by tumor cells. This study is the first to identify THBS4 as a powerful marker for diffuse-type gastric adenocarcinomas and to provide an initial characterization of its expression in the course of this disease. | [Susann F|[ouml]|rster, Stephan Gretschel, Thomas J|[ouml]|ns, Masakazu Yashiro, Wolfgang Kemmner] | Modern Pathology | 2011-06-24 | |
| naturepublishinggroup10.1038/nsmb.2067 | Misregulation of miR-1 processing is associated with heart defects in myotonic dystrophy | | [Fr�d�rique Rau, Fernande Freyermuth, Charlotte Fugier, Jean-Philippe Villemin, Marie-Christine Fischer, Bernard Jost, Doulaye Dembele, Genevi�ve Gourdon, Annie Nicole, Denis Duboc, Karim Wahbi, John W Day, Harutoshi Fujimura, Masanori P Takahashi, Didier Auboeuf, Natacha Dreumont, Denis Furling, Nicolas Charlet-Berguerand] | Nature Structural & Molecular Biology | 2011-06-19 | |
| naturepublishinggroup10.1038/icb.2011.56 | LPS hypersensitivity of gp130 mutant mice is independent of elevated haemopoietic TLR4 signaling | Among the many inflammatory mediators induced by the prototypical inflammatory stimulus lipopolysaccharide (LPS), which signals via Toll-like receptor (TLR)-4, interleukin (IL)-6 has recently been shown to feedback and augment TLR4 signaling when overproduced in LPS hypersensitive gp130F/F mice. This regulation by IL-6 in gp130F/F mice requires hyperactivation of the latent transcription factor signal transducer and activator of transcription (STAT) 3 via the IL-6 signaling receptor subunit gp130. However, the identity of LPS/TLR4-responsive inflammatory signaling pathways and gene networks, which are modulated by IL-6 (via gp130/STAT3), and the extent to which the tissue and cellular context of this regulation contributes to LPS-induced endotoxic shock in gp130F/F mice, are unknown. We report here that in LPS-treated macrophages from gp130F/F mice, gp130 hyperactivation upregulated the LPS-induced expression of inflammatory mediators downstream of Janus kinase (JAK)/STAT, nuclear factor κ-light-chain-enhancer of activated B cells, interferon regulatory factor and c-Jun N-terminal kinase/p38 mitogen-activated protein kinase pathways. Notably, however, LPS administration to bone marrow chimeras indicated that heightened LPS/TLR4 signaling in haemopoietic-derived gp130F/F immune cells is dispensable for the hypersensitivity of gp130F/F mice to LPS-induced endotoxemia. To understand the molecular consequences of gp130 hyperactivity in non-haemopoietic tissue on LPS-induced systemic inflammation, global gene expression profiling of livers from LPS-treated gp130F/F mice was performed and identified 264 hepatic LPS-responsive genes, which are differentially regulated by hyperactive gp130 signaling. Collectively, the substantial transcriptional reprogramming of LPS-responsive genes in gp130F/F mice emphasizes non-haemopoietic gp130 signaling as a key regulator of systemic inflammatory responses during LPS-induced endotoxemia. | [Claire J Greenhill, Jodee Gould, Matthias Ernst, Paul J Hertzog, Ashley Mansell, Brendan J Jenkins] | Immunology and Cell Biology | 2011-06-14 | |
| naturepublishinggroup10.1038/nature10106 | Direct reprogramming of somatic cells is promoted by maternal transcription factor Glis1 | Induced pluripotent stem cells (iPSCs) are generated from somatic cells by the transgenic expression of three transcription factors collectively called OSK: Oct3/4 (also called Pou5f1), Sox2 and Klf41. However, the conversion to iPSCs is inefficient. The proto-oncogene Myc enhances the efficiency of iPSC generation by OSK but it also increases the tumorigenicity of the resulting iPSCs2. Here we show that the Gli-like transcription factor Glis1 (Glis family zinc finger 1) markedly enhances the generation of iPSCs from both mouse and human fibroblasts when it is expressed together with OSK. Mouse iPSCs generated using this combination of transcription factors can form germline-competent chimaeras. Glis1 is enriched in unfertilized oocytes and in embryos at the one-cell stage. DNA microarray analyses show that Glis1 promotes multiple pro-reprogramming pathways, including Myc, Nanog, Lin28, Wnt, Essrb and the mesenchymal–epithelial transition. These results therefore show that Glis1 effectively promotes the direct reprogramming of somatic cells during iPSC generation. | [Momoko Maekawa, Kei Yamaguchi, Tomonori Nakamura, Ran Shibukawa, Ikumi Kodanaka, Tomoko Ichisaka, Yoshifumi Kawamura, Hiromi Mochizuki, Naoki Goshima, Shinya Yamanaka] | Nature | 2011-06-08 | |
| naturepublishinggroup10.1038/labinvest.2011.87 | Diabetes causes multiple genetic alterations and downregulates expression of DNA repair genes in the prostate | The molecular impact of diabetes mellitus on prostate gland has not been elucidated. In this study, we performed a whole-genome cDNA microarray analysis using a streptozotocin-induced diabetic rat model to identify the effects of diabetes on the gene expression profiles in prostate. Our study shows that diabetes causes changes in the expression of multiple genes, particularly those related to cell proliferation and differentiation, oxidative stress, DNA damage repair, cell cycle checkpoints, angiogenesis and apoptosis. These findings were confirmed by real-time polymerase chain reaction and immunohistochemical staining using rat and human prostate tissue. We also used a cell culture model (human normal prostatic RWPE-1 cell line) to study the direct effect of high glucose. We found that high glucose caused increased intracellular oxidative stress and DNA damage, as well as downregulation of anti-oxidative enzymes and DNA damage repair genes MRE11 and XRCC3. Our findings provide important insights into understanding the pathogenesis of the diabetes-induced changes in prostate as well as identifying potential therapeutic targets for future studies. | [Chunwei Ye, Xiaojuan Li, Yu Wang, Yuying Zhang, Mengyin Cai, Baoyi Zhu, Panwei Mu, Xuan Xia, Yi Zhao, Jianping Weng, Xin Gao, Xingqiao Wen] | Laboratory Investigation | 2011-06-06 | |
| naturepublishinggroup10.1038/emboj.2011.181 | Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex | The SAGA complex is a conserved, multifunctional co-activator that has broad roles in eukaryotic transcription. Previous studies suggested that Tra1, the largest SAGA component, is required either for SAGA assembly or for SAGA recruitment by DNA-bound transcriptional activators. In contrast to Saccharomyces cerevisiae and mouse, a tra1Δ mutant is viable in Schizosaccharomyces pombe, allowing us to test these issues in vivo. We find that, in a tra1Δ mutant, SAGA assembles and is recruited to some, but not all, promoters. Consistent with these findings, Tra1 regulates the expression of only a subset of SAGA-dependent genes. We previously reported that the SAGA subunits Gcn5 and Spt8 have opposing regulatory roles during S. pombe sexual differentiation. We show here that, like Gcn5, Tra1 represses this pathway, although by a distinct mechanism. Thus, our study reveals that Tra1 has specific regulatory roles, rather than global functions, within SAGA. | [Dominique Helmlinger, Samuel Marguerat, Judit Vill|[eacute]|n, Danielle L Swaney, Steven P Gygi, J|[uuml]|rg B|[auml]|hler, Fred Winston] | The EMBO Journal | 2011-06-03 | |
| naturepublishinggroup10.1038/embor.2011.78 | Antagonistic regulation of EMT by TIF1|[gamma]| and Smad4 in mammary epithelial cells | TGF-β is a potent inducer of epithelial-to-mesenchymal transition (EMT), a process involved in tumour invasion. TIF1γ participates in TGF-β signalling. To understand the role of TIF1γ in TGF-β signalling and its requirement for EMT, we analysed the TGF-β1 response of human mammary epithelial cell lines. A strong EMT increase was observed in TIF1γ-silenced cells after TGF-β1 treatment, whereas Smad4 inactivation completely blocked this process. Accordingly, the functions of several TIF1γ target genes can be linked to EMT, as shown by microarray analysis. As a negative regulator of Smad4, TIF1γ could be crucial for the regulation of TGF-β signalling. Furthermore, TIF1γ binds to and represses the plasminogen activator inhibitor 1 promoter, demonstrating a direct role of TIF1γ in TGF-β-dependent gene expression. This study shows the molecular relationship between TIF1γ and Smad4 in TGF-β signalling and EMT. | [C|[eacute]|dric Hesling, Laurent Fattet, Guillaume Teyre, Delphine Jury, Philippe Gonzalo, Jonathan Lopez, Christophe Vanbelle, Anne-Pierre Morel, Germain Gillet, Ivan Mikaelian, Ruth Rimokh] | EMBO reports | 2011-05-20 | |
| naturepublishinggroup10.1038/emboj.2011.151 | AP-2|[gamma]| regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription | Oestrogen receptor α (ERα) is key player in the progression of breast cancer. Recently, the cistrome and interactome of ERα were mapped in breast cancer cells, revealing the importance of spatial organization in oestrogen-mediated transcription. However, the underlying mechanism of this process is unclear. Here, we show that ERα binding sites (ERBS) identified from the Chromatin Interaction Analysis-Paired End DiTag of ERα are enriched for AP-2 motifs. We demonstrate the transcription factor, AP-2γ, which has been implicated in breast cancer oncogenesis, binds to ERBS in a ligand-independent manner. Furthermore, perturbation of AP-2γ expression impaired ERα DNA binding, long-range chromatin interactions, and gene transcription. In genome-wide analyses, we show that a large number of AP-2γ and ERα binding events converge together across the genome. The majority of these shared regions are also occupied by the pioneer factor, FoxA1. Molecular studies indicate there is functional interplay between AP-2γ and FoxA1. Finally, we show that most ERBS associated with long-range chromatin interactions are colocalized with AP-2γ and FoxA1. Together, our results suggest AP-2γ is a novel collaborative factor in ERα-mediated transcription. | [Si Kee Tan, Zhen Hua Lin, Cheng Wei Chang, Vipin Varang, Kern Rei Chng, You Fu Pan, Eu Leong Yong, Wing Kin Sung, Edwin Cheung] | The EMBO Journal | 2011-05-13 | |
| naturepublishinggroup10.1038/nature09999 | A novel tumour-suppressor function for the Notch pathway in myeloid leukaemia | Notch signalling is a central regulator of differentiation in a variety of organisms and tissue types1. Its activity is controlled by the multi-subunit γ-secretase (γSE) complex2. Although Notch signalling can play both oncogenic and tumour-suppressor roles in solid tumours, in the haematopoietic system it is exclusively oncogenic, notably in T-cell acute lymphoblastic leukaemia, a disease characterized by Notch1-activating mutations3. Here we identify novel somatic-inactivating Notch pathway mutations in a fraction of patients with chronic myelomonocytic leukaemia (CMML). Inactivation of Notch signalling in mouse haematopoietic stem cells (HSCs) results in an aberrant accumulation of granulocyte/monocyte progenitors (GMPs), extramedullary haematopoieisis and the induction of CMML-like disease. Transcriptome analysis revealed that Notch signalling regulates an extensive myelomonocytic-specific gene signature, through the direct suppression of gene transcription by the Notch target Hes1. Our studies identify a novel role for Notch signalling during early haematopoietic stem cell differentiation and suggest that the Notch pathway can play both tumour-promoting and -suppressive roles within the same tissue. | [Apostolos Klinakis, Camille Lobry, Omar Abdel-Wahab, Philmo Oh, Hiroshi Haeno, Silvia Buonamici, Inge van De Walle, Severine Cathelin, Thomas Trimarchi, Elisa Araldi, Cynthia Liu, Sherif Ibrahim, Miroslav Beran, Jiri Zavadil, Argiris Efstratiadis, Tom Taghon, Franziska Michor, Ross L. Levine, Iannis Aifantis] | Nature | 2011-05-11 | |
| naturepublishinggroup10.1038/cdd.2011.48 | Polycomb protein EZH2 regulates cancer cell fate decision in response to DNA damage | Polycomb protein histone methyltransferase enhancer of Zeste homologe 2 (EZH2) is frequently overexpressed in human malignancy and is implicated in cancer cell proliferation and invasion. However, it is largely unknown whether EZH2 has a role in modulating DNA damage response. Here, we show that EZH2 is an important determinant of cell fate decision in response to genotoxic stress. EZH2 depletion results in abrogation of both cell cycle G1 and G2/M checkpoints, directing DNA damage response toward predominant apoptosis in both p53-proficient and p53-deficient cancer cells, but not in normal cells. Mechanistically, EZH2 regulates DNA damage response in p53 wild-type cells mainly through transcriptional repression of FBXO32, which binds to and directs p21 for proteasome-mediated degradation, whereas it affects p53-deficient cells through regulating Chk1 activation by a distinct mechanism. Furthermore, pharmacological depletion of EZH2 phenocopies the effects of EZH2 knockdown on cell cycle checkpoints and apoptosis. These data unravel a crucial role of EZH2 in determining the cancer cell outcome following DNA damage and suggest that therapeutic targeting oncogenic EZH2 might serve as a strategy for improving conventional chemotherapy in a given malignancy. | [Z Wu, S T Lee, Y Qiao, Z Li, P L Lee, Y J Lee, X Jiang, J Tan, M Aau, C Z H Lim, Q Yu] | Cell Death & Differentiation | 2011-05-06 | |
| naturepublishinggroup10.1038/ki.2011.122 | The inducible deletion of Drosha and microRNAs in mature podocytes results in a collapsing glomerulopathy | Micro-RNAs (miRNAs) are short (average 22 nucleotides) noncoding regulatory RNAs that inhibit gene expression by targeting complementary 3′-untranslated regions of protein-encoding mRNAs for translational repression or degradation. miRNAs play key roles in both the function and differentiation of many cell types. Drosha and Dicer, two RNAase III enzymes, function in a stepwise manner to generate a mature miRNA. Previous studies have shown that podocyte-specific deletion of Dicer during development results in proteinuric renal disease and collapsing glomerulopathy (CG); however, Dicer has functions other than the generation of miRNAs. Here we found that the podocyte-specific deletion of Drosha results in a similar phenotype to Dicer mutants, confirming that the Dicer mutant phenotype is due to the loss of miRNAs. Moreover, the inducible deletion of Drosha in 2- to 3-month-old mice (Tet-On system) resulted in CG. Thus, continuous generation of miRNAs are required for the normal function of mature podocytes and their loss leads to CG. Identifying these miRNAs may provide new insight into disease pathogenesis and novel therapeutic targets in various podocytopathies. | [Olga Zhdanova, Shekhar Srivastava, Lie Di, Zhai Li, Leila Tchelebi, Sara Dworkin, Duncan B Johnstone, Jiri Zavadil, Mark M Chong, Dan R Littman, Lawrence B Holzman, Laura Barisoni, Edward Y Skolnik] | Kidney International | 2011-05-04 | x11 |
| naturepublishinggroup10.1038/onc.2011.129 | E2F1 suppresses Wnt|[sol]||[beta]|-catenin activity through transactivation of |[beta]|-catenin interacting protein ICAT | Deregulation of the pRb/E2F or Wnt/β-catenin pathway occurs frequently in human cancers, which is often associated with inappropriate cell proliferation. Although the oncogenic roles of pRb/E2F1 and Wnt/β-catenin pathways have been well studied, the functional interaction between the two pathways has only recently been characterized. In particular, E2F1 has been recently reported to negatively regulate Wnt/β-catenin activity in human colorectal cancers, though the mechanism underlying this regulation is not fully understood. Here we provide evidence that β-catenin interacting protein 1 (CTNNBIP1), also known as ICAT (inhibitor of β-catenin and TCF4), functions as a crucial node to mediate the cross talk between E2F1 and β-catenin signaling. We show that ICAT is a direct transcriptional target of E2F1, and that activation of ICAT by E2F1 is required for E2F1 to inhibit β-catenin activity. This study provides a mechanistic insight into the antagonistic interaction between E2F1 and β-catenin signaling. | [Z Wu, S Zheng, Z Li, J Tan, Q Yu] | Oncogene | 2011-05-02 | |
| naturepublishinggroup10.1038/nbt.1845 | Fibroblast growth factor 9 delivery during angiogenesis produces durable, vasoresponsive microvessels wrapped by smooth muscle cells | | [Matthew J Frontini, Zengxuan Nong, Robert Gros, Maria Drangova, Caroline O'Neil, Mona N Rahman, Oula Akawi, Hao Yin, Christopher G Ellis, J Geoffrey Pickering] | Nature Biotechnology | 2011-04-17 | |
| naturepublishinggroup10.1038/nature09907 | A diverse range of gene products are effectors of the type I interferon antiviral response | The type I interferon response protects cells against invading viral pathogens. The cellular factors that mediate this defence are the products of interferon-stimulated genes (ISGs). Although hundreds of ISGs have been identified since their discovery more than 25 years ago1, 2, 3, only a few have been characterized with respect to antiviral activity. For most ISG products, little is known about their antiviral potential, their target specificity and their mechanisms of action. Using an overexpression screening approach, here we show that different viruses are targeted by unique sets of ISGs. We find that each viral species is susceptible to multiple antiviral genes, which together encompass a range of inhibitory activities. To conduct the screen, more than 380 human ISGs were tested for their ability to inhibit the replication of several important human and animal viruses, including hepatitis C virus, yellow fever virus, West Nile virus, chikungunya virus, Venezuelan equine encephalitis virus and human immunodeficiency virus type-1. Broadly acting effectors included IRF1, C6orf150 (also known as MB21D1), HPSE, RIG-I (also known as DDX58), MDA5 (also known as IFIH1) and IFITM3, whereas more targeted antiviral specificity was observed with DDX60, IFI44L, IFI6, IFITM2, MAP3K14, MOV10, NAMPT (also known as PBEF1), OASL, RTP4, TREX1 and UNC84B (also known as SUN2). Combined expression of pairs of ISGs showed additive antiviral effects similar to those of moderate type I interferon doses. Mechanistic studies uncovered a common theme of translational inhibition for numerous effectors. Several ISGs, including ADAR, FAM46C, LY6E and MCOLN2, enhanced the replication of certain viruses, highlighting another layer of complexity in the highly pleiotropic type I interferon system. | [John W. Schoggins, Sam J. Wilson, Maryline Panis, Mary Y. Murphy, Christopher T. Jones, Paul Bieniasz, Charles M. Rice] | Nature | 2011-04-10 | |
| naturepublishinggroup10.1038/emboj.2011.105 | Glutathione revisited: a vital function in iron metabolism and ancillary role in thiol-redox control | Glutathione contributes to thiol-redox control and to extra-mitochondrial iron–sulphur cluster (ISC) maturation. To determine the physiological importance of these functions and sort out those that account for the GSH requirement for viability, we performed a comprehensive analysis of yeast cells depleted of or containing toxic levels of GSH. Both conditions triggered an intense iron starvation-like response and impaired the activity of extra-mitochondrial ISC enzymes but did not impact thiol-redox maintenance, except for high glutathione levels that altered oxidative protein folding in the endoplasmic reticulum. While iron partially rescued the ISC maturation and growth defects of GSH-depleted cells, genetic experiments indicated that unlike thioredoxin, glutathione could not support by itself the thiol-redox duties of the cell. We propose that glutathione is essential by its requirement in ISC assembly, but only serves as a thioredoxin backup in cytosolic thiol-redox maintenance. Glutathione-high physiological levels are thus meant to insulate its cytosolic function in iron metabolism from variations of its concentration during redox stresses, a model challenging the traditional view of it as prime actor in thiol-redox control. | [Chitranshu Kumar, Aeid Igbaria, Beno|[icirc]|t D'Autreaux, Anne-Ga|[euml]|lle Planson, Christophe Junot, Emmanuel Godat, Anand K Bachhawat, Agn|[egrave]|s Delaunay-Moisan, Michel B Toledano] | The EMBO Journal | 2011-04-08 | |
| naturepublishinggroup10.1038/leu.2011.53 | Clinical and biological implications of MYC activation: a common difference between MGUS and newly diagnosed multiple myeloma | Events mediating transformation from the pre-malignant monoclonal gammopathy of undetermined significance (MGUS) to multiple myeloma (MM) are unknown. We analyzed gene expression data sets generated on the Affymetrix U133 platform from 22 MGUS and 101 MM patients using gene-set enrichment analysis. Genes overexpressed in MM were enriched for cell cycle, proliferation and MYC activation gene sets. Upon dissecting the relationship between MYC and cell-cycle gene sets, we identified and validated an MYC activation signature dissociated from proliferation. Applying this signature, MYC is activated in 67% of myeloma, but not in MGUS. This was further confirmed by immunohistochemistry (IHC) using membrane CD138 and nuclear MYC double staining. We also showed that almost all tumors with RAS mutations expressed the MYC activation signature, and multiple mechanisms may be involved in activating MYC. MYC activation, whether assessed by gene-expression signature or IHC, is associated with hyperdiploid MM and shorter survival even in tumors that are not proliferative. Bortezomib treatment is able to overcome the survival disadvantage in patients with MYC activation. | [W-J Chng, G F Huang, T H Chung, S B Ng, N Gonzalez-Paz, T Troska-Price, G Mulligan, M Chesi, P L Bergsagel, R Fonseca] | Leukemia | 2011-04-05 | |
| naturepublishinggroup10.1038/ni.2020 | The transcription factor E4BP4 regulates the production of IL-10 and IL-13 in CD4+ T cells | | [Yasutaka Motomura, Hiroshi Kitamura, Atsushi Hijikata, Yuko Matsunaga, Koichiro Matsumoto, Hiromasa Inoue, Koji Atarashi, Shohei Hori, Hiroshi Watarai, Jinfang Zhu, Masaru Taniguchi, Masato Kubo] | Nature Immunology | 2011-04-03 | |
| naturepublishinggroup10.1038/ajg.2011.83 | Gene Expression Profiling and Response Signatures Associated With Differential Responses to Infliximab Treatment in Ulcerative Colitis | | [Gary Toedter, Katherine Li, Colleen Marano, Keying Ma, Sarah Sague, C Chris Huang, Xiao-Yu Song, Paul Rutgeerts, Fr|[eacute]|d|[eacute]|ric Baribaud] | The American Journal of Gastroenterology | 2011-03-29 | |
| naturepublishinggroup10.1038/ncb2210 | MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins | | [Kasey C. Vickers, Brian T. Palmisano, Bassem M. Shoucri, Robert D. Shamburek, Alan T. Remaley] | Nature Cell Biology | 2011-03-20 | |
| naturepublishinggroup10.1038/emboj.2011.52 | The unfolded protein response transducer IRE1|[alpha]| prevents ER stress-induced hepatic steatosis | The endoplasmic reticulum (ER) is the cellular organelle responsible for protein folding and assembly, lipid and sterol biosynthesis, and calcium storage. The unfolded protein response (UPR) is an adaptive intracellular stress response to accumulation of unfolded or misfolded proteins in the ER. In this study, we show that the most conserved UPR sensor inositol-requiring enzyme 1 α (IRE1α), an ER transmembrane protein kinase/endoribonuclease, is required to maintain hepatic lipid homeostasis under ER stress conditions through repressing hepatic lipid accumulation and maintaining lipoprotein secretion. To elucidate physiological roles of IRE1α-mediated signalling in the liver, we generated hepatocyte-specific Ire1α-null mice by utilizing an albumin promoter-controlled Cre recombinase-mediated deletion. Deletion of Ire1α caused defective induction of genes encoding functions in ER-to-Golgi protein transport, oxidative protein folding, and ER-associated degradation (ERAD) of misfolded proteins, and led to selective induction of pro-apoptotic UPR trans-activators. We show that IRE1α is required to maintain the secretion efficiency of selective proteins. In the absence of ER stress, mice with hepatocyte-specific Ire1α deletion displayed modest hepatosteatosis that became profound after induction of ER stress. Further investigation revealed that IRE1α represses expression of key metabolic transcriptional regulators, including CCAAT/enhancer-binding protein (C/EBP) β, C/EBPδ, peroxisome proliferator-activated receptor γ (PPARγ), and enzymes involved in triglyceride biosynthesis. IRE1α was also found to be required for efficient secretion of apolipoproteins upon disruption of ER homeostasis. Consistent with a role for IRE1α in preventing intracellular lipid accumulation, mice with hepatocyte-specific deletion of Ire1α developed severe hepatic steatosis after treatment with an ER stress-inducing anti-cancer drug Bortezomib, upon expression of a misfolding-prone human blood clotting factor VIII, or after partial hepatectomy. The identification of IRE1α as a key regulator to prevent hepatic steatosis provides novel insights into ER stress mechanisms in fatty liver diseases associated with toxic liver injuries. | [Kezhong Zhang, Shiyu Wang, Jyoti Malhotra, Justin R Hassler, Sung Hoon Back, Guohui Wang, Lin Chang, Wenbo Xu, Hongzhi Miao, Roberta Leonardi, Y Eugene Chen, Suzanne Jackowski, Randal J Kaufman] | The EMBO Journal | 2011-03-15 | |
| naturepublishinggroup10.1038/mt.2011.24 | A DNA Microarray-based Analysis of the Host Response to a Nonviral Gene Carrier: A Strategy for Improving the Immune Response | The purpose of this study was to investigate the host response to systemically administered lipid nanoparticles (NPs) encapsulating plasmid DNA (pDNA) in the spleen using a DNA microarray. As a model for NPs, we used a multifunctional envelope-type nano device (MEND). Microarray analysis revealed that 1,581 of the differentially expressed genes could be identified by polyethylene glycol (PEG)-unmodified NP using a threefold change relative to the control. As the result of PEGylation, the NP treatment resulted in the reduction in the expression of most of the genes. However, the expression of type I interferon (IFN) was specifically increased by PEGylation. Based on the microarray and a pathway analysis, we hypothesize that PEGylation inhibited the endosomal escape of NP, and extended the interaction of toll-like receptor-9 (TLR9) with CpG-DNA accompanied by the production of type I IFN. This hypothesis was tested by introducing a pH-sensitive fusogenic peptide, GALA, which enhances the endosomal escape of PEGylated NP. As expected, type I IFN was reduced and interleukin-6 (IL-6) remained at the baseline. These findings indicate that a carrier design based on microarray analysis and the manipulation of intracellular trafficking constitutes a rational strategy for reducing the host immune response to NPs. | [Hiroto Hatakeyama, Erika Ito, Momoko Yamamoto, Hidetaka Akita, Yasuhiro Hayashi, Kazuaki Kajimoto, Noritada Kaji, Yoshinobu Baba, Hideyoshi Harashima] | Molecular Therapy | 2011-03-08 | |
| naturepublishinggroup10.1038/onc.2011.12 | Prdm14 initiates lymphoblastic leukemia after expanding a population of cells resembling common lymphoid progenitors | Understanding the heterogeneous genetic mechanisms of tumor initiation in lymphoid leukemias (LL) will lead to improvements in prognostic classification and treatment regimens. In previous studies of mouse leukemias, we showed that retroviral insertion at the ecotropic viral insertion site 32 locus leads to increased expression of Prdm14, a pluripotency gene implicated in the self-renewal capacity of embryonic stem cells and the early stages of breast cancer. Here, we show that PRDM14 is also overexpressed in ~25% of human lymphoid neoplasms, with increased frequencies in T-cell acute LL and hyperdiploid precursor B-cell acute LL. To test if Prdm14 overexpression could initiate leukemia, mice were transduced with bone marrow cells transfected with a Prdm14 expression vector. LLs developed in 96% of female mice and 42% of male mice. Before the onset of leukemia, differentiation of transduced cells was biased up to 1000-fold toward cells with features of common lymphoid progenitors (CLPs), and lymphoid differentiation showed a relative block at the pro-B stage. Microarray gene expression analysis of expanded CLP-like cells before the onset of leukemia demonstrated upregulation of genes involved in pluripotency, tumor initiation, early B-lineage commitment, Wnt/Ras signaling and the epithelial-to-mesenchymal transition. Among the dysregulated genes were imprinted genes and non-coding RNAs including Dlk1 and Meg3, which are also key pluripotency mediators. Heightened expression of the estrogen-dependent oncogene, Myb, in tumors suggests a basis for the increased frequency of cancer in female mice. These data provide the first direct evidence for the association of Prdm14 with cancer initiation in an in vivo mouse model and in human lymphoid malignancies, while suggesting mechanisms for Prdm14's mode of action. | [E J Dettman, S J Simko, B Ayanga, B L Carofino, J F Margolin, H C Morse, M J Justice] | Oncogene | 2011-02-21 | |
| naturepublishinggroup10.1038/cddis.2011.1 | Anti-apoptotic function of Xbp1 as an IL-3 signaling molecule in hematopoietic cells | Cytokine signaling is critical for proliferation, survival and differentiation of hematopoietic cell, and interleukin-3 (IL-3) is required for maintenance of many hematopoietic cell lines, such as BaF3. We have isolated apoptosis-resistant clones of BaF3 using retroviral insertional mutagenesis and the Xbp1 locus was identified as a retroviral integration site. Expression and splicing of the Xbp1 transcript was conserved in the resistant clone but was promptly disappeared on IL-3 withdrawal in parental BaF3. IL-3 stimulation of BaF3 cells enhanced Xbp1 promoter activity and induced phosphorylation of the endoplasmic reticulum stress sensor protein IRE1, resulting in the increase in Xbp1S that activates unfolded protein response. When downstream signaling from IL-3 was blocked by LY294002 and/or dn-Stat5, Xbp1 expression was downregulated and IRE1 phosphorylation was suppressed. Inhibition of IL-3 signaling as well as knockdown of Xbp1-induced apoptosis in BaF3 cells. In contrast, constitutive expression of Xbp1S protected BaF3 from apoptosis during IL-3 depletion. However, cell cycle arrest at the G1 stage was observed in BaF3 and myeloid differentiation was induced in IL-3-dependent 32Dcl3 cells. Expression of apoptosis-, cell cycle- and differentiation-related genes was modulated by Xbp1S expression. These results indicate that the proper transcriptional and splicing regulation of Xbp1 by IL-3 signaling is important in homeostasis of hematopoietic cells. | [M Kurata, Y Yamazaki, Y Kanno, S Ishibashi, T Takahara, M Kitagawa, T Nakamura] | Cell Death & Disease | 2011-02-01 | |
| naturepublishinggroup10.1038/jhg.2011.14 | Genetic and clinical analysis in a Chinese parkinsonism-predominant spinocerebellar ataxia type 2 family | Parkinson's disease is a degenerative central nervous system disorder that often impairs motor skills, speech and other functions. We discovered a large Chinese family showing primarily parkinsonism symptoms with autosomal dominant inheritance. Six affected individuals in the family showed typical parkinsonism symptoms, including pill-rolling tremor. Two other affected individuals showed cerebellar ataxia symptoms. A whole-genome scan using the 50K single nucleotide polymorphism array with three different linkage methods detected two positive regions on chromosome 12q24.1 and 5q13.3. The ATXN2 gene, responsible for spinocerebellar ataxia type 2 (SCA2) was located precisely in the center of the positive region on chromosome 12. Further analysis of SCA2 revealed heterozygous pathological CAG expansions in the family. The affected individuals’ symptoms were typical of parkinsonism, but complex. Inverse correlation between CAG repeat size and age of onset is not obvious in this pedigree. This parkinsonism-predominant SCA2 family shared the same disease gene locus with other ‘standard’ SCA2 families, but it is possible that variations in one or more modifier genes might account for the parkinsonism-predominant SCA2 predisposition observed in this pedigree. | [Hao Sun, Wataru Satake, Changjun Zhang, Yoshitaka Nagai, Youyong Tian, Shouzhi Fu, Jiankun Yu, Yaping Qian, Yuan Qian, Jiayou Chu, Tatsushi Toda] | Journal of Human Genetics | 2011-02-10 | |
| naturepublishinggroup10.1038/bjc.2011.23 | The tumour-suppressive function of miR-1 and miR-133a targeting TAGLN2 in bladder cancer | | [H Yoshino, T Chiyomaru, H Enokida, K Kawakami, S Tatarano, K Nishiyama, N Nohata, N Seki, M Nakagawa] | British Journal of Cancer | 2011-02-08 | |
| naturepublishinggroup10.1038/aps.2010.204 | Genome-wide analysis of microRNA and mRNA expression signatures in hydroxycamptothecin-resistant gastric cancer cells | | [Xue-mei Wu, Xiang-qiang Shao, Xian-xin Meng, Xiao-na Zhang, Li Zhu, Shi-xu Liu, Jian Lin, Hua-sheng Xiao] | Acta Pharmacologica Sinica | 2011-02-01 | |
| naturepublishinggroup10.1038/nature09646 | Bifidobacteria can protect from enteropathogenic infection through production of acetate | The human gut is colonized with a wide variety of microorganisms, including species, such as those belonging to the bacterial genus Bifidobacterium, that have beneficial effects on human physiology and pathology1, 2, 3. Among the most distinctive benefits of bifidobacteria are modulation of host defence responses and protection against infectious diseases4, 5, 6. Nevertheless, the molecular mechanisms underlying these effects have barely been elucidated. To investigate these mechanisms, we used mice associated with certain bifidobacterial strains and a simplified model of lethal infection with enterohaemorrhagic Escherichia coli O157:H7, together with an integrated ‘omics’ approach. Here we show that genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain bifidobacteria contribute to protecting mice against death induced by E. coli O157:H7. We found that this effect can be attributed, at least in part, to increased production of acetate and that translocation of the E. coli O157:H7 Shiga toxin from the gut lumen to the blood was inhibited. We propose that acetate produced by protective bifidobacteria improves intestinal defence mediated by epithelial cells and thereby protects the host against lethal infection. | [Shinji Fukuda, Hidehiro Toh, Koji Hase, Kenshiro Oshima, Yumiko Nakanishi, Kazutoshi Yoshimura, Toru Tobe, Julie M. Clarke, David L. Topping, Tohru Suzuki, Todd D. Taylor, Kikuji Itoh, Jun Kikuchi, Hidetoshi Morita, Masahira Hattori, Hiroshi Ohno] | Nature | 2011-01-26 | |
| naturepublishinggroup10.1038/leu.2010.301 | The transcription factor PlagL2 activates Mpl transcription and signaling in hematopoietic progenitor and leukemia cells | Cytokine signaling pathways are frequent targets of oncogenic mutations in acute myeloid leukemia (AML), promoting proliferation and survival. We have previously shown that the transcription factor PLAGL2 promotes proliferation and cooperates with the leukemia fusion protein Cbfβ-SMMHC in AML development. Here, we show that PLAGL2 upregulates expression of the thrombopoietin receptor Mpl, using two consensus sites in its proximal promoter. We also show that Mpl overexpression efficiently cooperates with Cbfβ-SMMHC in development of leukemia in mice. Finally, we demonstrate that PlagL2-expressing leukemic cells show hyper-activation of Jak2 and downstream STAT5, Akt and Erk1/2 pathways in response to Thpo ligand. These results show that PlagL2 expression activates expression of Mpl in hematopoietic progenitors, and that upregulation of wild-type Mpl provides an oncogenic signal in cooperation with CBFβ-SMMHC in mice. | [S F Landrette, D Madera, F He, L H Castilla] | Leukemia | 2011-01-25 | |
| naturepublishinggroup10.1038/onc.2010.602 | Myc|[sol]|miR-378|[sol]|TOB2|[sol]|cyclin D1 functional module regulates oncogenic transformation | The c-Myc transcription factor activates a cascade of downstream targets to form a complex transcriptional program that ultimately leads to cellular transformation. Although a large number of protein-encoding genes as well as non-coding RNAs were identified as Myc targets, only a few have been validated to be functionally important for c-Myc-driven transformation. Here, we identify a microRNA (miRNA), miR-378, as a novel target of the c-Myc oncoprotein that is able to cooperate with activated Ras or HER2 to promote cellular transformation. Mechanistically, miR-378 achieves this oncogenic effect, at least in part, by targeting and inhibiting the anti-proliferative BTG family member, TOB2, which is further elucidated as a candidate tumor suppressor to transcriptionally repress proto-oncogene cyclin D1. Therefore, our study identifies miR-378-TOB2-cyclin D1 as a functional module to mediate the cross talk between Myc and Ras signaling in cellular transformation. | [M Feng, Z Li, M Aau, C H Wong, X Yang, Q Yu] | Oncogene | 2011-01-17 | |
| naturepublishinggroup10.1038/ncomms1155 | Neural stem and progenitor cells shorten S-phase on commitment to neuron production | | [Yoko Arai, Jeremy N. Pulvers, Christiane Haffner, Britta Schilling, Ina Nüsslein, Federico Calegari, Wieland B. Huttner] | Nature Communications | 2011-01-11 | |
| naturepublishinggroup10.1038/ncb2137 | HoxA3 is an apical regulator of haemogenic endothelium | During development, haemogenesis occurs invariably at sites of vasculogenesis. Between embryonic day (E) 9.5 and E10.5 in mice, endothelial cells in the caudal part of the dorsal aorta generate haematopoietic stem cells1, 2 and are referred to as haemogenic endothelium3, 4, 5, 6, 7, 8. The mechanisms by which haematopoiesis is restricted to this domain, and how the morphological transformation from endothelial to haematopoietic is controlled are unknown. We show here that HoxA3, a gene uniquely expressed in the embryonic but not yolk sac vasculature, restrains haematopoietic differentiation of the earliest endothelial progenitors, and induces reversion of the earliest haematopoietic progenitors into CD41-negative endothelial cells. This reversible modulation of endothelial–haematopoietic state is accomplished by targeting key haematopoietic transcription factors for downregulation, including Runx1, Gata1, Gfi1B, Ikaros, and PU.1. Through loss-of-function, and gain-of-function epistasis experiments, and the identification of antipodally regulated targets, we show that among these factors, Runx1 is uniquely able to erase the endothelial program set up by HoxA3. These results suggest both why a frank endothelium does not precede haematopoiesis in the yolk sac, and why haematopoietic stem cell generation requires Runx1 expression only in endothelial cells. | [Michelina Iacovino, Diana Chong, Istvan Szatmari, Lynn Hartweck, Danielle Rux, Arianna Caprioli, Ondine Cleaver, Michael Kyba] | Nature Cell Biology | 2010-12-19 | 7.3.1 |
| naturepublishinggroup10.1038/nature09691 | Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro | Studies in embryonic development have guided successful efforts to direct the differentiation of human embryonic and induced pluripotent stem cells (PSCs) into specific organ cell types in vitro1, 2. For example, human PSCs have been differentiated into monolayer cultures of liver hepatocytes and pancreatic endocrine cells3, 4, 5, 6 that have therapeutic efficacy in animal models of liver disease7, 8 and diabetes9, respectively. However, the generation of complex three-dimensional organ tissues in vitro remains a major challenge for translational studies. Here we establish a robust and efficient process to direct the differentiation of human PSCs into intestinal tissue in vitro using a temporal series of growth factor manipulations to mimic embryonic intestinal development10. This involved activin-induced definitive endoderm formation11, FGF/Wnt-induced posterior endoderm pattering, hindgut specification and morphogenesis12, 13, 14, and a pro-intestinal culture system15, 16 to promote intestinal growth, morphogenesis and cytodifferentiation. The resulting three-dimensional intestinal ‘organoids’ consisted of a polarized, columnar epithelium that was patterned into villus-like structures and crypt-like proliferative zones that expressed intestinal stem cell markers17. The epithelium contained functional enterocytes, as well as goblet, Paneth and enteroendocrine cells. Using this culture system as a model to study human intestinal development, we identified that the combined activity of WNT3A and FGF4 is required for hindgut specification whereas FGF4 alone is sufficient to promote hindgut morphogenesis. Our data indicate that human intestinal stem cells form de novo during development. We also determined that NEUROG3, a pro-endocrine transcription factor that is mutated in enteric anendocrinosis18, is both necessary and sufficient for human enteroendocrine cell development in vitro. PSC-derived human intestinal tissue should allow for unprecedented studies of human intestinal development and disease. | [Jason R. Spence, Christopher N. Mayhew, Scott A. Rankin, Matthew F. Kuhar, Jefferson E. Vallance, Kathryn Tolle, Elizabeth E. Hoskins, Vladimir V. Kalinichenko, Susanne I. Wells, Aaron M. Zorn, Noah F. Shroyer, James M. Wells] | Nature | 2010-12-12 | |
| naturepublishinggroup10.1038/nature09632 | A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns | Parallels between phylogeny and ontogeny have been discussed for almost two centuries, and a number of theories have been proposed to explain such patterns1. Especially elusive is the phylotypic stage, a phase during development where species within a phylum are particularly similar to each other2, 3, 4, 5, 6. Although this has formerly been interpreted as a recapitulation of phylogeny1, it is now thought to reflect an ontogenetic progression phase2, where strong constraints on developmental regulation and gene interactions exist2, 3. Several studies have shown that genes expressed during this stage evolve at a slower rate, but it has so far not been possible to derive an unequivocal molecular signature associated with this stage7, 8, 9, 10, 11, 12, 13, 14, 15. Here we use a combination of phylostratigraphy16 and stage-specific gene expression data to generate a cumulative index that reflects the evolutionary age of the transcriptome at given ontogenetic stages. Using zebrafish ontogeny and adult development as a model, we find that the phylotypic stage does indeed express the oldest transcriptome set and that younger sets are expressed during early and late development, thus faithfully mirroring the hourglass model of morphological divergence2, 3. Reproductively active animals show the youngest transcriptome, with major differences between males and females. Notably, ageing animals express increasingly older genes. Comparisons with similar data sets from flies and nematodes show that this pattern occurs across phyla. Our results indicate that an old transcriptome marks the phylotypic phase and that phylogenetic differences at other ontogenetic stages correlate with the expression of newly evolved genes. | [Tomislav Domazet-Lošo, Diethard Tautz] | Nature | 2010-12-08 | |
| naturepublishinggroup10.1038/onc.2010.538 | Analysis of Brca1-deficient mouse mammary glands reveals reciprocal regulation of Brca1 and c-kit | Disruption of the breast cancer susceptibility gene Brca1 results in defective lobular-alveolar development in the mammary gland and a predisposition to breast tumourigenesis in humans and in mice. Recent evidence suggests that BRCA1 loss in humans is associated with an expansion of the luminal progenitor cell compartment in the normal breast and tumours with a luminal progenitor-like expression profile. To further investigate the role of BRCA1 in the mammary gland, we examined the consequences of Brca1 loss in mouse mammary epithelial cells in vitro and in vivo. Here, we show that Brca1 loss is associated with defective morphogenesis of SCp2 and HC11 mouse mammary epithelial cell lines and that in the MMTV-Cre Brca1Co/Co mouse model of Brca1 loss, there is an accumulation of luminal progenitor (CD61+CD29loCD24+) cells during pregnancy. By day 1 of lactation, there are marked differences in the expression of 1379 genes, with most significantly altered pathways and networks, including lactation, the immune response and cancer. One of the most differentially expressed genes was the luminal progenitor marker, c-kit. Immunohistochemical analysis revealed that the increase in c-kit levels is associated with an increase in c-kit positivity. Interestingly, an inverse association between Brca1 and c-kit expression was also observed during mammary epithelial differentiation, and small interfering RNA-mediated knockdown of Brca1 resulted in a significant increase in c-kit mRNA levels. We found no evidence that c-kit plays a direct role in regulating differentiation of HC11 cells, suggesting that Brca1-mediated induction of c-kit probably contributes to Brca1-associated tumourigenesis via another cellular process, and that c-kit is likely to be a marker rather than a mediator of defective lobular-alveolar development resulting from Brca1 loss. | [C E Smart, A Wronski, J D French, S L Edwards, M-L Asselin-Labat, N Waddell, K Peters, B L Brewster, K Brooks, K Simpson, N Manning, S R Lakhani, S Grimmond, G J Lindeman, J E Visvader, M A Brown] | Oncogene | 2010-12-06 | 7.3 |
| naturepublishinggroup10.1038/ismej.2010.177 | Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon | We applied constrained ordination numerical ecology methods to data produced with a human intestinal tract-specific phylogenetic microarray (the Aus-HIT Chip) to examine the microbial diversity associated with matched biopsy tissue samples taken from the caecum, transverse colon, sigmoid colon and rectum of 10 healthy patients. Consistent with previous studies, the profiles revealed a marked intersubject variability; however, the numerical ecology methods of analysis allowed the subtraction of the subject effect from the data and revealed, for the first time, evidence of a longitudinal gradient for specific microbes along the colorectum. In particular, probes targeting Streptococcus and Enterococcus spp. produced strongest signals with caecal and transverse colon samples, with a gradual decline through to the rectum. Conversely, the analyses suggest that several members of the Enterobacteriaceae increase in relative abundance towards the rectum. These collective differences were substantiated by the multivariate analysis of quantitative PCR data. We were also able to identify differences in the microarray profiles, especially for the streptococci and Faecalibacterium prausnitzii, on the basis of gender. The results derived by these multivariate analyses are biologically intuitive and suggest that the biogeography of the colonic mucosa can be monitored for changes through cross-sectional and/or inception cohort studies. | [Daniel Aguirre de C|[aacute]|rcer, P|[aacute]|raic |[Oacute]| Cu|[iacute]|v, Tingting Wang, Seungha Kang, Daniel Worthley, Vicki Whitehall, Iain Gordon, Chris McSweeney, Barbara Leggett, Mark Morrison] | The ISME Journal | 2010-12-02 | x10 |
| naturepublishinggroup10.1038/cgt.2010.71 | Dlxin-1, a member of MAGE family, inhibits cell proliferation, invasion and tumorigenicity of glioma stem cells | We have previously reported the presence of Dlxin-1, a member of the melanoma antigen gene (MAGE) family, in the brain and showed its function as a cell cycle arrest protein, suggesting that Dlxin-1 may have anti-proliferative functions in rapidly growing tumors. Using the cancer stem cell hypothesis, which attributes the initiation and progression of brain tumors to the cancer-initiating stem cells, we have investigated the role of Dlxin-1 in the glioma stem cells propagated by us as a cell culture system comprising of HNGC-2 cells. Our studies provide evidence about the role of Dlxin-1 as an anti-tumorigenic protein in the highly chemo-resistant glioma stem cells. Next, we show that these anti-proliferative effects are manifested by Dlxin-1 through down regulation of the activities of MMP-2 and MMP-9, and through interaction of Dlxin-1 with its target protein P311 that is involved in glioma cell invasion. In summary, we establish the roles for Dlxin-1, one as an anti-tumorigenic and anti-invasive protein in high-grade gliomas and the other as an inducer of differentiation of glioma stem cells. These two attributes, in conjunction, result in conversion of the drug-resistant brain tumor stem cells to the tumor-attenuated cells that may now be more amenable to effective therapeutic targeting. | [E M Reddy, S T Chettiar, N Kaur, R Ganeshkumar, V Shepal, N C Shanbhag, A Shiras] | Cancer Gene Therapy | 2010-11-26 | |
| naturepublishinggroup10.1038/onc.2010.523 | Efficient in vivo microRNA targeting of liver metastasis | Targeting oncogenic microRNAs (miRNAs) is emerging as a promising strategy for cancer therapy. In this study, we provide proof of principle for the safety and efficacy of miRNA targeting against metastatic tumors. We tested the impact of targeting miR-182, a pro-metastatic miRNA frequently overexpressed in melanoma, the in vitro silencing of which represses invasion and induces apoptosis. Specifically, we assessed the effect of anti-miR-182 oligonucleotides synthesized with 2′ sugar modifications and a phosphorothioate backbone in a mouse model of melanoma liver metastasis. Luciferase imaging showed that mice treated with anti-miR-182 had a lower burden of liver metastases compared with control. We confirmed that miR-182 levels were effectively downregulated in the tumors of anti-miR-treated mice compared with tumors of control-treated mice, both in the liver and in the spleen. This effect was accompanied by an upregulation of multiple miR-182 direct targets. Transcriptional profiling of tumors treated with anti-miR-182 or with control oligonucleotides revealed an enrichment of genes controlling survival, adhesion and migration modulated in response to anti-miR-182 treatment. These data indicate that in vivo administration of anti-miRs allows for efficient miRNA targeting and concomitant upregulation of miRNA-controlled genes. Our results demonstrate that the use of anti-miR-182 is a promising therapeutic strategy for metastatic melanoma and provide a solid basis for testing similar strategies in human metastatic tumors. | [C Huynh, M F Segura, A Gaziel-Sovran, S Menendez, F Darvishian, L Chiriboga, B Levin, D Meruelo, I Osman, J Zavadil, E G Marcusson, E Hernando] | Oncogene | 2010-11-22 | |
| naturepublishinggroup10.1038/labinvest.2010.187 | Isolation of alveolar epithelial type II progenitor cells from adult human lungs | Resident stem/progenitor cells in the lung are important for tissue homeostasis and repair. However, a progenitor population for alveolar type II (ATII) cells in adult human lungs has not been identified. The aim of this study is to isolate progenitor cells from adult human lungs with the ability to differentiate into ATII cells. We isolated colony-forming cells that had the capability for self-renewal and the potential to generate ATII cells in vitro. These undifferentiated progenitor cells expressed surface markers of mesenchymal stem cells (MSCs) and surfactant proteins associated with ATII cells, such as CD90 and pro-surfactant protein-C (pro-SP-C), respectively. Microarray analyses indicated that transcripts associated with lung development were enriched in the pro-SP-C+/CD90+ cells compared with bone marrow-MSCs. Furthermore, pathological evaluation indicated that pro-SP-C and CD90 double-positive cells were present within alveolar walls in normal lungs, and significantly increased in ATII cell hyperplasias contributing to alveolar epithelial repair in damaged lungs. Our findings demonstrated that adult human lungs contain a progenitor population for ATII cells. This study is a first step toward better understanding of stem cell biology in adult human lung alveoli. | [Naoya Fujino, Hiroshi Kubo, Takaya Suzuki, Chiharu Ota, Ahmed E Hegab, Mei He, Satoshi Suzuki, Takashi Suzuki, Mitsuhiro Yamada, Takashi Kondo, Hidemasa Kato, Mutsuo Yamaya] | Laboratory Investigation | 2010-11-15 | |
| naturepublishinggroup10.1038/leu.2010.253 | The E2A-HLF oncogenic fusion protein acts through Lmo2 and Bcl-2 to immortalize hematopoietic progenitors | The oncogenic fusion protein E2A–HLF is a chimeric transcription factor that arises from the t(17;19) translocation in childhood B-cell acute lymphoblastic leukemias (B-precursor ALL) and is associated with very poor outcome. We show that retroviral-mediated expression of E2A–HLF alone is sufficient to immortalize primary lymphoid progenitors. We identify Lmo2 and Bcl-2 as direct target genes downstream of E2A–HLF. We use real-time PCR analysis to show that LMO2 and BCL-2 expression is preferentially upregulated both in biopsy material from t(17;19) B-precursor ALL patients and lymphoid cell lines derived from t(17;19) leukemias. Co-expression of Lmo2 and Bcl-2 was sufficient to immortalize lymphoid progenitor cells resulting in a similar phenotype to that induced by E2A–HLF alone. Both shRNA-mediated knockdown of Lmo2 expression and pharmacological inhibition of BCL-2 function in E2A–HLF immortalized cells severely compromised their viability. These data suggest that both Lmo2 and Bcl-2 are required for the action of E2A–HLF in leukemogenesis. | [J de Boer, J Yeung, J Ellu, R Ramanujachar, B Bornhauser, O Solarska, M Hubank, O Williams, H J M Brady] | Leukemia | 2010-11-12 | 5.1 |
| naturepublishinggroup10.1038/modpathol.2010.193 | A novel role for TNFAIP2: its correlation with invasion and metastasis in nasopharyngeal carcinoma | Tumor necrosis factor alpha (TNFα) is an inflammatory cytokine that is present in the microenvironment of many tumors and is known to promote tumor progression. To examine how TNFα modulates the progression and metastasis of nasopharyngeal carcinoma, we used Affymetrix chips to identify TNFα-inducible genes that are dysregulated in this tumor. Elevated expression of TNFAIP2, which encodes TNFα-inducible protein 2 and not previously known to be associated with cancer, was found and confirmed by quantitative RT-PCR of TNFAIP2 expression in nasopharyngeal carcinoma and adjacent normal tissues. Immunohistochemical analysis showed that the TNFAIP2 protein was highly expressed in tumor cells. Analysis of 95 nasopharyngeal carcinoma biopsy specimens revealed that high TNFAIP2 expression was significantly correlated with high-level intratumoral microvessel density (P=0.005) and low distant metastasis-free survival (P=0.001). A multivariate analysis further confirmed that TNFAIP2 was an independent prognostic factor for nasopharyngeal carcinoma (P=0.002). In vitro, TNFα treatment of nasopharyngeal carcinoma HK1 cells was found to induce TNFAIP2 expression, and siRNA-based knockdown of TNFAIP2 dramatically reduced the migration and invasion of nasopharyngeal carcinoma HK1 cells. These results collectively suggest for the first time that TNFAIP2 is a cell migration-promoting protein and its expression predicts distant metastasis. Our data suggest that TNFAIP2 may serve as an independent prognostic indicator for nasopharyngeal carcinoma. | [Lih-Chyang Chen, Chia-Chun Chen, Ying Liang, Ngan-Ming Tsang, Yu-Sun Chang, Chuen Hsueh] | Modern Pathology | 2010-11-05 | |
| naturepublishinggroup10.1038/ng.704 | Natural variation at Strubbelig Receptor Kinase 3 drives immune-triggered incompatibilities between Arabidopsis thaliana accessions | Accumulation of genetic incompatibilities within species can lead to reproductive isolation and, potentially, speciation. In this study, we show that allelic variation at SRF3 (Strubbelig Receptor Family 3), encoding a receptor-like kinase, conditions the occurrence of incompatibility between Arabidopsis thaliana accessions. The geographical distribution of SRF3 alleles reveals that allelic forms causing epistatic incompatibility with a Landsberg erecta allele at the RPP1 resistance locus are present in A. thaliana accessions in central Asia. Incompatible SRF3 alleles condition for an enhanced early immune response to pathogens as compared to the resistance-dampening effect of compatible SRF3 forms in isogenic backgrounds. Variation in disease susceptibility suggests a basis for the molecular patterns of a recent selective sweep detected at the SRF3 locus in central Asian populations. | [Rubén Alcázar, Ana V García, Ilkka Kronholm, Juliette de Meaux, Maarten Koornneef, Jane E Parker, Matthieu Reymond] | Nature Genetics | 2010-10-31 | |
| naturepublishinggroup10.1038/ncb2108 | Angiocrine factors from Akt-activated endothelial cells balance self-renewal and differentiation of haematopoietic stem cells | | [Hideki Kobayashi, Jason M. Butler, Rebekah O'Donnell, Mariko Kobayashi, Bi-Sen Ding, Bryant Bonner, Vi K. Chiu, Daniel J. Nolan, Koji Shido, Laura Benjamin, Shahin Rafii] | Nature Cell Biology | 2010-10-24 | |
| naturepublishinggroup10.1038/nature09447 | Generation of pathogenic TH17 cells in the absence of TGF-[bgr] signalling | CD4+ T-helper cells that selectively produce interleukin (IL)-17 (TH17), are critical for host defence and autoimmunity1, 2, 3, 4. Although crucial for TH17 cells in vivo5, 6, IL-23 has been thought to be incapable of driving initial differentiation. Rather, IL-6 and transforming growth factor (TGF)-β1 have been proposed to be the factors responsible for initiating specification7, 8, 9, 10. Here we show that TH17 differentiation can occur in the absence of TGF-β signalling. Neither IL-6 nor IL-23 alone efficiently generated TH17 cells; however, these cytokines in combination with IL-1β effectively induced IL-17 production in naive precursors, independently of TGF-β. Epigenetic modification of the Il17a, Il17f and Rorc promoters proceeded without TGF-β1, allowing the generation of cells that co-expressed RORγt (encoded by Rorc) and T-bet. T-bet+RORγt+ TH17 cells are generated in vivo during experimental allergic encephalomyelitis, and adoptively transferred TH17 cells generated with IL-23 without TGF-β1 were pathogenic in this disease model. These data indicate an alternative mode for TH17 differentiation. Consistent with genetic data linking IL23R with autoimmunity, our findings re-emphasize the importance of IL-23 and therefore may have therapeutic implications. | [Kamran Ghoreschi, Arian Laurence, Xiang-Ping Yang, Cristina M. Tato, Mandy J. McGeachy, Joanne E. Konkel, Haydeé L. Ramos, Lai Wei, Todd S. Davidson, Nicolas Bouladoux, John R. Grainger, Qian Chen, Yuka Kanno, Wendy T. Watford, Hong-Wei Sun, Gérard Eberl, Ethan M. Shevach, Yasmine Belkaid, Daniel J. Cua, WanJun Chen, John J. O’Shea] | Nature | 2010-10-20 | |
| naturepublishinggroup10.1038/labinvest.2010.166 | Mirnome analysis reveals novel molecular determinants in the pathogenesis of diet-induced nonalcoholic fatty liver disease | Nonalcoholic fatty liver disease (NAFLD) is an emerging disease with a broad spectrum of liver conditions. The complex molecular pathogenesis of NAFLD is still unclear. In this study, we conducted an analysis of microRNA (miRNA) expression profiles in liver of rats made NAFLD by different diets. To this aim, Sprague-Dawley rats were fed ad libitum for 3 months with different diets: standard diet (SD), diet enriched in fats and low in carbohydrates (HFD), SD with high fructose (SD-HF) and diet with high levels of fats and fructose (HFD-HF). Our results demonstrated that the treatment with different dietetic regimens caused a significant increase of the body weight and the alteration of some metabolic parameters compared with control animals, as well as various liver injuries. The miRNAs analysis showed the significant downregulation of three miRNAs (miR-122, miR-451 and miR-27) and the upregulation of miR-200a, miR-200b and miR-429 in HFD, SD-HF and HFD-HF rats. Besides, miR-21 expression was significantly decreased only in fructose-enriched diets. These miRNAs target molecules involved in the control of lipid and carbohydrate metabolism, signal transduction, cytokine and chemokine-mediated signaling pathway and apoptosis. Western blot analysis of PKCδ, LITAF, ALDOLASE-A, p38MAPK, PTEN, LIPIN1, EPHRIN-A1, EPHA2 and FLT1 showed a diet-induced deregulation of all these proteins. Interestingly, the expression pattern of LITAF, PTEN, LIPIN1, EPHRIN-A1, EPHA2 and FLT1 might be well explained by the trend of their specific mRNAs, by potentially regulatory miRNAs, or both. In conclusion, we highlight for the first time the potential involvement of novel determinants (miRNAs and proteins) in the molecular pathogenesis of diet-induced NAFLD. | [Anna Alisi, Letizia Da Sacco, Giovannella Bruscalupi, Fiorella Piemonte, Nadia Panera, Rita De Vito, Silvia Leoni, Gian Franco Bottazzo, Andrea Masotti, Valerio Nobili] | Laboratory Investigation | 2010-10-18 | |
| naturepublishinggroup10.1038/labinvest.2010.170 | DNA binding-dependent glucocorticoid receptor activity promotes adipogenesis via Kr|[uuml]|ppel-like factor 15 gene expression | Glucocorticoids, such as dexamethasone, have been used as in vitro inducers of adipogenesis. However, the roles of the glucocorticoid receptor (GR) in adipogenesis have not been well characterized yet. Here, we show that inhibition of GR activity using the GR antagonist RU486 prevents human mesenchymal stem cell and mouse embryonic fibroblast (MEF) differentiation into adipocytes. Moreover, in MEFs isolated from GR knockout (GRnull) and GRdim mice deficient in GR DNA-binding activity, adipogenesis was blocked. We identified glucocorticoid response element sites in the first intron of KLF15 by bioinformatical promoter analysis and confirmed their functional relevance by demonstrating GR interaction by chromatin immunoprecipitation. Moreover, transfection of MEFs with siRNA for KLF15 significantly attenuated the expressions of adipogenic-marker genes and the lipid accumulation. Our results provide a new mechanism for understanding glucocorticoids-dependent adipogenesis and that GR promotes adipogenesis via KLF15 gene expression as a transcriptional direct target. | [Maki Asada, Alexander Rauch, Hirohito Shimizu, Hiromi Maruyama, Shigeru Miyaki, Masafumi Shibamori, Hideki Kawasome, Hironobu Ishiyama, Jan Tuckermann, Hiroshi Asahara] | Laboratory Investigation | 2010-10-18 | |
| naturepublishinggroup10.1038/onc.2010.452 | Functional characterization of Wilms tumor-suppressor WTX and tumor-associated mutants | The WTX, Wilms tumor-associated tumor-suppressor gene, is present on the X chromosome and a single WTX mutation may be sufficient to promote carcinogenesis. Unlike the WT1 tumor suppressor, a transcription factor, WTX lacks conserved functional protein domains. To study the function of WTX, we constructed inducible cell lines expressing WTX and tumor-associated WTX mutants. Induction of WTX inhibited cell growth and caused G1/G0 arrest. In contrast, a short, tumor-associated truncation mutant of WTX358 only slightly inhibited cell growth without a significant cell-cycle arrest, although expression of a longer truncation mutant WTX565 led to the growth inhibition and cell-cycle arrest to a similar extent as wild-type WTX. Like WT1, WTX slowed growth and caused cell-cycle arrest through p21 induction. Gene expression profiling showed that these two tumor-suppressors regulated genes in similar pathways, including those implicated in control of the cellular growth, cell cycle, cell death, cancer and cardiovascular system development. When gene expression changes mediated by wild-type WTX were compared with those affected by mutant forms, WTX565 showed a 55% overlap (228 genes) in differentially regulated genes, whereas WTX358 regulated only two genes affected by wild-type WTX, implying that amino-acid residues 358–561 are critical for WTX function. | [M K-H Kim, D J Min, M Rabin, J D Licht] | Oncogene | 2010-10-18 | |
| naturepublishinggroup10.1038/labinvest.2010.175 | Mitochondrial damage-induced impairment of angiogenesis in the aging rat kidney | Decreased expression of vascular endothelial growth factor (VEGF) in the renal tubules is thought to cause progressive loss of the renal microvasculature with age. Mitochondrial dysfunction may be a principal phenomenon underlying the process of aging. The relation between VEGF expression and mitochondrial dysfunction in aging is not fully understood. We hypothesized that mitochondrial dysfunction blocks VEGF expression and contributes to impaired angiogenesis in the aging kidney. The aim of this study was to assess the role of mitochondria in VEGF expression in the aging rat kidney. We evaluated the accumulation of 8-hydroxy-2′-deoxyguanosine in mitochondrial DNA, as well as mitochondrial dysfunction, as assessed by electron microscopy of mitochondrial structure and histochemical staining for respiratory chain complex IV, in aging rat kidney. An increase in hypoxic area and a decrease in peritubular capillaries were detected in the cortex of aging rat kidneys; however, upregulation of VEGF expression was not observed. The expression of VEGF in proximal tubular epithelial cells in response to hypoxia was suppressed by the mitochondrial electron transfer inhibitor myxothiazol. Mitochondrial DNA-deficient cells also failed to upregulate VEGF expression under hypoxic conditions. These results indicate that impairment of VEGF upregulation, possibly as a result of mitochondrial dysfunction, contributes to impaired angiogenesis, which in turn leads to renal injury in the aging rat kidney. | [Minoru Satoh, Sohachi Fujimoto, Hideyuki Horike, Masahito Ozeki, Hajime Nagasu, Naruya Tomita, Tamaki Sasaki, Naoki Kashihara] | Laboratory Investigation | 2010-10-04 | |
| naturepublishinggroup10.1038/nature09409 | ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours | Gastrointestinal stromal tumour (GIST) is the most common human sarcoma and is primarily defined by activating mutations in the KIT or PDGFRA receptor tyrosine kinases1, 2. KIT is highly expressed in interstitial cells of Cajal (ICCs)—the presumed cell of origin for GIST—as well as in haematopoietic stem cells, melanocytes, mast cells and germ cells2, 3. Yet, families harbouring germline activating KIT mutations and mice with knock-in Kit mutations almost exclusively develop ICC hyperplasia and GIST4, 5, 6, 7, suggesting that the cellular context is important for KIT to mediate oncogenesis. Here we show that the ETS family member ETV1 is highly expressed in the subtypes of ICCs sensitive to oncogenic KIT mediated transformation8, and is required for their development. In addition, ETV1 is universally highly expressed in GISTs and is required for growth of imatinib-sensitive and resistant GIST cell lines. Transcriptome profiling and global analyses of ETV1-binding sites suggest that ETV1 is a master regulator of an ICC-GIST-specific transcription network mainly through enhancer binding. The ETV1 transcriptional program is further regulated by activated KIT, which prolongs ETV1 protein stability and cooperates with ETV1 to promote tumorigenesis. We propose that GIST arises from ICCs with high levels of endogenous ETV1 expression that, when coupled with an activating KIT mutation, drives an oncogenic ETS transcriptional program. This differs from other ETS-dependent tumours such as prostate cancer, melanoma and Ewing sarcoma where genomic translocation or amplification drives aberrant ETS expression9, 10, 11. It also represents a novel mechanism of oncogenic transcription factor activation. | [Ping Chi, Yu Chen, Lei Zhang, Xingyi Guo, John Wongvipat, Tambudzai Shamu, Jonathan A. Fletcher, Scott Dewell, Robert G. Maki, Deyou Zheng, Cristina R. Antonescu, C. David Allis, Charles L. Sawyers] | Nature | 2010-10-03 | |
| naturepublishinggroup10.1038/nprot.2010.108 | Analytical platform for metabolome analysis of microbial cells using methyl chloroformate derivatization followed by gas chromatography-mass spectrometry | | [Kathleen F Smart, Raphael B M Aggio, Jeremy R Van Houtte, Silas G Villas-Bôas] | Nature Protocols | 2010-09-30 | |
| naturepublishinggroup10.1038/nn.2646 | SOX9 induces and maintains neural stem cells | | [Charlotte E Scott, Sarah L Wynn, Abdul Sesay, Catarina Cruz, Martin Cheung, Maria-Victoria Gomez Gaviro, Sarah Booth, Bo Gao, Kathryn S E Cheah, Robin Lovell-Badge, James Briscoe] | Nature Neuroscience | 2010-09-26 | |
| naturepublishinggroup10.1038/cdd.2010.109 | Coordinated waves of gene expression during neuronal differentiation of embryonic stem cells as basis for novel approaches to developmental neurotoxicity testing | As neuronal differentiation of embryonic stem cells (ESCs) recapitulates embryonic neurogenesis, disturbances of this process may model developmental neurotoxicity (DNT). To identify the relevant steps of in vitro neurodevelopment, we implemented a differentiation protocol yielding neurons with desired electrophysiological properties. Results from focussed transcriptional profiling suggested that detection of non-cytotoxic developmental disturbances triggered by toxicants such as retinoic acid (RA) or cyclopamine was possible. Therefore, a broad transcriptional profile of the 20-day differentiation process was obtained. Cluster analysis of expression kinetics, and bioinformatic identification of overrepresented gene ontologies revealed waves of regulation relevant for DNT testing. We further explored the concept of superimposed waves as descriptor of ordered, but overlapping biological processes. The initial wave of transcripts indicated reorganization of chromatin and epigenetic changes. Then, a transient upregulation of genes involved in the formation and patterning of neuronal precursors followed. Simultaneously, a long wave of ongoing neuronal differentiation started. This was again superseded towards the end of the process by shorter waves of neuronal maturation that yielded information on specification, extracellular matrix formation, disease-associated genes and the generation of glia. Short exposure to lead during the final differentiation phase, disturbed neuronal maturation. Thus, the wave kinetics and the patterns of neuronal specification define the time windows and end points for examination of DNT. | [B Zimmer, P B Kuegler, B Baudis, A Genewsky, V Tanavde, W Koh, B Tan, T Waldmann, S Kadereit, M Leist] | Cell Death & Differentiation | 2010-09-24 | 9.0 |
| naturepublishinggroup10.1038/ki.2010.330 | Transcriptional inhibition of progressive renal disease by gene silencing pyrrole|[ndash]|imidazole polyamide targeting of the transforming growth factor-|[beta]|1 promoter | Pyrrole–imidazole (PI) polyamides are small synthetic molecules that recognize and attach to the minor groove of DNA, thereby inhibiting gene transcription by blocking transcription factor binding. These derivatives can act as gene silencers inhibiting target gene expression under stimulatory conditions such as disease. To evaluate PI polyamides as treatments for the progression of renal diseases, we examined morphological effects, pharmacological properties, and the specificity of PI polyamides targeted to the transforming growth factor (TGF)-β1 promoter during salt-induced hypertensive nephrosclerosis in Dahl salt-sensitive rats. The targeted PI polyamide markedly reduced glomerulosclerosis and interstitial fibrosis without side effects. PI polyamide significantly decreased expression of TGF-β1 and extracellular matrix in the renal cortex. Microarray analysis found that only 3% of the transcripts were affected by PI polyamide, but this included decreased expression of extracellular matrix, TGF-β1-related cytokines, angiogenic, and cell stabilizing factors, proteinases, and renal injury-related factors. Thus, targeted PI polyamides are potential gene silencers for diseases not treatable by current remedies. | [Hiroyuki Matsuda, Noboru Fukuda, Takahiro Ueno, Mayumi Katakawa, Xiaofei Wang, Takayoshi Watanabe, Sei-Ichi Matsui, Takahiko Aoyama, Kosuke Saito, Toshikazu Bando, Yoshiaki Matsumoto, Hiroaki Nagase, Koichi Matsumoto, Hiroshi Sugiyama] | Kidney International | 2010-09-22 | 7.3.1 |
| naturepublishinggroup10.1038/onc.2010.432 | Blocking Wnt signaling by SFRP-like molecules inhibits in vivo cell proliferation and tumor growth in cells carrying active |[beta]|-catenin | Constitutive activation of Wnt/β-catenin signaling in cancer results from mutations in pathway components, which frequently coexist with autocrine Wnt signaling or epigenetic silencing of extracellular Wnt antagonists. Among the extracellular Wnt inhibitors, the secreted frizzled-related proteins (SFRPs) are decoy receptors that contain soluble Wnt-binding frizzled domains. In addition to SFRPs, other endogenous molecules harboring frizzled motifs bind to and inhibit Wnt signaling. One of such molecules is V3Nter, a soluble SFRP-like frizzled polypeptide that binds to Wnt3a and inhibits Wnt signaling and expression of the β-catenin target genes cyclin D1 and c-myc. V3Nter is derived from the cell surface extracellular matrix component collagen XVIII. Here, we used HCT116 human colon cancer cells carrying the ΔS45 activating mutation in one of the alleles of β-catenin to show that V3Nter and SFRP-1 decrease baseline and Wnt3a-induced β-catenin stabilization. Consequently, V3Nter reduces the growth of human colorectal cancer xenografts by specifically controlling cell proliferation and cell cycle progression, without affecting angiogenesis or apoptosis, as shown by decreased [3H]-thymidine (in vitro) or BrdU (in vivo) incorporation, clonogenesis assays, cell cycle analysis and magnetic resonance imaging in living mice. Additionally, V3Nter switches off the β-catenin target gene expression signature in vivo. Moreover, experiments with β-catenin allele-targeted cells showed that the ΔS45 β-catenin allele hampers, but does not abrogate, inhibition of Wnt signaling by SFRP-1 or by the SFRP-like frizzled domain. Finally, neither SFRP-1 nor V3Nter affect β-catenin signaling in SW480 cells carrying nonfunctional Adenomatous polyposis coli. Thus, SFRP-1 and the SFRP-like molecule V3Nter can inhibit tumor growth of β-catenin-activated tumor cells in vivo. | [E Lavergne, I Hendaoui, C Coulouarn, C Ribault, J Leseur, P-A Eliat, S Mebarki, A Corlu, B Cl|[eacute]|ment, O Musso] | Oncogene | 2010-09-20 | |
| naturepublishinggroup10.1038/nature09375 | Formate-driven growth coupled with H2 production | Although a common reaction in anaerobic environments, the conversion of formate and water to bicarbonate and H2 (with a change in Gibbs free energy of ΔG° = +1.3 kJ mol−1) has not been considered energetic enough to support growth of microorganisms. Recently, experimental evidence for growth on formate was reported for syntrophic communities of Moorella sp. strain AMP and a hydrogen-consuming Methanothermobacter species and of Desulfovibrio sp. strain G11 and Methanobrevibacter arboriphilus strain AZ1. The basis of the sustainable growth of the formate-users is explained by H2 consumption by the methanogens, which lowers the H2 partial pressure, thus making the pathway exergonic2. However, it has not been shown that a single strain can grow on formate by catalysing its conversion to bicarbonate and H2. Here we report that several hyperthermophilic archaea belonging to the Thermococcus genus are capable of formate-oxidizing, H2-producing growth. The actual ΔG values for the formate metabolism are calculated to range between −8 and −20 kJ mol−1 under the physiological conditions where Thermococcus onnurineus strain NA1 are grown. Furthermore, we detected ATP synthesis in the presence of formate as a sole energy source. Gene expression profiling and disruption identified the gene cluster encoding formate hydrogen lyase, cation/proton antiporter and formate transporter, which were responsible for the growth of T. onnurineus NA1 on formate. This work shows formate-driven growth by a single microorganism with protons as the electron acceptor, and reports the biochemical basis of this ability. | [Yun Jae Kim, Hyun Sook Lee, Eun Sook Kim, Seung Seob Bae, Jae Kyu Lim, Rie Matsumi, Alexander V. Lebedinsky, Tatyana G. Sokolova, Darya A. Kozhevnikova, Sun-Shin Cha, Sang-Jin Kim, Kae Kyoung Kwon, Tadayuki Imanaka, Haruyuki Atomi, Elizaveta A. Bonch-Osmolovskaya, Jung-Hyun Lee, Sung Gyun Kang] | Nature | | |
| naturepublishinggroup10.1038/cddis.2010.49 | Novel p63 target genes involved in paracrine signaling and keratinocyte differentiation | The transcription factor p63 is required for proper epidermal barrier formation and maintenance. Herein, we used chromatin immunoprecipitation coupled with DNA sequencing to identify novel p63 target genes involved in normal human epidermal keratinocyte (NHEKs) growth and differentiation. We identified over 2000 genomic sites bound by p63, of which 82 were also transcriptionally regulated by p63 in NHEKs. Through the discovery of interleukin-1-α as a p63 target gene, we identified that p63 is a regulator of epithelial–mesenchymal crosstalk. Further, three-dimensional organotypic co-cultures revealed TCF7L1, another novel p63 target gene, as a regulator of epidermal proliferation and differentiation, providing a mechanism by which p63 maintains the proliferative potential of basal epidermal cells. The discovery of new target genes links p63 to diverse signaling pathways required for epidermal development, including regulation of paracrine signaling to proliferative potential. Further mechanistic insight into p63 regulation of epidermal cell growth and differentiation is provided by the identification of a number of novel p63 target genes in this study. | [C E Barton, K N Johnson, D M Mays, K Boehnke, Y Shyr, P Boukamp, J A Pietenpol] | Cell Death & Disease | 2010-09-01 | |
| naturepublishinggroup10.1038/nature09337 | A cryptic sensor for HIV-1 activates antiviral innate immunity in dendritic cells | Dendritic cells serve a key function in host defence, linking innate detection of microbes to activation of pathogen-specific adaptive immune responses1, 2. Whether there is cell-intrinsic recognition of human immunodeficiency virus (HIV) by host innate pattern-recognition receptors and subsequent coupling to antiviral T-cell responses is not yet known3. Dendritic cells are largely resistant to infection with HIV-14, but facilitate infection of co-cultured T-helper cells through a process of trans-enhancement5, 6. Here we show that, when dendritic cell resistance to infection is circumvented7, 8, HIV-1 induces dendritic cell maturation, an antiviral type I interferon response and activation of T cells. This innate response is dependent on the interaction of newly synthesized HIV-1 capsid with cellular cyclophilin A (CYPA) and the subsequent activation of the transcription factor IRF3. Because the peptidylprolyl isomerase CYPA also interacts with HIV-1 capsid to promote infectivity, our results indicate that capsid conformation has evolved under opposing selective pressures for infectivity versus furtiveness. Thus, a cell-intrinsic sensor for HIV-1 exists in dendritic cells and mediates an antiviral immune response, but it is not typically engaged owing to the absence of dendritic cell infection. The virulence of HIV-1 may be related to evasion of this response, the manipulation of which may be necessary to generate an effective HIV-1 vaccine. | [Nicolas Manel, Brandon Hogstad, Yaming Wang, David E. Levy, Derya Unutmaz, Dan R. Littman] | Nature | | 0 |
| naturepublishinggroup10.1038/mt.2010.186 | In-frame Dystrophin Following Exon 51-Skipping Improves Muscle Pathology and Function in the Exon 52|[ndash]|Deficient mdx Mouse | A promising therapeutic approach for Duchenne muscular dystrophy (DMD) is exon skipping using antisense oligonucleotides (AOs). In-frame deletions of the hinge 3 region of the dystrophin protein, which is encoded by exons 50 and 51, are predicted to cause a variety of phenotypes. Here, we performed functional analyses of muscle in the exon 52–deleted mdx (mdx52) mouse, to predict the function of in-frame dystrophin following exon 51-skipping, which leads to a protein lacking most of hinge 3. A series of AOs based on phosphorodiamidate morpholino oligomers was screened by intramuscular injection into mdx52 mice. The highest splicing efficiency was generated by a two-oligonucleotide cocktail targeting both the 5′ and 3′ splice sites of exon 51. After a dose-escalation study, we systemically delivered this cocktail into mdx52 mice seven times at weekly intervals. This induced 20–30% of wild-type (WT) dystrophin expression levels in all muscles, and was accompanied by amelioration of the dystrophic pathology and improvement of skeletal muscle function. Because the structure of the restored in-frame dystrophin resembles human dystrophin following exon 51-skipping, our results are encouraging for the ongoing clinical trials for DMD. Moreover, the therapeutic dose required can provide a suggestion of the theoretical equivalent dose for humans. | [Yoshitsugu Aoki, Akinori Nakamura, Toshifumi Yokota, Takashi Saito, Hitoshi Okazawa, Tetsuya Nagata, Shin'ichi Takeda] | Molecular Therapy | 2010-09-07 | |
| naturepublishinggroup10.1038/onc.2010.412 | Control of mammary tumor differentiation by SKI-606 (bosutinib) | C-Src is infrequently mutated in human cancers but it mediates oncogenic signals of many activated growth factor receptors and thus remains a key target for cancer therapy. However, the broad function of Src in many cell types and processes requires evaluation of Src-targeted therapeutics within a normal developmental and immune-competent environment. In an effort to understand the appropriate clinical use of Src inhibitors, we tested an Src inhibitor, SKI-606 (bosutinib), in the MMTV-PyVmT transgenic mouse model of breast cancer. Tumor formation in this model is dependent on the presence of Src, but the necessity of Src kinase activity for tumor formation has not been determined. Furthermore, Src inhibitors have not been examined in an autochthonous tumor model that permits assessment of effects on different stages of tumor progression. Here we show that oral administration of SKI-606 inhibited the phosphorylation of Src in mammary tumors and caused a rapid decrease in the Ezh2 Polycomb group histone H3K27 methyltransferase and an increase in epithelial organization. SKI-606 prevented the appearance of palpable tumors in over 50% of the animals and stopped tumor growth in older animals with pre-existing tumors. These antitumor effects were accompanied by decreased cellular proliferation, altered tumor blood vessel organization and dramatically increased differentiation to lactational and epidermal cell fates. SKI-606 controls the development of mammary tumors by inducing differentiation. | [L Hebbard, G Cecena, J Golas, J Sawada, L G Ellies, A Charbono, R Williams, R E Jimenez, M Wankell, K T Arndt, S Q DeJoy, R A Rollins, V Diesl, M Follettie, L Chen, E Rosfjord, R D Cardiff, M Komatsu, F Boschelli, R G Oshima] | Oncogene | 2010-09-06 | |
| naturepublishinggroup10.1038/modpathol.2010.164 | MicroRNA expression profiling in benign (sporadic and hereditary) and recurring adrenal pheochromocytomas | MicroRNAs are involved in the pathogenesis of several tumors, however, there have been no data on microRNA expression in pheochromocytomas to date. The objective of our study was to perform microRNA expression profiling in sporadic and hereditary benign, and recurring adrenomedullary tumors. Furthermore, the applicability of formalin-fixed paraffin-embedded tissue samples for the analysis of microRNA expression in pheochromocytomas was examined. MicroRNA expression data of three matched frozen and formalin-fixed paraffin-embedded samples were correlated. A total of 21 formalin-fixed paraffin-embedded samples (sporadic benign, multiple endocrine neoplasia 2, von Hippel-Lindau disease, sporadic recurring) were subjected to microRNA expression profiling using microarrays. MicroRNAs with significant differences in expression were validated and sample sizes were extended including tumors from neurofibromatosis type 1 patients by real-time quantitative reverse-transcription PCR (n=33). MicroRNA target prediction was carried out by TargetScan and MicroCosm Targets. Pathway analysis of targets was performed by Ingenuity Pathway Analysis and DIANA mirPath. Furthermore, microRNA expression profiles of a malignant pheochromocytoma and a pair of primary and recurrent tumors were studied by TaqMan Human MicroRNA Cards. MicroRNA expression correlated well between frozen and formalin-fixed paraffin-embedded samples (70–92%). Microarray analysis revealed 16 significantly differentially expressed microRNAs. Five of these were validated by real-time RT-PCR. miR-139-3p, miR-541 and miR-765 were significantly differentially expressed between sporadic benign and von Hippel-Lindau-related pheochromocytomas. Significantly higher expression of miR-885-5p and miR-1225-3p was found in multiple endocrine neoplasia type 2 and sporadic recurring pheochromocytomas, respectively. Pathway analysis revealed the possible involvement of Notch- and G-protein-coupled receptor signaling in tumor recurrence. MicroRNA expression profiles in the primary recurrent and recurring malignant comparisons have been similar. In conclusion, we have proved that formalin-fixed paraffin-embedded samples can be used for the analysis of microRNA expression in pheochromocytomas. MicroRNA expression patterns differ between various sporadic, hereditary and recurring tumors and miR-1225-3p may be useful for identifying recurring pheochromocytomas. | [Zs|[oacute]|fia T|[ouml]|mb|[ouml]|l, Katalin |[Eacute]|der, Attila Kov|[aacute]|cs, Peter M Szab|[oacute]|, Janina Kulka, Istv|[aacute]|n Lik|[oacute]|, Attila Zalatnai, Gergely R|[aacute]|cz, Mikl|[oacute]|s T|[oacute]|th, Attila Pat|[oacute]|cs, Andr|[aacute]|s Falus, K|[aacute]|roly R|[aacute]|cz, Peter Igaz] | Modern Pathology | 2010-09-03 | |
| naturepublishinggroup10.1038/ni.1929 | The transcription cofactor Hopx is required for regulatory T cell function in dendritic cell-mediated peripheral T cell unresponsiveness | | [Daniel Hawiger, Yisong Y Wan, Elizabeth E Eynon, Richard A Flavell] | Nature Immunology | 2010-08-29 | |
| naturepublishinggroup10.1038/aps.2010.147 | Regulation of Nrf2- and AP-1-mediated gene expression by epigallocatechin-3-gallate and sulforaphane in prostate of Nrf2-knockout or C57BL/6J mice and PC-3 AP-1 human prostate cancer cells | | [Sujit Nair, Avantika Barve, Tin-Oo Khor, Guo-xiang Shen, Wen Lin, Jefferson Y Chan, Li Cai, Ah-Ng Kong] | Acta Pharmacologica Sinica | 2010-08-23 | |
| naturepublishinggroup10.1038/cgt.2010.45 | Multivalent immunity targeting tumor-associated antigens by intra-lymph node DNA-prime, peptide-boost vaccination | Active immunotherapy of cancer has yet to yield effective therapies in the clinic. To evaluate the translatability of DNA-based vaccines we analyzed the profile of T-cell immunity by plasmid vaccination in a murine model, using transcriptome microarray analysis and flow cytometry. DNA vaccination resulted in specific T cells expressing low levels of co-inhibitory molecules (most notably PD-1), strikingly different from the expression profile elicited by peptide immunization. In addition, the T-cell response primed through this dual-antigen-expressing plasmid (MART-1/Melan-A and tyrosinase) translated into a substantial proliferation capacity and functional conversion to antitumor effector cells after tyrosinase and MART-1/Melan-A peptide analog boost. Furthermore, peptide boost rescued the immune response against the subdominant tyrosinase epitope. This immunization approach could be adapted to elicit potent immunity against multiple tumor antigens, resulting in a broader immune response that was more effective in targeting human tumor cells. Finally, this study sheds light on a novel mechanism of immune homeostasis through synchronous regulation of co-inhibitory molecules on T cells, highly relevant to heterologous prime boost approaches involving DNA vaccines as priming agents. | [K A Smith, Z Qiu, R Wong, V L Tam, B L Tam, D K Joea, A Quach, X Liu, M Pold, U M Malyankar, A Bot] | Cancer Gene Therapy | 2010-08-20 | |
| naturepublishinggroup10.1038/nature09247 | An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis | Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis, is a major cause of morbidity and mortality worldwide. Efforts to control it are hampered by difficulties with diagnosis, prevention and treatment1, 2. Most people infected with M. tuberculosis remain asymptomatic, termed latent TB, with a 10% lifetime risk of developing active TB disease. Current tests, however, cannot identify which individuals will develop disease3. The immune response to M. tuberculosis is complex and incompletely characterized, hindering development of new diagnostics, therapies and vaccines4, 5. Here we identify a whole-blood 393 transcript signature for active TB in intermediate and high-burden settings, correlating with radiological extent of disease and reverting to that of healthy controls after treatment. A subset of patients with latent TB had signatures similar to those in patients with active TB. We also identify a specific 86-transcript signature that discriminates active TB from other inflammatory and infectious diseases. Modular and pathway analysis revealed that the TB signature was dominated by a neutrophil-driven interferon (IFN)-inducible gene profile, consisting of both IFN-γ and type I IFN-αβ signalling. Comparison with transcriptional signatures in purified cells and flow cytometric analysis suggest that this TB signature reflects changes in cellular composition and altered gene expression. Although an IFN-inducible signature was also observed in whole blood of patients with systemic lupus erythematosus (SLE), their complete modular signature differed from TB, with increased abundance of plasma cell transcripts. Our studies demonstrate a hitherto underappreciated role of type I IFN-αβ signalling in the pathogenesis of TB, which has implications for vaccine and therapeutic development. Our study also provides a broad range of transcriptional biomarkers with potential as diagnostic and prognostic tools to combat the TB epidemic. | [Matthew P. R. Berry, Christine M. Graham, Finlay W. McNab, Zhaohui Xu, Susannah A. A. Bloch, Tolu Oni, Katalin A. Wilkinson, Romain Banchereau, Jason Skinner, Robert J. Wilkinson, Charles Quinn, Derek Blankenship, Ranju Dhawan, John J. Cush, Asuncion Mejias, Octavio Ramilo, Onn M. Kon, Virginia Pascual, Jacques Banchereau, Damien Chaussabel, Anne O’Garra] | Nature | | |
| naturepublishinggroup10.1038/sj.bjc.6605811 | miR-489 is a tumour-suppressive miRNA target PTPN11 in hypopharyngeal squamous cell carcinoma (HSCC) | | [N Kikkawa, T Hanazawa, L Fujimura, N Nohata, H Suzuki, H Chazono, D Sakurai, S Horiguchi, Y Okamoto, N Seki] | British Journal of Cancer | 2010-08-10 | |
| naturepublishinggroup10.1038/onc.2010.332 | Transcriptional upregulation of histone deacetylase 2 promotes Myc-induced oncogenic effects | Myc oncoproteins and histone deacetylases (HDACs) modulate gene transcription and enhance cancer cell proliferation, and HDAC inhibitors are among the most promising new classes of anticancer drugs. Here, we show that N-Myc and c-Myc upregulated HDAC2 gene expression in neuroblastoma and pancreatic cancer cells, respectively, which contributed to N-Myc- and c-Myc-induced cell proliferation. Cyclin G2 (CCNG2) was commonly repressed by N-Myc and HDAC2 in neuroblastoma cells and by c-Myc and HDAC2 in pancreatic cancer cells, and could be reactivated by HDAC inhibitors. 5-bromo-2′-deoxyuridine incorporation assays showed that transcriptional repression of CCNG2 was, in part, responsible for N-Myc-, c-Myc- and HDAC2-induced cell proliferation. Dual crosslinking chromatin immunoprecipitation assay demonstrated that N-Myc acted as a transrepressor by recruiting the HDAC2 protein to Sp1-binding sites at the CCNG2 gene core promoter. Moreover, HDAC2 was upregulated, and CCNG2 downregulated, in pre-cancerous and neuroblastoma tissues from N-Myc transgenic mice, and c-Myc overexpression correlated with upregulation of HDAC2 and repression of CCNG2 in tumour tissues from pancreatic cancer patients. Taken together, our data indicate the critical roles of upregulation of HDAC2 and suppression of CCNG2 in Myc-induced oncogenesis, and have significant implications for the application of HDAC inhibitors in the prevention and treatment of Myc-driven cancers. | [G M Marshall, S Gherardi, N Xu, Z Neiron, T Trahair, C J Scarlett, D K Chang, P Y Liu, K Jankowski, N Iraci, M Haber, M D Norris, J Keating, E Sekyere, G Jonquieres, F Stossi, B S Katzenellenbogen, A V Biankin, G Perini, T Liu] | Oncogene | 2010-08-09 | |
| naturepublishinggroup10.1038/ismej.2010.128 | Salmonella transcriptional signature in Tetrahymena phagosomes and role of acid tolerance in passage through the protist | Salmonella enterica Typhimurium remains undigested in the food vacuoles of the common protist, Tetrahymena. Contrary to its interaction with Acanthamoeba spp., S. Typhimurium is not cytotoxic to Tetrahymena and is egested as viable cells in its fecal pellets. Through microarray gene expression profiling we investigated the factors in S. Typhimurium that are involved in its resistance to digestion by Tetrahymena. The transcriptome of S. Typhimurium in Tetrahymena phagosomes showed that 989 and 1282 genes were altered in expression compared with that in water and in LB culture medium, respectively. A great proportion of the upregulated genes have a role in anaerobic metabolism and the use of alternate electron acceptors. Many genes required for survival and replication within macrophages and human epithelial cells also had increased expression in Tetrahymena, including mgtC, one of the most highly induced genes in all three cells types. A ΔmgtC mutant of S. Typhimurium did not show decreased viability in Tetrahymena, but paradoxically, was egested at a higher cell density than the wild type. The expression of adiA and adiY, which are involved in arginine-dependent acid resistance, also was increased in the protozoan phagosome. A ΔadiAY mutant had lower viability after passage through Tetrahymena, and a higher proportion of S. Typhimurium wild-type cells within pellets remained viable after exposure to pH 3.4 as compared with uningested cells. Our results provide evidence that acid resistance has a role in the resistance of Salmonella to digestion by Tetrahymena and that passage through the protist confers physiological advantages relevant to its contamination cycle. | [Marc Yi Ming Rehfuss, Craig Thomas Parker, Maria Theresa Brandl] | The ISME Journal | 2010-08-05 | |
| naturepublishinggroup10.1038/modpathol.2010.146 | Unique microRNA profile in Dupuytren's contracture supports deregulation of |[beta]|-catenin pathway | Dupuytren's contracture, a proliferative disease of unknown origin, is characterized by an abnormal fibroblast proliferation process. Evidence from numerous microRNA (miRNA) studies shows that miRNAs have a vital function in many biological processes, for instance, in cellular signaling networks, cell growth, tissue differentiation, and cell proliferation. Our aim was to characterize, to our knowledge for the first time, the miRNA-expression profile of Dupuytren's contracture. The miRNAs identified may have a function in the pathogenesis of Dupuytren's contracture by targeting and regulating important pathways. We compared the miRNA-expression profile of 29 Dupuytren's contracture patients with that of control samples (fibroblast cells and palmar fascia). Some of the miRNAs identified in our Dupuytren's contracture samples, including miR-29c, miR-130b, miR-101, miR-30b, and miR-140-3p, were found to regulate important genes related to the β-catenin pathway: WNT5A, ZIC1, and TGFB1. Expression profiles of these genes reanalyzed from published gene-expression data from similar patient material correlated with our miRNA results. Analysis was also performed for groups of patients with recurrent/non-recurrent and patients with hereditary/non-hereditary Dupuytren's contracture, but no significant differences appeared in miRNA-expression profiles of these groups. Identification of unique miRNA expression in Dupuytren's contracture may lead to the development of novel molecular therapy for its treatment. | [Neda Mosakhani, Mohamed Guled, Leo Lahti, Ioana Borze, Minna Forsman, Virve P|[auml]||[auml]|kk|[ouml]|nen, Jorma Ryh|[auml]|nen, Sakari Knuutila] | Modern Pathology | 2010-07-30 | |
| naturepublishinggroup10.1038/emboj.2010.172 | Zic2 regulates the expression of Sert to modulate eye-specific refinement at the visual targets | The development of the nervous system is a time-ordered and multi-stepped process that requires neural specification, axonal navigation and arbor refinement at the target tissues. Previous studies have demonstrated that the transcription factor Zic2 is necessary and sufficient for the specification of retinal ganglion cells (RGCs) that project ipsilaterally at the optic chiasm midline. Here, we report that, in addition, Zic2 controls the refinement of eye-specific inputs in the visual targets by regulating directly the expression of the serotonin transporter (Sert), which is involved in the modulation of activity-dependent mechanisms during the wiring of sensory circuits. In agreement with these findings, RGCs that express Zic2 ectopically show defects in axonal refinement at the visual targets and respond to pharmacological blockage of Sert, whereas Zic2-negative contralateral RGCs do not. These results link, at the molecular level, early events in neural differentiation with late activity-dependent processes and propose a mechanism for the establishment of eye-specific domains at the visual targets. | [Cristina Garc|[iacute]|a-Frigola, Elo|[iacute]|sa Herrera] | The EMBO Journal | 2010-07-30 | |
| naturepublishinggroup10.1038/cr.2010.93 | Organ-specific enhancement of metastasis by spontaneous ploidy duplication and cell size enlargement | Aneuploidy is commonly observed in breast cancer and is associated with poor prognosis. One frequent type of aneuploidy, hypertetraploidy, may derive from ploidy duplication of hyperdiploid cells. However, the pathological consequences of ploidy duplication in breast cancer progression have not been characterized. Here, we present an experimental system demonstrating spontaneous appearance of hypertetraploid cells from organ-specific metastatic variants of the MDA-MB-231 breast cancer cell line through ploidy duplication in vitro and in vivo. The hypertetraploid progenies showed increased metastatic potential to lung and brain, but not to bone, which may be partially explained by the distinct capillary structures in these organs that confer differential lodging advantages to tumor cells with enlarged size. Our results suggest a potential mechanistic link between ploidy duplication and enhancement of metastatic potentials, as was observed in previous clinical studies of breast cancer. | [Xin Lu, Xuemin Lu, Yibin Kang] | Cell Research | 2010-07-13 | 7.3 |
| naturepublishinggroup10.1038/sj.bjc.6605751 | The tumour-suppressive miR-29a|[sol]|b1 cluster is regulated by CEBPA and blocked in human AML | | [M Eyholzer, S Schmid, L Wilkens, B U Mueller, T Pabst] | British Journal of Cancer | 2010-07-13 | |
| naturepublishinggroup10.1038/ni.1901 | Deletion of the RNA-binding proteins ZFP36L1 and ZFP36L2 leads to perturbed thymic development and T lymphoblastic leukemia | | [Daniel J Hodson, Michelle L Janas, Alison Galloway, Sarah E Bell, Simon Andrews, Cheuk M Li, Richard Pannell, Christian W Siebel, H Robson MacDonald, Kim De Keersmaecker, Adolfo A Ferrando, Gerald Grutz, Martin Turner] | Nature Immunology | 2010-07-11 | |
| naturepublishinggroup10.1038/nature09202 | Striatal microRNA controls cocaine intake through CREB signalling | | [Jonathan A. Hollander, Heh-In Im, Antonio L. Amelio, Jannet Kocerha, Purva Bali, Qun Lu, David Willoughby, Claes Wahlestedt, Michael D. Conkright, Paul J. Kenny] | Nature | | |
| naturepublishinggroup10.1038/tpj.2010.55 | Changes in the gene expression profile of gastric cancer cells in response to ibuprofen: a gene pathway analysis | Nonsteroidal anti-inflammatory drugs possess antiproliferative activities that can affect cancer cells. The aim of this study was to examine the antiproliferative effects of ibuprofen on the MKN-45 cell line. Cells were treated with ibuprofen for 24, 48 or 72 h, and cell proliferation was evaluated by cell counting and [3H]-thymidine incorporation. Using microarray technology, we studied changes in the gene expression profiles over time after ibuprofen treatment. Ibuprofen induced a dose- and time-dependent reduction in cell number without altering cell viability. Genes involved in the ‘biological oxidation’ and ‘G1/S checkpoint’ pathways were the most significantly represented at 24 h, whereas genes involved in the ‘cell cycle’ and ‘DNA replication’ pathways were represented at 48 and 72 h. Genes associated with the ‘apoptosis’ pathway were also significantly represented at 72 h. Modulation of the expression of p53 and p53-induced genes (CDKN1A/p21 and GADD45), which are involved in the G1/S transition, suggested an effect of ibuprofen on cell-cycle progression. Using flow cytometry, we observed an early block in the G1 phase of the cell cycle after ibuprofen treatment. In addition, P450 family transcripts were upregulated and intracellular reactive oxygen species (ROS) was increased following 12 h of ibuprofen treatment. Ibuprofen induced ROS, which resulted in cellular alterations that promoted a p53-dependent G1 blockade. These findings suggest that ibuprofen exerts its antiproliferative actions through cell-cycle control and the induction of apoptosis. Both of these mechanisms appear to be independent of ibuprofen's anti-inflammatory effects. | [P Bonelli, F M Tuccillo, R Calemma, F Pezzetti, A Borrelli, R Martinelli, A De Rosa, D Esposito, R Palaia, G Castello] | The Pharmacogenomics Journal | 2010-06-15 | |
| naturepublishinggroup10.1038/sj.bjc.6605741 | Detection of oesophageal cancer biomarkers by plasma proteomic profiling of human cell line xenografts in response to chemotherapy | | [P Kelly, V Appleyard, K Murray, F Paulin, D Lamont, L Baker, S Suttie, D Exon, A Thompson] | British Journal of Cancer | 2010-06-15 | |
| naturepublishinggroup10.1038/sj.bjc.6605723 | Osteosarcoma is characterised by reduced expression of markers of osteoclastogenesis and antigen presentation compared with normal bone | | [L Endo-Munoz, A Cumming, S Sommerville, I Dickinson, N A Saunders] | British Journal of Cancer | 2010-06-15 | |
| naturepublishinggroup10.1038/ni.1889 | Revised map of the human progenitor hierarchy shows the origin of macrophages and dendritic cells in early lymphoid development | | [Sergei Doulatov, Faiyaz Notta, Kolja Eppert, Linh T Nguyen, Pamela S Ohashi, John E Dick] | Nature Immunology | 2010-06-13 | |
| naturepublishinggroup10.1038/leu.2010.130 | BAALC-associated gene expression profiles define IGFBP7 as a novel molecular marker in acute leukemia | Over expression of BAALC (brain and acute leukemia, cytoplasmic) predicts an inferior outcome in acute myeloid leukemia (AML) and acute lymphoblastic leukemia patients. To identify BAALC-associated genes that give insights into its functional role in chemotherapy resistance, gene expression signatures differentiating high from low BAALC expressers were generated from normal CD34+ progenitors, T-acute lymphoblastic leukemia (T-ALL) and AML samples. The insulin-like growth factor binding protein 7 (IGFBP7) was one of the four genes (CD34, CD133, natriuretic peptide receptor C (NPR3), IGFBP7) coexpressed with BAALC and common to the three entities. In T-ALL, high IGFBP7-expression was associated with an immature phenotype of early T-ALL (P<0.001), expression of CD34 (P<0.001) and CD33 (P<0.001). Moreover, high IGFBP7-expression predicted primary therapy resistance (P=0.03) and inferior survival in T-ALL (P=0.03). In vitro studies revealed that IGFBP7 protein significantly inhibited the proliferation of leukemia cell lines (Jurkat cells: 42% reduction, P=0.002; KG1a cells: 65% reduction, P<0.001). In conclusion, IGFBP7 was identified as a BAALC coexpressed gene. Furthermore, high IGFBP7 was associated with stem cell features and treatment failure in T-ALL. In contrast to BAALC, which likely represents only a surrogate marker of treatment failure in acute leukemia, IGFBP7 regulates the proliferation of leukemic cells and might be involved in chemotherapy resistance. | [S Heesch, C Schlee, M Neumann, A Stroux, A K|[uuml]|hnl, S Schwartz, T Haferlach, N Goekbuget, D Hoelzer, E Thiel, W-K Hofmann, C D Baldus] | Leukemia | 2010-06-10 | |
| naturepublishinggroup10.1038/msb.2010.38 | Global coordination of transcriptional control and mRNA decay during cellular differentiation | | [Maria J Amorim, Cristina Cotobal, Caia Duncan, Juan Mata] | Nature a - z index | 2010-06-08 | |
| naturepublishinggroup10.1038/emboj.2010.109 | Topoisomerase I regulates open chromatin and controls gene expression in vivo | DNA topoisomerases regulate the topological state of the DNA double helix and are key enzymes in the processes of DNA replication, transcription and genome stability. Using the fission yeast model Schizosaccharomyces pombe, we investigate genome wide how DNA topoisomerases I and II affect chromatin dynamics and gene expression in vivo. We show that topoisomerase I activity is directly required for efficient nucleosome disassembly at gene promoter regions. Lack of topoisomerase activity results in increased nucleosome occupancy, perturbed histone modifications and reduced transcription from these promoters. Strong correlative evidence suggests that topoisomerase I cooperates with the ATP-dependent chromatin remodeller Hrp1 in nucleosome disassembly. Our study links topoisomerase activity to the maintenance of open chromatin and regulating transcription in vivo. | [Micka|[euml]|l Durand-Dubief, Jenna Persson, Ulrika Norman, Edgar Hartsuiker, Karl Ekwall] | The EMBO Journal | 2010-06-04 | 8.0 |
| naturepublishinggroup10.1038/leu.2010.118 | Differential expression of NF-|[kappa]|B target genes in MALT lymphoma with and without chromosome translocation: insights into molecular mechanism | Mucosa-associated lymphoid tissue (MALT) lymphoma is characterized by t(11;18)(q21;q21)/API2-MALT1, t(1;14)(p22;q32)/BCL10-IGH and t(14;18)(q32;q21)/IGH-MALT1, which commonly activate the nuclear factor (NF)-κB pathway. Gastric MALT lymphomas harboring such translocations usually do not respond to Helicobacter pylori eradication, while most of those without translocation can be cured by antibiotics. To understand the molecular mechanism of these different MALT lymphoma subgroups, we performed gene expression profiling analysis of 21 MALT lymphomas (13 translocation-positive, 8 translocation-negative). Gene set enrichment analysis (GSEA) of the NF-κB target genes and 4394 additional gene sets covering various cellular pathways, biological processes and molecular functions have shown that translocation-positive MALT lymphomas are characterized by an enhanced expression of NF-κB target genes, particularly toll like receptor (TLR)6, chemokine, CC motif, receptor (CCR)2, cluster of differentiation (CD)69 and B-cell CLL/lymphoma (BCL)2, while translocation-negative cases were featured by active inflammatory and immune responses, such as interleukin-8, CD86, CD28 and inducible T-cell costimulator (ICOS). Separate analyses of the genes differentially expressed between translocation-positive and -negative cases and measurement of gene ontology term in these differentially expressed genes by hypergeometric test reinforced the above findings by GSEA. Finally, expression of TLR6, in the presence of TLR2, enhanced both API2-MALT1 and BCL10-mediated NF-κB activation in vitro. Our findings provide novel insights into the molecular mechanism of MALT lymphomas with and without translocation, potentially explaining their different clinical behaviors. | [R A Hamoudi, A Appert, H Ye, A Ruskone-Fourmestraux, B Streubel, A Chott, M Raderer, L Gong, I Wlodarska, C De Wolf-Peeters, K A MacLennan, L de Leval, P G Isaacson, M-Q Du] | Leukemia | 2010-06-03 | 7.3.1 |
| naturepublishinggroup10.1038/ni.1883 | The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling | | [Hua Tang, Weiping Cao, Sudhir Pai Kasturi, Rajesh Ravindran, Helder I Nakaya, Kousik Kundu, Niren Murthy, Thomas B Kepler, Bernard Malissen, Bali Pulendran] | Nature Immunology | 2010-05-23 | |
| naturepublishinggroup10.1038/ki.2010.138 | Altered modulation of WNT|[ndash]||[beta]|-catenin and PI3K|[sol]|Akt pathways in IgA nephropathy | Immunoglobulin A nephropathy (IgAN) is the most common form of primary glomerulonephritis worldwide. The basic defect lies within the IgA immune system and in peripheral blood leukocytes, rather than local kidney abnormalities. To define the intracellular mechanisms leading to the disease, we conducted a microarray study to identify genes and pathways differentially modulated in peripheral blood leukocytes isolated from 12 IgAN patients and 8 healthy controls. The genes whose expression discriminated between the IgAN patients and controls were primarily involved in canonical WNT–β-catenin and PI3K/Akt pathways. We also tested peripheral blood mononuclear cells and their subpopulations isolated from an independent group of IgAN patients and healthy controls. There were low protein levels of inversin and PTEN, key regulators of WNT–β-catenin and PI3K/Akt, in IgAN patients, suggesting hyperactivation of these pathways. Also, there were increased phospho-Akt protein levels and nuclear β-catenin accumulation with an enhanced peripheral blood mononuclear cell proliferation rate. Subpopulation analysis uncovered a major irregularity of WNT signaling in monocytes. Hence, hyperactivation of these pathways may provide insight into mechanisms contributing to the pathogenesis of IgAN. | [Sharon N Cox, Fabio Sallustio, Grazia Serino, Paola Pontrelli, Raffaella Verrienti, Francesco Pesce, Diletta D Torres, Nicola Ancona, Patrizia Stifanelli, Gianluigi Zaza, Francesco P Schena] | Kidney International | 2010-05-19 | |
| naturepublishinggroup10.1038/labinvest.2010.97 | Human 21T breast epithelial cell lines mimic breast cancer progression in vivo and in vitro and show stage-specific gene expression patterns | Early breast cancer progression involves advancement through specific morphological stages including atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive mammary carcinoma (IMC), although not necessarily always in a linear fashion. Observational studies have examined genetic, epigenetic and gene expression differences in breast tissues representing these stages of progression, but model systems which would allow for experimental testing of specific factors influencing transition through these stages are scarce. The 21T series cell lines, all originally derived from the same patient with metastatic breast cancer, have been proposed to represent a mammary tumor progression series. We report here that three of the 21T cell lines indeed mimic specific stages of human breast cancer progression (21PT-derived cells, ADH; 21NT-derived cells, DCIS; 21MT-1 cells, IMC) when grown in the mammary fat pad of nude mice, albeit after a year. To develop a more rapid, readily manipulatable in vitro assay for examining the biological differences between these cell lines, we have used a 3D Matrigel system. When the three cell lines were grown in 3D Matrigel, they showed characteristic morphologies, in which quantifiable aspects of stage-specific in vivo behaviors (ie, differences in acinar structure formation, cell polarization, colony morphology, cell proliferation, cell invasion) were recapitulated in a reproducible fashion. Gene expression profiling revealed a characteristic pattern for each of the three cell lines. Interestingly, Wnt pathway alterations are particularly predominant in the early transition from 21PTci (ADH) to 21NTci (DCIS), whereas alterations in expression of genes associated with control of cell motility and invasion phenomena are more prominent in the later transition of 21NTci (DCIS) to 21MT-1 (IMC). This system thus reveals potential therapeutic targets and will provide a means of testing the influences of identified genes on transitions between these stages of pre-malignant to malignant growth. | [Lesley H Souter, Joseph D Andrews, Guihua Zhang, Amy C Cook, Carl O Postenka, Waleed Al-Katib, Hon S Leong, David I Rodenhiser, Ann F Chambers, Alan B Tuck] | Laboratory Investigation | 2010-05-10 | 7.3 |
| naturepublishinggroup10.1038/onc.2010.129 | Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate | Limited information is available regarding epigenomic events mediating initiation and progression of tobacco-induced lung cancers. In this study, we established an in vitro system to examine epigenomic effects of cigarette smoke in respiratory epithelia. Normal human small airway epithelial cells and cdk-4/hTERT-immortalized human bronchial epithelial cells (HBEC) were cultured in normal media with or without cigarette smoke condensate (CSC) for up to 9 months under potentially relevant exposure conditions. Western blot analysis showed that CSC mediated dose- and time-dependent diminution of H4K16Ac and H4K20Me3, while increasing relative levels of H3K27Me3; these histone alterations coincided with decreased DNA methyltransferase 1 (DNMT1) and increased DNMT3b expression. Pyrosequencing and quantitative RT–PCR experiments revealed time-dependent hypomethylation of D4Z4, NBL2, and LINE-1 repetitive DNA sequences; up-regulation of H19, IGF2, MAGE-A1, and MAGE-A3; activation of Wnt signaling; and hypermethylation of tumor suppressor genes such as RASSF1A and RAR-β, which are frequently silenced in human lung cancers. Array-based DNA methylation profiling identified additional novel DNA methylation targets in soft-agar clones derived from CSC-exposed HBEC; a CSC gene expression signature was also identified in these cells. Progressive genomic hypomethylation and locoregional DNA hypermethylation induced by CSC coincided with a dramatic increase in soft-agar clonogenicity. Collectively, these data indicate that cigarette smoke induces ‘cancer-associated’ epigenomic alterations in cultured respiratory epithelia. This in vitro model may prove useful for delineating early epigenetic mechanisms regulating gene expression during pulmonary carcinogenesis. | [F Liu, J K Killian, M Yang, R L Walker, J A Hong, M Zhang, S Davis, Y Zhang, M Hussain, S Xi, M Rao, P A Meltzer, D S Schrump] | Oncogene | 2010-05-03 | 7.3 |
| naturepublishinggroup10.1038/onc.2010.143 | Homeobox gene IRX1 is a tumor suppressor gene in gastric carcinoma | The IRX1 tumor suppressor gene is located on 5p15.33, a cancer susceptibility locus. Loss of heterozygosity of 5p15.33 in gastric cancer was identified in our previous work. In this study, we analyzed the molecular features and function of IRX1. We found that IRX1 expression was lost or reduced in gastric cancer. However, no mutations were identified in IRX1-encoding regions. IRX1 transcription was suppressed by hypermethylation, and the expression of IRX1 mRNA was partially restored in gastric cancer cells after 5-Aza-dC treatment. Restoring IRX1 expression in SGC-7901 and NCI-N87 gastric cancer cells inhibited growth, invasion and tumorigenesis in vitro and in vivo. We identified a number of target genes by global microarray analysis after IRX1 transfection combined with real-time PCR and chromatin immunoprecipitation assay. BDKRB2, an angiogenesis-related gene, HIST2H2BE and FGF7, cell proliferation and invasion-related genes, were identified as direct IRX1 target genes. The hypermethylation of IRX1 was not only detected in primary gastric cancer tissues but also in the peripheral blood of gastric cancer patients, suggesting IRX1 could potentially serve as a biomarker for gastric cancer. | [X Guo, W Liu, Y Pan, P Ni, J Ji, L Guo, J Zhang, J Wu, J Jiang, X Chen, Q Cai, J Li, Q Gu, B Liu, Z Zhu, Y Yu] | Oncogene | 2010-05-03 | |
| naturepublishinggroup10.1038/leu.2010.78 | A transcriptome-wide approach reveals the key contribution of NFI-A in promoting erythroid differentiation of human CD34|[plus]| progenitors and CML cells | | [L M Starnes, A Sorrentino, M Ferracin, M Negrini, E Pelosi, C Nervi, C Peschle] | Leukemia | 2010-04-29 | |
| naturepublishinggroup10.1038/nm.2130 | A CD8+ T cell transcription signature predicts prognosis in autoimmune disease | Autoimmune diseases are common and debilitating, but their severe manifestations could be reduced if biomarkers were available to allow individual tailoring of potentially toxic immunosuppressive therapy. Gene expression–based biomarkers facilitating such tailoring of chemotherapy in cancer, but not autoimmunity, have been identified and translated into clinical practice1, 2. We show that transcriptional profiling of purified CD8+ T cells, which avoids the confounding influences of unseparated cells3, 4, identifies two distinct subject subgroups predicting long-term prognosis in two autoimmune diseases, antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), a chronic, severe disease characterized by inflammation of medium-sized and small blood vessels5, and systemic lupus erythematosus (SLE), characterized by autoantibodies, immune complex deposition and diverse clinical manifestations ranging from glomerulonephritis to neurological dysfunction6. We show that the subset of genes defining the poor prognostic group is enriched for genes involved in the interleukin-7 receptor (IL-7R) pathway and T cell receptor (TCR) signaling and those expressed by memory T cells. Furthermore, the poor prognostic group is associated with an expanded CD8+ T cell memory population. These subgroups, which are also found in the normal population and can be identified by measuring expression of only three genes, raise the prospect of individualized therapy and suggest new potential therapeutic targets in autoimmunity. | [Eoin F McKinney, Paul A Lyons, Edward J Carr, Jane L Hollis, David R W Jayne, Lisa C Willcocks, Maria Koukoulaki, Alvis Brazma, Vojislav Jovanovic, D Michael Kemeny, Andrew J Pollard, Paul A MacAry, Afzal N Chaudhry, Kenneth G C Smith] | Nature Medicine | 2010-04-18 | 7.2 |
| naturepublishinggroup10.1038/cdd.2010.40 | Ultrastructural and transcriptional profiling of neuropathological misregulation of CREB function | We compare here the neurodegenerative processes observed in the hippocampus of bitransgenic mice with chronically altered levels of cAMP-response element-binding protein (CREB) function. The combination of genome-wide transcriptional profiling of degenerating hippocampal tissue with microscopy analyses reveals that the sustained inhibition of CREB function in A-CREB mice is associated with dark neuron degeneration, whereas its strong chronic activation in VP16-CREB mice primarily causes excitotoxic cell death and inflammation. Furthermore, the meta-analysis with gene expression profiles available in public databases identifies relevant common markers to other neurodegenerative processes and highlights the importance of the immune response in neurodegeneration. Overall, these analyses define the ultrastructural and transcriptional signatures associated with these two forms of hippocampal neurodegeneration, confirm the importance of fine-tuned regulation of CREB-dependent gene expression for CA1 neuron survival and function, and provide novel insight into the function of CREB in the etiology of neurodegenerative processes. | [L M Valor, D Jancic, R Lujan, A Barco] | Cell Death & Differentiation | 2010-04-16 | |
| naturepublishinggroup10.1038/nature08875 | APCDD1 is a novel Wnt inhibitor mutated in hereditary hypotrichosis simplex | Hereditary hypotrichosis simplex is a rare autosomal dominant form of hair loss characterized by hair follicle miniaturization1, 2. Using genetic linkage analysis, we mapped a new locus for the disease to chromosome 18p11.22, and identified a mutation (Leu9Arg) in the adenomatosis polyposis down-regulated 1 (APCDD1) gene in three families. We show that APCDD1 is a membrane-bound glycoprotein that is abundantly expressed in human hair follicles, and can interact in vitro with WNT3A and LRP5—two essential components of Wnt signalling. Functional studies show that APCDD1 inhibits Wnt signalling in a cell-autonomous manner and functions upstream of β-catenin. Moreover, APCDD1 represses activation of Wnt reporters and target genes, and inhibits the biological effects of Wnt signalling during both the generation of neurons from progenitors in the developing chick nervous system, and axis specification in Xenopus laevis embryos. The mutation Leu9Arg is located in the signal peptide of APCDD1, and perturbs its translational processing from the endoplasmic reticulum to the plasma membrane. APCDD1(L9R) probably functions in a dominant-negative manner to inhibit the stability and membrane localization of the wild-type protein. These findings describe a novel inhibitor of the Wnt signalling pathway with an essential role in human hair growth. As APCDD1 is expressed in a broad repertoire of cell types3, our findings indicate that APCDD1 may regulate a diversity of biological processes controlled by Wnt signalling. | [Yutaka Shimomura, Dritan Agalliu, Alin Vonica, Victor Luria, Muhammad Wajid, Alessandra Baumer, Serena Belli, Lynn Petukhova, Albert Schinzel, Ali H. Brivanlou, Ben A. Barres, Angela M. Christiano] | Nature | 2010-04-15 | |
| naturepublishinggroup10.1038/onc.2010.84 | T-box 2 represses NDRG1 through an EGR1-dependent mechanism to drive the proliferation of breast cancer cells | T-box 2 (TBX2) is a transcription factor involved in mammary development and is known to be overexpressed in a subset of aggressive breast cancers. TBX2 has previously been shown to repress growth control genes such as p14ARF and p21WAF1/cip1. In this study we show that TBX2 drives proliferation in breast cancer cells and this is abrogated after TBX2 small interfering RNA (siRNA) knockdown or after the expression of a dominant-negative TBX2 protein. Using microarray analysis we identified a large cohort of novel TBX2-repressed target genes including the breast tumour suppressor NDRG1 (N-myc downregulated gene 1). We show that TBX2 targets NDRG1 through a previously undescribed mechanism involving the recruitment of early growth response 1 (EGR1). We show EGR1 is required for the ability of TBX2 to repress NDRG1 and drive cell proliferation. We show that TBX2 interacts with EGR1 and that TBX2 requires EGR1 to target the NDRG1 proximal promoter. Abrogation of either TBX2 or EGR1 expression is accompanied by the upregulation of cell senescence and apoptotic markers. NDRG1 can recapitulate these effects when transfected into TBX2-expressing cells. Together, these data identify a novel mechanism for TBX2-driven oncogenesis and highlight the importance of NDRG1 as a growth control gene in breast tissue. | [K L Redmond, N T Crawford, H Farmer, Z C D'Costa, G J O'Brien, N E Buckley, R D Kennedy, P G Johnston, D P Harkin, P B Mullan] | Oncogene | 2010-03-29 | |
| naturepublishinggroup10.1038/labinvest.2010.71 | Fibroblast-derived HB-EGF promotes Cdx2 expression in esophageal squamous cells | The molecular basis of attaining columnar phenotype in Barrett's esophagus is poorly understood. One hypothesis states that factors locally produced by cells of mesenchymal origin in chronic reflux esophagitis induce metaplastic transformation. This study was performed to elucidate the factors secreted from fibroblasts that cause columnar phenotype in adjacent squamous epithelium. Human fibroblast cells were exposed to acidified medium for 20 min, followed by medium neutralization for 2 h, and then total RNA was hybridized to Sentrix Human-6 Expression BeadChips. Furthermore, esophageal mucosal biopsy specimens from reflux esophagitis patients were examined for HB-EGF expression using immunohistochemistry. In addition, cells from the human esophageal squamous epithelial cell line HET1A were treated with recombinant HB-EGF, and changes in expressions of Cdx2 and columnar markers were analyzed. The gene expression profile revealed significant upregulation of a variety of growth factors and inflammatory chemokines in response to acid exposure. Among them, HB-EGF was upregulated more than 10-fold. Biopsy specimens from reflux esophagitis patients showed a strong expression of HB-EGF in fibroblast cells underlying the damaged epithelium. Furthermore, in vitro stimulation of HET1A cells with HB-EGF increased Cdx2 in dose-dependent manners. Functional analysis of human Cdx2 promoter also revealed its upregulation by HB-EGF stimulation, showing the role of potential responsive elements (AP-1 and NF-κB) for its transcriptional activation. Moreover, the columnar markers cytokeratin 7 and villin were also upregulated by HB-EGF stimulation. HB-EGF induces several genes characteristics of columnar phenotypes of esophageal squamous epithelium in a paracrine manner. | [Farzana B Rahman, Yasunori Kadowaki, Shunji Ishihara, Hiroshi Tobita, Hiroshi Imaoka, Hiroyuki Fukuhara, Md Monowar Aziz, Kenji Furuta, Yuji Amano, Yoshikazu Kinoshita] | Laboratory Investigation | 2010-03-29 | 7.3 |
| naturepublishinggroup10.1038/jhg.2010.24 | An integrated genomic analysis of gene-function correlation on schizophrenia susceptibility genes | Schizophrenia is a highly complex inheritable disease characterized by numerous genetic susceptibility elements, each contributing a modest increase in risk for the disease. Although numerous linkage or association studies have identified a large set of schizophrenia-associated loci, many are controversial. In addition, only a small portion of these loci overlaps with the large cumulative pool of genes that have shown changes of expression in schizophrenia. Here, we applied a genomic gene-function approach to identify susceptibility loci that show direct effect on gene expression, leading to functional abnormalities in schizophrenia. We carried out an integrated analysis by cross-examination of the literature-based susceptibility loci with the schizophrenia-associated expression gene list obtained from our previous microarray study (Journal of Human Genetics (2009) 54: 665–75) using bioinformatic tools, followed by confirmation of gene expression changes using qPCR. We found nine genes (CHGB, SLC18A2, SLC25A27, ESD, C4A/C4B, TCP1, CHL1 and CTNNA2) demonstrate gene-function correlation involving: synapse and neurotransmission; energy metabolism and defense mechanisms; and molecular chaperone and cytoskeleton. Our findings further support the roles of these genes in genetic influence and functional consequences on the development of schizophrenia. It is interesting to note that four of the nine genes are located on chromosome 6, suggesting a special chromosomal vulnerability in schizophrenia. | [Tearina T Chu, Ying Liu] | Journal of Human Genetics | 2010-03-26 | |
| naturepublishinggroup10.1038/jhg.2010.26 | Screening of genes involved in chromosome segregation during meiosis I: toward the identification of genes responsible for infertility in humans | Prophase I of male meiosis during early spermatogenesis involves dynamic chromosome segregation processes, including synapsis, meiotic recombination and cohesion. Genetic defects in the genes that participate in these processes consistently cause reproduction failure in mice. To identify candidate genes responsible for infertility in humans, we performed gene expression profiling of mouse spermatogenic cells undergoing meiotic prophase I. Cell fractions enriched in spermatogonia, leptotene/zygotene spermatocytes or pachytene spermatocytes from developing mouse testis were separately isolated by density gradient sedimentation and subjected to microarray analysis. A total of 726 genes were identified that were upregulated in leptotene/zygotene spermatocytes. To evaluate the screening efficiency for meiosis-specific genes, we randomly selected 12 genes from this gene set and characterized each gene product using reverse transcription (RT)-PCR of RNA from gonadal tissues, in situ hybridization on testicular tissue sections and subcellular localization analysis of the encoded protein. Four of the 12 genes were confirmed as genes expressed in meiotic stage and 2 of these 4 genes were novel, previously uncharacterized genes. Among the three confirmation methods that were used, RT-PCR appeared to be the most efficient method for further screening. These 726 candidates for human infertility genes might serve as a useful resource for next-generation sequencing combined with exon capture by microarray. | [Hiroshi Kogo, Hiroe Kowa-Sugiyama, Kouji Yamada, Hasbaira Bolor, Makiko Tsutsumi, Tamae Ohye, Hidehito Inagaki, Mariko Taniguchi, Tatsushi Toda, Hiroki Kurahashi] | Journal of Human Genetics | 2010-03-26 | |
| naturepublishinggroup10.1038/onc.2010.80 | Meta-analysis of adrenocortical tumour genomics data: novel pathogenic pathways revealed | Sporadic adrenocortical tumours are common, but their pathogenesis is poorly elucidated. In this study, we present a meta-analysis and review of gene expression microarray and comparative genome hybridization (CGH) studies performed to date on these tumours, including our own data. Data of whole genome microarray studies from altogether 164 tumours (97 benign, 67 malignant) and 18 normal tissues were reclassified and reanalysed. Significant gene sets and cytogenetic changes from publications without available genomic data were also examined including 269 benign, 215 malignant tumour and 30 normal tissues. In our experimental study, 11 tumour and four normal samples were analysed by parallel mRNA and CGH profiling. Data were examined by an integrative bioinformatics approach (GeneSpring, Gene Set Enrichment Analysis and Ingenuity Pathway Analysis softwares) searching for common gene expression changes and paralleling chromosome aberrations. Both meta-analysis of available mRNA and CGH profiling data and our experimental study revealed three major pathogenetic pathways: (1) cell cycle, (2) retinoic acid signalling (including lipopolysaccharide/Toll like receptor 4 pathway), (3) complement system and antigen presentation. These pathways include novel, previously undescribed pathomechanisms of adrenocortical tumours, and associated gene products may serve as diagnostic markers of malignancy and therapeutic targets. | [P M Szab|[oacute]|, V Tam|[aacute]|si, V Moln|[aacute]|r, M Andr|[aacute]|sfalvy, Z T|[ouml]|mb|[ouml]|l, R Farkas, K K|[ouml]|vesdi, A Pat|[oacute]|cs, M T|[oacute]|th, C Szalai, A Falus, K R|[aacute]|cz, P Igaz] | Oncogene | 2010-03-22 | 10.0 |
| naturepublishinggroup10.1038/leu.2010.31 | Deregulated gene expression pathways in myelodysplastic syndrome hematopoietic stem cells | To gain insight into the molecular pathogenesis of the myelodysplastic syndromes (MDS), we performed global gene expression profiling and pathway analysis on the hematopoietic stem cells (HSC) of 183 MDS patients as compared with the HSC of 17 healthy controls. The most significantly deregulated pathways in MDS include interferon signaling, thrombopoietin signaling and the Wnt pathways. Among the most significantly deregulated gene pathways in early MDS are immunodeficiency, apoptosis and chemokine signaling, whereas advanced MDS is characterized by deregulation of DNA damage response and checkpoint pathways. We have identified distinct gene expression profiles and deregulated gene pathways in patients with del(5q), trisomy 8 or −7/del(7q). Patients with trisomy 8 are characterized by deregulation of pathways involved in the immune response, patients with −7/del(7q) by pathways involved in cell survival, whereas patients with del(5q) show deregulation of integrin signaling and cell cycle regulation pathways. This is the first study to determine deregulated gene pathways and ontology groups in the HSC of a large group of MDS patients. The deregulated pathways identified are likely to be critical to the MDS HSC phenotype and give new insights into the molecular pathogenesis of this disorder, thereby providing new targets for therapeutic intervention. | [A Pellagatti, M Cazzola, A Giagounidis, J Perry, L Malcovati, M G Della Porta, M J|[auml]|dersten, S Killick, A Verma, C J Norbury, E Hellstr|[ouml]|m-Lindberg, J S Wainscoat, J Boultwood] | Leukemia | 2010-03-11 | |
| naturepublishinggroup10.1038/sj.bjc.6605571 | Hierarchical clustering of immunohistochemical analysis of the activated ErbB|[sol]|PI3K|[sol]|Akt|[sol]|NF-|[kappa]|B signalling pathway and prognostic significance in prostate cancer | | [I H Koumakpayi, C Le Page, A-M Mes-Masson, F Saad] | British Journal of Cancer | 2010-03-09 | |
| naturepublishinggroup10.1038/nmeth.1436 | Visualization of omics data for systems biology | High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have many visualization methods and tools to choose from. The challenge is to create clear, meaningful and integrated visualizations that give biological insight, without being overwhelmed by the intrinsic complexity of the data. In this review, we discuss how visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data, and we highlight emerging new directions. | [Nils Gehlenborg, Se|[aacute]|n I O'Donoghue, Nitin S Baliga, Alexander Goesmann, Matthew A Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum, Anne-Claude Gavin] | Nature Methods | 2010-03-01 | |
| naturepublishinggroup10.1038/leu.2010.20 | Frequent mutation of the polycomb-associated gene ASXL1 in the myelodysplastic syndromes and in acute myeloid leukemia | | [J Boultwood, J Perry, A Pellagatti, M Fernandez-Mercado, C Fernandez-Santamaria, M J Calasanz, M J Larrayoz, M Garcia-Delgado, A Giagounidis, L Malcovati, M G Della Porta, M J|[auml]|dersten, S Killick, E Hellstr|[ouml]|m-Lindberg, M Cazzola, J S Wainscoat] | Leukemia | 2010-02-25 | |
| naturepublishinggroup10.1038/ncb2023 | Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity | | [Marcel W. Coolen, Clare Stirzaker, Jenny Z. Song, Aaron L. Statham, Zena Kassir, Carlos S. Moreno, Andrew N. Young, Vijay Varma, Terence P. Speed, Mark Cowley, Paul Lacaze, Warren Kaplan, Mark D. Robinson, Susan J. Clark] | Nature a - z index | 2010-02-21 | |
| naturepublishinggroup10.1038/jid.2009.187 | Measurement of CD4|[plus]| and CD8|[plus]| T-Lymphocyte Cytokine Secretion and Gene Expression Changes in p-Phenylenediamine Allergic Patients and Tolerant Individuals | Factors predisposing to individual susceptibility to contact allergic dermatitis are ill defined. This study was designed to characterize the response of allergic and tolerant individuals’ T-lymphocytes after exposure to p-phenylenediamine (PPD). Peripheral blood mononuclear cells (PBMCs) from allergic patients proliferated when treated with PPD and Bandrowski's base (BB) and secreted IL-1α, -1β, -4, -5, -6, -8, -10, and -13; IFN-γ; tumor necrosis factor-α; MIP-1α/β; MCP-1 (monocyte chemotactic protein-1); and RANTES. PBMCs from tolerant individuals were stimulated to proliferate only with BB, and they secreted significantly lower levels of Th2 cytokines. Principal component analysis showed that genes are differentially expressed between the patient groups. A network-based analysis of microarray data showed upregulation of T helper type 2 (Th2) gene pathways, including IL-9, in allergic patients, but a regulatory gene profile in tolerant individuals. Real-time PCR confirmed the observed increase in Th2 cytokine gene transcription in allergic patients. Purified CD4+ and CD8+ T cells from allergic patients were stimulated to proliferate and secrete Th2 cytokines following antigen exposure. Only CD4+ T cells from tolerant individuals were stimulated by BB, and levels of Th2 cytokines were 80% lower. The nature of the antigenic determinant stimulating PBMCs and levels of Th2 cytokines, including IL-9, was confirmed in a validation cohort. These studies show increased activity of Th2 cytokines in CD4+ and CD8+ T cells from individuals with allergic contact dermatitis. | [Eve M Coulter, Claire Jenkinson, John Farrell, Sidonie N Lavergne, Camilla Pease, Andrew White, Maja Aleksic, David Basketter, Dominic P Williams, Clodagh King, Munir Pirmohamed, B Kevin Park, Dean J Naisbitt] | Journal of Investigative Dermatology | 2009-08-06 | |
| naturepublishinggroup10.1038/nchembio.194 | Redox-sensitive cysteines bridge p300/CBP-mediated acetylation and FoxO4 activity | Cellular damage invoked by reactive oxygen species plays a key role in the pathobiology of cancer and aging. Forkhead box class O (FoxO) transcription factors are involved in various cellular processes including cell cycle regulation, apoptosis and resistance to reactive oxygen species, and studies in animal models have shown that these transcription factors are of vital importance in tumor suppression, stem cell maintenance and lifespan extension. Here we report that the activity of FoxO in human cells is directly regulated by the cellular redox state through a unique mechanism in signal transduction. We show that reactive oxygen species induce the formation of cysteine-thiol disulfide–dependent complexes of FoxO and the p300/CBP acetyltransferase, and that modulation of FoxO biological activity by p300/CBP-mediated acetylation is fully dependent on the formation of this redox-dependent complex. These findings directly link cellular redox status to the activity of the longevity protein FoxO. | [Tobias B Dansen, Lydia M M Smits, Miranda H van Triest, Peter L J de Keizer, Dik van Leenen, Marian Groot Koerkamp, Anna Szypowska, Amanda Meppelink, Arjan B Brenkman, Junji Yodoi, Frank C P Holstege, Boudewijn M T Burgering] | Nature Chemical Biology | 2009-08-02 | |
| naturepublishinggroup10.1038/nprot.2009.88 | Monitoring peptidase activities in complex proteomes by MALDI-TOF mass spectrometry | Measuring enzymatic activities in biological fluids is a form of activity-based proteomics and may be utilized as a means of developing disease biomarkers. Activity-based assays allow amplification of output signals, thus potentially visualizing low-abundant enzymes on a virtually transparent whole-proteome background. The protocol presented here describes a semiquantitative in vitro assay of proteolytic activities in complex proteomes by monitoring breakdown of designer peptide substrates using robotic extraction and a matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) mass spectrometric readout. Relative quantitation of the peptide metabolites is carried out by comparison with spiked internal standards, followed by statistical analysis of the resulting mini-peptidome. Partial automation provides reproducibility and throughput essential for comparing large sample sets. The approach may be used for diagnostic or predictive purposes and it enables profiling of 96 samples in 30 h. It could be tailored to many diagnostic and pharmaco-dynamic purposes as a readout of catalytic and metabolic activities in body fluids or tissues. | [Josep Villanueva, Arpi Nazarian, Kevin Lawlor, Paul Tempst] | Nature Protocols | 2009-07-23 | |
| naturepublishinggroup10.1038/sj.bjc.6605153 | Androgen-related expression of G-proteins in ovarian cancer | | [L A Sheach, E M Adeney, A Kucukmetin, S J Wilkinson, A D Fisher, A Elattar, C N Robson, R J Edmondson] | British Journal of Cancer | 2009-07-21 | 00 |
| naturepublishinggroup10.1038/nature08210 | A role for Lin28 in primordial germ-cell development and germ-cell malignancy | The rarity and inaccessibility of the earliest primordial germ cells (PGCs) in the mouse embryo thwart efforts to investigate molecular mechanisms of germ-cell specification. stella (also called Dppa3) marks the rare founder population of the germ lineage1, 2. Here we differentiate mouse embryonic stem cells carrying a stella transgenic reporter into putative PGCs in vitro. The Stella+ cells possess a transcriptional profile similar to embryo-derived PGCs, and like their counterparts in vivo, lose imprints in a time-dependent manner. Using inhibitory RNAs to screen candidate genes for effects on the development of Stella+ cells in vitro, we discovered that Lin28, a negative regulator of let-7 microRNA processing3, 4, 5, 6, is essential for proper PGC development. Furthermore, we show that Blimp1 (also called Prdm1), a let-7 target and a master regulator of PGC specification7, 8, 9, can rescue the effect of Lin28 deficiency during PGC development, thereby establishing a mechanism of action for Lin28 during PGC specification. Overexpression of Lin28 promotes formation of Stella+ cells in vitro and PGCs in chimaeric embryos, and is associated with human germ-cell tumours. The differentiation of putative PGCs from embryonic stem cells in vitro recapitulates the early stages of gamete development in vivo, and provides an accessible system for discovering novel genes involved in germ-cell development and malignancy. | [Jason A. West, Srinivas R. Viswanathan, Akiko Yabuuchi, Kerianne Cunniff, Ayumu Takeuchi, In-Hyun Park, Julia E. Sero, Hao Zhu, Antonio Perez-Atayde, A. Lindsay Frazier, M. Azim Surani, George Q. Daley] | Nature | 2009-07-05 | |
| naturepublishinggroup10.1038/jid.2009.105 | Transient Expression of Ephrin B2 in Perinatal Skin Is Required for Maintenance of Keratinocyte Homeostasis | The formation of functional skin entails multiple key signals that are implicated repeatedly in distinct processes during embryogenesis. Although Eph receptors and their membrane-bound ephrin ligands play a role in a wide variety of embryonic processes, their function in skin development has not been addressed. Here, we show that ephrin B2 is transiently expressed in hair buds during embryogenesis and in dermal mesenchymal cells during the perinatal period. Keratinocyte-specific ephrin B2-targeted mutant mice exhibit no skin phenotype, whereas postnatal systemic ephrin B2 ablation results in the enhancement of keratinocyte proliferation. Although the same treatment results in a defect of vascular remodeling, our analyses showed that the keratinocyte phenotype is not caused by hypoxia due to vascular defects. Interestingly, we found an enhanced expression of IL-1 family molecules, which have been implicated in the regulation of keratinocyte proliferation. On the basis of these observations, we propose that the transient expression of ephrin B2 in perinatal dermal mesenchymal cells plays a role in adjusting the activity of the mesenchymal microenvironment that regulates proliferation of keratinocytes. | [Gyohei Egawa, Masatake Osawa, Akiyoshi Uemura, Yoshiki Miyachi, Shin-Ichi Nishikawa] | Journal of Investigative Dermatology | 2009-07-02 | |
| naturepublishinggroup10.1038/ni.1747 | Mina, an Il4 repressor, controls T helper type 2 bias | T helper type 2 (TH2) bias, which is the propensity of naive CD4+ T cells to differentiate into interleukin 4 (IL-4)-secreting TH2 cells, is a genetic trait that affects susceptibility to infectious, autoimmune and allergic diseases. TH2 bias correlates with the amount of IL-4 initially secreted by newly activated helper T cells that feeds back positively through the pathway of the IL-4 receptor and the transcription factors STAT6 and GATA-3 to drive TH2 development. Here we identify Mina, a member of the jumonji C (JmjC) protein family, as a genetic determinant of TH2 bias. Mina specifically bound to and repressed the Il4 promoter. Mina overexpression in transgenic mice impaired Il4 expression, whereas its knockdown in primary CD4+ T cells led to Il4 derepression. Our findings collectively provide mechanistic insight into an Il4-regulatory pathway that controls helper T cell differentiation and genetic variation in TH2 bias. | [Mariko Okamoto, Melanie Van Stry, Linda Chung, Madoka Koyanagi, Xizhang Sun, Yoshie Suzuki, Osamu Ohara, Hiroshi Kitamura, Atsushi Hijikata, Masato Kubo, Mark Bix] | Nature Immunology | 2009-06-28 | |
| naturepublishinggroup10.1038/tpj.2009.22 | Corticosteroid effects on blood gene expression in Duchenne muscular dystrophy | Though Deflazacort and prednisone improve clinical endpoints in Duchenne muscular dystrophy (DMD) patients, Deflazacort produces fewer side effects. As mechanisms of improvement and side effect differences remain unknown, we evaluated effects of corticosteroid administration on gene expression in blood of DMD patients. Whole blood was obtained from 14 children and adolescents with DMD treated with corticosteroids (DMD-STEROID) and 20 DMD children and adolescents naïve to corticosteroids (DMD). The DMD-STEROID group was further subdivided into Deflazacort and prednisone groups. Affymetrix U133 Plus 2.0 expression microarrays were used to evaluate mRNA expression. Expression of 524 probes changed with corticosteroids, including genes in iron trafficking and the chondroitin sulfate biosynthesis pathway. Deflazacort compared with prednisone yielded 508 regulated probes, including many involved in adipose metabolism. These genes and pathways help explain mechanisms of efficacy and side effects of corticosteroids, and could provide new treatment targets for DMD and other neuromuscular disorders. | [L Lit, F R Sharp, M Apperson, D Z Liu, W L Walker, I Liao, H Xu, B P Ander, B Wong] | The Pharmacogenomics Journal | 2009-06-02 | 7.2 |
| naturepublishinggroup10.1038/nature08036 | Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger | Histone H3 lysine 4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities1. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states1, 2. The dysregulation of PHD fingers has been implicated in several human diseases, including cancers and immune or neurological disorders3. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the carboxy-terminal PHD finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias4, 5, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98–PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98–PHD fusions act as 'chromatin boundary factors', dominating over polycomb-mediated gene silencing to 'lock' developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD finger, an 'effector' of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development. | [Gang G. Wang, Jikui Song, Zhanxin Wang, Holger L. Dormann, Fabio Casadio, Haitao Li, Jun-Li Luo, Dinshaw J. Patel, C. David Allis] | Nature | 2009-05-10 | |
| naturepublishinggroup10.1038/nature08021 | Genes that mediate breast cancer metastasis to the brain | The molecular basis for breast cancer metastasis to the brain is largely unknown1, 2. Brain relapse typically occurs years after the removal of a breast tumour2, 3, 4, suggesting that disseminated cancer cells must acquire specialized functions to take over this organ. Here we show that breast cancer metastasis to the brain involves mediators of extravasation through non-fenestrated capillaries, complemented by specific enhancers of blood–brain barrier crossing and brain colonization. We isolated cells that preferentially infiltrate the brain from patients with advanced disease. Gene expression analysis of these cells and of clinical samples, coupled with functional analysis, identified the cyclooxygenase COX2 (also known as PTGS2), the epidermal growth factor receptor (EGFR) ligand HBEGF, and the 2,6-sialyltransferase ST6GALNAC5 as mediators of cancer cell passage through the blood–brain barrier. EGFR ligands and COX2 were previously linked to breast cancer infiltration of the lungs, but not the bones or liver5, 6, suggesting a sharing of these mediators in cerebral and pulmonary metastases. In contrast, ST6GALNAC5 specifically mediates brain metastasis. Normally restricted to the brain7, the expression of ST6GALNAC5 in breast cancer cells enhances their adhesion to brain endothelial cells and their passage through the blood–brain barrier. This co-option of a brain sialyltransferase highlights the role of cell-surface glycosylation in organ-specific metastatic interactions. | [Paula D. Bos, Xiang H.-F. Zhang, Cristina Nadal, Weiping Shu, Roger R. Gomis, Don X. Nguyen, Andy J. Minn, Marc J. van de Vijver, William L. Gerald, John A. Foekens, Joan Massagu|[eacute]|] | Nature | 2009-05-06 | |
| naturepublishinggroup10.1038/ng.370 | Aberrant ERG expression cooperates with loss of PTEN to promote cancer progression in the prostate | Chromosomal translocations involving the ERG locus are frequent events in human prostate cancer pathogenesis; however, the biological role of aberrant ERG expression is controversial1. Here we show that aberrant expression of ERG is a progression event in prostate tumorigenesis. We find that prostate cancer specimens containing the TMPRSS2-ERG rearrangement are significantly enriched for loss of the tumor suppressor PTEN. In concordance with these findings, transgenic overexpression of ERG in mouse prostate tissue promotes marked acceleration and progression of high-grade prostatic intraepithelial neoplasia (HGPIN) to prostatic adenocarcinoma in a Pten heterozygous background. In vitro overexpression of ERG promotes cell migration, a property necessary for tumorigenesis, without affecting proliferation. ADAMTS1 and CXCR4, two candidate genes strongly associated with cell migration, were upregulated in the presence of ERG overexpression. Thus, ERG has a distinct role in prostate cancer progression and cooperates with PTEN haploinsufficiency to promote progression of HGPIN to invasive adenocarcinoma. | [Brett S Carver, Jennifer Tran, Anuradha Gopalan, Zhenbang Chen, Safa Shaikh, Arkaitz Carracedo, Andrea Alimonti, Caterina Nardella, Shohreh Varmeh, Peter T Scardino, Carlos Cordon-Cardo, William Gerald, Pier Paolo Pandolfi] | Nature Genetics | 2009-04-26 | |
| naturepublishinggroup10.1038/ng.312 | Tiny RNAs associated with transcription start sites in animals | It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. As part of the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within -60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5' ends of tiRNAs show peak density 10–30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes. | [Ryan J Taft, Evgeny A Glazov, Nicole Cloonan, Cas Simons, Stuart Stephen, Geoffrey J Faulkner, Timo Lassmann, Alistair R R Forrest, Sean M Grimmond, Kate Schroder, Katharine Irvine, Takahiro Arakawa, Mari Nakamura, Atsutaka Kubosaki, Kengo Hayashida, Chika Kawazu, Mitsuyoshi Murata, Hiromi Nishiyori, Shiro Fukuda, Jun Kawai, Carsten O Daub, David A Hume, Harukazu Suzuki, Valerio Orlando, Piero Carninci, Yoshihide Hayashizaki, John S Mattick] | Nature Genetics | 2009-04-19 | 7.3.1 |
| naturepublishinggroup10.1038/onc.2009.68 | Microarray coupled to quantitative RT|[ndash]|PCR analysis of androgen-regulated genes in human LNCaP prostate cancer cells | The androgen receptor (AR) mediates the growth-stimulatory effects of androgens in prostate cancer cells. Identification of androgen-regulated genes in prostate cancer cells is therefore of considerable importance for defining the mechanisms of prostate-cancer development and progression. Although several studies have used microarrays to identify AR-regulated genes in prostate cancer cell lines and in prostate tumours, we present here the results of gene expression microarray profiling of the androgen-responsive LNCaP prostate-cancer cell line treated with R1881 for the identification of androgen-regulated genes. We show that the expression of 319 genes is stimulated by 24 h after R1881 addition, with a similar number (300) of genes being significantly repressed. Expression of the upregulated genes, as well as of 60 of the most robustly downregulated genes, was carried out using quantitative RT–PCR (Q-RT–PCR) over a time-course of R1881 treatment from 0 to 72 h. Q-RT–PCR was also carried out following treatment with other AR agonists (dihydrotestosterone, estradiol and medroxyprogesterone) and antagonists (cyproterone acetate, hydroxyflutamide and bicalutamide). This study provides a comprehensive analysis of androgen-regulated gene expression in the LNCaP prostate cancer cell line, and identifies a number of androgen-regulated genes, not described previously, as candidates for mediating androgen responses in prostate cancer cells. | [S Ngan, E A Stronach, A Photiou, J Waxman, S Ali, L Buluwela] | Oncogene | 2009-04-13 | |
| naturepublishinggroup10.1038/ncb1858 | Absence of nucleolar disruption after impairment of 40S ribosome biogenesis reveals an rpL11-translation-dependent mechanism of p53 induction | Impaired ribosome biogenesis is attributed to nucleolar disruption and diffusion of a subset of 60S ribosomal proteins, particularly ribosomal protein (rp)L11, into the nucleoplasm, where they inhibit MDM2, leading to p53 induction and cell-cycle arrest1, 2, 3, 4. Previously, we demonstrated that deletion of the 40S rpS6 gene in mouse liver prevents hepatocytes from re-entering the cell cycle after partial hepatectomy5. Here, we show that this response leads to an increase in p53, which is recapitulated in culture by rpS6-siRNA treatment and rescued by the simultaneous depletion of p53. However, disruption of biogenesis of 40S ribosomes had no effect on nucleolar integrity, although p53 induction was mediated by rpL11, leading to the finding that the cell selectively upregulates the translation of mRNAs with a polypyrimidine tract at their 5'-transcriptional start site (5'-TOP mRNAs), including that encoding rpL11, on impairment of 40S ribosome biogenesis. Increased 5'-TOP mRNA translation takes place despite continued 60S ribosome biogenesis and a decrease in global translation. Thus, in proliferative human disorders involving hypomorphic mutations in 40S ribosomal proteins6, 7, specific targeting of rpL11 upregulation would spare other stress pathways that mediate the potential benefits of p53 induction8. | [Stefano Fumagalli, Alessandro Di Cara, Arti Neb-Gulati, Francois Natt, Sandy Schwemberger, Jonathan Hall, George F. Babcock, Rosa Bernardi, Pier Paolo Pandolfi, George Thomas] | Nature Cell Biology | 2009-03-15 | |
| naturepublishinggroup10.1038/cdd.2009.18 | Molecular stages of rapid and uniform neuralization of human embryonic stem cells | Insights into early human development are fundamental for our understanding of human biology. Efficient differentiation of human embryonic stem cells (hESCs) into neural precursor cells is critical for future cell-based therapies. Here, using defined conditions, we characterized a new method for rapid and uniform differentiation of hESCs into committed neural precursor cells (designated C-NPCs). Dynamic gene expression analysis identified several distinct stages of ESC neuralization and revealed functional modules of coregulated genes and pathways. The first wave of gene expression changes, likely corresponding to the transition through primitive ectoderm, started at day 3, preceding the formation of columnar neuroepithelial rosettes. The second wave started at day 5, coinciding with the formation of rosettes. The majority of C-NPCs were positive for both anterior and posterior markers of developing neuroepithelium. In culture, C-NPCs became electrophysiologically functional neurons; on transplantation into neonatal mouse brains, C-NPCs integrated into the cortex and olfactory bulb, acquiring appropriate neuronal morphologies and markers. Compared to rosette-NPCs,1 C-NPCs exhibited limited in vitro expansion capacity and did not express potent oncogenes such as PLAG1 or RSPO3. Concordantly, we never detected tumors or excessive neural proliferation after transplantation of C-NPCs into mouse brains. In conclusion, our study provides a framework for future analysis of molecular signaling during ESC neuralization. | [R Bajpai, G Coppola, M Kaul, M Talantova, F Cimadamore, M Nilbratt, D H Geschwind, S A Lipton, A V Terskikh] | Cell Death & Differentiation | 2009-03-13 | |
| naturepublishinggroup10.1038/jid.2009.51 | The Unfolded Protein Response Is Activated in Differentiating Epidermal Keratinocytes | The unfolded protein response (UPR), which is induced by stress to the endoplasmic reticulum (ER), is involved in the functional alteration of certain cells, such as the differentiation of B cells to plasma cells. The aim of this study is to determine whether the UPR is activated during epidermal keratinocyte (KC) differentiation. Here, we show that the expression of the UPR-induced proteins Bip/GRP78 and HRD1 was increased in cells in the supra-basal layers of normal human epidermis that contain KCs undergoing differentiation as well as in skin-equivalent cultured KCs. However, Bip/GRP78 and HRD1 were poorly expressed in proliferating KCs in squamous cell carcinoma and psoriasis vulgaris tissues. The epidermal growth factor receptor tyrosine kinase inhibitor, PD153035, which induces KC differentiation, upregulated UPR-induced marker mRNAs and proteins. Furthermore, microarray analyses and quantitative PCR revealed that ER stress-inducing reagents, tunicamycin (TU), thapsigargin, and brefeldin A, altered the expression of genes essential for human epidermal KC differentiation, including C/EBPβ, KLF4, and ABCA12 in vitro. However, ABCA12 and KLF4 mRNA did not increase with TU treatment after siRNA-mediated knockdown of XBP-1. Taken together, our findings strongly suggest that the UPR is activated during normal epidermal KC differentiation and induces C/EBPβ, KLF4, and ABCA12 mRNAs. | [Kazumitsu Sugiura, Yoshinao Muro, Kyoko Futamura, Kenji Matsumoto, Noriko Hashimoto, Yuji Nishizawa, Tetsuro Nagasaka, Hirohisa Saito, Yasushi Tomita, Jiro Usukura] | Journal of Investigative Dermatology | 2009-03-12 | |
| naturepublishinggroup10.1038/mt.2009.22 | High Mobility Group Box2 Promoter-controlled Suicide Gene Expression Enables Targeted Glioblastoma Treatment | Achievement of specific tumor cell targeting remains a challenge for glioma gene therapy. We observed that the human high mobility group box2 (HMGB2) gene had a low level of expression in normal human brain tissues, but was significantly upregulated in glioblastoma tissues. With progressive truncation of a 5′-upstream sequence of the HMGB2 gene, we identified a 0.5-kb fragment displaying a high transcriptional activity in glioblastoma cells, but a low activity in normal brain cells. To test the feasibility of using the HMGB2 promoter sequence in targeted cancer therapy, we constructed a baculoviral vector expressing the herpes simplex virus thymidine kinase (HSVtk) gene driven by the HMGB2 promoter. Transduction with the viral vector induced cell death in glioblastoma cell lines in the presence of ganciclovir (GCV), but did not affect the survival of human astrocytes and neurons. In a mouse xenograft model, intratumor injection of the baculoviral vector suppressed the growth of human glioblastoma cells and prolonged the survival of tumor-bearing mice. Our results suggest that the novel 5′ sequence of HMGB2 gene has a potential to be used as an efficient, tumor-selective promoter in targeted vectors for glioblastoma gene therapy. | [Poonam Balani, Jerome Boulaire, Ying Zhao, Jieming Zeng, Jiakai Lin, Shu Wang] | Molecular Therapy | 2009-02-24 | |
| naturepublishinggroup10.1038/emboj.2009.39 | The transcription factor OsNAC4 is a key positive regulator of plant hypersensitive cell death | The hypersensitive response (HR) is a common feature of plant immune responses and a type of programmed cell death. However, little is known about the induction mechanism of HR cell death. We report that overexpression of OsNAC4, which encodes a plant-specific transcription factor, leads to HR cell death accompanied by the loss of plasma membrane integrity, nuclear DNA fragmentation and typical morphological changes. In OsNAC4 knock-down lines, HR cell death is markedly decreased in response to avirulent bacterial strains. After induction by an avirulent pathogen recognition signal, OsNAC4 is translocated into the nucleus in a phosphorylation-dependent manner. A microarray analysis showed that the expression of 139 genes including OsHSP90 and IREN, encoding a Ca2+-dependent nuclease, were different between the OsNAC4 knock-down line and control line during HR cell death. During the induction of HR cell death, OsHSP90 is involved in the loss of plasma membrane integrity, whereas IREN causes nuclear DNA fragmentation. Overall, our results indicate that two important events occurring during HR cell death are regulated by independent pathways. | [Takashi Kaneda, Yuri Taga, Ryota Takai, Megumi Iwano, Hiroyoshi Matsui, Seiji Takayama, Akira Isogai, Fang-Sik Che] | The EMBO Journal | 2009-02-19 | |
| naturepublishinggroup10.1038/ijo.2009.3 | Using gene expression to predict the secretome of differentiating human preadipocytes | | [D M Mutch, C Rouault, M Keophiphath, D Lacasa, K Cl|[eacute]|ment] | International Journal of Obesity | 2009-02-17 | |
| naturepublishinggroup10.1038/nature07815 | IFN|[agr]| activates dormant haematopoietic stem cells in vivo | Maintenance of the blood system is dependent on dormant haematopoietic stem cells (HSCs) with long-term self-renewal capacity. After injury these cells are induced to proliferate to quickly re-establish homeostasis1. The signalling molecules promoting the exit of HSCs out of the dormant stage remain largely unknown. Here we show that in response to treatment of mice with interferon- (IFN), HSCs efficiently exit G0 and enter an active cell cycle. HSCs respond to IFN treatment by the increased phosphorylation of STAT1 and PKB/Akt (also known as AKT1), the expression of IFN target genes, and the upregulation of stem cell antigen-1 (Sca-1, also known as LY6A). HSCs lacking the IFN/ receptor (IFNAR)2, STAT1 (ref. 3) or Sca-1 (ref. 4) are insensitive to IFN stimulation, demonstrating that STAT1 and Sca-1 mediate IFN-induced HSC proliferation. Although dormant HSCs are resistant to the anti-proliferative chemotherapeutic agent 5-fluoro-uracil1, 5, HSCs pre-treated (primed) with IFN and thus induced to proliferate are efficiently eliminated by 5-fluoro-uracil exposure in vivo. Conversely, HSCs chronically activated by IFN are functionally compromised and are rapidly out-competed by non-activatable Ifnar-/- cells in competitive repopulation assays. Whereas chronic activation of the IFN pathway in HSCs impairs their function, acute IFN treatment promotes the proliferation of dormant HSCs in vivo. These data may help to clarify the so far unexplained clinical effects of IFN on leukaemic cells6, 7, and raise the possibility for new applications of type I interferons to target cancer stem cells8. | [Marieke A. G. Essers, Sandra Offner, William E. Blanco-Bose, Zoe Waibler, Ulrich Kalinke, Michel A. Duchosal, Andreas Trumpp] | Nature | 2009-02-11 | |
| naturepublishinggroup10.1038/onc.2008.495 | Regulation of microRNA expression by HMGA1 proteins | The High Mobility Group proteins HMGA1 are nuclear architectural factors that play a critical role in a wide range of biological processes. Since recent studies have identified the microRNAs (miRNAs) as important regulators of gene expression, modulating critical cellular functions such as proliferation, apoptosis and differentiation, the aim of our work was to identify the miRNAs that are physiologically regulated by HMGA1 proteins. To this purpose, we have analysed the miRNA expression profile of mouse embryonic fibroblasts (MEFs) carrying two, one or no Hmga1 functional alleles using a microarray (miRNA microarray). By this approach, we found a miRNA expression profile that differentiates Hmga1-null MEFs from the wild-type ones. In particular, a significant decrease in miR-196a-2, miR-101b, miR-331 and miR-29a was detected in homozygous Hmga1-knockout MEFs in comparison with wild-type cells. Consistently, these miRNAs are downregulated in most of the analysed tissues of Hmga1-null mice in comparison with the wild-type mice. ChIP assay shows that HMGA1 is able to bind regions upstream of these miRNAs. Moreover, we identified the HMGA2 gene product as a putative target of miR-196a-2, suggesting that HMGA1 proteins are able to downregulate the expression of the other member of the HMGA family through the regulation of the miR-196a-2 expression. Finally, ATXN1 and STC1 gene products have been identified as targets of miR-101b. Therefore, it is reasonable to hypothesize that HMGA1 proteins are involved in several functions by regulating miRNA expression. | [I De Martino, R Visone, M Fedele, F Petrocca, D Palmieri, J M Hoyos, F Forzati, C M Croce, A Fusco] | Oncogene | 2009-01-26 | |
| naturepublishinggroup10.1038/sj.bjc.6604857 | HOX transcription factors are potential therapeutic targets in non-small-cell lung cancer (targeting HOX genes in lung cancer) | The HOX genes are a family of homeodomain-containing transcription factors that determine the identity of cells and tissues during embryonic development. They are also known to behave as oncogenes in some haematological malignancies. In this study, we show that the expression of many of the HOX genes is highly elevated in primary non-small-cell lung cancers (NSCLCs) and in the derived cell lines A549 and H23. Furthermore, blocking the activity of HOX proteins by interfering with their binding to the PBX co-factor causes these cells to undergo apoptosis in vitro and reduces the growth of A549 tumours in vivo. These findings suggest that the interaction between HOX and PBX proteins is a potential therapeutic target in NSCLC. | [L Plowright, K J Harrington, H S Pandha, R Morgan] | British Journal of Cancer | 2009-01-20 | |
| naturepublishinggroup10.1038/onc.2008.472 | Downregulation of SRF|[ndash]|FOS|[ndash]|JUNB pathway in fumarate hydratase deficiency and in uterine leiomyomas | Defects of metabolic enzymes result in a variety of manifestations not logically explained by the primary metabolic function. Dominant defects of fumarate hydratase (FH) result in predisposition to cutaneous and uterine leiomyomas, and renal cell cancer. FH is a metabolic enzyme of the tricarboxylic acid cycle, and its tumor-suppressor mechanism is not fully understood. We compared the consequences of FH deficiency and respiratory chain (RC) deficiency using global expression pattern of diploid primary fibroblasts. This approach utilized the information that RC defects do not seem to predispose to tumorigenesis, and the aim was to identify FH-specific signaling effects that might have relevance to tumor formation. These results were then compared to global expression patterns of FH-deficient and sporadic uterine leiomyoma data sets. We show here that FH-deficient fibroblasts share a common transcriptional fingerprint with FH-deficient and sporadic leiomyomas, highlighting the downregulation of serum response factor (SRF)-regulated transcripts, particularly the FOS–JUNB pathway. We confirmed the downregulation of this pathway at transcriptional and protein level. SRF has a fundamental function in the differentiation of smooth muscle progenitor cells, and its downregulation both in diploid FH-deficient primary fibroblasts and in leiomyomas suggests an early function in the mechanism of uterine leiomyoma formation in FH deficiency. Concordantly, the phosphorylated form of SRF, known to activate transcription, is undetectable in leiomyomas whereas clearly detected in several nuclei in the differentiated myometrium. A similar transcriptional SRF-pathway fingerprint in FH-deficient and sporadic leiomyomas emphasizes the potential importance of this pathway in primary events leading to leiomyomatosis. | [N Raimundo, S Vanharanta, L A Aaltonen, I Hovatta, A Suomalainen] | Oncogene | 2009-01-19 | |
| naturepublishinggroup10.1038/nn.2257 | CREB regulation of nucleus accumbens excitability mediates social isolation|[ndash]|induced behavioral deficits | Here, we characterized behavioral abnormalities induced by prolonged social isolation in adult rodents. Social isolation induced both anxiety- and anhedonia-like symptoms and decreased cAMP response element–binding protein (CREB) activity in the nucleus accumbens shell (NAcSh). All of these abnormalities were reversed by chronic, but not acute, antidepressant treatment. However, although the anxiety phenotype and its reversal by antidepressant treatment were CREB-dependent, the anhedonia-like symptoms were not mediated by CREB in NAcSh. We found that decreased CREB activity in NAcSh correlated with increased expression of certain K+ channels and reduced electrical excitability of NAcSh neurons, which was sufficient to induce anxiety-like behaviors and was reversed by chronic antidepressant treatment. Together, our results describe a model that distinguishes anxiety- and depression-like behavioral phenotypes, establish a selective role of decreased CREB activity in NAcSh in anxiety-like behavior, and provide a mechanism by which antidepressant treatment alleviates anxiety symptoms after social isolation. | [Deanna L Wallace, Ming-Hu Han, Danielle L Graham, Thomas A Green, Vincent Vialou, Sergio D I|[ntilde]|iguez, Jun-Li Cao, Anne Kirk, Sumana Chakravarty, Arvind Kumar, Vaishnav Krishnan, Rachael L Neve, Don C Cooper, Carlos A Bola|[ntilde]|os, Michel Barrot, Colleen A McClung, Eric J Nestler] | Nature Neuroscience | 2009-01-18 | |
| naturepublishinggroup10.1038/leu.2008.357 | Molecular profile of CD34|[plus]| stem|[sol]|progenitor cells according to JAK2V617F mutation status in essential thrombocythemia | | [L Catani, R Zini, D Sollazzo, E Ottaviani, A M Vannucchi, S Ferrari, M Baccarani, N Vianelli, R M Lemoli, R Manfredini] | Leukemia | 2009-01-08 | |
| naturepublishinggroup10.1038/ng.266 | Tandem array|[ndash]|based expression screens identify host mRNA targets of virus-encoded microRNAs | MicroRNAs (miRNAs) are short noncoding RNAs of cellular1 and viral origin2, 3, 4, 5, 6, 7 that post-transcriptionally regulate gene expression through imperfect base pairing to their mRNA targets. Because the recognition sequences of miRNAs for their targets are short and may be discontinuous, bioinformatic prediction of targets is difficult. Here we present an approach to the experimental identification of the mRNA targets of miRNAs encoded by the Kaposi's sarcoma–associated herpesvirus (KSHV). KSHV encodes 17 miRNAs, derived from 12 pre-miRNAs expressed from a single locus during viral latency2, 5, 6, 7, 8, 9, 10. We conducted multiple screens that examine small changes in transcript abundance under different conditions of miRNA expression or inhibition and then searched the identified transcripts for seed sequence matches. Using this strategy, we identified BCLAF1, encoding Bcl2-associated factor, as a target for miR-K5, and further analysis revealed that several other KSHV miRNAs also target this gene product. Our results support that this type of expression profiling provides a potentially general approach to the identification of miRNA targets. | [Joseph M Ziegelbauer, Christopher S Sullivan, Don Ganem] | Nature Genetics | 2008-12-21 | |
| naturepublishinggroup10.1038/jid.2008.392 | Dual Role of COUP-TF-Interacting Protein 2 in Epidermal Homeostasis and Permeability Barrier Formation | COUP-TF-interacting protein 2 (CTIP2; also known as Bcl11b) is a transcription factor that plays key roles in the development of the central nervous and immune systems. CTIP2 is also highly expressed in the developing epidermis, and at lower levels in the dermis and in adult skin. Analyses of mice harboring a germline deletion of CTIP2 revealed that the protein plays critical roles in skin during development, particularly in keratinocyte proliferation and late differentiation events, as well as in the development of the epidermal permeability barrier. At the core of all of these actions is a relatively large network of genes, described herein, that is regulated directly or indirectly by CTIP2. The analysis of conditionally null mice, in which expression of CTIP2 was ablated specifically in epidermal keratinocytes, suggests that CTIP2 functions in both cell and non-cell autonomous contexts to exert regulatory influence over multiple phases of skin development, including barrier establishment. Considered together, our results suggest that CTIP2 functions as a top-level regulator of skin morphogenesis. | [Olga Golonzhka, Xiaobo Liang, Nadia Messaddeq, Jean-Marc Bornert, Adam L Campbell, Daniel Metzger, Pierre Chambon, Gitali Ganguli-Indra, Mark Leid, Arup K Indra] | Journal of Investigative Dermatology | 2008-12-18 | |
| naturepublishinggroup10.1038/nature07583 | Signalling through RHEB-1 mediates intermittent fasting-induced longevity in C. elegans | Dietary restriction is the most effective and reproducible intervention to extend lifespan in divergent species1. In mammals, two regimens of dietary restriction, intermittent fasting (IF) and chronic caloric restriction, have proven to extend lifespan and reduce the incidence of age-related disorders2. An important characteristic of IF is that it can increase lifespan even when there is little or no overall decrease in calorie intake2. The molecular mechanisms underlying IF-induced longevity, however, remain largely unknown. Here we establish an IF regimen that effectively extends the lifespan of Caenorhabditis elegans, and show that the low molecular weight GTPase RHEB-1 has a dual role in lifespan regulation; RHEB-1 is required for the IF-induced longevity, whereas inhibition of RHEB-1 mimics the caloric-restriction effects. RHEB-1 exerts its effects in part by the insulin/insulin growth factor (IGF)-like signalling effector DAF-16 in IF. Our analyses demonstrate that most fasting-induced upregulated genes require RHEB-1 function for their induction, and that RHEB-1 and TOR signalling are required for the fasting-induced downregulation of an insulin-like peptide, INS-7. These findings identify the essential role of signalling by RHEB-1 in IF-induced longevity and gene expression changes, and suggest a molecular link between the IF-induced longevity and the insulin/IGF-like signalling pathway. | [Sakiko Honjoh, Takuya Yamamoto, Masaharu Uno, Eisuke Nishida] | Nature | 2008-12-14 | |
| naturepublishinggroup10.1038/ncb1816 | An inducible autoregulatory loop between HIPK2 and Siah2 at the apex of the hypoxic response | Oxygen deprivation (hypoxia) results in reprogrammed gene expression patterns that induce multifaceted cellular responses. Here we identify a regulated interaction between the serine/threonine kinase HIPK2 and the ubiquitin E3 ligase Siah2 as a mechanism controlling the hypoxic response. Under normoxic conditions, several mechanisms ensure HIPK2 stability: only a fraction of HIPK2 is found in association with Siah2, whereas HIPK2-mediated phosphorylation of this E3 ligase at positions 26, 28 and 68 weakens mutual binding and destabilizes its phosphorylated interaction partner. Hypoxic conditions allow a markedly increased HIPK2/Siah2 interaction and result in efficient polyubiquitylation and proteasomal degradation of the kinase. Accordingly, hypoxia-induced HIPK2 elimination is markedly reduced in Siah2-deficient cells. As HIPK2 has an important role as a negative regulator of gene expression, its elimination from promoter-associated repressor complexes allows the induction of a substantial fraction of hypoxia-induced genes. | [Marco A. Calzado, Laureano de la Vega, Andreas M|[ouml]|ller, David D. L. Bowtell, M. Lienhard Schmitz] | Nature Cell Biology | 2008-11-30 | |
| naturepublishinggroup10.1038/ni.1688 | Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans | A major challenge in vaccinology is to prospectively determine vaccine efficacy. Here we have used a systems biology approach to identify early gene 'signatures' that predicted immune responses in humans vaccinated with yellow fever vaccine YF-17D. Vaccination induced genes that regulate virus innate sensing and type I interferon production. Computational analyses identified a gene signature, including complement protein C1qB and eukaryotic translation initiation factor 2 alpha kinase 4—an orchestrator of the integrated stress response—that correlated with and predicted YF-17D CD8+ T cell responses with up to 90% accuracy in an independent, blinded trial. A distinct signature, including B cell growth factor TNFRS17, predicted the neutralizing antibody response with up to 100% accuracy. These data highlight the utility of systems biology approaches in predicting vaccine efficacy. | [Troy D Querec, Rama S Akondy, Eva K Lee, Weiping Cao, Helder I Nakaya, Dirk Teuwen, Ali Pirani, Kim Gernert, Jiusheng Deng, Bruz Marzolf, Kathleen Kennedy, Haiyan Wu, Soumaya Bennouna, Herold Oluoch, Joseph Miller, Ricardo Z Vencio, Mark Mulligan, Alan Aderem, Rafi Ahmed, Bali Pulendran] | Nature Immunology | 2008-11-23 | |
| naturepublishinggroup10.1038/cdd.2008.166 | Mitochondrial dysfunction triggered by loss of HtrA2 results in the activation of a brain-specific transcriptional stress response | Cellular stress responses can be activated following functional defects in organelles such as mitochondria and the endoplasmic reticulum. Mitochondrial dysfunction caused by loss of the serine protease HtrA2 leads to a progressive movement disorder in mice and has been linked to parkinsonian neurodegeneration in humans. Here, we demonstrate that loss of HtrA2 results in transcriptional upregulation of nuclear genes characteristic of the integrated stress response, including the transcription factor CHOP, selectively in the brain. We also show that loss of HtrA2 results in the accumulation of unfolded proteins in the mitochondria, defective mitochondrial respiration and enhanced production of reactive oxygen species that contribute to the induction of CHOP expression and to neuronal cell death. CHOP expression is also significantly increased in Parkinson's disease patients’ brain tissue. We therefore propose that this brain-specific transcriptional response to stress may be important in the advance of neurodegenerative diseases. | [N Moisoi, K Klupsch, V Fedele, P East, S Sharma, A Renton, H Plun-Favreau, R E Edwards, P Teismann, M D Esposti, A D Morrison, N W Wood, J Downward, L M Martins] | Cell Death & Differentiation | 2008-11-21 | |
| naturepublishinggroup10.1038/nsmb.1516 | Bach1 inhibits oxidative stress|[ndash]|induced cellular senescence by impeding p53 function on chromatin | Cellular senescence is one of the key strategies to suppress expansion of cells with mutations. Senescence is induced in response to genotoxic and oxidative stress. Here we show that the transcription factor Bach1 (BTB and CNC homology 1, basic leucine zipper transcription factor 1), which inhibits oxidative stress-inducible genes, is a crucial negative regulator of oxidative stress–induced cellular senescence. Bach1-deficient murine embryonic fibroblasts showed a propensity to undergo more rapid and profound p53-dependent premature senescence than control wild-type cells in response to oxidative stress. Bach1 formed a complex that contained p53, histone deacetylase 1 and nuclear co-repressor N-coR. Bach1 was recruited to a subset of p53 target genes and contributed to impeding p53 action by promoting histone deacetylation. Because Bach1 is regulated by oxidative stress and heme, our data show that Bach1 connects oxygen metabolism and cellular senescence as a negative regulator of p53. | [Yoshihiro Dohi, Tsuyoshi Ikura, Yutaka Hoshikawa, Yasutake Katoh, Kazushige Ota, Ayako Nakanome, Akihiko Muto, Shinji Omura, Tsutomu Ohta, Akihiro Ito, Minoru Yoshida, Tetsuo Noda, Kazuhiko Igarashi] | Nature Structural & Molecular Biology | 2008-11-16 | |
| naturepublishinggroup10.1038/onc.2008.391 | Decreased expression of CXXC4 promotes a malignant phenotype in renal cell carcinoma by activating Wnt signaling | The Wnt signaling pathway is involved in normal embryonic development and controls the homeostatic self-renewal of stem cells in adult tissues. Constitutive activation of Wnt signaling contributes to cancer development and progression. We identified a CXXC4 homozygous deletion at 4q24 in an aggressive renal cell carcinoma (RCC) using single-nucleotide polymorphism (SNP) arrays. CXXC4 encodes Idax, which negatively regulates Wnt signaling by binding to the PDZ domain of Dishevelled. CXXC4 mRNA levels in tumor samples were significantly lower in patients with metastases compared with those without (P=0.0016). Patients whose tumors had lower CXXC4 expression than normal kidney showed a poorer cause-specific survival outcome than those with higher expression (P=0.0095). Decreased expression of CXXC4 also correlated with cytoplasmic staining of β-catenin. Knockdown of CXXC4 induced the nuclear translocation of β-catenin and altered expression of a set of genes involved in cell proliferation, invasion and survival. Furthermore, reduced expression of CXXC4 by small interfering RNAs promoted cell proliferation and inhibited apoptosis after 5-FU and doxorubicin treatment in RCC cells. These data suggest that CXXC4 plays a critical role in tumor progression of RCC through Wnt signaling. Wnt signaling could thus be a potential molecular target in RCC indicating decreased CXXC4 expression. | [T Kojima, T Shimazui, S Hinotsu, A Joraku, T Oikawa, K Kawai, R Horie, H Suzuki, R Nagashima, K Yoshikawa, T Michiue, M Asashima, H Akaza, K Uchida] | Oncogene | 2008-10-20 | |
| naturepublishinggroup10.1038/jid.2008.290 | Mutations in the Lipase H Gene Underlie Autosomal Recessive Woolly Hair|[sol]|Hypotrichosis | Woolly hair (WH) is characterized by the presence of fine and tightly curled hair. WH can appear as a symptom of some systemic diseases, or without associated findings (nonsyndromic WH). Nonsyndromic WH is known to be inherited as either an autosomal-dominant (OMIM 194300) or recessive (ARWH; OMIM 278150) trait. In this study, we identified 11 consanguineous families of Pakistani origin with ARWH, as well as associated features including sparse and hypopigmented hair shafts. We first checked for mutations in the P2RY5 gene, which encodes an orphan G-protein-coupled receptor that we recently identified as a cause of ARWH. However, none of the 11 families had mutations in the P2RY5 gene. To identify the disease locus, we performed linkage studies in one of these families using the Affymetrix 10K array, and identified a region of suggestive linkage on chromosome 3q27. This region contains the lipase H (LIPH) gene which has been recently shown to underlie an autosomal-recessive form of hypotrichosis. Mutation analysis resulted in the identification of a total of 5 pathogenic mutations in the LIPH of all 11 families analyzed. These results show that LIPH is a second causative gene for ARWH/hypotrichosis, giving rise to a phenotype clinically indistinguishable from P2RY5 mutations. | [Yutaka Shimomura, Muhammad Wajid, Lynn Petukhova, Lawrence Shapiro, Angela M Christiano] | Journal of Investigative Dermatology | 2008-10-02 | |
| naturepublishinggroup10.1038/nbt.1497 | Notch signaling respecifies the hemangioblast to a cardiac fate | To efficiently generate cardiomyocytes from embryonic stem (ES) cells in culture it is essential to identify key regulators of the cardiac lineage and to develop methods to control them. Using a tet-inducible mouse ES cell line to enforce expression of a constitutively activated form of the Notch 4 receptor, we show that signaling through the Notch pathway can efficiently respecify hemangioblasts to a cardiac fate, resulting in the generation of populations consisting of >60% cardiomyocytes. Microarray analyses reveal that this respecification is mediated in part through the coordinated regulation of the BMP and Wnt pathways by Notch signaling. Together, these findings have uncovered a potential role for the Notch pathway in cardiac development and provide an approach for generating large numbers of cardiac progenitors from ES cells. | [Vincent C Chen, Robert Stull, Daniel Joo, Xin Cheng, Gordon Keller] | Nature Biotechnology | 2008-09-28 | |
| naturepublishinggroup10.1038/ng.203 | Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease | Inflammatory bowel disease (IBD) is a common inflammatory disorder with complex etiology that involves both genetic and environmental triggers, including but not limited to defects in bacterial clearance, defective mucosal barrier and persistent dysregulation of the immune response to commensal intestinal bacteria. IBD is characterized by two distinct phenotypes: Crohn's disease (CD) and ulcerative colitis (UC). Previously reported GWA studies have identified genetic variation accounting for a small portion of the overall genetic susceptibility to CD and an even smaller contribution to UC pathogenesis. We hypothesized that stratification of IBD by age of onset might identify additional genes associated with IBD. To that end, we carried out a GWA analysis in a cohort of 1,011 individuals with pediatric-onset IBD and 4,250 matched controls. We identified and replicated significantly associated, previously unreported loci on chromosomes 20q13 (rs2315008[T] and rs4809330[A]; P = 6.30 10-8 and 6.95 10-8, respectively; odds ratio (OR) = 0.74 for both) and 21q22 (rs2836878[A]; P = 6.01 10-8; OR = 0.73), located close to the TNFRSF6B and PSMG1 genes, respectively. | [Subra Kugathasan, Robert N Baldassano, Jonathan P Bradfield, Patrick M A Sleiman, Marcin Imielinski, Stephen L Guthery, Salvatore Cucchiara, Cecilia E Kim, Edward C Frackelton, Kiran Annaiah, Joseph T Glessner, Erin Santa, Tara Willson, Andrew W Eckert, Erin Bonkowski, Julie L Shaner, Ryan M Smith, F George Otieno, Nicholas Peterson, Debra J Abrams, Rosetta M Chiavacci, Robert Grundmeier, Petar Mamula, Gitit Tomer, David A Piccoli, Dimitri S Monos, Vito Annese, Lee A Denson, Struan F A Grant, Hakon Hakonarson] | Nature Genetics | 2008-08-31 | |
| naturepublishinggroup10.1038/nature07317 | STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling | The cellular innate immune system is essential for recognizing pathogen infection and for establishing effective host defence. But critical molecular determinants responsible for facilitating an appropriate immune response—following infection with DNA and RNA viruses, for example—remain to be identified. Here we report the identification, following expression cloning, of a molecule (STING; stimulator of interferon genes) that appears essential for effective innate immune signalling processes. It comprises five putative transmembrane regions, predominantly resides in the endoplasmic reticulum and is able to activate both NF-B and IRF3 transcription pathways to induce expression of type I interferon (IFN- and IFN- ) and exert a potent anti-viral state following expression. In contrast, loss of STING rendered murine embryonic fibroblasts extremely susceptible to negative-stranded virus infection, including vesicular stomatitis virus. Further, STING ablation abrogated the ability of intracellular B-form DNA, as well as members of the herpesvirus family, to induce IFN-, but did not significantly affect the Toll-like receptor (TLR) pathway. Yeast two-hybrid and co-immunoprecipitation studies indicated that STING interacts with RIG-I and with SSR2 (also known as TRAP), which is a member of the translocon-associated protein (TRAP) complex required for protein translocation across the endoplasmic reticulum membrane following translation1, 2. Ablation by RNA interference of both TRAP and translocon adaptor SEC61 was subsequently found to inhibit STING's ability to stimulate expression of IFN-. Thus, as well as identifying a regulator of innate immune signalling, our results imply a potential role for the translocon in innate signalling pathways activated by select viruses as well as intracellular DNA. | [Hiroki Ishikawa, Glen N. Barber] | Nature | 2008-08-24 | |
| naturepublishinggroup10.1038/nature07210 | T-cell-expressed proprotein convertase furin is essential for maintenance of peripheral immune tolerance | Furin is one of seven proprotein convertase family members that promote proteolytic maturation of proproteins1. It is induced in activated T cells and is reported to process a variety of substrates including the anti-inflammatory cytokine transforming growth factor (TGF)-1 (refs 2–4), but the non-redundant functions of furin versus other proprotein convertases in T cells are unclear. Here we show that conditional deletion of furin in T cells allowed for normal T-cell development but impaired the function of regulatory and effector T cells, which produced less TGF-1. Furin-deficient T regulatory (Treg) cells were less protective in a T-cell transfer colitis model and failed to induce Foxp3 in normal T cells. Additionally, furin-deficient effector cells were inherently over-active and were resistant to suppressive activity of wild-type Treg cells. Thus, our results indicate that furin is indispensable in maintaining peripheral tolerance, which is due, at least in part, to its non-redundant, essential function in regulating TGF-1 production. Targeting furin has emerged as a strategy in malignant and infectious disease5, 6. Our results suggest that inhibiting furin might activate immune responses, but may result in a breakdown in peripheral tolerance. | [Marko Pesu, Wendy T. Watford, Lai Wei, Lili Xu, Ivan Fuss, Warren Strober, John Andersson, Ethan M. Shevach, Martha Quezado, Nicolas Bouladoux, Anton Roebroek, Yasmine Belkaid, John Creemers, John J. O|[rsquo]|Shea] | Nature | 2008-08-13 | |
| naturepublishinggroup10.1038/labinvest.2008.74 | Placental expression of ceruloplasmin in pregnancies complicated by severe preeclampsia | There is consensus that ischemia/reperfusion injury associated with preeclampsia (PE) promotes both placental damage and the release of factors leading to maternal endothelium dysfunction, a hallmark of this potentially life-threatening syndrome. These factors include plasminogen activator inhibitor-1 (PAI-1) and soluble fms-like tyrosine kinase-1 (sFlt-1). The goal of this study was to further characterize placental factors involved in the pathophysiology of PE. Thus, DNA microarray gene profiling was utilized to identify mRNA differentially regulated in placentas from women with severe PE compared to both preterm (PC) and term control (TC) groups. Microarray studies detected an upregulation of mRNA for ceruloplasmin, a copper-containing iron transport protein with antioxidant ferroxidase properties, in PE compared to PC and TC placentas, respectively. Quantitative real-time PCR confirmed these results by demonstrating significant increases in ceruloplasmin mRNA in PE vs PC and TC placentas. Supporting previous reports, the expression of sFlt-1 and PAI-1 were also upregulated in PE placentas. Immunohistochemistry localized ceruloplasmin to the intervillous space in PE and PC placentas, whereas stronger syncytial staining was noted in PE. Western blotting confirmed a significant increase in ceruloplasmin levels in placental tissue in PE compared to PC groups. PCR identified the presence of mRNA for ceruloplasmin in primary cultures of syncytiotrophoblasts, but not villous-derived fibroblasts, suggesting that syncytium is the site of ceruloplasmin synthesis in placenta. Hypoxic treatment (1% O2) of syncytiotrophoblasts enhanced levels of ceruloplasmin mRNA approximately 25-fold, a significantly greater upregulation than that noted for PAI-1 and sFlt-1, suggesting that enhanced ceruloplasmin expression is a sensitive marker of syncytial hypoxia. We suggest that syncytial ceruloplasmin and its associated ferroxidase activity, induced by the hypoxia accompanying severe PE, is important in an endogenous cellular program to mitigate the damaging effects of subsequent reperfusion injury at this site. | [Seth Guller, Catalin S Buhimschi, Yula Y Ma, Se Te J Huang, Liubin Yang, Edward Kuczynski, Eduardo Zambrano, Charles J Lockwood, Irina A Buhimschi] | Laboratory Investigation | 2008-08-04 | |
| naturepublishinggroup10.1038/onc.2008.251 | Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays | Propensity for subsequent distant metastasis in head and neck squamous-cell carcinoma (HNSCC) was analysed using 186 primary tumours from patients initially treated by surgery that developed (M) or did not develop (NM) metastases as the first recurrent event. Transcriptome (Affymetrix HGU133_Plus2, QRT–PCR) and array-comparative genomic hybridization data were collected. Non-supervised hierarchical clustering based on Affymetrix data distinguished tumours differing in pathological differentiation, and identified associated functional changes. Propensity for metastasis was not associated with these subgroups. Using QRT–PCR data we identified a four-gene model (PSMD10, HSD17B12, FLOT2 and KRT17) that predicts M/NM status with 77% success in a separate 79-sample validation group of HNSCC samples. This prediction is independent of clinical criteria (age, lymph node status, stage, differentiation and localization). The most significantly altered transcripts in M versus NM were significantly associated to metastasis-related functions, including adhesion, mobility and cell survival. Several genomic modifications were significantly associated with M/NM status (most notably gains at 4q11–22 and Xq12–28; losses at 11q14–24 and 17q11 losses) and partly linked to transcription modifications. This work yields a basis for the development of prognostic molecular signatures, markers and therapeutic targets for HNSCC metastasis. | [D S Rickman, R Millon, A De Reynies, E Thomas, C Wasylyk, D Muller, J Abecassis, B Wasylyk] | Oncogene | 2008-08-04 | |
| naturepublishinggroup10.1038/sj.bjc.6604486 | Identification of claudin-4 as a marker highly overexpressed in both primary and metastatic prostate cancer | In the quest for markers of expression and progression for prostate cancer (PCa), the majority of studies have focussed on molecular data exclusively from primary tumours. Although expression in metastases is inferred, a lack of correlation with secondary tumours potentially limits their applicability diagnostically and therapeutically. Molecular targets were identified by examining expression profiles of prostate cell lines using cDNA microarrays. Those genes identified were verified on PCa cell lines and tumour samples from both primary and secondary tumours using real-time RT–PCR, western blotting and immunohistochemistry. Claudin-4, coding for an integral membrane cell-junction protein, was the most significantly (P<0.00001) upregulated marker in both primary and metastatic tumour specimens compared with benign prostatic hyperplasia at both RNA and protein levels. In primary tumours, claudin-4 was more highly expressed in lower grade (Gleason 6) lesions than in higher grade (Gleason 7) cancers. Expression was prominent throughout metastases from a variety of secondary sites in fresh-frozen and formalin-fixed specimens from both androgen-intact and androgen-suppressed patients. As a result of its prominent expression in both primary and secondary PCas, together with its established role as a receptor for Clostridium perfringens enterotoxin, claudin-4 may be useful as a potential marker and therapeutic target for PCa metastases. | [K A Landers, H Samaratunga, L Teng, M Buck, M J Burger, B Scells, M F Lavin, R A Gardiner] | British Journal of Cancer | 2008-07-22 | |
| naturepublishinggroup10.1038/leu.2008.191 | High-resolution analysis of chromosome copy number alterations in angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma, unspecified, with single nucleotide polymorphism-typing microarrays | Angioimmunoblastic T-cell lymphoma (AILT) and peripheral T-cell lymphoma, unspecified (PTCL-u) are relatively frequent subtypes of T- or natural killer cell lymphoma. To characterize the structural anomalies of chromosomes associated with these disorders, we here determined chromosome copy number alterations (CNAs) and loss of heterozygosity (LOH) at >55 000 single nucleotide polymorphism loci for clinical specimens of AILT (n=40) or PTCL-u (n=33). Recurrent copy number gain common to both conditions was detected on chromosomes 8, 9 and 19, whereas common LOH was most frequent for a region of chromosome 2. AILT- or PTCL-u-specific CNAs or LOH were also identified at 21 regions, some spanning only a few hundred base pairs. We also identified prognosis-related CNAs or LOH by several approaches, including Cox's proportional hazard analysis. Among the genes that mapped to such loci, a poor prognosis was linked to overexpression of CARMA1 at 7p22 and of MYCBP2 at 13q22, with both genes being localized within regions of frequent copy number gain. For a frequent LOH region at 2q34, we also identified IKAROS family zinc-finger 2 cDNAs encoding truncated proteins. Our data indicate that AILT and PTCL-u consist of heterogeneous subgroups with distinct transforming genetic alterations. | [S-i Fujiwara, Y Yamashita, N Nakamura, Y L Choi, T Ueno, H Watanabe, K Kurashina, M Soda, M Enomoto, H Hatanaka, S Takada, M Abe, K Ozawa, H Mano] | Leukemia | 2008-07-17 | |
| naturepublishinggroup10.1038/nsmb.1452 | Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast | SWI/SNF chromatin-remodeling complexes have crucial roles in transcription and other chromatin-related processes. The analysis of the two members of this class in Saccharomyces cerevisiae, SWI/SNF and RSC, has heavily contributed to our understanding of these complexes. To understand the in vivo functions of SWI/SNF and RSC in an evolutionarily distant organism, we have characterized these complexes in Schizosaccharomyces pombe. Although core components are conserved between the two yeasts, the compositions of S. pombe SWI/SNF and RSC differ from their S. cerevisiae counterparts and in some ways are more similar to metazoan complexes. Furthermore, several of the conserved proteins, including actin-like proteins, are markedly different between the two yeasts with respect to their requirement for viability. Finally, phenotypic and microarray analyses identified widespread requirements for SWI/SNF and RSC on transcription including strong evidence that SWI/SNF directly represses iron-transport genes. | [Brendon J Monahan, Judit Vill|[eacute]|n, Samuel Marguerat, J|[uuml]|rg B|[auml]|hler, Steven P Gygi, Fred Winston] | Nature Structural & Molecular Biology | 2008-07-11 | |
| naturepublishinggroup10.1038/cgt.2008.40 | Molecular analysis of human cancer cells infected by an oncolytic HSV-1 reveals multiple upregulated cellular genes and a role for SOCS1 in virus replication | Oncolytic herpes simplex viruses (oHSVs) are promising anticancer therapeutics. We sought to characterize the functional genomic response of human cancer cells to oHSV infection using G207, an oHSV previously evaluated in a phase I trial. Five human malignant peripheral nerve sheath tumor cell lines, with differing sensitivity to oHSV, were infected with G207 for 6 h. Functional genomic analysis of virus-infected cells demonstrated large clusters of downregulated cellular mRNAs and smaller clusters of those upregulated, including 21 genes commonly upregulated in all five lines. Of these, 7 are known to be HSV-1 induced and 14 represent novel virus-regulated genes. Gene ontology analysis revealed that a majority of G207-upregulated genes are involved in Janus kinase/signal transducer and activator of transcription signaling, transcriptional regulation, nucleic acid metabolism, protein synthesis and apoptosis. Ingenuity networks highlighted nodes for AP-1 subunits and interferon signaling via STAT1, suppressor of cytokine signaling-1 (SOCS1), SOCS3 and RANTES. As biological confirmation, we found that virus-mediated upregulation of SOCS1 correlated with sensitivity to G207 and that depletion of SOCS1 impaired virus replication by >10-fold. Further characterization of roles provided by oHSV-induced cellular genes during virus replication may be utilized to predict oncolytic efficacy and to provide rational strategies for designing next-generation oncolytic viruses. | [Y Y Mahller, B Sakthivel, W H Baird, B J Aronow, Y-H Hsu, T P Cripe, R Mehrian-Shai] | Cancer Gene Therapy | 2008-06-13 | |
| naturepublishinggroup10.1038/mi.2008.13 | Acute appendicitis is characterized by a uniform and highly selective pattern of inflammatory gene expression | Acute appendicitis (AA) is the most common life-threatening surgical emergency in pediatrics. To characterize the nature of the inflammatory response in AA, gene expression profiles were generated. We found remarkable uniformity in the genes that were differentially expressed between patients with appendicitis and control groups. Sixty-four probe sets were differentially expressed in samples from patients with both severe and mild appendicitis compared to control samples, and within this group we were able to identify four dominant clusters. Interestingly, expression levels of interleukin (IL)-8 significantly correlated with histologic score, and expression of IL-8 protein was observed within both neutrophils and mononuclear cells by immunohistochemistry, suggesting a possible role in the etiology of appendicitis. Although there was some overlap between genes reported to be differentially expressed in Crohn's disease (CD) and those observed in AA, differential expression of genes involved in interferon responses that characterize CD was not observed. | [C G Murphy, J N Glickman, K Tomczak, Y Y Wang, A H Beggs, M W Shannon, B H Horwitz] | Mucosal Immunology | 2008-07-01 | |
| naturepublishinggroup10.1038/labinvest.2008.42 | Deterioration of atherosclerosis in mice lacking angiotensin II type 1A receptor in bone marrow-derived cells | The renin–angiotensin system (RAS) modulates end-organ damages, resulting in cardiovascular and kidney diseases. Experiments both in vitro and in vivo demonstrate that the angiotensin II (Ang II) type 1 (AT1) receptor pathway also exerts pro-inflammatory and pro-atherogenic effects on bone marrow-derived cells (BMDCs). Here, we investigated how AT1 receptor expression by BMDCs contributes to atherosclerosis and kidney injury in vivo by transplanting BM into RAS-activated transgenic mice. There was no difference in the extent of kidney damage between mice receiving BM transplants from mutant mice lacking the angiotensin II type 1a receptor (AT1a) gene and mice receiving transplants from wild-type (WT) mice. However, mice receiving transplants from AT1a ‘knockout’ (KO) mice displayed accelerated lethality and atherosclerotic lesions. These results indicated that the effects of AT1a receptor on BMDCs are organ dependent. Microarray expression profiling of macrophages from AT1a-KO mice revealed significant changes in the mRNA levels for a number of genes implicated in atherosclerosis. In accordance with the in vivo atherosclerosis results, AT1a-KO macrophages exhibited greater uptake of modified lipoproteins relative to macrophages from WT mice. We propose that the expression of AT1a receptor by BMDCs limits atherosclerosis in vivo. | [Hideki Kato, Junji Ishida, Katsumasa Nagano, Kaori Honjo, Takeshi Sugaya, Norifumi Takeda, Fumihiro Sugiyama, Ken-ichi Yagami, Toshiro Fujita, Masaomi Nangaku, Akiyoshi Fukamizu] | Laboratory Investigation | 2008-05-19 | |
| naturepublishinggroup10.1038/pcan.2008.27 | Molecular targeting of Bcl-2 overcomes prostate cancer cell adaptation to XIAP gene downregulation | X-linked inhibitor of apoptosis (XIAP) is a suppressor of apoptosis that supports an increased survival and resistance to chemotherapy of human prostate cancer (PCa) cells. Effects of transient (24 h) and chronic (beyond 1 month) downregulation of XIAP in DU145 hormone refractory prostate cancer (HRPC) cells were studied. We found that transient downregulation of XIAP by siRNAs resulted in an increase of apoptosis and a decrease in Bcl-2 levels and sensitized PCa cells to cisplatin. XIAP downregulation by shRNA vector stable transfection led to upregulation of Bcl-2 protein. Our results identify the adaptability of PCa cells to chronic loss of XIAP in part through upregulation of Bcl-2 and indicate that multitargeting approach is the most effective application in the chemotherapy of human HRPC. | [Y Nakano, V Bilim, K Yuuki, A Muto, T Kato, A Nagaoka, Y Tomita] | Prostate Cancer and Prostatic Diseases | 2008-05-13 | |
| naturepublishinggroup10.1038/jid.2008.124 | Unraveling the Mysteries of IGF-1 Signaling in Melanoma | The inherent ability of a cell to undergo apoptosis governs a number of developmental processes essential to proper mammalian development. Into adulthood, the pathways that potentiate the apoptotic response are extremely diverse and finely regulated to prevent potential diseases. Of these, cancer is often associated with loss of an apoptotic response. Hanahan and Weinberg (2000) list evasion of apoptosis as a hallmark feature acquired during neoplastic transformation. The impact of this event is dramatic on several levels; avoidance of apoptosis not only prevents programmed cell death in an array of cell types but also promotes chemotherapeutic resistance during anticancer regimens. | [John T Lee, Patricia Brafford, Meenhard Herlyn] | Journal of Investigative Dermatology | 2008-06-01 | |
| naturepublishinggroup10.1038/modpathol.2008.57 | Array comparative genomic hybridization analysis of olfactory neuroblastoma | Olfactory neuroblastoma is an unusual neuroectodermal malignancy, which is thought to arise at the olfactory membrane of the sinonasal tract. Due to its rarity, little is understood regarding its molecular and cytogenetic abnormalities. The aim of the current study is to identify specific DNA copy number changes in olfactory neuroblastoma. Thirteen dissected tissue samples were analyzed using array comparative genomic hybridization. Our results show that gene copy number profiles of olfactory neuroblastoma samples are complex. The most frequent changes included gains at 7q11.22–q21.11, 9p13.3, 13q, 20p/q, and Xp/q, and losses at 2q31.1, 2q33.3, 2q37.1, 6q16.3, 6q21.33, 6q22.1, 22q11.23, 22q12.1, and Xp/q. Gains were more frequent than losses, and high-stage tumors showed more alterations than low-stage olfactory neuroblastoma. Frequent changes in high-stage tumors were gains at 13q14.2–q14.3, 13q31.1, and 20q11.21–q11.23, and loss of Xp21.1 (in 66% of cases). Gains at 5q35, 13q, and 20q, and losses at 2q31.1, 2q33.3, and 6q16–q22, were present in 50% of cases. The identified regions of gene copy number change have been implicated in a variety of tumors, especially carcinomas. In addition, our results indicate that gains in 20q and 13q may be important in the progression of this cancer, and that these regions possibly harbor genes with functional relevance in olfactory neuroblastoma. | [Mohamed Guled, Samuel Myllykangas, Henry F Frierson, Stacey E Mills, Sakari Knuutila, Edward B Stelow] | Modern Pathology | 2008-04-11 | |
| naturepublishinggroup10.1038/jcbfm.2008.22 | Gene expression in peripheral blood differs after cardioembolic compared with large-vessel atherosclerotic stroke: biomarkers for the etiology of ischemic stroke | There are no biomarkers that differentiate cardioembolic from large-vessel atherosclerotic stroke, although the treatments differ for each and ~30% of strokes and transient ischemic attacks have undetermined etiologies using current clinical criteria. We aimed to define gene expression profiles in blood that differentiate cardioembolic from large-vessel atherosclerotic stroke. Peripheral blood samples were obtained from healthy controls and acute ischemic stroke patients (<3, 5, and 24 h). RNA was purified, labeled, and applied to Affymetrix Human U133 Plus 2.0 Arrays. Expression profiles in the blood of cardioembolic stroke patients are distinctive from those of large-vessel atherosclerotic stroke patients. Seventy-seven genes differ at least 1.5-fold between them, and a minimum number of 23 genes differentiate the two types of stroke with at least 95.2% specificity and 95.2% sensitivity for each. Genes regulated in large-vessel atherosclerotic stroke are expressed in platelets and monocytes and modulate hemostasis. Genes regulated in cardioembolic stroke are expressed in neutrophils and modulate immune responses to infectious stimuli. This new method can be used to predict whether a stroke of unknown etiology was because of cardioembolism or large-vessel atherosclerosis that would lead to different therapy. These results have wide ranging implications for similar disorders. | [Huichun Xu, Yang Tang, Da-Zhi Liu, Ruiqiong Ran, Bradley P Ander, Michelle Apperson, Xin She Liu, Jane C Khoury, Jeffrey P Gregg, Arthur Pancioli, Edward C Jauch, Kenneth R Wagner, Piero Verro, Joseph P Broderick, Frank R Sharp] | Journal of Cerebral Blood Flow & Metabolism | 2008-04-02 | |
| naturepublishinggroup10.1038/nature06880 | Control of Treg and TH17 cell differentiation by the aryl hydrocarbon receptor | Regulatory T cells (Treg) expressing the transcription factor Foxp3 control the autoreactive components of the immune system. The development of Treg cells is reciprocally related to that of pro-inflammatory T cells producing interleukin-17 (TH17). Although Treg cell dysfunction and/or TH17 cell dysregulation are thought to contribute to the development of autoimmune disorders, little is known about the physiological pathways that control the generation of these cell lineages. Here we report the identification of the ligand-activated transcription factor aryl hydrocarbon receptor (AHR) as a regulator of Treg and TH17 cell differentiation in mice. AHR activation by its ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin induced functional Treg cells that suppressed experimental autoimmune encephalomyelitis. On the other hand, AHR activation by 6-formylindolo[3,2-b]carbazole interfered with Treg cell development, boosted TH17 cell differentiation and increased the severity of experimental autoimmune encephalomyelitis in mice. Thus, AHR regulates both Treg and TH17 cell differentiation in a ligand-specific fashion, constituting a unique target for therapeutic immunomodulation. | [Francisco J. Quintana, Alexandre S. Basso, Antonio H. Iglesias, Thomas Korn, Mauricio F. Farez, Estelle Bettelli, Mario Caccamo, Mohamed Oukka, Howard L. Weiner] | Nature | 2008-03-23 | |
| naturepublishinggroup10.1038/nature06738 | Thyrotrophin in the pars tuberalis triggers photoperiodic response | Molecular mechanisms regulating animal seasonal breeding in response to changing photoperiod are not well understood. Rapid induction of gene expression of thyroid-hormone-activating enzyme (type 2 deiodinase, DIO2) in the mediobasal hypothalamus (MBH) of the Japanese quail (Coturnix japonica) is the earliest event yet recorded in the photoperiodic signal transduction pathway. Here we show cascades of gene expression in the quail MBH associated with the initiation of photoinduced secretion of luteinizing hormone. We identified two waves of gene expression. The first was initiated about 14 h after dawn of the first long day and included increased thyrotrophin (TSH) -subunit expression in the pars tuberalis; the second occurred approximately 4 h later and included increased expression of DIO2. Intracerebroventricular (ICV) administration of TSH to short-day quail stimulated gonadal growth and expression of DIO2 which was shown to be mediated through a TSH receptor–cyclic AMP (cAMP) signalling pathway. Increased TSH in the pars tuberalis therefore seems to trigger long-day photoinduced seasonal breeding. | [Nobuhiro Nakao, Hiroko Ono, Takashi Yamamura, Tsubasa Anraku, Tsuyoshi Takagi, Kumiko Higashi, Shinobu Yasuo, Yasuhiro Katou, Saburo Kageyama, Yumiko Uno, Takeya Kasukawa, Masayuki Iigo, Peter J. Sharp, Atsushi Iwasawa, Yutaka Suzuki, Sumio Sugano, Teruyuki Niimi, Makoto Mizutani, Takao Namikawa, Shizufumi Ebihara, Hiroki R. Ueda, Takashi Yoshimura] | Nature | 2008-03-20 | |
| naturepublishinggroup10.1038/leu.2008.67 | Dose-dependent repression of T-cell and natural killer cell genes by PU.1 enforces myeloid and B-cell identity | The Ets transcription factor PU.1, encoded by the gene Sfpi1, functions in a concentration-dependent manner to promote myeloid and B-cell development and has been implicated in myeloid and lymphoid leukemias. To determine the consequences of reducing PU.1 concentration during hematopoiesis, we analyzed mice with two distinct hypomorphic alleles of Sfpi1 that produce PU.1 at 20% (BN) or 2% (Blac) of wild-type levels. Myeloid development was impaired in these mice, but less severely than in Sfpi1 null mice. To identify the downstream target genes that respond to changes in PU.1 concentration, we analyzed ex vivo interleukin-3 dependent myeloid cell lines established from Sfpi1BN/BN, Sfpi1Blac/Blac and Sfpi1- /- fetal liver cells. Unexpectedly, many T-cell and natural killer cell genes were expressed in Sfpi1- /- cells and repressed in a dose-dependent manner in Sfpi1Blac/Blac and Sfpi1BN/BN cells. This pattern of dose-dependent T/NK-cell gene repression also occurred in ex vivo interleukin-7 dependent progenitor B cell lines. These results suggest that PU.1 functions in a concentration-dependent manner to repress T-cell and natural killer cell fates while promoting myeloid and B-cell fates. | [M B Kamath, I B Houston, A J Janovski, X Zhu, S Gowrisankar, A G Jegga, R P DeKoter] | Leukemia | 2008-03-20 | |
| naturepublishinggroup10.1038/emboj.2008.51 | Liver-specific deletion of histone deacetylase 3 disrupts metabolic transcriptional networks | Histone deacetylase 3 (Hdac3) is an enzymatic component of transcriptional repression complexes recruited by the nuclear hormone receptors. Inactivation of Hdac3 in cancer cell lines triggered apoptosis, and removal of Hdac3 in the germ line of mice caused embryonic lethality. Therefore, we deleted Hdac3 in the postnatal mouse liver. These mice developed hepatomegaly, which was the result of hepatocyte hypertrophy, and these morphological changes coincided with significant imbalances between carbohydrate and lipid metabolism. Loss of Hdac3 triggered changes in gene expression consistent with inactivation of repression mediated by nuclear hormone receptors. Loss of Hdac3 also increased the levels of Ppar2, and treatment of these mice with a Ppar antagonist partially reversed the lipid accumulation in the liver. In addition, gene expression analysis identified mammalian target of rapamycin signalling as being activated after deletion of Hdac3, and inhibition by rapamycin affected the accumulation of neutral lipids in Hdac3-null livers. Thus, Hdac3 regulates metabolism through multiple signalling pathways in the liver, and deletion of Hdac3 disrupts normal metabolic homeostasis. | [Sarah K Knutson, Brenda J Chyla, Joseph M Amann, Srividya Bhaskara, Stacey S Huppert, Scott W Hiebert] | The EMBO Journal | 2008-03-20 | |
| naturepublishinggroup10.1038/embor.2008.34 | Gene induction following wounding of wild-type versus macrophage-deficient Drosophila embryos | By using a microarray screen to compare gene responses after sterile laser wounding of wild-type and ‘macrophageless’ serpent mutant Drosophila embryos, we show the wound-induced programmes that are independent of a pathogenic response and distinguish which of the genes are macrophage dependent. The evolutionarily conserved nature of this response is highlighted by our finding that one such new inflammation-associated gene, growth arrest and DNA damage-inducible gene 45 (GADD45), is upregulated in both Drosophila and murine repair models. Comparison of unwounded wild-type and serpent mutant embryos also shows a portfolio of ‘macrophage-specific’ genes, which suggest analogous functions with vertebrate inflammatory cells. Besides identifying the various classes of wound- and macrophage-related genes, our data indicate that sterile injury per se, in the absence of pathogens, triggers induction of a ‘pathogen response’, which might prime the organism for what is likely to be an increased risk of infection. | [Brian Stramer, Mark Winfield, Tanya Shaw, Thomas H Millard, Sarah Woolner, Paul Martin] | EMBO reports | 2008-03-14 | |
| naturepublishinggroup10.1038/nature06781 | SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis | Mechanisms underlying global changes in gene expression during tumour progression are poorly understood. SATB1 is a genome organizer that tethers multiple genomic loci and recruits chromatin-remodelling enzymes to regulate chromatin structure and gene expression. Here we show that SATB1 is expressed by aggressive breast cancer cells and its expression level has high prognostic significance (P < 0.0001), independent of lymph-node status. RNA-interference-mediated knockdown of SATB1 in highly aggressive (MDA-MB-231) cancer cells altered the expression of >1,000 genes, reversing tumorigenesis by restoring breast-like acinar polarity and inhibiting tumour growth and metastasis in vivo. Conversely, ectopic SATB1 expression in non-aggressive (SKBR3) cells led to gene expression patterns consistent with aggressive-tumour phenotypes, acquiring metastatic activity in vivo. SATB1 delineates specific epigenetic modifications at target gene loci, directly upregulating metastasis-associated genes while downregulating tumour-suppressor genes. SATB1 reprogrammes chromatin organization and the transcription profiles of breast tumours to promote growth and metastasis; this is a new mechanism of tumour progression. | [Hye-Jung Han, Jose Russo, Yoshinori Kohwi, Terumi Kohwi-Shigematsu] | Nature | 2008-03-13 | |
| naturepublishinggroup10.1038/mp.2008.30 | Family-based association testing strongly implicates DRD2 as a risk gene for schizophrenia in Han Chinese from Taiwan | The gene that codes for dopamine receptor D2 (DRD2 on chromosome 11q23) has long been a prime functional and positional candidate risk gene for schizophrenia. Collectively, prior case–control studies found a reliable effect of the Ser311Cys DRD2 polymorphism (rs1801028) on risk for schizophrenia, but few other polymorphisms in the gene had ever been evaluated and no adequately powered family-based association study has been performed to date. Our objective was to test 21 haplotype-tagging and all three known nonsynonymous single-nucleotide polymorphisms (SNPs) in DRD2 for association with schizophrenia in a family-based study of 2408 Han Chinese, including 1214 affected individuals from 616 families. We did not find a significant effect of rs1801028, but we did find significant evidence for association of schizophrenia with two multi-marker haplotypes spanning blocks of strong linkage disequilibrium (LD) and nine individual SNPs (Ps<0.05). Importantly, two SNPs (rs1079727 and rs2283265) and both multi-marker haplotypes spanning entire LD blocks (including one that contained rs1801028) remained significant after correcting for multiple testing. These results further add to the body of data implicating DRD2 as a schizophrenia risk gene; however, a causal variant(s) in DRD2 remains to be elucidated by further fine mapping of the gene, with particular attention given to the area surrounding the third through fifth exons. | [S J Glatt, S V Faraone, J A Lasky-Su, T Kanazawa, H-G Hwu, M T Tsuang] | Molecular Psychiatry | 2008-03-11 | |
| naturepublishinggroup10.1038/npp.2008.19 | Abnormal Indices of Cell Cycle Activity in Schizophrenia and their Potential Association with Oligodendrocytes | The goal of this study was to determine what signaling pathways may elicit myelin-specific gene expression deficits in schizophrenia (SZ). Microarray analyses indicated that genes associated with canonical cell cycle pathways were significantly affected in the anterior cingulate gyrus (ACG), the region exhibiting the most profound myelin-specific gene expression changes, in persons with SZ (N=16) as compared with controls (N=19). Detected gene expression changes of key regulators of G1/S phase transition and genes central to oligodendrocyte differentiation were validated using qPCR in the ACG in an independent cohort (Ns=45/34). The relative abundance of phosphorylated retinoblastoma protein (pRb) was increased in the white matter underlying the ACG in SZ subjects (Ns=12). The upregulation of cyclin D1 gene expression and the downregulation of p57Kip2, accompanied by increased cyclin D/CDK4-dependent phosphorylation of pRb, acting as a checkpoint for G1/S phase transition, suggest abnormal cell cycle re-entry in postmitotic oligodendrocytes in SZ. Furthermore, gene expression profiling of brain samples from myelin mutant animal models, quaking and myelin-associated glycoprotein (MAG) null mice, showed that cell cycle gene expression changes were not a necessary consequence of the reduced gene expression of structural myelin proteins, such as MAG. While, quaking, a known modulator of cell cycle activity during oligodendrocyte differentiation impairs the expression of multiple myelin genes, including those that are affected in SZ. These data suggest that the normal patterns of cell cycle gene and protein expression are disrupted in SZ and that this disruption may contribute to the oligodendroglial deficits observed in SZ. | [Pavel Katsel, Kenneth L Davis, Celeste Li, Weilun Tan, Elizabeth Greenstein, Lisa B Kleiner Hoffman, Vahram Haroutunian] | Neuropsychopharmacology | 2008-03-05 | |
| naturepublishinggroup10.1038/onc.2008.42 | Autocrine induction of invasion and metastasis by tumor-associated trypsin inhibitor in human colon cancer cells | From the conditioned medium of the human colon carcinoma cells, HT-29 5M21 (CM-5M21), expressing a spontaneous invasive phenotype, tumor-associated trypsin inhibitor (TATI) was identified and characterized by proteomics, cDNA microarray approaches and functional analyses. Both CM-5M21 and recombinant TATI, but not the K18Y-TATI mutant at the protease inhibitor site, trigger collagen type I invasion by several human adenoma and carcinoma cells of the colon and breast, through phosphoinositide-3-kinase, protein kinase C and Rho-GTPases/Rho kinase-dependent pathways. Conversely, the proinvasive action of TATI in parental HT29 cells was alleviated by the TATI antibody PSKAN2 and the K18Y-TATI mutant. Stable expression of K18Y-TATI in HT-29 5M21 cells downregulated tumor growth, angiogenesis and the expression of several metastasis-related genes, including CSPG4 (13.8-fold), BMP-7 (9.7-fold), the BMP antagonist CHORDIN (5.2-fold), IGFBP-2 and IGF2 (9.6- and 4.6-fold). Accordingly, ectopic expression of KY-TATI inhibited the development of lung metastases from HT-29 5M21 tumor xenografts in immunodeficient mice. These findings identify TATI as an autocrine transforming factor potentially involved in early and late events of colon cancer progression, including local invasion of the primary tumor and its metastatic spread. Targeting TATI, its molecular partners and effectors may bring novel therapeutic applications for high-grade human solid tumors in the digestive and urogenital systems. | [V Gouyer, D Fontaine, P Dumont, O de Wever, H Fontayne-Devaud, E Leteurtre, S Truant, D Delacour, H Drobecq, J-P Kerckaert, Y de Launoit, M Bracke, C Gespach, J-L Desseyn, G Huet] | Oncogene | 2008-03-03 | |
| naturepublishinggroup10.1038/nsmb.1399 | A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases | Dicer initiates RNA interference by generating small RNAs involved in various silencing pathways. Dicer participates in centromeric silencing, but its role in the epigenetic regulation of other chromatin domains has not been explored. Here we show that Dicer1 deficiency in Mus musculus leads to decreased DNA methylation, concomitant with increased telomere recombination and telomere elongation. These DNA-methylation defects correlate with decreased expression of Dnmt1, Dnmt3a and Dnmt3b DNA methyltransferases (Dnmts), and methylation levels can be recovered by their overexpression. We identify the retinoblastoma-like 2 protein (Rbl2) as responsible for decreased Dnmt expression in Dicer1-null cells, suggesting the existence of Dicer-dependent small RNAs that target Rbl2. We identify the miR-290 cluster as being downregulated in Dicer1-deficient cells and show that it silences Rbl2, thereby controlling Dnmt expression. These results identify a pathway by which miR-290 directly regulates Rbl2-dependent Dnmt expression, indirectly affecting telomere-length homeostasis. | [Roberta Benetti, Susana Gonzalo, Isabel Jaco, Purificaci|[oacute]|n Mu|[ntilde]|oz, Susana Gonzalez, Stefan Schoeftner, Elizabeth Murchison, Thomas Andl, Taiping Chen, Peter Klatt, En Li, Manuel Serrano, Sarah Millar, Gregory Hannon, Maria A Blasco] | Nature Structural & Molecular Biology | 2008-03-02 | |
| naturepublishinggroup10.1038/ng.100 | Disruption of P2RY5, an orphan G protein|[ndash]|coupled receptor, underlies autosomal recessive woolly hair | The genetic determinants of hair texture in humans are largely unknown. Several human syndromes exist in which woolly hair comprises a part of the phenotype; however, simple autosomal recessive inheritance of isolated woolly hair has only rarely been reported1, 2. To identify a gene involved in controlling hair texture, we performed genetic linkage analysis in six families of Pakistani origin with autosomal recessive woolly hair (ARWH; OMIM 278150). All six families showed linkage to chromosome 13q14.2–14.3 (Z = 17.97). In all cases, we discovered pathogenic mutations in P2RY5, which encodes a G protein–coupled receptor and is a nested gene residing within intron 17 of the retinoblastoma 1 (RB1) gene. P2RY5 is expressed in both Henle's and Huxley's layers of the inner root sheath of the hair follicle. Our findings indicate that disruption of P2RY5 underlies ARWH and, more broadly, uncover a new gene involved in determining hair texture in humans. | [Yutaka Shimomura, Muhammad Wajid, Yoshiyuki Ishii, Lawrence Shapiro, Lynn Petukhova, Derek Gordon, Angela M Christiano] | Nature Genetics | 2008-02-24 | |
| naturepublishinggroup10.1007/s10038-008-0255-5 | Association analyses confirming a susceptibility locus for intracranial aneurysm at chromosome 14q23 | Previous linkage analyses of intracranial aneurysm (IA) have proposed several genetic susceptibility loci; however, some loci remain contradictory. The objective of this study was to confirm these loci in a Japanese population using allelic and haplotype association analyses. We set high-density single nucleotide polymorphism markers in previously suggested IA loci and conducted an association analysis in 29 cases and 35 controls from a small community in Akita, Japan. Genotyping was carried out using the GeneChip 10 K mapping array, and the association analysis was performed using GeneSpring GT2 software. The result was confirmed in a replication cohort consisting of 237 cases and 253 controls from all over Japan. Only one variant, rs767603, at chromosome 14q23, was significantly associated with IA, both in allelic analysis (p = 0.00017, Bonferroni-corrected p = 0.021) and haplotype analysis (p = 0.00178, Bonferroni-corrected p = 0.048). This association was confirmed in the replication cohort (p = 0.0046 for allelic association, p = 0.0060 for haplotype association). Our findings confirm 14q23 to be a susceptibility locus for intracranial aneurysm. | [Yohei Mineharu, Kayoko Inoue, Sumiko Inoue, Kenji Kikuchi, Hikaru Ohishi, Kazuhiko Nozaki, Nobuo Hashimoto, Akio Koizumi] | Journal of Human Genetics | 2008-02-08 | |
| naturepublishinggroup10.1038/nprot.2008.4 | miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes | MicroRNAs (miRNAs) represent a class of short (22 nt) noncoding RNAs that control gene expression post-transcriptionally. Microarray technology is frequently applied to monitor miRNA expression levels but is challenged by (i) the short length of miRNAs that offers little sequence for appending detection molecules; (ii) low copy number of some miRNA; and (iii) a wide range of predicted melting temperatures (Tm) versus their DNA complementary sequences. We recently developed a microarray platform for genome-wide profiling of miRNAs (miChip) by applying locked nucleic acid (LNA)-modified capture probes. Here, we provide detailed protocols for the generation of the miChip microarray platform, the preparation and fluorescent labeling of small RNA containing total RNA, its hybridization to the immobilized LNA-modified capture probes and the post-hybridization handling of the microarray. Starting from the intact tissue sample, the entire protocol takes 3 d to yield highly accurate and sensitive data about miRNA expression levels. | [Mirco Castoldi, Sabine Schmidt, Vladimir Benes, Matthias W Hentze, Martina U Muckenthaler] | Nature Protocols | 2008-02-07 | |
| naturepublishinggroup10.1038/onc.2008.6 | MicroRNA signatures of TRAIL resistance in human non-small cell lung cancer | To define novel pathways that regulate susceptibility to tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) in non-small cell lung cancer (NSCLC), we have performed genome-wide expression profiling of microRNAs (miRs). We show that in TRAIL-resistant NSCLC cells, levels of different miRs are increased, and in particular, miR-221 and -222. We demonstrate that these miRs impair TRAIL-dependent apoptosis by inhibiting the expression of key functional proteins. Indeed, transfection with anti-miR-221 and -222 rendered CALU-1-resistant cells sensitive to TRAIL. Conversely, H460-sensitive cells treated with -221 and -222 pre-miRs become resistant to TRAIL. miR-221 and -222 target the 3′-UTR of Kit and p27kip1 mRNAs, but interfere with TRAIL signaling mainly through p27kip1. In conclusion, we show that high expression levels of miR-221 and -222 are needed to maintain the TRAIL-resistant phenotype, thus making these miRs as promising therapeutic targets or diagnostic tool for TRAIL resistance in NSCLC. | [M Garofalo, C Quintavalle, G Di Leva, C Zanca, G Romano, C Taccioli, C G Liu, C M Croce, G Condorelli] | Oncogene | 2008-02-04 | 7.2 |
| naturepublishinggroup10.1038/emboj.2008.13 | p73 poses a barrier to malignant transformation by limiting anchorage-independent growth | p53 is known to prevent tumour formation by restricting the proliferation of damaged or oncogene-expressing cells. In contrast, how the p53 family member p73 suppresses tumour formation remains elusive. Using a step-wise transformation protocol for human cells, we show that, in premalignant stages, expression of the transactivation-competent p73 isoform TAp73 is triggered in response to pRB pathway alterations. TAp73 expression at this stage of transformation results in increased sensitivity to chemotherapeutic drugs and oxidative stress and inhibits proliferation and survival at high cell density. Importantly, TAp73 triggers a transcriptional programme to prevent anchorage-independent growth, which is considered a crucial hallmark of fully transformed cells. An essential suppressor of anchorage-independent growth is KCNK1, which is directly transactivated by TAp73 and commonly downregulated in glioma, melanoma and ovarian cancer. Oncogenic Ras switches p73 expression from TAp73 to the oncogenic Np73 isoform in a phosphatidyl-inositol 3-kinase-dependent manner. Our results implicate TAp73 as a barrier to anchorage-independent growth and indicate that downregulation of TAp73 is a key transforming activity of oncogenic Ras mutants. | [Michaela Beitzinger, Lars Hofmann, Claudia Oswald, Rasa Beinoraviciute-Kellner, Markus Sauer, Heidi Griesmann, Anne Catherine Bretz, Christof Burek, Andreas Rosenwald, Thorsten Stiewe] | The EMBO Journal | 2008-01-31 | |
| naturepublishinggroup10.1038/oby.2007.76 | Islet-1: A Potentially Important Role for an Islet Cell Gene in Visceral Fat | | [Haiyan Li, Leonie K. Heilbronn, Dachun Hu, Ann M. Poynten, Miriam A. Blackburn, Deepali P. Shirkhedkar, Warren H. Kaplan, Adamandia D. Kriketos, Jiming Ye, Donald J. Chisholm] | Obesity | 2008-02-01 | |
| naturepublishinggroup10.1038/sj.jid.5701243 | Superficial, Nodular, and Morpheiform Basal-Cell Carcinomas Exhibit Distinct Gene Expression Profiles | Basal-cell carcinoma (BCC), the most common neoplasm in humans, occurs in a variety of morphological presentations. The mechanisms of BCC development downstream of the initial genetic mutations are not well understood, and different BCC morphological presentations might exhibit distinct gene expression patterns. We investigated superficial (n=8), nodular (n=8), and morpheiform (n=7) BCCs using 21K cDNA microarrays. Global gene expression profiles between respective BCC subtypes, and as compared with normal skin (n=8), were statistically defined by significance analysis of microarrays (SAM). Thirty-seven genes were subsequently validated by quantitative reverse transcriptase-PCR analysis using an expanded set of 31 BCCs. Gene ontology analysis indicated that gene expression patterns of BCC subtypes in multiple biological processes showed significant variation, particularly in genes associated with the mitogen-activated protein kinase (MAPK) pathway. Notably, genes involved in response to DNA-damage stimulus were uniquely upregulated in morpheiform BCCs. Our results indicate a relative similarity in gene expression between nodular and superficial BCC subtypes. In contrast, morpheiform BCCs are more diverse, with gene expression patterns consistent with their more “invasive” phenotype. These data may help us understand the complex behavior of BCC subtypes and may eventually lead to new therapeutic strategies. | [Mei Yu, David Zloty, Bryce Cowan, Jerry Shapiro, Anne Haegert, Robert H Bell, Larry Warshawski, Nicholas Carr, Kevin J McElwee] | Journal of Investigative Dermatology | 2008-01-17 | 7.2 |
| naturepublishinggroup10.1038/nm1699 | Endothelin B receptor mediates the endothelial barrier to T cell homing to tumors and disables immune therapy | In spite of their having sufficient immunogenicity, tumor vaccines remain largely ineffective. The mechanisms underlying this lack of efficacy are still unclear. Here we report a previously undescribed mechanism by which the tumor endothelium prevents T cell homing and hinders tumor immunotherapy. Transcriptional profiling of microdissected tumor endothelial cells from human ovarian cancers revealed genes associated with the absence or presence of tumor-infiltrating lymphocytes (TILs). Overexpression of the endothelin B receptor (ETBR) was associated with the absence of TILs and short patient survival time. The ETBR inhibitor BQ-788 increased T cell adhesion to human endothelium in vitro, an effect countered by intercellular adhesion molecule-1 (ICAM-1) blockade or treatment with NO donors. In mice, ETBR neutralization by BQ-788 increased T cell homing to tumors; this homing required ICAM-1 and enabled tumor response to otherwise ineffective immunotherapy in vivo without changes in systemic antitumor immune response. These findings highlight a molecular mechanism with the potential to be pharmacologically manipulated to enhance the efficacy of tumor immunotherapy in humans. | [Ronald J Buckanovich, Andrea Facciabene, Sarah Kim, Fabian Benencia, Dimitra Sasaroli, Klara Balint, Dionysios Katsaros, Anne O'Brien-Jenkins, Phyllis A Gimotty, George Coukos] | Nature Medicine | 2008-01-06 | |
| naturepublishinggroup10.1038/nature06534 | Reprogramming of human somatic cells to pluripotency with defined factors | Pluripotency pertains to the cells of early embryos that can generate all of the tissues in the organism. Embryonic stem cells are embryo-derived cell lines that retain pluripotency and represent invaluable tools for research into the mechanisms of tissue formation. Recently, murine fibroblasts have been reprogrammed directly to pluripotency by ectopic expression of four transcription factors (Oct4, Sox2, Klf4 and Myc) to yield induced pluripotent stem (iPS) cells. Using these same factors, we have derived iPS cells from fetal, neonatal and adult human primary cells, including dermal fibroblasts isolated from a skin biopsy of a healthy research subject. Human iPS cells resemble embryonic stem cells in morphology and gene expression and in the capacity to form teratomas in immune-deficient mice. These data demonstrate that defined factors can reprogramme human cells to pluripotency, and establish a method whereby patient-specific cells might be established in culture. | [In-Hyun Park, Rui Zhao, Jason A. West, Akiko Yabuuchi, Hongguang Huo, Tan A. Ince, Paul H. Lerou, M. William Lensch, George Q. Daley] | Nature | 2007-12-23 | |
| naturepublishinggroup10.1038/nm1669 | Antidepressant actions of the exercise-regulated gene VGF | Exercise has many health benefits, including antidepressant actions in depressed human subjects, but the mechanisms underlying these effects have not been elucidated. We used a custom microarray to identify a previously undescribed profile of exercise-regulated genes in the mouse hippocampus, a brain region implicated in mood and antidepressant response. Pathway analysis of the regulated genes shows that exercise upregulates a neurotrophic factor signaling cascade that has been implicated in the actions of antidepressants. One of the most highly regulated target genes of exercise and of the growth factor pathway is the gene encoding the VGF nerve growth factor, a peptide precursor previously shown to influence synaptic plasticity and metabolism. We show that administration of a synthetic VGF-derived peptide produces a robust antidepressant response in mice and, conversely, that mutation of VGF in mice produces the opposite effects. The results suggest a new role for VGF and identify VGF signaling as a potential therapeutic target for antidepressant drug development. | [Joshua G Hunsberger, Samuel S Newton, Alicia H Bennett, Catharine H Duman, David S Russell, Stephen R Salton, Ronald S Duman] | Nature Medicine | 2007-12-02 | 5.0 |
| naturepublishinggroup10.1038/sj.jid.5701149 | Gene Profiling of Keloid Fibroblasts Shows Altered Expression in Multiple Fibrosis-Associated Pathways | Keloids are benign tumors of the dermis that form during a protracted wound healing process. Susceptibility to keloid formation occurs predominantly in people of African and Asian descent. The key alteration(s) responsible for keloid formation has not been identified and there is no satisfactory treatment for this disorder. The altered regulatory mechanism is limited to dermal wound healing, although several diseases characterized by an exaggerated response to injury are prevalent in individuals of African ancestry. We have observed a complex pattern of phenotypic differences in keloid fibroblasts grown in standard culture medium or induced by hydrocortisone (HC). In this study Affymetrix-based microarray was performed on RNA obtained from fibroblasts cultured from normal scars and keloids grown in the absence and presence of HC. We observed differential regulation of approximately 500 genes of the 38,000 represented on the Affymetrix chip. Of particular interest was increased expression of several IGF-binding and IGF-binding-related proteins and decreased expression of a subset of Wnt pathway inhibitors and multiple IL-1-inducible genes. Increased expression of connective tissue growth factor and insulin-like growth factor binding protein-3 was observed in keloid fibroblasts only in the presence of HC. These findings support a role for multiple fibrosis-related pathways in the pathogenesis of keloids. | [Joan C Smith, Braden E Boone, Susan R Opalenik, Scott M Williams, Shirley B Russell] | Journal of Investigative Dermatology | 2007-11-08 | |
| naturepublishinggroup10.1038/sj.clpt.6100376 | Microarray Analysis of the Global Alterations in the Gene Expression in the Placentas From Cigarette-smoking Mothers | The effects of maternal cigarette smoking on the transcriptome of human full-term placentas were investigated by a microarray analysis. QPCR was performed for a selected set of metabolizing genes. Differentially expressed genes were selected by fold change (1.5-fold) and analysis of variance (P<0.05) between the control and smoker groups. The expression of 174 probe sets was affected significantly. Chronic cigarette smoking induced the expression of CYP1A1. A trend toward a decrease in the expression of several steroid hormone-metabolizing enzymes, including CYP19A1, was detected. The expression of phase II enzymes was not altered, and no enriched categories were observed among the regulated genes, except for aryl hydrocarbon receptor (AhR)-CYP1A1. The unaltered expression of phase II enzymes may result in an increase in the levels of active metabolites and elevated oxidative chemical stress in the placenta and the fetus. On the basis of our results, it seems that cigarette smoke acts as a hormone disrupter in the placenta. | [P Huuskonen, M Storvik, M Reinisalo, P Honkakoski, J Rys|[auml]|, J Hakkola, M Pasanen] | Clinical Pharmacology & Therapeutics | 2007-10-27 | |
| naturepublishinggroup10.1038/sj.onc.1210858 | Breast cancer metastases are molecularly distinct from their primary tumors | Metastases have been widely thought to arise from rare, selected, mutation-bearing cells in the primary tumor. Recently, however, it has been proposed that breast tumors are imprinted ab initio with metastatic ability. Thus, there is a debate over whether ‘phenotypic’ disease progression is really associated with ‘molecular’ progression. We profiled 26 matched primary breast tumors and lymph node metastases and identified 270 probesets that could discriminate between the two categories. We then used an independent cohort of breast tumors (81 samples) and unmatched distant metastases (32 samples) to validate and refine this list down to a 126-probeset list. A representative subset of these genes was subjected to analysis by in situ hybridization, on a third independent cohort (57 primary breast tumors and matched lymph node metastases). This not only confirmed the expression profile data, but also allowed us to establish the cellular origin of the signals. One-third of the analysed representative genes (4 of 11) were expressed by the epithelial component. The four epithelial genes alone were able to discriminate primary breast tumors from their metastases. Finally, engineered alterations in the expression of two of the epithelial genes (SERPINB5 and LTF) modified cell motility in vitro, in accordance with a possible causal role in metastasis. Our results show that breast cancer metastases are molecularly distinct from their primary tumors. | [M Vecchi, S Confalonieri, P Nuciforo, M A Vigan|[ograve]|, M Capra, M Bianchi, D Nicosia, F Bianchi, V Galimberti, G Viale, G Palermo, A Riccardi, R Campanini, M G Daidone, M A Pierotti, S Pece, P P Di Fiore] | Oncogene | 2007-10-22 | |
| naturepublishinggroup10.1038/nbt1350 | Chemotherapy-resistant human AML stem cells home to and engraft within the bone-marrow endosteal region | Acute myelogenous leukemia (AML) is the most common adult leukemia, characterized by the clonal expansion of immature myeloblasts initiating from rare leukemic stem (LS) cells1, 2, 3. To understand the functional properties of human LS cells, we developed a primary human AML xenotransplantation model using newborn nonobese diabetic/severe combined immunodeficient/interleukin (NOD/SCID/IL)2rnull mice carrying a complete null mutation of the cytokine c upon the SCID background4. Using this model, we demonstrated that LS cells exclusively recapitulate AML and retain self-renewal capacity in vivo. They home to and engraft within the osteoblast-rich area of the bone marrow, where AML cells are protected from chemotherapy-induced apoptosis. Quiescence of human LS cells may be a mechanism underlying resistance to cell cycle–dependent cytotoxic therapy. Global transcriptional profiling identified LS cell–specific transcripts that are stable through serial transplantation. These results indicate the potential utility of this AML xenograft model in the development of novel therapeutic strategies targeted at LS cells. | [Fumihiko Ishikawa, Shuro Yoshida, Yoriko Saito, Atsushi Hijikata, Hiroshi Kitamura, Satoshi Tanaka, Ryu Nakamura, Toru Tanaka, Hiroko Tomiyama, Noriyuki Saito, Mitsuhiro Fukata, Toshihiro Miyamoto, Bonnie Lyons, Koichi Ohshima, Naoyuki Uchida, Shuichi Taniguchi, Osamu Ohara, Koichi Akashi, Mine Harada, Leonard D Shultz] | Nature Biotechnology | 2007-10-21 | |
| naturepublishinggroup10.1038/sj.cdd.4402227 | Serum|[sol]|glucocorticoid-induced protein kinase-1 facilitates androgen receptor-dependent cell survival | Androgen receptor (AR) is a critical factor in the development and progression of prostate cancer. We and others recently demonstrated that eliminating AR expression leads to apoptotic cell death in AR-positive prostate cancer cells. To understand the mechanisms of AR-dependent survival, we performed a genome-wide search for AR-regulated survival genes. We found that serum/glucocorticoid-induced protein kinase-1 (SGK-1) mRNA levels were significantly upregulated after androgen stimulation, which was confirmed to be AR dependent. Promoter analysis revealed that the AR interacted with the proximal and distal regions of the sgk1 promoter, leading to sgk-1 promoter activation after androgen stimulation. Functional assays demonstrated that SGK-1 was indispensable for the protective effect of androgens on cell death induced by serum starvation. SGK-1 overexpression not only rescued cells from AR small-interfering RNA (siRNA)-induced apoptosis, but also enhanced AR transactivation, even in the absence of androgen. Additionally, SGK-1 siRNA reduced AR transactivation, indicating a positive feedback effect of SGK-1 expression on AR-mediated gene expression and cellular survival. Taken together, our data suggest that SGK-1 is an androgen-regulated gene that plays a pivotal role in AR-dependent survival and gene expression. | [I Shanmugam, G Cheng, P F Terranova, J B Thrasher, C P Thomas, B Li] | Cell Death & Differentiation | 2007-10-12 | |
| naturepublishinggroup10.1038/sj.emboj.7601876 | Critical roles for a genetic code alteration in the evolution of the genus Candida | During the last 30 years, several alterations to the standard genetic code have been discovered in various bacterial and eukaryotic species. Sense and nonsense codons have been reassigned or reprogrammed to expand the genetic code to selenocysteine and pyrrolysine. These discoveries highlight unexpected flexibility in the genetic code, but do not elucidate how the organisms survived the proteome chaos generated by codon identity redefinition. In order to shed new light on this question, we have reconstructed a Candida genetic code alteration in Saccharomyces cerevisiae and used a combination of DNA microarrays, proteomics and genetics approaches to evaluate its impact on gene expression, adaptation and sexual reproduction. This genetic manipulation blocked mating, locked yeast in a diploid state, remodelled gene expression and created stress cross-protection that generated adaptive advantages under environmental challenging conditions. This study highlights unanticipated roles for codon identity redefinition during the evolution of the genus Candida, and strongly suggests that genetic code alterations create genetic barriers that speed up speciation. | [Raquel M Silva, Jo|[atilde]|o A Paredes, Gabriela R Moura, Bruno Manadas, Tatiana Lima-Costa, Rita Rocha, Isabel Miranda, Ana C Gomes, Marian JG Koerkamp, Michel Perrot, Frank CP Holstege, H|[eacute]|lian Boucherie, Manuel A S Santos] | The EMBO Journal | 2007-10-11 | |
| naturepublishinggroup10.1038/sj.leu.2404961 | Transcriptional dysregulation mediated by RUNX1-RUNX1T1 in normal human progenitor cells and in acute myeloid leukaemia | The t(8;21)(q22;q22) occurs frequently in acute myelogenous leukaemia and gives rise to the transcription factor fusion protein, RUNX1-RUNX1T1 (also known as AML1-ETO). To identify the genes dysregulated by the aberrant transcriptional activity of RUNX1-RUNX1T1, we used microarrays to determine the effect of this mutation on gene expression in human progenitor cells and during subsequent development. Gene signatures of these developmental subsets were very dissimilar indicating that effects of RUNX1-RUNX1T1 are highly context dependent. We focused on gene changes associated with the granulocytic lineage and identified a clinically relevant subset of these by comparison with 235 leukaemia patient transcriptional signatures. We confirmed the overexpression of a number of significant genes (Sox4, IL-17BR, CD200 and -catenin). Further, we show that overexpression of CD200 and -catenin is also associated with the inv(16) abnormality which like RUNX1-RUNX1T1 disrupts core binding factor activity. We investigated the functional significance of CD200 and -catenin overexpression in normal human progenitor cells. The effect of IL17 on growth was also assessed. Individually, none of these changes were sufficient to recapitulate the effects of RUNX1-RUNX1T1 on normal development. These data provide the most comprehensive and pertinent assessment of the effect of RUNX1-RUNX1T1 on gene expression and demonstrate the highly context-dependent effects of this fusion gene. | [A Tonks, L Pearn, M Musson, A Gilkes, K I Mills, A K Burnett, R L Darley] | Leukemia | 2007-09-27 | 7.3 |
| naturepublishinggroup10.1038/sj.jid.5701068 | SERPINE1 (PAI-1) Is a Prominent Member of the Early G0 |[rarr]| G1 Transition |[ldquo]|Wound Repair|[rdquo]| Transcriptome in p53 Mutant Human Keratinocytes | | [Li Qi, Stephen P Higgins, Qi Lu, Rohan Samarakoon, Cynthia E Wilkins-Port, Qunhui Ye, Craig E Higgins, Lisa Staiano-Coico, Paul J Higgins] | Journal of Investigative Dermatology | 2007-09-20 | |
| naturepublishinggroup10.1038/sj.onc.1210767 | Sonic Hedgehog regulates Hes1 through a novel mechanism that is independent of canonical Notch pathway signalling | Aberrant regulation of signalling mechanisms that normally orchestrate embryonic development, such as the Hedgehog, Wnt and Notch pathways, is a common feature of tumorigenesis. In order to better understand the neoplastic events mediated by Hedgehog signalling, we identified over 200 genes regulated by Sonic Hedgehog in multipotent mesodermal cells. Widespread crosstalk with other developmental signalling pathways is evident, suggesting a complex network of interactions that challenges the often over-simplistic representation of these pathways as simple linear entities. Hes1, a principal effector of the Notch pathway, was found to be a target of Sonic Hedgehog in both C3H/10T1/2 mesodermal and MNS70 neural cells. Desert Hedgehog also elicited a strong Hes1 response. While Smoothened function was found necessary for upregulation of Hes1 in response to Sonic Hedgehog, the mechanism does not require γ-secretase-mediated cleavage of Notch receptors, and appears to involve transcription factors other than RBP-Jκ. Thus, we have defined a novel mechanism for Hes1 regulation in stem-like cells that is independent of canonical Notch signalling. | [W J Ingram, K I McCue, T H Tran, A R Hallahan, B J Wainwright] | Oncogene | 2007-09-17 | |
| naturepublishinggroup10.1038/sj.onc.1210800 | JAK kinases overexpression promotes in vitro cell transformation | Constitutive activation of the JAK-STAT pathway is frequent in cancer and contributes to oncogenesis. Here, we took advantage of the Ba/F3 cell line, a murine proB cell line dependent on IL-3 for growth, to analyse mechanisms of constitutive STAT activation in vitro. Cytokine-independent and tumorigenic Ba/F3 cell lines were derived from a two-step selection process. Cells transfected with a defective IL-9 receptor acquire IL-9 responsiveness during a first step of selection, and progress after a second selection step to autonomously growing tumorigenic cells. Microarray analysis pointed to JAK1 overexpression as a key genetic event in this transformation. Overexpression of JAK1 not only increased the sensitivity to IL-9 but also allowed a second selection step toward cytokine-independent growth with constitutive STAT activation. This progression was dependent on a functional FERM and kinase JAK1 domain. Similar results were observed after JAK2, JAK3 and TYK2 overexpression. All autonomous cell lines showed an activation of STAT5, ERK1–2 and AKT but only TYK2-overexpressing cell lines showed a constitutive activation of STAT3. Thus, JAK overexpression can be considered as one of the oncogenic events leading to the constitutive activation of the JAK-STAT pathway. | [L Knoops, T Hornakova, Y Royer, S N Constantinescu, J-C Renauld] | Oncogene | 2007-09-17 | |
| naturepublishinggroup10.1038/ni1511 | Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17|[ndash]|producing T cell responses | The intestinal immune system must elicit robust immunity against harmful pathogens but must also restrain immune responses directed against commensal microbes and dietary antigens. The mechanisms that maintain this dichotomy are poorly understood. Here we describe a population of CD11b+F4/80+CD11c- macrophages in the lamina propria that expressed several anti-inflammatory molecules, including interleukin 10 (IL-10), but little or no proinflammatory cytokines, even after stimulation with Toll-like receptor ligands. These macrophages induced, by a mechanism dependent on IL-10, retinoic acid and exogenous transforming growth factor-, the differentiation of Foxp3+ regulatory T cells. In contrast, lamina propria CD11b+ dendritic cells elicited IL-17 production. This IL-17 production was suppressed by lamina propria macrophages, indicating that a dynamic interaction between these subsets may influence the balance between immune activation and tolerance. | [Timothy L Denning, Yi-chong Wang, Seema R Patel, Ifor R Williams, Bali Pulendran] | Nature Immunology | 2007-09-16 | |
| naturepublishinggroup10.1038/sj.leu.2404934 | Translocation t(4;14) retains prognostic significance even in the setting of high-risk molecular signature | | [W J Chng, W M Kuehl, P L Bergsagel, R Fonseca] | Leukemia | 2007-09-06 | |
| naturepublishinggroup10.1038/sj.pcan.4501007 | Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens | Formalin-fixed paraffin-embedded (FFPE) prostate specimens are rich sources of molecular pathological information. However, FFPE-based microarray analysis of tissue samples may be hampered by the degradation and chemical alteration of RNA molecules due to the preservation procedure. In this report, we employed a probe analyses of Affymetrix oligonucleotide arrays at individual probe level to compensate for the potential loss of gene identifications associated with compromised mRNA quality in FFPE preparations. Furthermore, to increase the sample quality, we utilized laser capture microdissection of prostate tumor and benign epithelial cells. Remarkably, combination of these approaches recapitulated the common prostate cancer-associated gene expression alteration. Identification of prostate cancer associated-gene expression alterations such as AMACR, Kallikrein gene family and genes associated with androgen signaling such as PDEF and STEAP were consistent with previous findings reported in prostate cancer. These data suggest that combination of laser capture dissection with computational enhancement of microarray data may be useful for the assessment of gene expression changes in FFPE prostate cancer specimens. | [B Furusato, S Shaheduzzaman, G Petrovics, A Dobi, M Seifert, L Ravindranath, M E Nau, T Werner, M Vahey, D G McLeod, S Srivastava, I A Sesterhenn] | Prostate Cancer and Prostatic Diseases | 2007-09-04 | |
| naturepublishinggroup10.1038/nature06055 | Tip60 is a haplo-insufficient tumour suppressor required for an oncogene-induced DNA damage response | The acetyl-transferase Tip60 might influence tumorigenesis in multiple ways1. First, Tip60 is a co-regulator of transcription factors that either promote or suppress tumorigenesis, such as Myc and p532, 3, 4. Second, Tip60 modulates DNA-damage response (DDR) signalling1, and a DDR triggered by oncogenes can counteract tumour progression5, 6. Using E–myc transgenic mice that are heterozygous for a Tip60 gene (Htatip) knockout allele (hereafter denoted as Tip60+/– mice), we show that Tip60 counteracts Myc-induced lymphomagenesis in a haplo-insufficient manner and in a time window that is restricted to a pre- or early-tumoral stage. Tip60 heterozygosity severely impaired the Myc-induced DDR7, 8, 9 but caused no general DDR defect in B cells. Myc- and p53-dependent transcription were not affected, and neither were Myc-induced proliferation, activation of the ARF–p53 tumour suppressor pathway or the resulting apoptotic response10, 11, 12, 13. We found that the human TIP60 gene (HTATIP) is a frequent target for mono-allelic loss in human lymphomas and head-and-neck and mammary carcinomas, with concomitant reduction in mRNA levels. Immunohistochemical analysis also demonstrated loss of nuclear TIP60 staining in mammary carcinomas. These events correlated with disease grade and frequently concurred with mutation of p53. Thus, in both mouse and human, Tip60 has a haplo-insufficient tumour suppressor activity that is independent from—but not contradictory with—its role within the ARF–p53 pathway1, 2, 3, 14, 15, 16. We suggest that this is because critical levels of Tip60 are required for mounting an oncogene-induced DDR in incipient tumour cells5, 6, the failure of which might synergize with p53 mutation towards tumour progression17, 18, 19, 20. | [Chiara Gorrini, Massimo Squatrito, Chiara Luise, Nelofer Syed, Daniele Perna, Landon Wark, Francesca Martinato, Domenico Sardella, Alessandro Verrecchia, Samantha Bennett, Stefano Confalonieri, Matteo Cesaroni, Francesco Marchesi, Milena Gasco, Eugenio Scanziani, Maria Capra, Sabine Mai, Paolo Nuciforo, Tim Crook, John Lough, Bruno Amati] | Nature | 2007-08-30 | |
| naturepublishinggroup10.1038/sj.bjc.6603948 | Network-based analysis of calcium-binding protein genes identifies Grp94 as a target in human oral carcinogenesis | To characterise Ca2+-binding protein gene expression changes in oral squamous cell carcinomas (OSCCs), we compared the gene expression profiles in OSCC-derived cell lines with normal oral tissues. One hundred Ca2+-binding protein genes differentially expressed in OSCCs were identified, and genetic pathways associated with expression changes were generated. Among genes mapped to the network with the highest significance, glucose-regulated protein 94 kDa (Grp94) was evaluated further for mRNA and protein expression in the OSCC cell lines, primary OSCCs, and oral premalignant lesions (OPLs). A significant (P<0.001) overexpression of Grp94 protein was observed in all cell lines compared to normal oral epithelium. Immunohistochemical analysis showed highly expressed Grp94 in primary OSCCs and OPLs, whereas most of the corresponding normal tissues had no protein immunoreaction. Real-time quantitative reverse transcriptase-PCR data agreed with the protein expression status. Moreover, overexpression of Grp94 in primary tumours was significantly (P<0.001) correlated with poor disease-free survival. The results suggested that Grp94 may have potential clinical application as a novel diagnosis and prognostic biomarker for human OSCCs. | [H Nomura, K Uzawa, Y Yamano, K Fushimi, T Ishigami, Y Kato, K Saito, D Nakashima, M Higo, Y Kouzu, K Ono, K Ogawara, M Shiiba, H Bukawa, H Yokoe, H Tanzawa] | British Journal of Cancer | 2007-08-28 | |
| naturepublishinggroup10.1038/nm1629 | High levels of GDF15 in thalassemia suppress expression of the iron regulatory protein hepcidin | In thalassemia, deficient globin-chain production during erythropoiesis results in anemia1, 2, 3. Thalassemia may be further complicated by iron overload (frequently exacerbated by blood transfusion), which induces numerous endocrine diseases, hepatic cirrhosis, cardiac failure and even death4. Accumulation of iron in the absence of blood transfusions may result from inappropriate suppression of the iron-regulating peptide hepcidin by an erythropoietic mechanism5. To test this hypothesis, we examined erythroblast transcriptome profiles from 15 healthy, nonthalassemic donors. Growth differentiation factor 15 (GDF15), a member of the transforming growth factor- superfamily, showed increased expression and secretion during erythroblast maturation. Healthy volunteers had mean GDF15 serum concentrations of 450 50 pg/ml. In comparison, individuals with -thalassemia syndromes had elevated GDF15 serum levels (mean 66,000 9,600 pg/ml; range 4,800–248,000 pg/ml; P < 0.05) that were positively correlated with the levels of soluble transferrin receptor, erythropoietin and ferritin. Serum from thalassemia patients suppressed hepcidin mRNA expression in primary human hepatocytes, and depletion of GDF15 reversed hepcidin suppression. These results suggest that GDF15 overexpression arising from an expanded erythroid compartment contributes to iron overload in thalassemia syndromes by inhibiting hepcidin expression. | [Toshihiko Tanno, Natarajan V Bhanu, Patricia A Oneal, Sung-Ho Goh, Pamela Staker, Y Terry Lee, John W Moroney, Christopher H Reed, Naomi LC Luban, Rui-Hong Wang, Thomas E Eling, Richard Childs, Tomas Ganz, Susan F Leitman, Suthat Fucharoen, Jeffery L Miller] | Nature Medicine | 2007-08-26 | |
| naturepublishinggroup10.1038/nbt1331 | High-frequency generation of viable mice from engineered bi-maternal embryos | Mammalian development to adulthood typically requires both maternal and paternal genomes, because genomic imprinting places stringent limitations on mammalian development, strictly precluding parthenogenesis1, 2. Here we report the generation of bi-maternal embryos that develop at a high success rate equivalent to the rate obtained with in vitro fertilization of normal embryos. These bi-maternal mice developed into viable and fertile female adults. The bi-maternal embryos, distinct from parthenogenetic or gynogenetic conceptuses, were produced by the construction of oocytes from fully grown oocytes and nongrowing oocytes that contain double deletions in the H19 differentially methylated region (DMR) and the Dlk1-Dio3 intergenic germline–derived DMR. The results provide conclusive evidence that imprinted genes regulated by these two paternally methylated imprinting-control regions are the only paternal barrier that prevents the normal development of bi-maternal mouse fetuses to term. | [Manabu Kawahara, Qiong Wu, Nozomi Takahashi, Shinnosuke Morita, Kaori Yamada, Mitsuteru Ito, Anne C Ferguson-Smith, Tomohiro Kono] | Nature Biotechnology | 2007-08-19 | |
| naturepublishinggroup10.1038/sj.bjc.6603906 | NF-|[kappa]|B activation in inflammatory breast cancer is associated with oestrogen receptor downregulation, secondary to EGFR and|[sol]|or ErbB2 overexpression and MAPK hyperactivation | Activation of NF-B in inflammatory breast cancer (IBC) is associated with loss of estrogen receptor (ER) expression, indicating a potential crosstalk between NF-B and ER. In this study, we examined the activation of NF-B in IBC and non-IBC with respect to ER and EGFR and/or ErbB2 expression and MAPK hyperactivation. A qRT–PCR based ER signature was evaluated in tumours with and without transcriptionally active NF-B, as well as correlated with the expression of eight NF-B target genes. Using a combined ER/NF-B signature, hierarchical clustering was executed. Hyperactivation of MAPK was investigated using a recently described MAPK signature (Creighton et al, 2006), and was linked to tumour phenotype, ER and EGFR and/or ErbB2 overexpression. The expression of most ER-modulated genes was significantly elevated in breast tumours without transcriptionally active NF-B. In addition, the expression of most ER-modulated genes was significantly anticorrelated with the expression of most NF-B target genes, indicating an inverse correlation between ER and NF-B activation. Clustering using the combined ER and NF-B signature revealed one cluster mainly characterised by low NF-B target gene expression and a second one with elevated NF-B target gene expression. The first cluster was mainly characterised by non-IBC specimens and IHC ER+ breast tumours (13 out of 18 and 15 out of 18 respectively), whereas the second cluster was mainly characterised by IBC specimens and IHC ER- breast tumours (12 out of 19 and 15 out of 19 respectively) (Pearson 2, P<0.0001 and P<0.0001 respectively). Hyperactivation of MAPK was associated with both ER status and tumour phenotype by unsupervised hierarchical clustering using the MAPK signature and was significantly reflected by overexpression of EGFR and/or ErbB2. NF-B activation is linked to loss of ER expression and activation in IBC and in breast cancer in general. The inverse correlation between NF-B activation and ER activation is due to EGFR and/or ErbB2 overexpression, resulting in NF-B activation and ER downregulation. | [S J Van Laere, I Van der Auwera, G G Van den Eynden, P van Dam, E A Van Marck, P B Vermeulen, L Y Dirix] | British Journal of Cancer | 2007-08-14 | |
| naturepublishinggroup10.1038/sj.pcan.4500997 | Differential gene expression in the peripheral zone compared to the transition zone of the human prostate gland | Gene expression profiles may lend insight into whether prostate adenocarcinoma (CaP) predominantly occurs in the peripheral zone (PZ) compared to the transition zone (TZ). From human prostates, tissue sets consisting of PZ and TZ were isolated to investigate whether there is a differential level of gene expression between these two regions of this gland. Gene expression profiling using Affymetrix Human Genome U133 plus 2.0 arrays coupled with quantitative real-time reverse transcriptase-PCR was employed. Genes associated with neurogenesis, signal transduction, embryo implantation and cell adhesion were found to be expressed at a higher level in the PZ. Those overexpressed in the TZ were associated with neurogenesis development, signal transduction, cell motility and development. Whether such differential gene expression profiles may identify molecular mechanisms responsible for susceptibility to CaP remains to be ascertained. | [E E Noel, N Ragavan, M J Walsh, S Y James, S S Matanhelia, C M Nicholson, Y-J Lu, F L Martin] | Prostate Cancer and Prostatic Diseases | 2007-07-24 | |
| naturepublishinggroup10.1038/sj.onc.1210648 | Epigenetic regulation of microRNA-370 by interleukin-6 in malignant human cholangiocytes | Interleukin-6 (IL-6) is overexpressed and contributes to tumor cell growth in cholangiocarcinoma. Enforced IL-6 production can alter the expression of specific microRNAs (miRNAs) involved in tumor growth, and moreover can modulate expression of methylation-dependent genes. Thus, we assessed the methylation-dependent regulation of miRNA expression in human malignant cholangiocytes stably transfected to overexpress IL-6. The expression of the methyltransferases DNA methyltransferase enzyme-1 and HASJ4442 was increased by IL-6 overexpression, but was decreased by the methylation inhibitor 5-aza-2′-deoxycytidine (5-aza-CdR). Expression profiling identified seven miRNAs that were significantly downregulated by IL-6 overexpression (<0.4-fold) and upregulated (>2-fold) by 5-aza-CdR. One of these, miR-370, is embedded in a CpG island. Although 5-aza-CdR increased miR-370 expression by 2.1-fold in malignant cells, the expression in nonmalignant cells was unchanged. The oncogene mitogen-activated protein kinase kinase kinase 8 (MAP3K8) was identified as a target of miR-370, and its expression was decreased by 5-aza-CdR in cholangiocarcinoma cells. Overexpression of IL-6 reduced miR-370 expression and reinstated MAP3K8 expression in vitro as well as in tumor cell xenografts in vivo. Thus, IL-6 may contribute to tumor growth by modulation of expression of selected miRNAs, such as miR-370. These studies define a mechanism by which inflammation-associated cytokines can epigenetically modulate gene expression and directly contribute to tumor biology. | [F Meng, H Wehbe-Janek, R Henson, H Smith, T Patel] | Oncogene | 2007-07-09 | |
| naturepublishinggroup10.1038/ng2072 | Loss of GLIS2 causes nephronophthisis in humans and mice by increased apoptosis and fibrosis | Nephronophthisis (NPHP), an autosomal recessive kidney disease, is the most frequent genetic cause of end-stage renal failure in the first three decades of life. Positional cloning of the six known NPHP genes1, 2, 3, 4 has linked its pathogenesis to primary cilia function3, 5. Here we identify mutation of GLIS2 as causing an NPHP-like phenotype in humans and mice, using positional cloning and mouse transgenics, respectively. Kidneys of Glis2 mutant mice show severe renal atrophy and fibrosis starting at 8 weeks of age. Differential gene expression studies on Glis2 mutant kidneys demonstrate that genes promoting epithelial-to-mesenchymal transition and fibrosis are upregulated in the absence of Glis2. Thus, we identify Glis2 as a transcription factor mutated in NPHP and demonstrate its essential role for the maintenance of renal tissue architecture through prevention of apoptosis and fibrosis. | [Massimo Attanasio, N Henriette Uhlenhaut, Vitor H Sousa, John F O'Toole, Edgar Otto, Katrin Anlag, Claudia Klugmann, Anna-Corina Treier, Juliana Helou, John A Sayer, Dominik Seelow, Gudrun N|[uuml]|rnberg, Christian Becker, Albert E Chudley, Peter N|[uuml]|rnberg, Friedhelm Hildebrandt, Mathias Treier] | Nature Genetics | 2007-07-08 | |
| naturepublishinggroup10.1038/nature05972 | New cell lines from mouse epiblast share defining features with human embryonic stem cells | The application of human embryonic stem (ES) cells in medicine and biology has an inherent reliance on understanding the starting cell population. Human ES cells differ from mouse ES cells and the specific embryonic origin of both cell types is unclear. Previous work suggested that mouse ES cells could only be obtained from the embryo before implantation in the uterus1, 2, 3, 4, 5. Here we show that cell lines can be derived from the epiblast, a tissue of the post-implantation embryo that generates the embryo proper. These cells, which we refer to as EpiSCs (post-implantation epiblast-derived stem cells), express transcription factors known to regulate pluripotency, maintain their genomic integrity, and robustly differentiate into the major somatic cell types as well as primordial germ cells. The EpiSC lines are distinct from mouse ES cells in their epigenetic state and the signals controlling their differentiation. Furthermore, EpiSC and human ES cells share patterns of gene expression and signalling responses that normally function in the epiblast. These results show that epiblast cells can be maintained as stable cell lines and interrogated to understand how pluripotent cells generate distinct fates during early development. | [Paul J. Tesar, Josh G. Chenoweth, Frances A. Brook, Timothy J. Davies, Edward P. Evans, David L. Mack, Richard L. Gardner, Ronald D. G. McKay] | Nature | 2007-06-27 | |
| naturepublishinggroup10.1038/sj.ki.5002172 | Gene expression profiling in the remnant kidney model of wild type and kinin B1 and B2 receptor knockout mice | Angiotensin-converting enzyme inhibitors are the most efficient pharmacologic agents to delay the development of end-stage renal disease (ESRD). This is a multipharmacologic approach that inhibits angiotensin II formation while increasing kinin concentrations. Considerable attention has been focused on the role of decreased angiotensin II levels; however, the role of increased kinin levels is gaining in interest. Kinins affect cellular physiology by interacting with one of two receptors being the more inducible B1 and the more constitutive B2 receptors. This study utilizes the mouse remnant kidney of 20 weeks duration as a model of ESRD. Whole mouse genome microarrays were used to evaluate gene expression in the remnant kidneys of wild type, B1 and B2 receptor knockout animals. The microarray data indicate that gene families involved in vascular damage, inflammation, fibrosis, and proteinuria were upregulated, whereas gene families involved in cell growth, metabolism, lipid, and protein biosynthesis were downregulated in the remnant kidneys. Interestingly, the microarray analyses coupled to histological evaluations are suggestive of a possible protective role of kinins operating through the B2 receptor subtype in this model of renal disease. The results highlight the potential of microarray technology for unraveling complex mechanisms contributing to chronic renal failure. | [J P Schanstra, M Bachvarova, E Neau, J L Bascands, D Bachvarov] | Kidney International | 2007-06-20 | |
| naturepublishinggroup10.1038/sj.mt.6300215 | Targeted Inflammation During Oncolytic Virus Therapy Severely Compromises Tumor Blood Flow | Oncolytic viruses (OVs) are selected or designed to eliminate malignancies by direct infection and lysis of cancer cells. In contrast to this concept of direct tumor lysis by viral infection, we observed that a significant portion of the in vivo tumor killing activity of two OVs, vesicular stomatitis virus (VSV) and vaccinia virus is caused by indirect killing of uninfected tumor cells. Shortly after administering the oncolytic virus we observed limited virus infection, coincident with a loss of blood flow to the interior of the tumor that correlated with induction of apoptosis in tumor cells. Transcript profiling of tumors showed that virus infection resulted in a dramatic transcriptional activation of pro-inflammatory genes including the neutrophil chemoattractants CXCL1 and CXCL5. Immunohistochemical examination of infected tumors revealed infiltration by neutrophils correlating with chemokine induction. Depletion of neutrophils in animals prior to VSV administration eliminated uninfected tumor cell apoptosis and permitted more extensive replication and spreading of the virus throughout the tumor. Taken all together, these results indicate that targeted recruitment of neutrophils to infected tumor beds enhances the killing of malignant cells. We propose that activation of inflammatory cells can be used for enhancing the effectiveness of oncolytic virus therapeutics, and that this approach should influence the planning of therapeutic doses. | [Caroline J Breitbach, Jennifer M Paterson, Chantal G Lemay, Theresa J Falls, Allison McGuire, Kelley A Parato, David F Stojdl, Manijeh Daneshmand, Kelly Speth, David Kirn, J Andrea McCart, Harold Atkins, John C Bell] | Molecular Therapy | 2007-06-19 | |
| naturepublishinggroup10.1038/sj.icb.7100078 | Interleukin-1|[alpha]| regulates antimicrobial peptide expression in human keratinocytes | Human epidermis and epithelium serve as physiologic barriers to protect against noxious and infectious agents. Contributing to the defense against infection, epithelial cells express antimicrobial peptides (AMPs). The expression of AMPs in keratinocytes is generally regulated directly by bacteria and indirectly by proinflammatory cytokines. Bacteria may also regulate AMP expression by inducing keratinocyte expression of the autonomous proinflammatory cytokine, interleukin-1 (IL-1). To test the hypothesis that AMP expression may be regulated by cell autonomous cytokines, we investigated the effect of IL-1 on the expression of AMPs in human keratinocytes (HaCaT cells) by microarray, northern blot, reverse transcriptase (RT)–PCR and western blot analyses. IL-1 increased expression of mRNA in a dose- and time-dependent manner specific for lipocalin 2, S100A8, S100A9 and secretory leukocyte protease inhibitor (SLPI) more than twofold relative to nonstimulated cells (control), and slightly upregulated S100A7 and -defensin-2. Furthermore, the expression of lipocalin 2, S100A7, S100A8, S100A9 and SLPI proteins were upregulated by IL-1. On the other hand, HaCaT cells expressed mRNA specific for other AMPs, including cystatin 3, adrenomedullin, RNase-7 and mucin 5, which were unaffected by IL-1 treatment. These results suggest that the autonomous keratinocyte cytokine, IL-1, selectively upregulates the expression of AMPs which may modulate innate epithelial cell immunity in skin and mucosa. | [Mika Bando, Yuka Hiroshima, Masatoshi Kataoka, Yasuo Shinohara, Mark C Herzberg, Karen F Ross, Toshihiko Nagata, Jun-ichi Kido] | Immunology and Cell Biology | 2007-06-05 | |
| naturepublishinggroup10.1038/nature05836 | Gene-specific control of inflammation by TLR-induced chromatin modifications | Toll-like receptors (TLRs) induce a multi-component inflammatory response that must be tightly regulated to avoid tissue damage. Most known regulatory mechanisms target TLR signalling pathways and thus broadly inhibit multiple aspects of the inflammatory response. Given the functional diversity of TLR-induced genes, we proposed that additional, gene-specific regulatory mechanisms exist to allow individual aspects of the TLR-induced response to be differentially regulated. Using an in vitro system of lipopolysaccharide tolerance in murine macrophages, we show that TLR-induced genes fall into two categories on the basis of their functions and regulatory requirements. We demonstrate that representatives from the two classes acquire distinct patterns of TLR-induced chromatin modifications. These gene-specific chromatin modifications are associated with transient silencing of one class of genes, which includes pro-inflammatory mediators, and priming of the second class, which includes antimicrobial effectors. These findings illustrate an adaptive response in macrophages and reveal component-specific regulation of inflammation. | [Simmie L. Foster, Diana C. Hargreaves, Ruslan Medzhitov] | Nature | 2007-05-30 | |
| naturepublishinggroup10.1038/sj.onc.1210552 | Identification of candidate genes involved in neuroblastoma progression by combining genomic and expression microarrays with survival data | Identifying genes, whose expression is consistently altered by chromosomal gains or losses, is an important step in defining genes of biological relevance in a wide variety of tumour types. However, additional criteria are needed to discriminate further among the large number of candidate genes identified. This is particularly true for neuroblastoma, where multiple genomic copy number changes of proven prognostic value exist. We have used Affymetrix microarrays and a combination of fluorescent in situ hybridization and single nucleotide polymorphism (SNP) microarrays to establish expression profiles and delineate copy number alterations in 30 primary neuroblastomas. Correlation of microarray data with patient survival and analysis of expression within rodent neuroblastoma cell lines were then used to define further genes likely to be involved in the disease process. Using this approach, we identify >1000 genes within eight recurrent genomic alterations (loss of 1p, 3p, 4p, 10q and 11q, 2p gain, 17q gain, and the MYCN amplicon) whose expression is consistently altered by copy number change. Of these, 84 correlate with patient survival, with the minimal regions of 17q gain and 4p loss being enriched significantly for such genes. These include genes involved in RNA and DNA metabolism, and apoptosis. Orthologues of all but one of these genes on 17q are overexpressed in rodent neuroblastoma cell lines. A significant excess of SNPs whose copy number correlates with survival is also observed on proximal 4p in stage 4 tumours, and we find that deletion of 4p is associated with improved outcome in an extended cohort of tumours. These results define the major impact of genomic copy number alterations upon transcription within neuroblastoma, and highlight genes on distal 17q and proximal 4p for downstream analyses. They also suggest that integration of discriminators, such as survival and comparative gene expression, with microarray data may be useful in the identification of critical genes within regions of loss or gain in many human cancers. | [M |[Lstrok]|astowska, V Viprey, M Santibanez-Koref, I Wappler, H Peters, C Cullinane, P Roberts, A G Hall, D A Tweddle, A D J Pearson, I Lewis, S A Burchill, M S Jackson] | Oncogene | 2007-05-28 | |
| naturepublishinggroup10.1038/ni1472 | Lymphoid reservoirs of antigen-specific memory T helper cells | How vaccines control the development of antigen-specific effector and memory T helper cells is central to protective immunity but remains poorly understood. Here we found that protein vaccination selected high-affinity, CXCR5+ICOShi follicular B-helper T cells (TFH cells) that developed in draining lymphoid tissue to regulate B cell responses. In the memory phase, reservoirs of antigen-specific CXCR5+ICOSlo TFH cells persisted with less effector activity but accelerated antigen-recall ability. This new compartment of memory TFH cells was retained in draining lymphoid sites with antigen-specific memory B cells, persistent complexes of peptide and major histocompatibility complex class II and continued expression of CD69. Thus, protein vaccination promotes B cell immunity by selecting high-affinity effector TFH cells and creating lymphoid reservoirs of antigen-specific memory TFH cells in vivo. | [Nicolas Fazilleau, Michael D Eisenbraun, Laurent Malherbe, Jessica N Ebright, Rebecca R Pogue-Caley, Louise J McHeyzer-Williams, Michael G McHeyzer-Williams] | Nature Immunology | 2007-05-27 | |
| naturepublishinggroup10.1038/sj.onc.1210525 | Comparative expression profiling identifies an in vivo target gene signature with TFAP2B as a mediator of the survival function of PAX3|[sol]|FKHR | The chromosomal translocation t(2;13), characteristic for the aggressive childhood cancer alveolar rhabdomyosarcoma (aRMS), generates the chimeric transcription factor PAX3/FKHR with a well known oncogenic role. However, the molecular mechanisms mediating essential pathophysiological functions remain poorly defined. Here, we used comparative expression profiling of PAX3/FKHR silencing in vitro and PAX3/FKHR-specific gene signatures in vivo to identify physiologically important target genes. Hereby, 51 activated genes, both novel and known, were identified. We also found repression of skeletal muscle-specific genes suggesting that PAX3/FKHR blocks further differentiation of aRMS cells. Importantly, TFAP2B was validated as direct target gene mediating the anti-apoptotic function of PAX3/FKHR. Hence, we developed a pathophysiologically relevant transcriptional profile of PAX3/FKHR and identified a critical target gene for aRMS development. | [M Ebauer, M Wachtel, F K Niggli, B W Sch|[auml]|fer] | Oncogene | 2007-05-21 | |
| naturepublishinggroup10.1038/sj.mt.6300199 | Tissue-specific Aberrations of Gene Expression in HPRT-deficient Mice: Functional Complexity in a Monogenic Disease|[quest]| | We have used the hypoxanthine-guanine phosphoribosyltransferase (HPRT) enzyme-deficient mouse model of human Lesch-Nyhan disease (LND) to examine the tissue-specificity of altered global gene expression in a genetically "simple" monogenic human disease. We have identified a number of genes and gene families whose expression is aberrant in the mouse knockout model of the LND, and we have identified different patterns of aberrant gene expression in two principal target tissues associated with the disease phenotype, i.e., the central nervous system and the liver. The major neurological phenotype reflects dysfunction of the dopamine neurotransmitter system in the basal ganglia, and we have now identified aberrant expression of a small number of genes in HPRT-deficient striata. The abnormal metabolic phenotype of hyperuricemia in HPRT-deficient mice is also reflected in an aberrant gene expression in the liver. We interpret these findings to suggest that the genetic consequences of a primary HPRT knockout in the mouse produces transcriptional aberrations in a number of other genes that may play a role in the disease phenotype. Knowledge of these secondary genetic defects may help in the identification of targets for drug- and gene-based therapy. | [Shaochun Song, Theodore Friedmann] | Molecular Therapy | 2007-05-15 | |
| naturepublishinggroup10.1038/ni1470 | Activation of the lectin DC-SIGN induces an immature dendritic cell phenotype triggering Rho-GTPase activity required for HIV-1 replication | DC-SIGN, a C-type lectin expressed on dendritic cells (DCs), can sequester human immunodeficiency virus (HIV) virions in multivesicular bodies. Here, using large-scale gene expression profiling and tyrosine-phosphorylated proteome analyses, we characterized signaling mediated by DC-SIGN after activation by either HIV or a DC-SIGN-specific antibody. Activation of DC-SIGN resulted in downregulation of genes encoding major histocompatibility complex class II, Jagged 1 and interferon-response molecules and upregulation of the gene encoding transcription factor ATF3. Phosphorylated proteome analysis showed that HIV- or antibody-stimulated DC-SIGN signaling was mediated by the Rho guanine nucleotide–exchange factor LARG and led to increased Rho-GTPase activity. Activation of LARG in DCs exposed to HIV was required for the formation of virus–T cell synapses. Thus, HIV sequestration by and stimulation of DC-SIGN helps HIV evade immune responses and spread to cells. | [Ashleigh Hodges, Katherine Sharrocks, Mariola Edelmann, Dilair Baban, Arnaud Moris, Olivier Schwartz, Hal Drakesmith, Kay Davies, Benedikt Kessler, Andrew McMichael, Alison Simmons] | Nature Immunology | 2007-05-13 | |
| naturepublishinggroup10.1038/sj.onc.1210468 | ER|[alpha]||[ndash]|CITED1 co-regulated genes expressed during pubertal mammary gland development: implications for breast cancer prognosis | Expression microarray analysis identified over 930 genes regulated during puberty in the mouse mammary gland. Most prominent were genes whose expression increased in parallel with pubertal development and remained high thereafter. Members of the Wnt, transforming growth factor- and oestrogen-signalling pathways were significantly overrepresented. Comparison to expression data from CITED1 knockout mice identified a subset of oestrogen-responsive genes displaying altered expression in the absence of CITED1. Included in this subset are stanniocalcin2 (Stc2) and amphiregulin (Areg). Chromatin immunoprecipitation revealed that ER binds to oestrogen response elements in both the Stc2 and Areg genes in the mammary gland during puberty. Additionally, CITED1 and ER localize to the same epithelial cells of the pubertal mammary gland, supporting a role for interaction of these two proteins during normal development. In a human breast cancer data set, expression of Stc2, Areg and CITED1 parallel that of ER. Similar to ER, CITED1 expression correlates with good outcome in breast cancer, implying that potential maintenance of the ER–CITED1 co-regulated signalling pathway in breast tumours can indicate good prognosis. | [J McBryan, J Howlin, P A Kenny, T Shioda, F Martin] | Oncogene | 2007-05-07 | |
| naturepublishinggroup10.1038/modpathol.3800794 | Gene expression analysis of soft tissue sarcomas: characterization and reclassification of malignant fibrous histiocytoma | In soft tissue sarcomas, the diagnosis of malignant fibrous histiocytoma (MFH) has been a very controversial issue, and MFH is now considered to be reclassified into pleomorphic subtypes of other sarcomas. To characterize MFH genetically, we used an oligonucleotide microarray to analyze gene expression in 105 samples from 10 types of soft tissue tumors. Spindle cell and pleomorphic sarcomas, such as dedifferentiated liposarcoma, myxofibrosarcoma, leiomyosarcoma, malignant peripheral nerve sheath tumor (MPNST), fibrosarcoma and MFH, showed similar gene expression patterns compared to other tumors. Samples from those five sarcoma types could be classified into respective clusters based on gene expression by excluding MFH samples. We calculated distances between MFH samples and other five sarcoma types (dedifferentiated liposarcoma, myxofibrosarcoma, leiomyosarcoma, MPNST and fibrosarcoma) based on differentially expressed genes and evaluated similarities. Three of the 21 MFH samples showed marked similarities to one of the five sarcoma types, which were supported by histological findings. Although most of the remaining 18 MFH samples showed little or no histological resemblance to one of the five sarcoma types, 12 of them showed moderate similarities in terms of gene expression. These results explain the heterogeneity of MFH and show that the majority of MFHs could be reclassified into pleomorphic subtypes of other sarcomas. Taken together, gene expression profiling could be a useful tool to unveil the difference in the underlying molecular backgrounds, which leads to a rational taxonomy and diagnosis of a diverse group of soft tissue sarcomas. | [Robert Nakayama, Takeshi Nemoto, Hiro Takahashi, Tsutomu Ohta, Akira Kawai, Kunihiko Seki, Teruhiko Yoshida, Yoshiaki Toyama, Hitoshi Ichikawa, Tadashi Hasegawa] | Modern Pathology | 2007-04-27 | |
| naturepublishinggroup10.1038/sj.onc.1210450 | Loss of the retinoblastoma tumor suppressor: differential action on transcriptional programs related to cell cycle control and immune function | Functional inactivation of the retinoblastoma tumor suppressor gene product (RB) is a common event in human cancers. Classically, RB functions to constrain cellular proliferation, and loss of RB is proposed to facilitate the hyperplastic proliferation associated with tumorigenesis. To understand the repertoire of regulatory processes governed by RB, two models of RB loss were utilized to perform microarray analysis. In murine embryonic fibroblasts harboring germline loss of RB, there was a striking deregulation of gene expression, wherein distinct biological pathways were altered. Specifically, genes involved in cell cycle control and classically associated with E2F-dependent gene regulation were upregulated via RB loss. In contrast, a program of gene expression associated with immune function and response to pathogens was significantly downregulated with the loss of RB. To determine the specific influence of RB loss during a defined period and without the possibility of developmental compensation as occurs in embryonic fibroblasts, a second system was employed wherein Rb was acutely knocked out in adult fibroblasts. This model confirmed the distinct regulation of cell cycle and immune modulatory genes through RB loss. Analyses of cis-elements supported the hypothesis that the majority of those genes upregulated with RB loss are regulated via the E2F family of transcription factors. In contrast, those genes whose expression was reduced with the loss of RB harbored different promoter elements. Consistent with these analyses, we found that disruption of E2F-binding function of RB was associated with the upregulation of gene expression. In contrast, cells harboring an RB mutant protein (RB-750F) that retains E2F-binding activity, but is specifically deficient in the association with LXCXE-containing proteins, failed to upregulate these same target genes. However, downregulation of genes involved in immune function was readily observed with disruption of the LXCXE-binding function of RB. Thus, these studies demonstrate that RB plays a significant role in both the positive and negative regulations of transcriptional programs and indicate that loss of RB has distinct biological effects related to both cell cycle control and immune function. | [M P Markey, J Bergseid, E E Bosco, K Stengel, H Xu, C N Mayhew, S J Schwemberger, W A Braden, Y Jiang, G F Babcock, A G Jegga, B J Aronow, M F Reed, J Y J Wang, E S Knudsen] | Oncogene | 2007-04-23 | |
| naturepublishinggroup10.1038/sj.onc.1210467 | Loss of suppressor-of-fused function promotes tumorigenesis | The Sonic Hedgehog (SHH) signaling pathway is indispensable for development, and functions to activate a transcriptional program modulated by the GLI transcription factors. Here, we report that loss of a regulator of the SHH pathway, Suppressor of Fused (Sufu), resulted in early embryonic lethality in the mouse similar to inactivation of another SHH regulator, Patched1 (Ptch1). In contrast to Ptch1+/- mice, Sufu+/- mice were not tumor prone. However, in conjunction with p53 loss, Sufu+/- animals developed tumors including medulloblastoma and rhabdomyosarcoma. Tumors present in Sufu+/-p53-/- animals resulted from Sufu loss of heterozygosity. Sufu+/-p53-/- medulloblastomas also expressed a signature gene expression profile typical of aberrant SHH signaling, including upregulation of N-myc, Sfrp1, Ptch2 and cyclin D1. Finally, the Smoothened inhibitor, hedgehog antagonist, did not block growth of tumors arising from Sufu inactivation. These data demonstrate that Sufu is essential for development and functions as a tumor suppressor. | [Y Lee, R Kawagoe, K Sasai, Y Li, H R Russell, T Curran, P J McKinnon] | Oncogene | 2007-04-23 | |
| naturepublishinggroup10.1038/nature05756 | PTC124 targets genetic disorders caused by nonsense mutations | Nonsense mutations promote premature translational termination and cause anywhere from 5–70% of the individual cases of most inherited diseases1. Studies on nonsense-mediated cystic fibrosis have indicated that boosting specific protein synthesis from <1% to as little as 5% of normal levels may greatly reduce the severity or eliminate the principal manifestations of disease2, 3. To address the need for a drug capable of suppressing premature termination, we identified PTC124—a new chemical entity that selectively induces ribosomal readthrough of premature but not normal termination codons. PTC124 activity, optimized using nonsense-containing reporters, promoted dystrophin production in primary muscle cells from humans and mdx mice expressing dystrophin nonsense alleles, and rescued striated muscle function in mdx mice within 2–8 weeks of drug exposure. PTC124 was well tolerated in animals at plasma exposures substantially in excess of those required for nonsense suppression. The selectivity of PTC124 for premature termination codons, its well characterized activity profile, oral bioavailability and pharmacological properties indicate that this drug may have broad clinical potential for the treatment of a large group of genetic disorders with limited or no therapeutic options. | [Ellen M. Welch, Elisabeth R. Barton, Jin Zhuo, Yuki Tomizawa, Westley J. Friesen, Panayiota Trifillis, Sergey Paushkin, Meenal Patel, Christopher R. Trotta, Seongwoo Hwang, Richard G. Wilde, Gary Karp, James Takasugi, Guangming Chen, Stephen Jones, Hongyu Ren, Young-Choon Moon, Donald Corson, Anthony A. Turpoff, Jeffrey A. Campbell, M. Morgan Conn, Atiyya Khan, Neil G. Almstead, Jean Hedrick, Anna Mollin, Nicole Risher, Marla Weetall, Shirley Yeh, Arthur A. Branstrom, Joseph M. Colacino, John Babiak, William D. Ju, Samit Hirawat, Valerie J. Northcutt, Langdon L. Miller, Phyllis Spatrick, Feng He, Masataka Kawana, Huisheng Feng, Allan Jacobson, Stuart W. Peltz, H. Lee Sweeney] | Nature | 2007-04-22 | |
| naturepublishinggroup10.1038/nsmb1239 | Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection | Histone acetylation is important in regulating DNA accessibility. Multifunctional Sin3 proteins bind histone deacetylases (HDACs) to assemble silencing complexes that selectively target chromatin. We show that, in fission yeast, an essential HDAC, Clr6, exists in two distinct Sin3 core complexes. Complex I contains an essential Sin3 homolog, Pst1, and other factors, and predominantly targets gene promoters. Complex II contains a nonessential Sin3 homolog, Pst2, and several conserved proteins. It preferentially targets transcribed chromosomal regions and centromere cores. Defects in complex II abrogate global protective functions of chromatin, causing increased accessibility of DNA to genotoxic agents and widespread antisense transcripts that are processed by the exosome. Notably, the two Clr6 complexes differentially repress forward and reverse centromeric repeat transcripts, suggesting that these complexes regulate transcription in heterochromatin and euchromatin in similar manners, including suppression of spurious transcripts from cryptic start sites. | [Estelle Nicolas, Takatomi Yamada, Hugh P Cam, Peter C FitzGerald, Ryuji Kobayashi, Shiv I S Grewal] | Nature Structural & Molecular Biology | 2007-04-22 | |
| naturepublishinggroup10.1038/sj.mp.4001998 | Expression profiling in monozygotic twins discordant for bipolar disorder reveals dysregulation of the WNT signalling pathway | To identify genes dysregulated in bipolar disorder (BD1), we carried out global gene expression profiling using whole-genome microarrays. To minimize genetic variation in gene expression levels between cases and controls, we compared expression profiles in lymphoblastoid cell lines from monozygotic twin pairs discordant for the disease. We identified 82 genes that were differentially expressed by 1.3-fold in three BD1 cases compared to their co-twins, and which were statistically (P0.05) differentially expressed between the groups of BD1 cases and controls. Using quantitative reverse transcriptase-polymerase chain reaction, we confirmed the differential expression of some of these genes, including: KCNK1, MAL, PFN2, TCF7, PGK1 and PI4KCB, in at least two of the twin pairs. In contrast to the findings of a previous study by Kakiuchi and colleagues with similar discordant BD1 twin design, our data do not support the dysregulation of XBP1 and HSPA5. From pathway and gene ontology analysis, we identified upregulation of the WNT signalling pathway and the biological process of apoptosis. The differentially regulated genes and pathways identified in this study may provide insights into the biology of BD1. | [N Matigian, L Windus, H Smith, C Filippich, C Pantelis, J McGrath, B Mowry, N Hayward] | Molecular Psychiatry | 2007-04-17 | |
| naturepublishinggroup10.1038/sj.gene.6364389 | Study of proinflammatory responses induced by Yersinia pestis in human monocytes using cDNA arrays | Yersinia pestis, the causative agent of plague, is known to develop strategies to overcome the host immune mechanisms and survive in the host. The molecular changes induced by Y. pestis in the host are not well delineated. Here, we examined the early events triggered after the intracellular infection of Y. pestis in human monocytes and lymphocytes by analyzing the host transcriptional profiles using cDNA arrays. We found that sets of genes that, especially at early time periods, were highly upregulated in monocytes alone when compared with a mixed culture of lymphocytes and monocytes. Gene expression responses revealed genes coding for cytokines, chemokines, transcription factors, inflammatory and apoptosis-related genes. Protein levels were measured, and real-time polymerase chain reaction was used to validate the microarray results. Our data suggest that intracellular infection of human monocytes with Y. pestis results in a strong inflammatory response at early time periods and a downregulation of genes such as thromobomodulin, which may play a role in coagulation, resulting in disseminated intravascular coagulation, a primary cause of death in plague infected hosts. We provide evidence that genomic analysis can provide a solid foundation to mechanistic insights to explain some of the symptoms induced by Y. pestis. | [R Das, A Dhokalia, X-Z Huang, R Hammamieh, N Chakraborty, L E Lindler, M Jett] | Genes and Immunity | 2007-04-12 | |
| naturepublishinggroup10.1038/sj.jid.5700813 | Absence of Cutaneous TNF|[alpha]|-Producing CD4|[plus]| T Cells and TNF|[alpha]| may Allow for Fibrosis Rather than Epithelial Cytotoxicity in Murine Sclerodermatous Graft-Versus-Host Disease, a Model for Human Scleroderma | Graft-versus-host disease (GVHD) is a complication of hematopoietic cell transplantation and is a major source of morbidity and mortality. Two main forms of GVHD occur: cytotoxic GVHD (Cyt GVHD), in which TNF is a critical cytokine in epithelial injury, and sclerodermatous GVHD (Scl GVHD), in which TGF plays a major role in fibrosis. To understand the critical early events in GVHD and scleroderma, we are studying a murine model that uses differences in minor histocompatability antigens to generate Scl GVHD. We asked the question: what is the immune environment in this model that promotes fibrosis rather than the epithelial injury of Cyt GVHD? We found that in Scl GVHD, cutaneous CD4+ T cells produced IFN and IL-2 but not TNF, also absent by gene array analysis. The role of cutaneous CD4+ T cells in Scl GVHD may not be an active process through production of TGF, but may rather be a passive one due to lack of antigen-presenting cell (APC) support for CD4+ T cells and failure to produce TNF, a potent inhibitor of TGF-induced fibrosis as well as inducer of keratinocyte apoptosis. These APC–T cell interactions and the cytokine environment promote fibrosis rather than cytotoxic epithelial injury in skin in Scl GVHD. | [David Askew, Lixin Zhou, Cayun Wu, Guofen Chen, Anita C Gilliam] | Journal of Investigative Dermatology | 2007-04-12 | |
| naturepublishinggroup10.1038/sj.onc.1210441 | p53 and |[Delta]|Np63|[alpha]| differentially bind and regulate target genes involved in cell cycle arrest, DNA repair and apoptosis | The mechanism by which the p53 family of proteins coordinately regulates select target genes after various types of cell stress is not well understood. To further define factors that dictate regulation of target genes, we examined the binding of p53, Np63 and RNA polymerase II (pol II) to the regulatory regions of select target genes in primary human epidermal keratinocytes (HEKs) using chromatin immunoprecipitation. In rapidly proliferating cells, we observed constitutive binding of Np63 and varying levels of p53 binding, to consensus sites in target genes involved in cell cycle arrest, DNA repair and apoptosis. Following genotoxic stress, p53 occupancy increased whereas Np63 occupancy decreased at the majority of binding sites examined. Microarray analysis of transcripts isolated from HEKs ectopically expressing p53 and Np63 revealed an inverse regulation of select target genes by the two family members. Collectively, our results suggest that Np63 can function as a repressor of select p53 target genes involved in growth arrest, DNA repair and apoptosis, and that the location of the p53 consensus binding site(s) in a target gene may dictate whether pol II is constitutively bound in proliferating cells. | [K L Schavolt, J A Pietenpol] | Oncogene | 2007-04-02 | |
| naturepublishinggroup10.1038/nprot.2007.57 | Data analysis of assorted serum peptidome profiles | Discovery of biomarker patterns using proteomic techniques requires examination of large numbers of patient and control samples, followed by data mining of the molecular read-outs (e.g., mass spectra). Adequate signal processing and statistical analysis are critical for successful extraction of markers from these data sets. The protocol, specifically designed for use in conjunction with MALDI-TOF-MS-based serum peptide profiling, is a data analysis pipeline, starting with transfer of raw spectra that are interpreted using signal processing algorithms to define suitable features (i.e., peptides). We describe an algorithm for minimal entropy-based peak alignment across samples. Peak lists obtained in this way, and containing all samples, all peptide features and their normalized MS-ion intensities, can be evaluated, and results validated, using common statistical methods. We recommend visual inspection of the spectra to confirm all results, and have written freely available software for viewing and color-coding of spectral overlays. | [Josep Villanueva, John Philip, Lin DeNoyer, Paul Tempst] | Nature Protocols | 2007-03-29 | |
| naturepublishinggroup10.1038/sj.eye.6702779 | Significance of gene expression analysis in uveal melanoma in comparison to standard risk factors for risk assessment of subsequent metastases | | [U Petrausch, P Martus, H T|[ouml]|nnies, N E Bechrakis, D Lenze, S Wansel, M Hummel, N Bornfeld, E Thiel, M H Foerster, U Keilholz] | Eye | 2007-03-23 | 4.2 |
| naturepublishinggroup10.1038/sj.leu.2404594 | High expression of several tyrosine kinases and activation of the PI3K|[sol]|AKT pathway in mediastinal large B cell lymphoma reveals further similarities to Hodgkin lymphoma | Mediastinal large B-cell (MBL) and classical Hodgkin lymphoma (HL) have several pathogenic mechanisms in common. As we recently observed aberrant tyrosine kinase (TK) activities in HL, we now analysed also MBL for such activities. Indeed, MBL and HL were the only B-cell lymphomas where elevated cellular phospho-tyrosine contents were typical features. Three TKs, JAK2, RON and TIE1, not expressed in normal B cells, were each expressed in about 30% of MBL cases, and 75% of cases expressed at least one of the TKs. Among the intracellular pathways frequently triggered by TKs, the PI3K/AKT pathway was activated in about 40% of MBLs and essential for survival of MBL cell lines, whereas the RAF/mitogen-activated protein kinase pathway seemed to be inhibited. No activating mutations were detected in the three TKs in MBL cell lines and primary cases. RON and TIE1 were each also expressed in about 35% and JAK2 in about 53% of HL cases. JAK2 genomic gains are frequent in MBL and HL but we observed no strict correlation of JAK2 genomic status with JAK2 protein expression. In conclusion, aberrant TK activities are a further shared pathogenic mechanism of MBL and HL and may be interesting targets for therapeutic intervention. | [C Renn|[eacute]|, K Willenbrock, J I Martin-Subero, N Hinsch, C D|[ouml]|ring, E Tiacci, W Klapper, P M|[ouml]|ller, R K|[uuml]|ppers, M-L Hansmann, R Siebert, A Br|[auml]|uninger] | Leukemia | 2007-04-01 | |
| naturepublishinggroup10.1038/sj.clpt.6100081 | Gene Modulatory Effects, Pharmacokinetics, and Clinical Tolerance of Interferon-|[alpha]|1b: A Second Member of the Interferon-|[alpha]| Family | Interferon-1 (IFN-1), which may have a primary role in innate immunity, differs significantly in amino-acid sequence from IFN-2, the only recombinant IFN- with substantial clinical evaluation. Patients with metastatic malignancies received daily subcutaneous doses of 1.5–270 g/m2 of recombinant IFN-1b. Gene modulation, pharmacokinetics, tolerability, and disease response were determined. Significant (P<0.01) dose and gene-dependent increases of 2-10 fold occurred in IFN-stimulated genes, including four (tumor necrosis factor-related apoptosis-inducing ligand, cig 5, p56, GEM) never previously identified as increased in patients; significant increases (P<0.01) resulted at the lowest dose (1.5 g/m2; 1.5 104 human antiviral units/m2). Increases (P<0.01) were sustainable for >4 weeks. Peak levels of IFN-1b were at 3 h; an increase of approximately eightfold in both Cmax and AUC occurred between 15 g/m2 and 270 g/m2. Chronic toxicities of anorexia, weight loss, and fatigue were relatively uncommon. Eighteen patients were treated for >8 weeks; none experienced >grade 1 weight loss. Three patients at the highest dose developed grade 3 fatigue after 3 months, which required dose reduction or discontinuation. Patient acceptability of fatigue defined a dose for initiation of Phase II trials, 270 g/m2. Six patients (five with renal cell carcinoma) had progression-free survival for >1 year, including two who had partial responses. IFN-1b resulted in potent stimulation of IFN-regulated genes and tumor regressions in renal cell carcinoma. Unique gene modulatory effects, when coupled with the moderate severity of side effects and a potentially central role in innate immunity, provide rationale for further clinical evaluation of IFN-1 in virus infections and cancer. | [P Masci, T Olencki, L Wood, L Rybicki, B Jacobs, B Williams, P Faber, R Bukowski, K Tong, E C Borden] | Clinical Pharmacology & Therapeutics | 2007-03-01 | |
| naturepublishinggroup10.1038/sj.leu.2404605 | MicroRNA miR-181a correlates with morphological sub-class of acute myeloid leukaemia and the expression of its target genes in global genome-wide analysis | MicroRNAs (miRNAs) are short single-stranded RNAs that have a potentially important role in gene regulation. Using a quantitative real-time polymerase chain reaction assay specific to the mature miRNA, the expression level of a selected group of haematopoietic tissue-specific miRNAs was measured across a set of 30 primary adult acute myeloid leukaemia (AML) with a normal karyotype. The expression levels of each miRNA were correlated with the genome-wide mRNA expression profiles in the same leukaemias. This revealed that miR-181a correlated strongly with the AML morphological sub-type and with the expression of genes previously identified through sequence analysis as potential interaction targets. Three other miRNAs, miR-10a, miR-10b and miR-196a-1, showed a clear correlation with HOX gene expression. | [S Debernardi, S Skoulakis, G Molloy, T Chaplin, A Dixon-McIver, B D Young] | Leukemia | 2007-03-01 | |
| naturepublishinggroup10.1038/sj.leu.2404587 | Highly purified CD38|[plus]| and CD38|[minus]| sub-clones derived from the same chronic lymphocytic leukemia patient have distinct gene expression signatures despite their monoclonal origin | CD38 expression is an important prognostic marker in chronic lymphocytic leukemia (CLL) with high levels of CD38 associated with shorter overall survival. In this study, we used gene expression profiling and protein analysis of highly purified cell-sorted CD38+ and CD38- chronic lymphocytic leukemia cells to elucidate a molecular basis for the association between CD38 expression and inferior clinical outcome. Paired CD38+ and CD38- CLL cells derived from the same patient were shown to be monoclonal by VH gene sequencing but despite this, CD38+ CLL cells possessed a distinct gene expression profile when compared with their CD38- sub-clones. Importantly, CD38+ CLL cells relatively over expressed vascular endothelial growth factor (VEGF) and appeared to preferentially utilize an internal autocrine VEGF survival loop. Elevated VEGF expression was associated with increased expression of the anti-apoptotic protein Mcl-1. Inhibition of VEGF receptor signaling also resulted in a reduction in cell viability. In contrast, exogenous VEGF caused a significant increase in CD38- CLL cell viability and a marked induction of Mcl-1; both effects were less obvious in CD38+ CLL cells. Taken together, our data provide a biological rationale for the poor prognosis of CD38+ CLL and indicate that both VEGF and Mcl-1 may prove to be useful therapeutic targets. | [C Pepper, R Ward, T T Lin, P Brennan, J Starczynski, M Musson, C Rowntree, P Bentley, K Mills, G Pratt, C Fegan] | Leukemia | 2007-02-08 | 7.0 |
| naturepublishinggroup10.1038/sj.emboj.7601563 | Distinct C/EBP|[alpha]| motifs regulate lipogenic and gluconeogenic gene expression in vivo | The C/EBP transcription factor regulates hepatic nitrogen, glucose, lipid and iron metabolism. However, how it is able to independently control these processes is not known. Here, we use mouse knock-in mutagenesis to identify C/EBP domains that specifically regulate hepatic gluconeogenesis and lipogenesis. In vivo deletion of a proline–histidine rich domain (PHR), dephosphorylated at S193 by insulin signaling, dysregulated genes involved in the generation of acetyl-CoA and NADPH for triglyceride synthesis and led to increased hepatic lipogenesis. These promoters bound SREBP-1 as well as C/EBP, and the PHR was required for C/EBP-SREBP transcriptional synergy. In contrast, the highly conserved C/EBP CR4 domain was found to undergo liver-specific dephosphorylation of residues T222 and T226 upon fasting, and alanine mutation of these residues upregulated the hepatic expression of the gluconeogenic G6Pase and PEPCK mRNAs, but not PGC-1, leading to glucose intolerance. Our results show that pathway-specific metabolic regulation can be achieved through a single transcription factor containing context-sensitive regulatory domains, and indicate C/EBP phosphorylation as a PGC-1-independent mechanism for regulating hepatic gluconeogenesis. | [Thomas |[Aring]| Pedersen, Oxana Bereshchenko, Susana Garcia-Silva, Olga Ermakova, Elke Kurz, Susanne Mandrup, Bo T Porse, Claus Nerlov] | The EMBO Journal | 2007-02-08 | |
| naturepublishinggroup10.1038/sj.onc.1210208 | Gene expression analysis of early and advanced gastric cancers | Gastric carcinoma is one of the major causes of cancer mortality worldwide. Early detection results in excellent prognosis for patients with early cancer (EGC), whereas the prognosis of advanced cancer (AGC) patients remains poor. It is not clear whether EGC and AGC are molecularly distinct, and whether they represent progressive stages of the same tumor or different entities ab initio. Gene expression profiles of EGC and AGC were determined by Affymetrix technology and quantitative polymerase chain reaction. Representative regulated genes were further analysed by in situ hybridization (ISH) on tissue microarrays. Expression analysis allowed the identification of a signature that differentiates AGC from EGC. In addition, comparison with normal gastric mucosa indicated that the majority of alterations associated with EGC are retained in AGC, and that further expression changes mark the transition from EGC to AGC. Finally, ISH analysis showed that representative genes, differentially expressed in the invasive areas of EGC and AGC, are not differentially expressed in the non-invasive areas of the same tumors. Our data are more directly compatible with a progression model of gastric carcinogenesis, whereby EGC and AGC may represent different molecular stages of the same tumor. Finally, the identification of an AGC-specific signature might help devising novel therapeutic strategies for advanced gastric cancer. | [M Vecchi, P Nuciforo, S Romagnoli, S Confalonieri, C Pellegrini, G Serio, M Quarto, M Capra, G C Roviaro, E Contessini Avesani, C Corsi, G Coggi, P P Di Fiore, S Bosari] | Oncogene | 2007-02-05 | |
| naturepublishinggroup10.1038/sj.jid.5700714 | In Situ Identification of Genes Regulated Specifically in Fibroblasts of Human Basal Cell Carcinoma | Basal cell carcinoma (BCC) is characterized by slow growth, virtual absence of metastases, and strong stroma-dependency. Cancer-associated fibroblasts (CAFs) in the tumor stroma influence tumor growth, invasion, and metastasis. To comprehensively characterize CAFs of BCC in their in situ cancer environment, laser capture microdissection, linear gene amplification, microarray analysis, and quantitative real-time PCR (qRT-PCR) were combined. Pair-wise comparison of gene expression of microdissected CAFs and corresponding normal perifollicular fibroblasts identified 65 genes that were significantly upregulated in at least two of three different patients. Among the annotated genes, as many as 13 genes encoded secreted proteins, of which six were previously implicated as CAF-associated proteins in various tumor types. Four of the seven novel CAF genes – matrix Gla-protein, secreted frizzled-related protein 2, angiopoietin-related protein-2, and platelet-derived growth factor receptor-like protein – were selected for further analyses by qRT-PCR and were found to be frequently upregulated in CAFs of three independent BCC tissues. Analyses of CAFs from squamous cell cancer, prostate cancer, and colon cancer did not indicate that these genes were upregulated in these cancers. This study thus validates a novel approach for comprehensive characterization CAFs in their in situ environment of BCC. The results suggest a specific expression profile of CAFs in BCC possibly accounting for disease-specific pathological roles. | [Patrick Micke, Kai Kappert, Mitsuhiro Ohshima, Christina Sundquist, Stefan Scheidl, Per Lindahl, Carl-Henrik Heldin, Johan Botling, Fredrik Ponten, Arne |[Ouml]|stman] | Journal of Investigative Dermatology | 2007-02-01 | |
| naturepublishinggroup10.1038/ncpcardio0766 | Mitochondrial oxidative metabolism is required for the cardiac differentiation of stem cells | | [Susan Chung, Petras P Dzeja, Randolph S Faustino, Carmen Perez-Terzic, Atta Behfar, Andre Terzic] | Nature a - z index | 2007-02-01 | |
| naturepublishinggroup10.1038/ncpcardio0763 | Stem cells transform into a cardiac phenotype with remodeling of the nuclear transport machinery | | [Carmen Perez-Terzic, Randolph S Faustino, Brian J Boorsma, D Kent Arrell, Nicolas J Niederl|[auml]|nder, Atta Behfar, Andre Terzic] | Nature a - z index | 2007-02-01 | |
| naturepublishinggroup10.1038/ni1433 | DCs metabolize sunlight-induced vitamin D3 to 'program' T cell attraction to the epidermal chemokine CCL27 | During adaptive immune responses, dendritic cells activate T cells and endow them with specific homing properties. Mechanisms that 'imprint' specific tropisms, however, are not well defined. We show here that 1,25(OH)2D3, the active form of vitamin D3, signaled T cells to express CC chemokine receptor 10, which enabled them to migrate to the skin-specific chemokine CCL27 secreted by keratinocytes of the epidermis. In contrast, 1,25(OH)2D3 suppressed the gut-homing receptors 47 and CCR9. Vitamin D3, the inactive prohormone naturally generated in the skin by exposure to the sun, was processed by dendritic cells and T cells to the active metabolite, providing a mechanism for the local regulation of T cell 'epidermotropism'. Our findings support a model in which dendritic cells process and 'interpret' locally produced metabolites to 'program' T cell homing and microenvironmental positioning. | [Hekla Sigmundsdottir, Junliang Pan, Gudrun F Debes, Carsten Alt, Aida Habtezion, Dulce Soler, Eugene C Butcher] | Nature Immunology | 2007-01-28 | |
| naturepublishinggroup10.1038/sj.mt.6300038 | Oncolytic HSV and Erlotinib Inhibit Tumor Growth and Angiogenesis in a Novel Malignant Peripheral Nerve Sheath Tumor Xenograft Model | Malignant peripheral nerve sheath tumors (MPNSTs), driven in part by hyperactive Ras and epidermal growth factor receptor (EGFR) signaling, are often incurable. Testing of therapeutics for MPNST has been hampered by lack of adequate xenograft models. We previously documented that human MPNST cells are permissive for lytic infection by oncolytic herpes simplex viruses (oHSV). Herein we developed and characterized a xenograft model of human MPNST and evaluated the antitumor effects of oHSV mutants (G207 and hrR3) and the EGFR inhibitor, erlotinib. Additive cytotoxicity of these agents was found in human MPNST cell lines, suggesting that EGFR signaling is not critical for virus replication. Mice bearing human MPNST tumors treated with G207 or hrR3 by intraperitoneal or intratumoral injection showed tumor-selective virus biodistribution, virus replication, and reduced tumor burden. oHSV injection demonstrated more dramatic antitumor activity than erlotinib. Combination therapies showed a trend toward an increased antiproliferative effect. Both oHSV and erlotinib were antiangiogenic as measured by proangiogenic gene expression, effect on endothelial cells and xenograft vessel density. Overall, oHSVs showed highly potent antitumor effects against MPNST xenografts, an effect not diminished by EGFR inhibition. Our data suggest that inclusion of MPNSTs in clinical trials of oHSV is warranted. | [Yonatan Y Mahller, Sachin S Vaikunth, Mark A Currier, Shyra J Miller, Maria C Ripberger, Ya-Hsuan Hsu, Ruty Mehrian-Shai, Margaret H Collins, Timothy M Crombleholme, Nancy Ratner, Timothy P Cripe] | Molecular Therapy | 2007-02-01 | |
| naturepublishinggroup10.1038/sj.onc.1210185 | TLX1|[sol]|HOX11-induced hematopoietic differentiation blockade | Aberrant expression of the human homeobox-containing proto-oncogene TLX1/HOX11 inhibits hematopoietic differentiation programs in a number of murine model systems. Here, we report the establishment of a murine erythroid progenitor cell line, iEBHX1S-4, developmentally arrested by regulatable TLX1 expression. Extinction of TLX1 expression released the iEBHX1S-4 differentiation block, allowing erythropoietin-dependent acquisition of erythroid markers and hemoglobin synthesis. Coordinated activation of erythroid transcriptional networks integrated by the acetyltransferase co-activator CREB-binding protein (CBP) was suggested by bioinformatic analysis of the upstream regulatory regions of several conditionally induced iEBHX1S-4 gene sets. In accord with this notion, CBP-associated acetylation of GATA-1, an essential regulator of erythroid differentiation, increased concomitantly with TLX1 downregulation. Coimmunoprecipitation experiments and glutathione-S-transferase pull-down assays revealed that TLX1 directly binds to CBP, and confocal laser microscopy demonstrated that the two proteins partially colocalize at intranuclear sites in iEBHX1S-4 cells. Notably, the distribution of CBP in conditionally blocked iEBHX1S-4 cells partially overlapped with chromatin marked by a repressive histone methylation pattern, and downregulation of TLX1 coincided with exit of CBP from these heterochromatic regions. Thus, we propose that TLX1-mediated differentiation arrest may be achieved in part through a mechanism that involves redirection of CBP and/or its sequestration in repressive chromatin domains. | [I Riz, S S Akimov, S S Eaker, K K Baxter, H J Lee, L Mari|[ntilde]|o-Ram|[iacute]|rez, D Landsman, T S Hawley, R G Hawley] | Oncogene | 2007-01-08 | |
| naturepublishinggroup10.1038/sj.embor.7400849 | Novel c-MYC target genes mediate differential effects on cell proliferation and migration | The developmental and oncogenic roles of MYC proteins are well established, but the transcriptional targets mediating their functions remain elusive. Using small interfering RNA-mediated knockdown in breast and cervix carcinoma cell lines, which overexpress c-MYC, we show that c-MYC independently controls metabolism and cell proliferation, and can, depending on the cells, promote or inhibit migration. We identified new c-MYC target genes in these cell lines, and show that selective regulation of some targets correlates with the phenotypic responses of these different cell lines to c-MYC depletion. Notably, we show that a positive regulation of the WNT signalling pathway contributes to c-MYC pro-mitogenic effects in breast and cervix carcinoma cells. We also show that repression of CCL5/RANTES accounts for c-MYC anti-migratory effects in specific breast cancer cells. Our combined genomic and phenotypic analysis indicates that c-MYC functions are cellular-context-dependent and that selectively regulated genes are responsible for its differential properties. | [David Cappellen, Thomas Schlange, Matthieu Bauer, Francisca Maurer, Nancy E Hynes] | EMBO reports | 2006-12-08 | |
| naturepublishinggroup10.1038/sj.jid.5700638 | A Skin-Like Cytochrome P450 Cocktail Activates Prohaptens to Contact Allergenic Metabolites | Allergic contact dermatitis is a complex syndrome representing immunological responses to cutaneous exposure to protein-reactive chemicals. Although many contact sensitizers directly can elicit this disorder, others (prohaptens) require activation. Knowledge regarding the activating mechanisms remains limited, but one possibility is metabolic activation by cytochrome P450 (CYP) enzymes in the skin. We have, after quantitative reverse transcriptase-PCR studies of the CYP content in 18 human skin samples, developed an enriched skin-like recombinant human (rh) CYP cocktail using CYP1A1, 1B1, 2B6, 2E1, and 3A5. To validate the rhCYP cocktail, a prohaptenic conjugated diene ((5R)-5-isopropenyl-2-methyl-1-methylene-2-cyclohexene) was investigated using: the skin-like rhCYP cocktail, a liver-like rhCYP cocktail, single rhCYP enzymes, liver microsomes, keratinocytes, and a dendritic cell (DC) assay. The diene was activated to sensitizing epoxides in all non-cell-based incubations including the skin-like rhCYP cocktail. An exocyclic epoxide metabolite ((7R)-7-isopropenyl-4-methyl-1-oxaspiro[2.5]oct-4-ene) was found to be mainly responsible for the allergenic activity of the diene. This epoxide also induced pronounced DC activation indicated by upregulation of IL-8. The skin-like rhCYP cocktail provides a simplified alternative to using skin tissue preparations in mechanistic studies of CYP-mediated skin metabolism of prohaptens and offers the future possibility of designing in vitro predictive assays for assessment of allergenic activity of prohaptens. | [Moa Andresen Bergstr|[ouml]|m, Hagen Ott, Anna Carlsson, Mark Neis, Gabriele Zwadlo-Klarwasser, Charlotte A M Jonsson, Hans F Merk, Ann-Therese Karlberg, Jens M Baron] | Journal of Investigative Dermatology | 2006-11-23 | |
| naturepublishinggroup10.1038/nature06051 | Early events in the thymus affect the balance of effector and regulatory T cells | In cellular immunology the critical balance between effector and regulatory mechanisms is highlighted by serious immunopathologies attributable to mutations in Foxp3, a transcription factor required for a major subset of regulatory T (Tr) cells1, 2, 3. Thus, many studies have focused on the developmental origin of Tr cells, with the prevailing view that they emerge in the thymus from late-stage T-cell progenitors whose T-cell receptors (TCRs) engage high affinity (agonist) ligands4, 5, 6. This study questions the completeness of that interpretation. Here we show that without any obvious effect on TCR-mediated selection, the normal differentiation of mouse T cells into potent cytolytic and interferon--secreting effector cells is switched towards an aggregate regulatory phenotype by limiting the capacity of CD4+CD8+ T-cell progenitors to influence in trans early cell progenitors. Unexpectedly, we found that the propensity of early TCR-+ progenitors to differentiate into Foxp3+ Tr cells is also regulated in trans by CD4+CD8+ T-cell progenitor cells, before agonist selection. | [Daniel J. Pennington, Bruno Silva-Santos, Tobias Silberzahn, M|[oacute]|nica Esc|[oacute]|rcio-Correia, Martin J. Woodward, Scott J. Roberts, Adrian L. Smith, P. Julian Dyson, Adrian C. Hayday] | Nature | 2006-11-12 | 7.3 |
| naturepublishinggroup10.1038/sj.jid.5700616 | TIM-3 Is Expressed in Melanoma Cells and Is Upregulated in TGF-Beta Stimulated Mast Cells | Many studies detect elevated numbers of mast cells in tumors, but it is still controversial whether they are beneficial or detrimental for tumor cells. Furthermore, many tumors, such as melanomas, produce large quantities of transforming growth factor (TGF)- and during tumorigenesis the apoptotic and growth-inhibitory effects of TGF-s are lost. Based on these data we investigated the gene expression changes in TGF-I-treated human mast cells with DNA microarray and detected 45 differentially regulated genes, among them T-cell immunoglobulin and mucin domain-containing protein 3 (TIM-3). As the major sources of TIM-3 ligand galectin-9 are not tumor cells, but rather mast cells, this raises the possibility of an autocrine mechanism resulting in local immunosuppression through the elevated TIM-3 expression by TGF-I. Interestingly, not only melanoma tissue sections contained TIM-3-positive mast cells, but we detected this protein also in melanoma cells. Furthermore, TIM-3 was expressed in both WM35 and HT168-M1 melanoma cell lines at a higher level than in isolated epidermal melanocytes, which can contribute to the lower adhering capacity of tumor cells. In conclusion, the immunoregulatory molecule TIM-3 in TGF--stimulated mast cells and melanoma cells may support the survival of this tumor type. | [Zoltan Wiener, Barbara Kohalmi, Peter Pocza, Judit Jeager, Gergely Tolgyesi, Sara Toth, Eva Gorbe, Zoltan Papp, Andras Falus] | Journal of Investigative Dermatology | 2006-11-09 | |
| naturepublishinggroup10.1038/sj.pcan.4500915 | Characterization of the androgen receptor in a benign prostate tissue-derived human prostate epithelial cell line: RC-165N|[sol]|human telomerase reverse transcriptase | The majority of prostate epithelial cell lines stably expressing wild-type (wt) or mutant (mt) androgen receptor (AR) are derived from metastatic prostate cancers. Therefore, the wt AR-expressing RC-165N/human telomerase reverse transcriptase (hTERT) cell line derived from the benign prostate tissue of an African-American patient provides a unique opportunity to assess the functional status of AR in a cellular context not studied before. Although androgen-induced expression of known androgen responsive genes such as PMEPA1, and NDRG1 was observed in RC-165N/hTERT, this cell line expresses prostate-specific antigen (PSA) at significantly lower levels. Chromatin immunoprecipitation assay revealed androgen-dependent binding of AR to androgen response elements of PSA, PMEPA1 and NDRG1 genes. Similarities, as well as differences were noted in the expression of androgen responsive genes between RC-165N/hTERT and LNCaP cells. Comprehensive evaluations of AR functions in RC-165N/hTERT cells suggest that whereas some features of known AR functions are maintained in this benign prostatic tissue-derived cell line, other AR functions are not retained. Objective evaluations of similar cell lines will lead to the understanding of AR functions in prostate growth and differentiation. | [K-H Kim, A Dobi, S Shaheduzzaman, C L Gao, K Masuda, H Li, A Drukier, Y Gu, V Srikantan, J S Rhim, S Srivastava] | Prostate Cancer and Prostatic Diseases | 2006-10-31 | |
| naturepublishinggroup10.1038/nbt1255 | Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance | Plant microRNAs (miRNAs) regulate the abundance of target mRNAs by guiding their cleavage at the sequence complementary region. We have modified an Arabidopsis thaliana miR159 precursor to express artificial miRNAs (amiRNAs) targeting viral mRNA sequences encoding two gene silencing suppressors, P69 of turnip yellow mosaic virus (TYMV) and HC-Pro of turnip mosaic virus (TuMV). Production of these amiRNAs requires A. thaliana DICER-like protein 1. Transgenic A. thaliana plants expressing amiR-P69159 and amiR-HC-Pro159 are specifically resistant to TYMV and TuMV, respectively. Expression of amiR-TuCP159 targeting TuMV coat protein sequences also confers specific TuMV resistance. However, transgenic plants that express both amiR-P69159 and amiR-HC-Pro159 from a dimeric pre-amiR-P69159/amiR-HC-Pro159 transgene are resistant to both viruses. The virus resistance trait is displayed at the cell level and is hereditable. More important, the resistance trait is maintained at 15 °C, a temperature that compromises small interfering RNA–mediated gene silencing. The amiRNA-mediated approach should have broad applicability for engineering multiple virus resistance in crop plants. | [Qi-Wen Niu, Shih-Shun Lin, Jose Luis Reyes, Kuan-Chun Chen, Hui-Wen Wu, Shyi-Dong Yeh, Nam-Hai Chua] | Nature Biotechnology | 2006-10-22 | 7.3.1 |
| naturepublishinggroup10.1038/sj.emboj.7601390 | Genome-wide characterization of fission yeast DNA replication origins | Eukaryotic DNA replication is initiated from multiple origins of replication, but little is known about the global regulation of origins throughout the genome or in different types of cell cycles. Here, we identify 401 strong origins and 503 putative weaker origins spaced in total every 14 kb throughout the genome of the fission yeast Schizosaccharomyces pombe. The same origins are used during premeiotic and mitotic S-phases. We found that few origins fire late in mitotic S-phase and that activating the Rad3 dependent S-phase checkpoint by inhibiting DNA replication had little effect on which origins were fired. A genome-wide analysis of eukaryotic origin efficiencies showed that efficiency was variable, with large chromosomal domains enriched for efficient or inefficient origins. Average efficiency is twice as high during mitosis compared with meiosis, which can account for their different S-phase lengths. We conclude that there is a continuum of origin efficiency and that there is differential origin activity in the mitotic and meiotic cell cycles. | [Christian Heichinger, Christopher J Penkett, J|[uuml]|rg B|[auml]|hler, Paul Nurse] | The EMBO Journal | 2006-10-19 | |
| naturepublishinggroup10.1038/sj.tpj.6500420 | Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach | We describe a comprehensive translational approach for identifying candidate genes for alcoholism. The approach relies on the cross-matching of animal model brain gene expression data with human genetic linkage data, as well as human tissue data and biological roles data, an approach termed convergent functional genomics. An analysis of three animal model paradigms, based on inbred alcohol-preferring (iP) and alcohol-non-preferring (iNP) rats, and their response to treatments with alcohol, was used. A comprehensive analysis of microarray gene expression data from five key brain regions (frontal cortex, amygdala, caudate–putamen, nucleus accumbens and hippocampus) was carried out. The Bayesian-like integration of multiple independent lines of evidence, each by itself lacking sufficient discriminatory power, led to the identification of high probability candidate genes, pathways and mechanisms for alcoholism. These data reveal that alcohol has pleiotropic effects on multiple systems, which may explain the diverse neuropsychiatric and medical pathology in alcoholism. Some of the pathways identified suggest avenues for pharmacotherapy of alcoholism with existing agents, such as angiotensin-converting enzyme (ACE) inhibitors. Experiments we carried out in alcohol-preferring rats with an ACE inhibitor show a marked modulation of alcohol intake. Other pathways are new potential targets for drug development. The emergent overall picture is that physical and physiological robustness may permit alcohol-preferring individuals to withstand the aversive effects of alcohol. In conjunction with a higher reactivity to its rewarding effects, they may able to ingest enough of this nonspecific drug for a strong hedonic and addictive effect to occur. | [Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu] | The Pharmacogenomics Journal | 2006-10-10 | |
| naturepublishinggroup10.1038/sj.leu.2404403 | Prognostic value of chromosome 1q21 gain by fluorescent in situ hybridization and increase CKS1B expression in myeloma | A specific role for increased level of expression of CKS1B, as a consequence of chromosome 1q21 copy number gain, has been postulated as both pathogenic, as well as a powerful clinical prognostic factor in multiple myeloma (MM). The purpose of this study is to determine the clinical associations and prognostic impact of copy number gain at chromosome 1q21 (with a bacteria artificial chromosome clone containing CKS1B) and CKS1B gene level of expression in MM. We studied the chromosome region 1q21 for copy number change in a cohort of myeloma patients treated by high-dose therapy with stem-cell rescue (HDT) (n=159). A separate cohort of patients, treated by HDT was studied for CKS1B messenger RNA expression by gene expression profiling (n=67). 1q21 gain was then correlated with clinical parameters and survival. Gain of 1q21 copy number was detected in about a third of MM and was associated with more proliferative disease and poor-risk cytogenetic categories such as t(4;14), and chromosome 13 deletion. Both 1q21 gain and increase gene expression level were significantly associated with reduced survival. However, neither is an independent prognostic marker in MM on multivariate Cox proportional hazard analysis. | [R Fonseca, S A Van Wier, W J Chng, R Ketterling, M Q Lacy, A Dispenzieri, P L Bergsagel, S V Rajkumar, P R Greipp, M R Litzow, T Price-Troska, K J Henderson, G J Ahmann, M A Gertz] | Leukemia | 2006-10-05 | |
| naturepublishinggroup10.1016/j.ymthe.2006.03.024 | Multiple Innate Inflammatory Responses Induced after Systemic Adenovirus Vector Delivery Depend on a Functional Complement System | Excessive complement activation can result in extreme tissue damage and systemic inflammatory responses, similar to innate immune responses rapidly elicited after systemic adenovirus (Ad) injections. To determine if Ad interactions with the complement system impact upon Ad-induced innate immune responses, we injected Ad into complement-deficient, C3-knockout mice (C3-KO) or wild-type mice (WT) and quantitatively compared multiple anti-Ad innate immune responses in both strains of mice. In Ad-treated WT mice, we noted rapid increases in plasma KC levels (1 h post injection), followed by increases in IL-6, IFN-, RANTES, IL-12(p40), IL-5, G-CSF, and GM-CSF and subsequently thrombocytopenia. Conversely, in Ad-treated C3-KO mice, many of these inflammatory responses were significantly blunted, including the avoidance of Ad-induced thrombocytopenia. Global liver transcriptome responses in Ad-treated WT mice were assessed by RT-PCR-validated gene array analysis and were found to be also significantly affected by the lack of complement activity in Ad-treated C3-KO mice. Finally, our results confirmed the ability of high dose Ads to transduce hepatocytes despite a lack of complement activity. In summary, Ad interactions with the mammalian complement system are significant and likely initiate and/or exacerbate many of the inflammatory responses noted after systemic Ad injections. | [Anne Kiang, Zachary C. Hartman, Ruth S. Everett, Delila Serra, Haixiang Jiang, Michael M. Frank, Andrea Amalfitano] | Molecular Therapy | 2006-10-01 | |
| naturepublishinggroup10.1038/sj.onc.1210002 | Transforming function of the LSM1 oncogene in human breast cancers with the 8p11|[ndash]|12 amplicon | Amplification of the 8p11–12 region occurs in 15–20% of breast cancers, but the driving oncogene at this locus has yet to be definitively identified. We mapped the 8p11–12 amplicon in breast cancer cell lines and primary human breast cancers and identified the candidate oncogene human Sm-like protein (hLsm1, LSM1) based on increases in copy number and expression level relative to human mammary epithelial cells. To examine the oncogenic role of LSM1, we overexpressed this gene in MCF10A mammary epithelial cells and inhibited its production in the SUM44 breast cancer cell line, which has a natural amplification and overexpression of LSM1. Our data confirmed that LSM1 is an oncogene from the 8p11–12 amplicon by showing that hLsm1 overexpression induced growth factor-independent proliferation and soft agar colony formation in MCF10A cells, and hLsm1 inhibition in SUM44 cells dramatically reduced soft agar growth. Little is known about hLsm1 function other than its involvement in mRNA degradation; therefore, we used expression microarray analysis to investigate how hLsm1 affects cell transformation in MCF10A and SUM44 cells. We identified numerous genes altered following hLsm1 overexpression common to SUM44 breast cancer cells that play important roles in cell cycle regulation, cell proliferation and other cancer-promoting processes. Future work will continue to characterize these important changes to achieve a more complete understanding of the mechanism of hLsm1's effect on cancer progression. | [K L Streicher, Z Q Yang, S Draghici, S P Ethier] | Oncogene | 2006-09-25 | 7.0 |
| naturepublishinggroup10.1038/sj.leu.2404376 | Identification of a molecular signature for leukemic promyelocytes and their normal counterparts: focus on DNA repair genes | Acute promyelocytic leukemia (APL) is a clonal expansion of hematopoietic precursors blocked at the promyelocytic stage. Gene expression profiles of APL cells obtained from 16 patients were compared to eight samples of CD34+-derived normal promyelocytes. Malignant promyelocytes showed widespread changes in transcription in comparison to their normal counterpart and 1020 differentially expressed genes were identified. Discriminating genes include transcriptional regulators (FOS, JUN and HOX genes) and genes involved in cell cycle and DNA repair. The strong upregulation in APL of some transcripts (FLT3, CD33, CD44 and HGF) was also confirmed at protein level. Interestingly, a trend toward a transcriptional repression of genes involved in different DNA repair pathways was found in APL and confirmed by real-time polymerase chain reactor (PCR) in a new set of nine APLs. Our results suggest that both inefficient base excision repair and recombinational repair might play a role in APLs development. To investigate the expression pathways underlying the development of APL occurring as a second malignancy (sAPL), we included in our study eight cases of sAPL. Although both secondary and de novo APL were characterized by a strong homogeneity in expression profiling, we identified a small set of differentially expressed genes that discriminate sAPL from de novo cases. | [I Casorelli, E Tenedini, E Tagliafico, M F Blasi, A Giuliani, M Crescenzi, E Pelosi, U Testa, C Peschle, L Mele, D Diverio, M Breccia, F Lo-Coco, S Ferrari, M Bignami] | Leukemia | 2006-09-21 | |
| naturepublishinggroup10.1038/nrm2020 | Auxin in action: signalling, transport and the control of plant growth and development | Hormones have been at the centre of plant physiology research for more than a century. Research into plant hormones (phytohormones) has at times been considered as a rather vague subject, but the systematic application of genetic and molecular techniques has led to key insights that have revitalized the field. In this review, we will focus on the plant hormone auxin and its action. We will highlight recent mutagenesis and molecular studies, which have delineated the pathways of auxin transport, perception and signal transduction, and which together define the roles of auxin in controlling growth and patterning. | [William D. Teale, Ivan A. Paponov, Klaus Palme] | Nature Reviews Molecular Cell Biology | 2006-09-20 | |
| naturepublishinggroup10.1038/msb4100083 | When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation | | [M T A P Kresnowati, W A van Winden, M J H Almering, A ten Pierick, C Ras, T A Knijnenburg, P Daran-Lapujade, J T Pronk, J J Heijnen, J M Daran] | Nature a - z index | 2006-09-12 | |
| naturepublishinggroup10.1038/nbt1242 | Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project | Microarray-based expression profiling experiments typically use either a one-color or a two-color design to measure mRNA abundance. The validity of each approach has been amply demonstrated. Here we provide a simultaneous comparison of results from one- and two-color labeling designs, using two independent RNA samples from the Microarray Quality Control (MAQC) project, tested on each of three different microarray platforms. The data were evaluated in terms of reproducibility, specificity, sensitivity and accuracy to determine if the two approaches provide comparable results. For each of the three microarray platforms tested, the results show good agreement with high correlation coefficients and high concordance of differentially expressed gene lists within each platform. Cumulatively, these comparisons indicate that data quality is essentially equivalent between the one- and two-color approaches and strongly suggest that this variable need not be a primary factor in decisions regarding experimental microarray design. | [Tucker A Patterson, Edward K Lobenhofer, Stephanie B Fulmer-Smentek, Patrick J Collins, Tzu-Ming Chu, Wenjun Bao, Hong Fang, Ernest S Kawasaki, Janet Hager, Irina R Tikhonova, Stephen J Walker, Liang Zhang, Patrick Hurban, Francoise de Longueville, James C Fuscoe, Weida Tong, Leming Shi, Russell D Wolfinger] | Nature Biotechnology | 2006-09-08 | |
| naturepublishinggroup10.1038/4421067a | Microarrays: Quality control | | [Michael Eisenstein] | Nature a - z index | 2006-08-30 | |
| naturepublishinggroup10.1038/sj.leu.2404358 | Identification of a molecular signature predictive of sensitivity to differentiation induction in acute myeloid leukemia | Acute myeloid leukemia (AML) blasts are immature committed myeloid cells unable to spontaneously undergo terminal maturation, and characterized by heterogeneous sensitivity to natural differentiation inducers. Here, we show a molecular signature predicting the resistance or sensitivity of six myeloid cell lines to differentiation induced in vitro with retinoic acid or vitamin D. The identified signature was further validated by TaqMan assay for the prediction of response to an in vitro differentiation assay performed on 28 freshly isolated AML blast populations. The TaqMan assay successfully predicts the in vitro resistance or responsiveness of AML blasts to differentiation inducers. Furthermore, performing a meta-analysis of publicly available microarray data sets, we also show the accuracy of our prediction on known phenotypes and suggest that our signature could become useful for the identification of patients eligible for new therapeutic strategies. | [E Tagliafico, E Tenedini, R Manfredini, A Grande, F Ferrari, E Roncaglia, S Bicciato, R Zini, S Salati, E Bianchi, C Gemelli, M Montanari, T Vignudelli, T Zanocco-Marani, S Parenti, P Paolucci, G Martinelli, P P Piccaluga, M Baccarani, G Specchia, U Torelli, S Ferrari] | Leukemia | 2006-08-17 | |
| naturepublishinggroup10.1038/sj.jid.5700517 | Cutaneous Gene Expression by DNA Microarray in Murine Sclerodermatous Graft-Versus-Host Disease, a Model for Human Scleroderma | The molecular mechanisms governing skin fibrosis in murine sclerodermatous graft-versus-host disease (Scl GVHD) are not known. We used Affymetrix DNA microarrays representing >14,000 mouse genes to characterize global gene expression in skin during development of Scl GVHD in lethally irradiated BALB/c (H-2d) mice transplanted with B10.D2 (H-2d) bone marrow and spleen cells. These mice develop skin thickening, whereas control mice transplanted with syngeneic BALB/c (H-2d) bone marrow and spleen cells do not develop disease. We found consistent differences between mice with Scl GVHD and controls in cytokine messenger RNAs (mRNAs) for both Th1-like (IFN-) and Th2-like (IL-6, Il-10, and IL-13) inflammatory patterns. mRNAs for chemokines CCL2, CCL5, CCL17, IFN- inducible chemokines (CXCL9/Mig, CXCL10/IP-10, and CXCL11/I-TAC), and for growth factors such as platelet-derived growth factor-c, connective tissue growth factor, fibroblast growth factor 1, epidermal growth factor, nerve growth factor-, vascular endothelial growth factor (VEGF)-, and VEGF- were elevated, similar to human scleroderma. mRNAs for cell adhesion molecules, such as L-selectin (selectin lymphocyte), P-selectin (selectin platelet), E-selectin (selectin endothelium), and vascular cell adhesion molecule 1, were also upregulated. In separate experiments, we confirmed the increased synthesis of IFN- and IL-2, unchanged IL-10, and absence of tumor necrosis factor-, and IL-4 proteins by flow cytometry of isolated skin T cells. These constellations of immunologic changes provide a "fingerprint" for fibrosing autoimmune disease. They are useful to understand the pathogenesis of Scl GVHD, to identify markers for early diagnosis of disease, and to devise more effective strategies for intervention in early scleroderma and Scl GVHD. | [Lixin Zhou, David Askew, Caiyun Wu, Anita C Gilliam] | Journal of Investigative Dermatology | 2006-08-17 | |
| naturepublishinggroup10.1038/sj.onc.1209898 | A genomic analysis of adult T-cell leukemia | Adult T-cell leukemia (ATL) is an intractable malignancy of CD4+ T cells that is etiologically associated with infection by human T-cell leukemia virus-type I. Most individuals in the chronic stage of ATL eventually undergo progression to a highly aggressive acute stage. To clarify the mechanism responsible for this stage progression, we isolated CD4+ cells from individuals in the chronic (n=19) or acute (n=22) stages of ATL and subjected them to profiling of gene expression with DNA microarrays containing >44 000 probe sets. Changes in chromosome copy number were also examined for 24 cell specimens with the use of microarrays harboring 50 000 probe sets. Stage-dependent changes in gene expression profile and chromosome copy number were apparent. Furthermore, expression of the gene for MET, a receptor tyrosine kinase for hepatocyte growth factor (HGF), was shown to be specific to the acute stage of ATL, and the plasma concentration of HGF was increased in individuals in either the acute or chronic stage. HGF induced proliferation of a MET-positive ATL cell line, and this effect was blocked by antibodies to HGF. The HGF-MET signaling pathway is thus a potential therapeutic target for ATL. | [Y L Choi, K Tsukasaki, M C O'Neill, Y Yamada, Y Onimaru, K Matsumoto, J Ohashi, Y Yamashita, S Tsutsumi, R Kaneda, S Takada, H Aburatani, S Kamihira, T Nakamura, M Tomonaga, H Mano] | Oncogene | 2006-08-14 | |
| naturepublishinggroup10.1038/sj.onc.1209854 | Role of E2F3 expression in modulating cellular proliferation rate in human bladder and prostate cancer cells | Amplification and overexpression of the E2F3 gene at 6p22 in human bladder cancer is associated with increased tumour stage, grade and proliferation index, and in prostate cancer E2F3 overexpression is linked to tumour aggressiveness. We first used small interfering RNA technology to confirm the potential importance of E2F3 overexpression in bladder cancer development. Knockdown of E2F3 expression in bladder cells containing the 6p22 amplicon strongly reduced the extent of bromodeoxyuridine (BrdU) incorporation and the rate of cellular proliferation. In contrast, knockdown of CDKAL1/FLJ20342, another proposed oncogene, from this amplicon had no effect. Expression cDNA microarray analysis on bladder cancer cells following E2F3 knockdown was then used to identify genes regulated by E2F3, leading to the identification of known E2F3 targets such as Cyclin A and CDC2 and novel targets including pituitary tumour transforming gene 1, Polo-like kinase 1 (PLK1) and Caveolin-2. For both bladder and prostate cancer, we have proposed that E2F3 protein overexpression may cooperate with removal of the E2F inhibitor retinoblastoma tumor suppressor protein (pRB) to drive cellular proliferation. In support of this model, we found that ectopic expression of E2F3a enhanced the BrdU incorporation, a marker of cellular proliferation rate, of prostate cancer DU145 cells, which lack pRB, but had no effect on the proliferation rate of PC3 prostate cancer cells that express wild-type pRB. BrdU incorporation in PC3 cells could, however, be increased by overexpressing E2F3a in cells depleted of pRB. When taken together, these observations indicate that E2F3 levels have a critical role in modifying cellular proliferation rate in human bladder and prostate cancer. | [A Y Olsson, A Feber, S Edwards, R te Poele, I Giddings, S Merson, C S Cooper] | Oncogene | 2006-08-14 | |
| naturepublishinggroup10.1038/ng1864 | Molecular analysis of flies selected for aggressive behavior | | [Herman A Dierick, Ralph J Greenspan] | Nature Genetics | 2006-08-13 | |
| naturepublishinggroup10.1038/ng1855 | Augmentation of tumor angiogenesis by a Myc-activated microRNA cluster | | [Michael Dews, Asal Homayouni, Duonan Yu, Danielle Murphy, Cinzia Sevignani, Erik Wentzel, Emma E Furth, William M Lee, Greg H Enders, Joshua T Mendell, Andrei Thomas-Tikhonenko] | Nature Genetics | 2006-07-30 | |
| naturepublishinggroup10.1038/sj.npp.1301162 | Differential Regulation of Immediate-Early Gene Expression in the Prefrontal Cortex of Rats with a High vs Low Behavioral Response to Methamphetamine | Methamphetamine (METH) administration mimics many of the symptoms of mania and can produce psychosis after chronic use. Both rodents and man display interindividual variation in response to METH. The molecular mechanisms underlying these differences might be relevant to both stimulant addiction and endogenous psychosis. We treated 50 Sprague–Dawley rats acutely with METH (4.0 mg/kg) and 10 control rats with saline, and measured their behavior for 3 h after drug administration. Animals were divided into high responders (HR) (top 20%) and low responders (LR) (lowest 20%) based on their stereotypy response. They were killed 24 h after injection. Total RNA was extracted from the prefrontal cortex (PFC) and the expression of approximately 30 000 transcripts were analyzed using Affymetrix 230 2.0 GeneChips. Real-time reverse transcription-polymerase chain reaction was used to validate the expression of a select group of genes. Forty-three genes exhibited significant differences in expression in HR vs LR 24 h after METH treatment including a group of immediate-early genes (IEGs) (eg, c-fos, junB, NGFI-B, serum-regulated glucocorticoid kinase). These IEG expression differences were accompanied by the significant downregulation of many of these genes compared to saline in the HR but not LR, suggesting a differential responsiveness of signal transduction pathways in these two groups of rats. In addition, the expression of other transcription factors in the PFC was significantly different in HR compared to LR. These gene expression changes may contribute to individual differences in responsiveness to stimulants and the development of mania and psychosis. | [Paul D Shilling, Ronald Kuczenski, David S Segal, Thomas B Barrett, John R Kelsoe] | Neuropsychopharmacology | 2006-07-19 | |
| naturepublishinggroup10.1038/ni1362 | Detection of pathogenic intestinal bacteria by Toll-like receptor 5 on intestinal CD11c+ lamina propria cells | | [Satoshi Uematsu, Myoung Ho Jang, Nicolas Chevrier, Zijin Guo, Yutaro Kumagai, Masahiro Yamamoto, Hiroki Kato, Nagako Sougawa, Hidenori Matsui, Hirotaka Kuwata, Hiroaki Hemmi, Cevayir Coban, Taro Kawai, Ken J Ishii, Osamu Takeuchi, Masayuki Miyasaka, Kiyoshi Takeda, Shizuo Akira] | Nature Immunology | 2006-07-09 | |
| naturepublishinggroup10.1038/sj.ki.5001624 | Altered vitamin D metabolism in type II diabetic mouse glomeruli may provide protection from diabetic nephropathy | The db/db mouse develops features of type II diabetes mellitus as the result of impaired signaling through its abnormal leptin receptor. In spite of accurate metabolic features of diabetes, renal disease manifestations in these mice are not as severe as in humans suggesting the presence of protective genes. There is a growing body of evidence in humans for the relevance of vitamin D in diabetes. Here we followed a large cohort of db/db mice and their non-diabetic db/+ littermates. Transcriptional profiling revealed significant upregulation of 23 genes involved in Ca2+ homeostasis and vitamin D metabolism in db/db glomeruli relative to db/+ glomeruli. Increased glomerular expression of vitamin D3 1-hydroxylase, vitamin D binding protein, calbindins D9K and D28K, and calcyclin mRNA was confirmed by quantitative reverse transcription–polymerase chain reaction in 20-, 36-, and 52-week-old db/db glomeruli. Although vitamin D3 1-hydroxylase protein was primarily expressed and upregulated in db/db renal tubules, it was also expressed in glomerular podocytes in vivo. Serum 1,25-dihydroxyvitamin D3 and urinary Ca2+ excretion were increased >3-fold in db/db mice compared to db/+ mice. Cultured glomerular podocytes had mRNA for vitamin D3 1-hydroxylase, vitamin D receptor, and calbindin D28K, each of which was increased in high glucose conditions. High glucose also led to enhanced production of fibronectin and collagen IV protein, which was blocked by 1,25-dihydroxyvitamin D3. These results show that vitamin D metabolism is altered in db/db mice leading to metabolic and transcriptional effects. The podocyte is affected by paracrine and potentially autocrine effects of vitamin D, which may explain why db/db mice are resistant to progressive diabetic nephropathy. | [Y Wang, J Zhou, A W Minto, B K Hack, J J Alexander, M Haas, Y C Li, C W Heilig, R J Quigg] | Kidney International | 2006-07-05 | |
| naturepublishinggroup10.1038/sj.onc.1209770 | Proteomic analysis reveals successive aberrations in protein expression from healthy mucosa to invasive head and neck cancer | Development of head and neck squamous cell carcinoma (HNSCC) is a multistep process and in many cases involves a phenomenon coined 'field cancerization'. In order to identify changes in protein expression occurring at different stages of tumorigenesis and field cancerization, we analysed 113 HNSCCs and 73 healthy, 99 tumor-distant and 18 tumor-adjacent squamous mucosae by SELDI-TOF-MS on IMAC30 ProteinChip Arrays. Forty-eight protein peaks were differentially expressed between healthy mucosa and HNSCC. Calgizarrin (S100A11), the Cystein proteinase inhibitor Cystatin A, Acyl-CoA-binding protein, Stratifin (14-3-3 sigma), Histone H4, - and -Hemoglobin, a C-terminal fragment of -hemoglobin and the -defensins 1–3 were identified by mass spectrometry. The -defensins showed various alterations in expression as validated by immunohistochemistry (IHC). Supervised prediction analysis revealed excellent classification of healthy mucosa (94.5% correctly classified) and tumor samples (92.9% correctly classified). Application of this classifier to the tumor-adjacent and tumor-distant mucosa samples disclosed dramatic changes: only 59.6% of the tumor-distant biopsies were classified as normal, 27.3% were predicted as aberrant or HNSCC. Strikingly, 72% of the tumor-adjacent mucosae were predicted as aberrant. These data provide evidence for the existence of genetically altered fields with inconspicuous histology. Comparison of the protein profiles in the tumor-distant-samples with clinical outcome of 32 patients revealed a significant association between aberrant profiles with tumor relapse events (P=0.018; Fisher's exact test, two-tailed). We conclude that proteomic profiling in conjunction with protein identification greatly outperforms histopathological diagnosis and may have significant predictive power for clinical outcome and personalized risk assessment. | [M Roesch-Ely, M Nees, S Karsai, A Ruess, R Bogumil, U Warnken, M Schn|[ouml]|lzer, A Dietz, P K Plinkert, C Hofele, F X Bosch] | Oncogene | 2006-07-03 | |
| naturepublishinggroup10.1038/sj.onc.1209778 | Serrated carcinomas form a subclass of colorectal cancer with distinct molecular basis | Serrated colorectal carcinomas (CRCs) are morphologically different from conventional CRCs and have been proposed to follow a distinct pathway of CRC formation. Despite studies of single molecular events in this tumor type, the diagnosis of serrated CRC relies on morphology and the putative unique biological character of these tumors has not been established. Here we show that the gene expression profiling of 37 CRCs separated serrated and conventional CRCs into two distinct branches in unsupervised hierarchical clustering (P-value 7.8 10-7), and revealed 201 differentially expressed genes representing potential biomarkers for serrated CRC. Immunohistochemistry was utilized to verify the key findings in the 37 CRCs examined by expression profiling, and a separate validation set of 37 serrated and 86 conventional CRCs was examined to evaluate the candidate biomarkers in an extended sample material. Ephrin receptor B2, hypoxia-inducible factor 1-alpha and patched appeared as proteins important for genesis of serrated CRC. This study establishes serrated CRCs as a biologically distinct subclass of CRC and represents a step forward in the molecular classification of these cancers. The study also provides a platform to understand the molecular basis of serrated CRC and in long term may contribute to the development of specific treatment options for this tumor type. | [P Laiho, A Kokko, S Vanharanta, R Salovaara, H Sammalkorpi, H J|[auml]|rvinen, J-P Mecklin, T J Karttunen, K Tuppurainen, V Davalos, S Schwartz, D Arango, M J M|[auml]|kinen, L A Aaltonen] | Oncogene | 2006-07-03 | |
| naturepublishinggroup10.1038/sj.leu.2404274 | Consensus guidelines for microarray gene expression analyses in leukemia from three European leukemia networks | A plethora of studies have documented that gene expression profiling using DNA microarrays for various types of hematological malignancies provides novel information, which may have diagnostic and prognostic implications. However, to successfully use microarrays for this purpose, the quality and reproducibility of the whole procedure need to be guaranteed. Critical steps of the method are handling, processing and storage of the leukemic sample, purification of tumor cells (or lack thereof), RNA extraction methods, quality control of RNA, labeling techniques, hybridization, washing, scanning, spot filtering, normalization and initial interpretation, and finally the biostatistical analysis. These items have been extensively discussed and evaluated in different multi-center quality rounds within the three networks, that is, I-BFM-SG, the German Competence Network 'Acute and Chronic Leukemias' and the European LeukemiaNet. Based on the exchange of knowledge and experience between the three networks over the last few years, we have formulated guidelines for performing microarray experiments in leukemia. We confine ourselves to leukemias, but many of these requirements also apply to lymphomas or other clinical samples, including solid tumors. | [F J T Staal, G Cario, G Cazzaniga, T Haferlach, M Heuser, W-K Hofmann, K Mills, M Schrappe, M Stanulla, L U Wingen, J J M van Dongen, B Schlegelberger] | Leukemia | 2006-06-08 | |
| naturepublishinggroup10.1038/sj.onc.1209715 | Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells | Progression of prostate cancer to androgen independence is suspected to involve the androgen and protein kinase A (PKA) signaling pathways. Here for the first time, the transcriptomes associated with each pathway and common transcriptional targets in response to stimulation of both pathways were identified in human prostate cancer cells using Affymetrix GeneChip technology (Human Genome U133 plus2). Statistically significant changes in the levels of 858 genes in response to androgen and 303 genes in response to activation of the PKA pathway were determined using GeneSpring software. Expression of a subset of these genes (22) that were transcriptional targets for the androgen and/or PKA pathways were validated by reverse transcriptase–polymerase chain reaction and Western blot analyses. Application of small interfering RNAs to the androgen receptor (AR) revealed that in addition to KLK3, levels of expression of KLK2 and SESN1 were regulated by AR activated by both the androgen and PKA signaling pathways. SESN1 was identified as a gene repressed by activated AR. These results provide a broad view of the effects of the androgen and PKA signaling pathways on the transcriptional program of prostate cancer cells and indicate that only a limited number of genes are targeted by cross-talk between AR and PKA pathways. | [G Wang, S J M Jones, M A Marra, M D Sadar] | Oncogene | 2006-06-05 | |
| naturepublishinggroup10.1038/sj.jid.5700310 | Prominent Production of IL-20 by CD68|[plus]||[sol]|CD11c|[plus]| Myeloid-Derived Cells in Psoriasis: Gene Regulation and Cellular Effects | We assessed expression of IL-20 and its receptors in psoriasis, given the recent implication of IL-20 in epidermal hyperplasia. Psoriatic lesional (LS) skin consistently expressed more IL-20 mRNA than nonlesional (NL) skin. Immunoreactivity to IL-20 protein was greater in LS tissue and mainly localized to infiltrating CD68+/CD11c+ (myeloid-derived) dermal leukocytes. Because this contrasted with earlier reports of a keratinocyte source, we assessed IL-20 mRNA expression in a variety of cells in vitro, and confirmed a myeloid-derived cellular source (monocytes). Plastic adhesion, activation of 2 integrins, and incubation with tumor necrosis factor- stimulated expression in these cells. IL-20 receptor (IL-20R) and IL-20R mRNA was decreased in LS versus NL skin, which also contrasted with earlier findings. To investigate the relationship between IL-20 and disease activity, we examined psoriasis patients treated with the CD2-targeted agent alefacept. In therapeutic responders, lesional IL-20 mRNA decreased to NL levels, suggesting that CD2+ leukocytes may proximally regulate IL-20. Finally, to assess IL-20 function, we used microarrays to screen IL-20-treated keratinocytes, which demonstrated upregulation of disease-related and IFN--induced genes. Hence, IL-20 may influence inflammation through IFN-like effects. Together, these data indicate that IL-20 may be an important effector cytokine in psoriasis, and that its inhibition may represent a potential therapeutic target. | [Frank Wang, Edmund Lee, Michelle A Lowes, Asifa S Haider, Judilyn Fuentes-Duculan, Maria Veronica Abello, Francesca Chamian, Irma Cardinale, James G Krueger] | Journal of Investigative Dermatology | 2006-04-27 | |
| naturepublishinggroup10.1038/sj.ejhg.5201631 | Localization of candidate regions for a novel gene for Kartagener syndrome | Asymmetric positioning of internal organs is a characteristics of vertebrates. The normal left-right anatomic positioning, situs solitus, sometimes does not occur normaly, leading to laterality defects. Studies in animal models have shown that laterality decisions are mediated by a cascade of genes that lead to the asymmetric expression of Nodal, LEFTA, LEFTB and PITX2 in the lateral plate mesoderm. A search for mutations in genes implicated in left–right patterning in animal models allowed genes associated with heterotaxia defects in humans to be identified. However, these genes explain only a small percentage of human situs defects, suggesting that other genes must play a role. In this study, we report a consanguineous family of Turkish origin, composed of two unaffected parents and three children, two of whom presented Kartagener syndrome. On the basis of their family history, we hypothesize autosomal recessive mode of inheritance. A genotype analysis with polymorphic markers did not show linkage with any known genes or loci causing laterality disorders. Array CGH did not detect a duplication or microdeletion greater than 1 Mb as a possible cause. Genome wide screening using 10 K Affymetrix SNP chips was performed, allowing the identification of two regions of autozygosity, one in chromosome 1 and the other on chromosome 7. In the chromosome 1 locus, a strong candidate gene, encoding the kinesin-associated protein 3 (KIF3AP) was not mutated, based on SSCP/heteroduplex analysis and direct sequencing. These data provide a basis for the identification of a novel gene implicated in Kartagener syndrome. | [Ilse Gutierrez-Roelens, Thierry Sluysmans, Mark Jorissen, Mustapha Amyere, Miikka Vikkula] | European Journal of Human Genetics | 2006-04-26 | |
| naturepublishinggroup10.1038/sj.jid.5700224 | Heterogeneous Abnormalities of CCND1 and RB1 in Primary Cutaneous T-Cell Lymphomas Suggesting Impaired Cell Cycle Control in Disease Pathogenesis | Upregulation of cyclin D1/B-cell leukemia/lymphoma 1 (CCND1/BCL1) is present in most mantle cell lymphomas with the t(11;14)(q13;q32) translocation. However, little is known about the abnormalities of CCND1 and its regulator RB1 in primary cutaneous T-cell lymphomas (CTCL). We analyzed CCND and RB status in CTCL using fluorescent in situ hybridization (FISH), immunohistochemistry (IHC), and Affymetrix expression microarray. FISH revealed loss of CCND1/BCL1 in five of nine Sézary syndrome (SS) cases but gain in two cases, and RB1 loss in four of seven SS cases. IHC showed absent CCND1/BCL1 expression in 18 of 30 SS, 10 of 23 mycosis fungoides (MF), and three of 10 primary cutaneous CD30+ anaplastic large-cell lymphoma (C-ALCL). Increased CCND1/BCL1 expression was seen in nine MF, seven C-ALCL, and six SS cases. Absent RB1 expression was detected in 8 of 12 MF and 7 of 9 SS cases, and raised RB1 expression in 7 of 8 C-ALCL. Affymetrix revealed increased gene expression of CCND2 in four of eight CTCL cases, CCND3 in three cases, and CDKN2C in two cases with a normal expression of CCND1 and RB1. These findings suggest heterogeneous abnormalities of CCND and RB in CTCL, in which dysregulated CCND and RB1 may lead to impaired cell cycle control. | [Xin Mao, Guy Orchard, Eric C Vonderheid, Peter C Nowell, Martine Bagot, Armand Bensussan, Robin Russell-Jones, Bryan D Young, Sean J Whittaker] | Journal of Investigative Dermatology | 2006-04-13 | |
| naturepublishinggroup10.1038/sj.onc.1209502 | Oncogenic HRAS suppresses clusterin expression through promoter hypermethylation | Silencing of gene expression by methylation of CpG islands in regulatory elements is frequently observed in cancer. However, an influence of the most common oncogenic signalling pathways onto DNA methylation has not yet been investigated thoroughly. To address this issue, we identified genes suppressed in HRAS-transformed rat fibroblasts but upregulated after treatment with the demethylating agent 5-Aza-2-deoxycytidine and with the MEK1,2 inhibitor U0126. Analysis of gene expression by microarray and Northern blot analysis revealed the MEK/ERK target genes clusterin, matrix metalloproteinase 2 (Mmp2), peptidylpropyl isomerase C-associated protein, syndecan 4, Timp2 and Thbs1 to be repressed in the HRAS-transformed FE-8 cells in a MEK/ERK- and methylation-dependent manner. Hypermethylation of putative regulatory elements in HRAS-transformed cells as compared to immortalized fibroblasts was detected within a CpG island 14.5 kb upstream of clusterin, within the clusterin promoter and within a CpG island of the Mmp2 promoter by bisulphite sequencing. Furthermore, hypermethylation of the clusterin promoter was observed 10 days after induction of HRAS in immortalized rat fibroblasts and a clear correlation between reduced clusterin expression and hypermethlyation could also be observed in distinct rat tissues. These results suggest that silencing of individual genes by DNA methylation is controlled by oncogenic signalling pathways, yet the mechanisms responsible for initial target gene suppression are variable. | [P Lund, K Wei|[szlig]|haupt, T Mikeska, D Jammas, X Chen, R-J Kuban, U Ungeth|[uuml]|m, U Krapfenbauer, H-P Herzel, R Sch|[auml]|fer, J Walter, C Sers] | Oncogene | 2006-03-27 | |
| naturepublishinggroup10.1038/sj.onc.1209497 | Characterization of an imatinib-sensitive subset of high-grade human glioma cultures | High-grade gliomas, including glioblastomas, are malignant brain tumors for which improved treatment is urgently needed. Genetic studies have demonstrated the existence of biologically distinct subsets. Preliminary studies have indicated that platelet-derived growth factor (PDGF) receptor signaling contributes to the growth of some of these tumors. In this study, human high-grade glioma primary cultures were analysed for sensitivity to treatment with the PDGF receptor inhibitor imatinib/Glivec/Gleevec/STI571. Six out of 15 cultures displayed more than 40% growth inhibition after imatinib treatment, whereas seven cultures showed less than 20% growth inhibition. In the sensitive cultures, apoptosis contributed to growth inhibition. Platelet-derived growth factor receptor status correlated with imatinib sensitivity. Supervised analyses of gene expression profiles and real-time PCR analyses identified expression of the chemokine CXCL12/SDF-1 (stromal cell-derived factor 1) as a predictor of imatinib sensitivity. Exogenous addition of CXCL12 to imatinib-insensitive cultures conferred some imatinib sensitivity. Finally, coregulation of CXCL12 and PDGF -receptor was observed in glioblastoma biopsies. We have thus defined the characteristics of a novel imatinib-sensitive subset of glioma cultures, and provided evidence for a functional relationship between imatinib sensitivity and chemokine signaling. These findings will assist in the design and evaluation of clinical trials exploring therapeutic effects of imatinib on malignant brain tumors. | [D H|[auml]|gerstrand, G Hesselager, S Achterberg, U Wickenberg Bolin, M Kowanetz, M Kastemar, C-H Heldin, A Isaksson, M Nist|[eacute]|r, A |[Ouml]|stman] | Oncogene | 2006-03-20 | |
| naturepublishinggroup10.1038/sj.gene.6364294 | Overlapping BXSB congenic intervals, in combination with microarray gene expression, reveal novel lupus candidate genes | The BXSB mouse strain is an important model of glomerulonephritis observed in systemic lupus erythematosus (SLE). Linkage studies have successfully identified disease-susceptibility intervals; however, extracting the identity of the susceptibility gene(s) in such regions is the crucial next step. Congenic mouse strains present a defined genetic resource that is highly amenable to microarray analysis. We have performed microarray analysis using a series of chromosome 1 BXSB congenic mice with partially overlapping disease-susceptibility intervals. Simultaneous comparison of the four congenic lines allowed the identification of expression differences associated with both the initiation and progression of disease. Thus, we have identified a number of novel SLE disease gene candidates and have confirmed the identity of Ifi202 as a disease candidate in the BXSB strain. Sequencing of the promoter regions of Gas5 has revealed polymorphisms in the BXSB strain, which may account for the differential expression profile. Furthermore, the combination of the microarray results with the different phenotypes of these mice has allowed the identification of a number of expression differences that do not necessarily map to the congenic interval, but may be implicated in disease pathways. | [M E K Haywood, S J Rose, S Horswell, M J Lees, G Fu, M J Walport, B J Morley] | Genes and Immunity | 2006-03-16 | |
| naturepublishinggroup10.1038/sj.onc.1209494 | AURKA is one of the downstream targets of MAPK1|[sol]|ERK2 in pancreatic cancer | DUSP6/MKP-3, a specific inhibitor of MAPK1/ERK2, frequently loses its expression in primary pancreatic cancer tissues. This evidence suggests that constitutive activation of MAPK1 synergistically induced by frequent mutation of KRAS2 and the loss of function of DUSP6 plays key roles in pancreatic carcinogenesis and progression. By profiling of gene expressions associated with downregulation of MAPK1 induced by exogenous overexpression of DUSP6 in pancreatic cancer cells, we found that AURKA/STK15, the gene encoding Aurora-A kinase, which plays key roles in cellular mitosis, was among the downregulated genes along with its related genes, which included AURKB, TPX2 and CENPA. An association of expression and promoter activity of AURKA with MAPK activity was verified. Knockdown of ETS2 resulted in a reduction of AURKA expression. These results indicate that AURKA is a direct target of the MAPK pathway and that its overexpression in pancreatic cancer is induced by hyperactivation of the pathway, at least via ETS2. | [T Furukawa, N Kanai, H O Shiwaku, N Soga, A Uehara, A Horii] | Oncogene | 2006-03-13 | |
| naturepublishinggroup10.1038/ncpcardio0429 | Derivation of a cardiopoietic population from human mesenchymal stem cells yields cardiac progeny | | [Atta Behfar, Andre Terzic] | Nature a - z index | 2006-03-01 | |
| naturepublishinggroup10.1038/sj.onc.1209415 | An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen | Little is known of the underlying biology of estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer (BC), and few targeted therapies are available. Clinical heterogeneity of ER(-)/PR(-) tumors suggests that molecular subsets exist. We performed genome-wide expression analysis of 99 primary BC samples and eight BC cell lines in an effort to reveal distinct subsets, provide insight into their biology and potentially identify new therapeutic targets. We identified a subset of ER(-)/PR(-) tumors with paradoxical expression of genes known to be either direct targets of ER, responsive to estrogen, or typically expressed in ER(+) BC. Differentially expressed genes included SPDEF, FOXA1, XBP1, CYB5, TFF3, NAT1, APOD, ALCAM and AR (P<0.001). A classification model based on the expression signature of this tumor class identified molecularly similar BCs in an independent human BC data set and among BC cell lines (MDA-MB-453). This cell line demonstrated a proliferative response to androgen in an androgen receptor-dependent and ER-independent manner. In addition, the androgen-induced transcriptional program of MDA-MB-453 significantly overlapped the molecular signature of the unique ER(-)/PR(-) subclass of human tumors. This subset of BCs, characterized by a hormonally regulated transcriptional program and response to androgen, suggests the potential for therapeutic strategies targeting the androgen signaling pathway. | [A S Doane, M Danso, P Lal, M Donaton, L Zhang, C Hudis, W L Gerald] | Oncogene | 2006-02-20 | |
| naturepublishinggroup10.1038/sj.onc.1209442 | Identification of tumor markers and differentiation markers for molecular diagnosis of lung adenocarcinoma | To identify tumor markers and differentiation markers for lung adenocarcinoma (AdC), we analysed expression profiles of 14 500 genes against three cases of type II alveolar epithelial cells, bronchiolar epithelial cells, and bronchial epithelial cells, respectively, and 10 cases of AdC cells isolated by laser capture microdissection. Hierarchical clustering analysis indicated that AdC cells and noncancerous lung epithelial cells are significantly different in their expression profiles, and that different sets of differentiation markers are expressed among alveolar, bronchiolar and bronchial epithelial cells. Nine genes were identified as being highly expressed in AdC cells, but not expressed in noncancerous lung epithelial cells. Sixteen genes were identified as differentiation markers for lung epithelial cells. Real-time RT–PCR analysis of 45 lung AdC cases further revealed that expression of four tumor markers in AdC cells was significantly higher than that in noncancerous lung cells and that expression of ten differentiation markers was retained in a considerable fraction of lung AdC cases. Five tumor markers and seven differentiation markers were not expressed in peripheral blood cells. Similarities and differences in expression profiles between normal epithelial cells from different lung respiratory compartments and AdC cells demonstrated in this study will be informative for the molecular diagnosis of lung AdC. | [N Nakamura, K Kobayashi, M Nakamoto, T Kohno, H Sasaki, Y Matsuno, J Yokota] | Oncogene | 2006-02-20 | |
| naturepublishinggroup10.1038/sj.onc.1209418 | ST7-mediated suppression of tumorigenicity of prostate cancer cells is characterized by remodeling of the extracellular matrix | Multiple lines of evidence have provided compelling evidence for the existence of a tumor suppressor gene (TSG) on chromosome 7q31.1. ST7 may be the target of this genetic instability but its designation as a TSG is controversial. In this study, we show that, functionally, ST7 behaves as a tumor suppressor in human cancer. ST7 suppressed growth of PC-3 prostate cancer cells inoculated subcutaneously into severe combined immunodeficient mice, and increased the latency of tumor detection from 13 days in control tumors to 23 days. Re-expression of ST7 was also associated with suppression of colony formation under anchorage-independent conditions in MDA-MB-231 breast cancer cells and ST7 mRNA expression was downregulated in 44% of primary breast cancers. Expression profiling of PC-3 cells revealed that ST7 predominantly induces changes in genes involved in re-modeling the extracellular matrix such as SPARC, IGFBP5 and several matrix metalloproteinases. These data indicate that ST7 may mediate tumor suppression through modification of the tumor microenvironment. | [Cs-F Hooi, C Blancher, W Qiu, I M Revet, L H Williams, M L Ciavarella, R L Anderson, E W Thompson, A Connor, W A Phillips, I G Campbell] | Oncogene | 2006-02-13 | |
| naturepublishinggroup10.1038/sj.jid.5700157 | Genomic Analysis Defines a Cancer-Specific Gene Expression Signature for Human Squamous Cell Carcinoma and Distinguishes Malignant Hyperproliferation from Benign Hyperplasia | Using high-density oligonucleotide arrays, we measured expression of >12,000 genes in surgical excisions of invasive human squamous cell carcinomas (SCCs) versus site-matched control skin. This analysis defined >1,900 genes with altered expression in SCCs that were statistically different from controls. As SCCs are composed of epithelial cells, which are both hyperplastic and invasive, we sought to define gene sets associated with these biologic processes by comparing gene expression to psoriasis vulgaris, which is a condition of benign keratinocyte hyperplasia without invasiveness or pre-malignant potential. Through this analysis, we found genes that were commonly upregulated in both conditions and unique genes with increased expression in SCCs. Differential gene regulation in these two conditions was confirmed by real-time reverse transcription-PCR and immunohistochemistry. We found that benign hyperplasia is associated with upregulation of genes including DEFB4 (defensin B4), SERPINB3 (serine proteinase inhibitor, member 3), STAT1 (signal transducer and activator of transcription 1), K16 (keratin 16), CEACAMs (carcinoembryonic antigen-related cell adhesion molecules), and WNT 5A (wingless-type MMTV integration site family, member 5A). WNT receptor frizzled homolog 6 (FZD6) and prostaglandin-metabolizing enzyme hydroxyprostaglandin dehydrogenase were increased in SCC alone. Growth factor pleiotrophin (PTN) was expressed at higher levels in non-tumor-bearing skin adjacent to excised SCC. SCC was further characterized by upregulation of matrix metalloproteinases 1, 10, and 13, cathepsin L2, cystatin E/M as well as STAT3 and microseminoprotein, beta (MSMB), and downregulation of inducible nitric oxide synthase, granzyme B, CD8, and CD83. The current study defines a unique gene expression signature for cutaneous SCC in humans and suggests potential roles for WNT, FZD, and PTN in the pathogenesis of SCC. | [Asifa S Haider, Sara B Peters, Helen Kaporis, Irma Cardinale, Ji Fei, Jurg Ott, Miki Blumenberg, Ann M Bowcock, James G Krueger, John A Carucci] | Journal of Investigative Dermatology | 2006-02-09 | |
| naturepublishinggroup10.1038/sj.cdd.4401860 | Virally mediated MafB transduction induces the monocyte commitment of human CD34|[plus]| hematopoietic stem|[sol]|progenitor cells | Upregulation of specific transcription factors is a generally accepted mechanism to explain the commitment of hematopoietic stem cells along precise maturation lineages. Based on this premise, transduction of primary hematopoietic stem/progenitor cells with viral vectors containing the investigated transcription factors appears as a suitable experimental model to identify such regulators. Although MafB transcription factor is believed to play a role in the regulation of monocytic commitment, no demonstration is, to date, available supporting this function in normal human hematopoiesis. To address this issue, we retrovirally transduced cord blood CD34+ hematopoietic progenitors with a MafB cDNA. Immunophenotypic and morphological analysis of transduced cells demonstrated the induction of a remarkable monomacrophage differentiation. Microarray analysis confirmed these findings and disclosed the upregulation of macrophage-related transcription factors belonging to the AP-1, MAF, PPAR and MiT families. Altogether our data allow to conclude that MafB is a key regulator of human monocytopoiesis. | [C Gemelli, M Montanari, E Tenedini, T Zanocco Marani, T Vignudelli, M Siena, R Zini, S Salati, E Tagliafico, R Manfredini, A Grande, S Ferrari] | Cell Death & Differentiation | 2006-02-03 | |
| naturepublishinggroup10.1038/sj.gene.6364282 | Gingival epithelial cells heterozygous for Toll-like receptor 4 polymorphisms Asp299Gly and Thr399Ile are hypo-responsive to Porphyromonas gingivalis | The Toll-like receptor (TLR)4 is the major sensor for bacterial lipopolysaccharide and its two common co-segregating polymorphisms, Asp299Gly and Thr399Ile, which occur at a frequency of between 6 and 10%, have been associated with infectious diseases, LPS hypo-responsiveness and cardiovascular disease. Porphyromonas gingivalis is a Gram-negative bacterium implicated in chronic periodontitis and is a known TLR4 and TLR2 agonist. We obtained two gingival epithelial cell primary cultures from subjects heterozygous for the TLR4 polymorphism Asp299Gly and compared response characteristics with similar cells from patients (four) with the wild-type TLR4 genes. Cytokine responses and transcriptome profiles of gingival epithelial cell primary culture cells to TNF challenge were similar for all primary epithelial cell cultures. P. gingivalis challenge, however, gave markedly different responses for Asp299Gly heterozygous and wild-type epithelial cell cultures. The epithelial cells heterozygous for the TLR4 polymorphism Asp299Gly were functionally hypo-responsive, evidenced by differences in BD-2 mRNA expression, mRNA response profile by microarray analysis and by pro-inflammatory and chemokine cytokines at the protein and mRNA level. These findings emphasize variance in human epithelial cell TLRs, linked with Asp299Gly carriage, which results in a hypo-responsive epithelial cell phenotype less susceptible to Gram-negative diseases and associated systemic conditions. | [D F Kinane, H Shiba, P G Stathopoulou, H Zhao, D F Lappin, A Singh, M A Eskan, S Beckers, S Waigel, B Alpert, T B Knudsen] | Genes and Immunity | 2006-01-26 | |
| naturepublishinggroup10.1038/sj.onc.1209365 | Sustained trophism of the mammary gland is sufficient to accelerate and synchronize development of ErbB2|[sol]|Neu-induced tumors | Epidemiological studies indicate that parity enhances HER2/ErbB2/Neu-induced breast tumorigenesis. Furthermore, recent studies using multiparous, ErbB2/Neu-overexpressing mouse mammary tumor virus (MMTV-Neu) mice have shown that parity induces a population of cells that are targeted for ErbB2/Neu-induced transformation. Although parity accelerates mammary tumorigenesis, the pattern of tumor development in multiparous MMTV-Neu mice remains stochastic, suggesting that additional events are required for ErbB2/Neu to cause mammary tumors. Whether such events are genetic in nature or reflective of the dynamic hormonal control of the gland that occurs with pregnancy remains unclear. We postulated that young age at pregnancy initiation or chronic trophic maintenance of mammary epithelial cells might provide a cellular environment that significantly increases susceptibility to ErbB2/Neu-induced tumorigenesis. MMTV-Neu mice that were maintained pregnant or lactating beginning at 3 weeks of age demonstrated accelerated tumorigenesis, but this process was still stochastic, indicating that early pregnancy does not provide the requisite events of tumorigenesis. However, bitransgenic mice that were generated by breeding MMTV-Neu mice with a luteinizing hormone-overexpressing mouse model of ovarian hyperstimulation developed multifocal mammary tumors in an accelerated, synchronous manner compared to virgin MMTV-Neu animals. This synchrony of tumor development in the bitransgenic mice suggests that trophic maintenance of the mammary gland provides the additional events required for tumor formation and maintains the population of cells that are targeted by ErbB2/Neu for transformation. Both the synchrony of tumor appearance and the ability to characterize a window of commitment by ovariectomy/palpation studies permitted microarray analysis to evaluate changes in gene expression over a defined timeline that spans the progression from normal to preneoplastic mammary tissue. These approaches led to identification of several candidate genes whose expression changes in the mammary gland with commitment to ErbB2/Neu-induced tumorigenesis, suggesting that they may either be regulated by ErbB2/Neu and/or contribute to tumor formation. | [M D Landis, D D Seachrist, F W Abdul-Karim, R A Keri] | Oncogene | 2006-01-23 | |
| naturepublishinggroup10.1038/sj.bjc.6602933 | Gene expression profiling of primary cultures of ovarian epithelial cells identifies novel molecular classifiers of ovarian cancer | In order to elucidate the biological variance between normal ovarian surface epithelial (NOSE) and epithelial ovarian cancer (EOC) cells, and to build a molecular classifier to discover new markers distinguishing these cells, we analysed gene expression patterns of 65 primary cultures of these tissues by oligonucleotide microarray. Unsupervised clustering highlights three subgroups of tumours: low malignant potential tumours, invasive solid tumours and tumour cells derived from ascites. We selected 18 genes with expression profiles that enable the distinction of NOSE from these three groups of EOC with 92% accuracy. Validation using an independent published data set derived from tissues or primary cultures confirmed a high accuracy (87–96%). The distinctive expression pattern of a subset of genes was validated by quantitative reverse transcription–PCR. An ovarian-specific tissue array representing tissues from NOSE and EOC samples of various subtypes and grades was used to further assess the protein expression patterns of two differentially expressed genes (Msln and BMP-2) by immunohistochemistry. This study highlights the relevance of using primary cultures of epithelial ovarian cells as a model system for gene profiling studies and demonstrates that the statistical analysis of gene expression profiling is a useful approach for selecting novel molecular tumour markers. | [C Le Page, V Ouellet, J Madore, F Ren, T J Hudson, P N Tonin, D M Provencher, A-M Mes-Masson] | British Journal of Cancer | 2006-01-17 | |
| naturepublishinggroup10.1038/sj.ki.5000049 | Differential regulation of metzincins in experimental chronic renal allograft rejection: Potential markers and novel therapeutic targets | Chronic renal allograft rejection is characterized by alterations in the extracellular matrix compartment and in the proliferation of various cell types. These features are controlled, in part by the metzincin superfamily of metallo-endopeptidases, including matrix metalloproteinases (MMPs), a disintegrin and metalloproteinase (ADAM) and meprin. Therefore, we investigated the regulation of metzincins in the established Fisher to Lewis rat kidney transplant model. Studies were performed using frozen homogenates and paraffin sections of rat kidneys at day 0 (healthy controls) and during periods of chronic rejection at day +60 and day +100 following transplantation. The messenger RNA (mRNA) expression was examined by Affymetrix Rat Expression Array 230A GeneChip and by real-time Taqman polymerase chain reaction analyses. Protein expression was studied by zymography, Western blot analyses, and immunohistology. mRNA levels of MMPs (MMP-2/-11/-12/-14), of their inhibitors (tissue inhibitors of metalloproteinase (TIMP)-1/-2), ADAM-17 and transforming growth factor (TGF)-1 significantly increased during chronic renal allograft rejection. MMP-2 activity and immunohistological staining were augmented accordingly. The most important mRNA elevation was observed in the case of MMP-12. As expected, Western blot analyses also demonstrated increased production of MMP-12, MMP-14, and TIMP-2 (in the latter two cases as individual proteins and as complexes). In contrast, mRNA levels of MMP-9/-24 and meprin / had decreased. Accordingly, MMP-9 protein levels and meprin / synthesis and activity were downregulated significantly. Members of metzincin families (MMP, ADAM, and meprin) and of TIMPs are differentially regulated in chronic renal allograft rejection. Thus, an altered pattern of metzincins may represent novel diagnostic markers and possibly may provide novel targets for future therapeutic interventions. | [C C Berthier, N Lods, S A Joosten, C van Kooten, D Leppert, R L P Lindberg, A Kappeler, F Raulf, E E Sterchi, D Lottaz, H-P Marti] | Kidney International | 2006-01-01 | |
| naturepublishinggroup10.1038/sj.npp.1301002 | Chronic Olanzapine Treatment Causes Differential Expression of Genes in Frontal Cortex of Rats as Revealed by DNA Microarray Technique | Recent emerging biochemical data indicate that several important neuroregulatory genes and proteins may be involved in the etiology of schizophrenia and bipolar disorder. Additionally, the same genes appear to be targets of several psychotropic medications that are used to treat these disorders. Recent DNA microarray studies show that genes involved in synaptic neurotransmission, signal transduction, and glutamate/GABA regulation may be differentially regulated in brains of subjects with schizophrenia. We hypothesized that chronic administration of olanzapine to rats would alter expression of various genes that may be involved in the etiology of schizophrenia and mood disorders. Rats were administered olanzapine (N=20, 2 mg/kg/day) or sterile saline intraperitoneally (N=20) daily for 21 days. Control and olanzapine-treated frontal cortices were analyzed using cDNA microarray technology. The results showed significant downregulation of 31 genes and upregulation of 38 genes by greater than two-fold in the drug-treated brains vs controls. Our results provide evidence for altered regulation of genes involved with signal transduction and cell communication, metabolism and energy pathways, transport, immune response, nucleic acid metabolism, and neuronal growth factors. Real-time quantitative RT-PCR analysis verified the direction and magnitude of change in six genes of interest: calbindin 3, homer 1, regulator of G-protein signaling (RGS) 2, pyruvate kinase, Reelin and insulin 2. Western blotting showed significant upregulation in protein products for Reelin 410 and Reelin 180 kDa and downregulation for NMDA3B and RGS2. Our results show for the first time that olanzapine causes changes in levels of several important genes that may be involved in the etiology and treatment of schizophrenia and other psychiatric disorders. | [S Hossein Fatemi, Teri J Reutiman, Timothy D Folsom, Christopher Bell, Lisa Nos, Peter Fried, David A Pearce, Sushmita Singh, David P Siderovski, Francis S Willard, Mitsunori Fukuda] | Neuropsychopharmacology | 2006-01-11 | |
| naturepublishinggroup10.1038/sj.jcbfm.9600264 | Gene expression in blood changes rapidly in neutrophils and monocytes after ischemic stroke in humans: a microarray study | Ischemic brain and peripheral white blood cells release cytokines, chemokines and other molecules that activate the peripheral white blood cells after stroke. To assess gene expression in these peripheral white blood cells, whole blood was examined using oligonucleotide microarrays in 15 patients at 2.40.5, 5 and 24 h after onset of ischemic stroke and compared with control blood samples. The 2.4-h blood samples were drawn before patients were treated either with tissue-type plasminogen activator (tPA) alone or with tPA plus Eptifibatide (the Combination approach to Lysis utilizing Eptifibatide And Recombinant tPA trial). Most genes induced in whole blood at 2 to 3 h were also induced at 5 and 24 h. Separate studies showed that the genes induced at 2 to 24 h after stroke were expressed mainly by polymorphonuclear leukocytes and to a lesser degree by monocytes. These genes included: matrix metalloproteinase 9; S100 calcium-binding proteins P, A12 and A9; coagulation factor V; arginase I; carbonic anhydrase IV; lymphocyte antigen 96 (cluster of differentiation (CD)96); monocarboxylic acid transporter (6); ets-2 (erythroblastosis virus E26 oncogene homolog 2); homeobox gene Hox 1.11; cytoskeleton-associated protein 4; N-formylpeptide receptor; ribonuclease-2; N-acetylneuraminate pyruvate lyase; BCL6; glycogen phosphorylase. The fold change of these genes varied from 1.6 to 6.8 and these 18 genes correctly classified 10/15 patients at 2.4 h, 13/15 patients at 5 h and 15/15 patients at 24 h after stroke. These data provide insights into the inflammatory responses after stroke in humans, and should be helpful in diagnosis, understanding etiology and pathogenesis, and guiding acute treatment and development of new treatments for stroke. | [Yang Tang, Huichun Xu, XinLi Du, Lisa Lit, Wynn Walker, Aigang Lu, Ruiqiong Ran, Jeffrey P Gregg, Melinda Reilly, Art Pancioli, Jane C Khoury, Laura R Sauerbeck, Janice A Carrozzella, Judith Spilker, Joseph Clark, Kenneth R Wagner, Edward C Jauch, Dongwoo J Chang, Piero Verro, Joseph P Broderick, Frank R Sharp] | Journal of Cerebral Blood Flow & Metabolism | 2006-01-04 | |
| naturepublishinggroup10.1038/nature04225 | Hypomethylation-linked activation of PAX2 mediates tamoxifen-stimulated endometrial carcinogenesis | Tamoxifen, a selective oestrogen receptor modulator, has been used in the treatment of all stages of hormone-responsive breast cancer. However, tamoxifen shows partial oestrogenic activity in the uterus and its use has been associated with an increased incidence of endometrial cancer. The molecular explanation for these observations is not known. Here we show that tamoxifen and oestrogen have distinct but overlapping target gene profiles. Among the overlapping target genes, we identify a paired-box gene, PAX2, that is crucially involved in cell proliferation and carcinogenesis in the endometrium. Our experiments show that PAX2 is activated by oestrogen and tamoxifen in endometrial carcinomas but not in normal endometrium, and that this activation is associated with cancer-linked hypomethylation of the PAX2 promoter. | [Huijian Wu, Yupeng Chen, Jing Liang, Bin Shi, Ge Wu, Ying Zhang, Dan Wang, Ruifang Li, Xia Yi, Hua Zhang, Luyang Sun, Yongfeng Shang] | Nature | 2005-12-15 | |
| naturepublishinggroup10.1038/sj.onc.1209228 | DBC1 re-expression alters the expression of multiple components of the plasminogen pathway | Deleted in bladder cancer 1 (DBC1) is a candidate gene for the bladder tumour suppressor locus at 9q33.1. The function of the gene is currently unknown but a cross-species sequence comparison suggests an important role, as it is highly evolutionarily conserved. Here, we transfected a nonexpressing human bladder cancer cell line with a set of human DBC1 cDNA constructs. The effect on global expression patterns was assessed using cDNA microarrays. The cell clone with the lowest level of DBC1 expression showed induced expression of 26 genes including plasminogen activator inhibitor 2 (SERPINB5; 4.6-fold), heparin-binding EGF-like growth factor precursor (DTR; 4.2-fold), small proline-rich protein 2B (SPRR2B; 3.6-fold), metallothionein 1 isoforms (MT1B/MT1A/MT-1F; from 2.9- to 3.2-fold), tissue-type plasminogen activator precursor (PLAT; 2.8-fold) and urokinase-type plasminogen activator precursor (PLAU; 2.7-fold). In clustering analysis, both PLAT and PLAU clustered with the functionally related urokinase plasminogen activator surface receptor (PLAUR; 1.9-fold). Furthermore, 14 human bladder tumours were analysed by real-time quantitative PCR using gene-specific primers for selected (n=20) genes. The expression levels of SERPINB5, PLAU, PLAUR and MT1 correlated with the DBC1 levels, suggesting previously unknown involvement of DBC1 in the urokinase-plasminogen pathway. | [J P Louhelainen, C D Hurst, E Pitt, H Nishiyama, H A Pickett, M A Knowles] | Oncogene | 2005-12-12 | |
| naturepublishinggroup10.1038/sj.onc.1209283 | Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues | MicroRNAs (miRNAs) are a non-coding family of genes involved in post-transcriptional gene regulation. These transcripts are associated with cell proliferation, cell differentiation, cell death and carcinogenesis. We analysed the miRNA expression profiles in 25 pairs of hepatocellular carcinoma (HCC) and adjacent non-tumorous tissue (NT) and nine additional chronic hepatitis (CH) specimens using a human miRNA microarray. Targets and references samples were co-hybridized to a microarray containing whole human mature and precursor miRNA sequences. Whereas three miRNAs exhibited higher expression in the HCC samples than that in the NT samples, five miRNAs demonstrated lower expression in the HCC samples than in the NT samples (P<0.0001). Classification of samples as HCC or NT by using support vector machine algorithms based on these data provided an overall prediction accuracy of 97.8% (45/46). In addition, the expression levels of four miRNAs were inversely correlated with the degree of HCC differentiation (P<0.01). A comparison of CH and liver cirrhosis samples revealed significantly different pattern of miRNA expression (P<0.01). There were no differences, however, between hepatitis B-positive and hepatitis C-positive samples. This information may help clarify the molecular mechanisms involved in the progression of liver disease, potentially serving as a diagnostic tool of HCC. | [Y Murakami, T Yasuda, K Saigo, T Urashima, H Toyoda, T Okanoue, K Shimotohno] | Oncogene | 2005-12-05 | |
| naturepublishinggroup10.1111/j.0022-202X.2005.23971.x | Microarray Analysis of Gene Expression in Cultured Skin Substitutes Compared with Native Human Skin | Cultured skin substitutes (CSS), prepared using keratinocytes, fibroblasts, and biopolymers, can facilitate closure of massive burn wounds by increasing the availability of autologous tissue for grafting. But because they contain only two cell types, skin substitutes cannot replace all of the functions of native human skin. To better understand the physiological and molecular differences between CSS and native skin, we undertook a comprehensive analysis of gene expression in native skin, cultured keratinocytes, cultured fibroblasts, and skin substitutes using Affymetrix gene chip microarrays. Hierarchical tree clustering identified six major clusters of coordinately regulated genes, using a list of 1030 genes that were the most differentially expressed between groups. These clusters correspond to biomarker pools representing expression signatures for native skin, fibroblasts, keratinocytes, and cultured skin. The expression analysis revealed that entire clusters of genes were either up- or downregulated upon combination of fibroblasts and keratinocytes in cultured skin grafts. Further, several categories of genes were overexpressed in CSS compared with native skin, including genes associated with hyperproliferative skin or activated keratinocytes. The observed pattern of expression indicates that CSS in vitro, which display a well-differentiated epidermal layer, exhibit a hyperproliferative phenotype similar to wounded native skin. | [Andrea K Smiley, Jennifer M Klingenberg, Bruce J Aronow, Steven T Boyce, WJohn Kitzmiller, Dorothy M Supp] | Journal of Investigative Dermatology | 2005-12-01 | |
| naturepublishinggroup10.1038/ni1282 | A Toll-like receptor|[ndash]|independent antiviral response induced by double-stranded B-form DNA | | [Ken J Ishii, Cevayir Coban, Hiroki Kato, Ken Takahashi, Yuichi Torii, Fumihiko Takeshita, Holger Ludwig, Gerd Sutter, Koichi Suzuki, Hiroaki Hemmi, Shintaro Sato, Masahiro Yamamoto, Satoshi Uematsu, Taro Kawai, Osamu Takeuchi, Shizuo Akira] | Nature Immunology | 2005-11-13 | |
| naturepublishinggroup10.1038/sj.onc.1209183 | CITED1 homozygous null mice display aberrant pubertal mammary ductal morphogenesis | Expression microarray analysis identified CITED1 among a group of genes specifically upregulated in the pubertal mouse mammary gland. At puberty, CITED1 localizes to the luminal epithelial cell population of the mammary ducts and the body cells of the terminal end buds. Generation of CITED1 gene knockout mice showed that homozygous null mutants exhibit retarded mammary ductal growth at puberty and, in addition, dilated ductal structures with a lack of spatial restriction of the subtending branches. Analysis of CITED1 homozygous null and heterozygous null mammary gland gene expression using microarrays suggested that the mammary-specific phenotype seen in the homozygous null females is due to a disturbance in the transcription of a number of key mediators of pubertal ductal morphogenesis. These include estrogen and TGF responsive genes, such as the EGFR/ErbB2 ligand, amphiregulin, whose transcription we suggest is directly or indirectly regulated by CITED1. | [J Howlin, J McBryan, S Napoletano, T Lambe, E McArdle, T Shioda, F Martin] | Oncogene | 2005-11-07 | |
| naturepublishinggroup10.1038/sj.leu.2403997 | IGF-1R is overexpressed in poor-prognostic subtypes of multiple myeloma | | [W J Chng, A Gualberto, R Fonseca] | Leukemia | 2005-10-20 | |
| naturepublishinggroup10.1038/sj.onc.1209016 | Identification of novel tumour-associated genes differentially expressed in the process of squamous cell cancer development | Chemically induced mouse skin carcinogenesis represents the most extensively utilized animal model to unravel the multistage nature of tumour development and to design novel therapeutic concepts of human epithelial neoplasia. We combined this tumour model with comprehensive gene expression analysis and could identify a large set of novel tumour-associated genes that have not been associated with epithelial skin cancer development yet. Expression data of selected genes were confirmed by semiquantitative and quantitative RT-PCR as well as in situ hybridization and immunofluorescence analysis on mouse tumour sections. Enhanced expression of genes identified in our screen was also demonstrated in mouse keratinocyte cell lines that form tumours in vivo. Self-organizing map clustering was performed to identify different kinetics of gene expression and coregulation during skin cancer progression. Detailed analysis of differential expressed genes according to their functional annotation confirmed the involvement of several biological processes, such as regulation of cell cycle, apoptosis, extracellular proteolysis and cell adhesion, during skin malignancy. Finally, we detected high transcript levels of ANXA1, LCN2 and S100A8 as well as reduced levels for NDR2 protein in human skin tumour specimens demonstrating that tumour-associated genes identified in the chemically induced tumour model might be of great relevance for the understanding of human epithelial malignancies as well. | [L Hummerich, R M|[uuml]|ller, J Hess, F Kokocinski, M Hahn, G F|[uuml]|rstenberger, C Mauch, P Lichter, P Angel] | Oncogene | 2005-10-17 | |
| naturepublishinggroup10.1038/sj.onc.1209138 | Downregulation of E-cadherin by hepatitis B virus X antigen in hepatocellullar carcinoma | Hepatitis B virus (HBV)-encoded X antigen (HBxAg) contributes to the development of hepatocellular carcinoma (HCC). A frequent characteristic of HCC is reduced or absent expression of the cell adhesion protein, E-cadherin, although it is not known whether HBxAg plays a role. To address this, the levels of E-cadherin were determined in HBxAg-positive and -negative HepG2 cells in culture, and in tumor and surrounding nontumor liver from a panel of HBV carriers. The results showed an inverse relationship between HBxAg and E-cadherin expression both in tissue culture and in vivo. In HBxAg-positive cells, E-cadherin was suppressed at both the mRNA and protein levels. This was associated with hypermethylation of the E-cadherin promoter. Depressed E-cadherin correlated with HBxAg trans-activation function, as did the migration of HepG2 cells in vitro. Decreased expression of E-cadherin was also associated with the accumulation of -catenin in the cytoplasm and/or nuclei in tissues and cell lines, which is characteristic of activated -catenin. Additional work showed that HBxAg-activated -catenin. Together, these results suggest that the HBxAg is associated with decreased expression of E-cadherin, accumulation of -catenin in the cytoplasm and nucleus, and increased cell migration, which may contribute importantly to hepatocarcinogenesis. | [J Liu, Z Lian, S Han, M M Y Waye, H Wang, M-C Wu, K Wu, J Ding, P Arbuthnot, M Kew, D Fan, M A Feitelson] | Oncogene | 2005-10-10 | |
| naturepublishinggroup10.1038/sj.onc.1209105 | Oncogenic mutations cause dramatic, qualitative changes in the transcriptional activity of c-Myb | The v-Myb oncoprotein encoded by Avian Myeloblastosis Virus is highly oncogenic, induces leukemias in chickens and mice and transforms immature hematopoietic cells in vitro. The v-Myb protein is a mutated and truncated version of c-Myb, a DNA-binding transcription factor expressed in many cell types that is essential for normal hematopoiesis. Previous studies suggested that two types of differences, DNA binding domain mutations and the deletion of a C-terminal negative regulatory domain were important for increasing the transforming activity of v-Myb. Here, we combined structure-function studies of the v-Myb and c-Myb proteins with unbiased microarray-based transcription assays to compare the transcriptional specificities of the two proteins. In human cells, the v-Myb and c-Myb proteins displayed strikingly different activities and regulated overlapping, but largely distinct sets of target genes. Each type of mutation that distinguished v-Myb from c-Myb, including the N- and C-terminal deletions, DNA binding domain changes and mutations in the transcriptional activation domain, affected different sets of target genes and contributed to the different activities of c-Myb and v-Myb. The results suggest that v-Myb is not just a de-repressed version of c-Myb. Instead, it is a distinct transcriptional regulator with a unique set of activities. | [F Liu, W Lei, J P O'Rourke, S A Ness] | Oncogene | 2005-10-03 | |
| naturepublishinggroup10.1111/j.0022-202X.2005.23844.x | Co-Regulation of p16INK4a and Migratory Genes in Culture Conditions that Lead to Premature Senescence in Human Keratinocytes | Cellular stasis, also known as telomere-independent senescence, prevents many epithelial cells from becoming immortalized by telomerase alone. As human keratinocytes age in culture, protein levels of the tumor suppressor p16INK4a continue to increase, resulting in growth arrest independent of telomere length. Differences in culture conditions have been shown to modulate both p16INK4a expression and replicative capacity of human keratinocytes; however, the mechanism of p16INK4a induction under these conditions is unknown. Using multiple primary keratinocyte cell strains, we verified a delay in p16INK4a induction and an extended lifespan of human keratinocytes when grown in co-culture with post-mitotic fibroblast feeder cells as compared with keratinocytes grown on tissue culture plastic alone. Evaluation of gene expression levels in the two culture conditions by microarray analysis, and subsequent validation, demonstrated that keratinocytes cultured on plastic alone had significantly increased expression of many genes involved in keratinocyte migration and reduced expression levels of genes involved in keratinocyte differentiation. Higher levels of p16INK4a expression were present in cells that also displayed increased amounts of autophosphorylated focal adhesion kinase and urokinase plaminogen activator receptor (uPAR), both markers of keratinocyte migration. Furthermore, when tyrosine phosphorylation or urokinase-type plasminogen activator (uPA)/uPAR function was inhibited, both keratinocyte migration and p16INK4a expression were reduced. Our results indicate that keratinocytes cultured in the absence of feeder cells exhibit a migratory phenotype and suggest that p16INK4a is selectively induced under these conditions by a mechanism involving tyrosine kinase activity and the urokinase plasminogen activation system. | [Benjamin W Darbro, Galen B Schneider, Aloysius J Klingelhutz] | Journal of Investigative Dermatology | 2005-09-01 | |
| naturepublishinggroup10.1038/nature03713 | Regulation of Mycobacterium tuberculosis cell envelope composition and virulence by intramembrane proteolysis | Mycobacterium tuberculosis infection is a continuing global health crisis that kills 2 million people each year1. Although the structurally diverse lipids of the M. tuberculosis cell envelope each have non-redundant roles in virulence or persistence2, 3, 4, 5, 6, 7, the molecular mechanisms regulating cell envelope composition in M. tuberculosis are undefined. In higher eukaryotes, membrane composition is controlled by site two protease (S2P)-mediated cleavage of sterol regulatory element binding proteins8, 9, membrane-bound transcription factors that control lipid biosynthesis. S2P is the founding member of a widely distributed family of membrane metalloproteases10, 11 that cleave substrate proteins within transmembrane segments12. Here we show that a previously uncharacterized M. tuberculosis S2P homologue (Rv2869c) regulates M. tuberculosis cell envelope composition, growth in vivo and persistence in vivo. These results establish that regulated intramembrane proteolysis is a conserved mechanism controlling membrane composition in prokaryotes and show that this proteolysis is a proximal regulator of cell envelope virulence determinants in M. tuberculosis. | [Hideki Makinoshima, Michael S. Glickman] | Nature | 2005-07-21 | |
| naturepublishinggroup10.1038/sj.bjc.6602666 | Comparison of hypoxia transcriptome in vitro with in vivo gene expression in human bladder cancer | Hypoxia-inducible genes have been linked to the aggressive phenotype of cancer. However, nearly all work on hypoxia-regulated genes has been conducted in vitro on cell lines. We investigated the hypoxia transcriptome in primary human bladder cancer using cDNA microarrays to compare genes induced by hypoxia in vitro in bladder cancer cell line EJ28 with genes upregulated in 39 bladder tumour specimens (27 superficial and 12 invasive). We correlated array mRNA fold changes with carbonic anhydrase 9 (CA IX) staining of tumours as a surrogate marker of hypoxia. Of 6000 genes, 32 were hypoxia inducible in vitro more than two-fold, five of which were novel, including lactate transporter SLC16A3 and RNAse 4. Eight of 32 hypoxia-inducible genes in vitro were also upregulated on the vivo array. Vascular endothelial growth factor mRNA was upregulated two-fold by hypoxia and 2–18-fold in 31 out of 39 tumours. Glucose transporter 1 was also upregulated on both arrays mRNA, and fold changes on the in vivo array significantly correlated with CA IX staining of tumours (P=0.008). However, insulin-like growth factor binding protein 3 mRNA was the most strongly differentially expressed gene in both arrays and this confirmed its upregulation in urine of bladder cancer patients (n=157, P<0.01). This study defines genes suitable for an in vivo hypoxia 'profile', shows the heterogeneity of the hypoxia response and describes new hypoxia-regulated genes. | [J J Ord, E H Streeter, I S D Roberts, D Cranston, A L Harris] | British Journal of Cancer | 2005-07-19 | |
| naturepublishinggroup10.1038/ni1223 | Selected Toll-like receptor agonist combinations synergistically trigger a T helper type 1|[ndash]|polarizing program in dendritic cells | | [Giorgio Napolitani, Andrea Rinaldi, Francesco Bertoni, Federica Sallusto, Antonio Lanzavecchia] | Nature Immunology | 2005-07-03 | |
| naturepublishinggroup10.1038/sj.onc.1208802 | PKB|[sol]|Akt induces transcription of enzymes involved in cholesterol and fatty acid biosynthesis via activation of SREBP | Protein kinase B (PKB/Akt) has been shown to play a role in protection from apoptosis, cell proliferation and cell growth. It is also involved in mediating the effects of insulin, such as lipogenesis, glucose uptake and conversion of glucose into fatty acids and cholesterol. Sterol-regulatory element binding proteins (SREBPs) are the major transcription factors that regulate genes involved in fatty acid and cholesterol synthesis. It has been postulated that constitutive activation of the phosphatidylinositol 3 kinase/Akt pathway may be involved in fatty acid and cholesterol accumulation that has been described in several tumour types. In this study, we have analysed changes in gene expression in response to Akt activation using DNA microarrays. We identified several enzymes involved in fatty acid and cholesterol synthesis as targets for Akt-regulated transcription. Expression of these enzymes has previously been shown to be regulated by the SREBP family of transcription factors. Activation of Akt induces synthesis of full-length SREBP-1 and SREBP-2 proteins as well as expression of fatty acid synthase (FAS), the key regulatory enzyme in lipid biosynthesis. We also show that Akt leads to the accumulation of nuclear SREBP-1 but not SREBP-2, and that activation of SREBP is required for Akt-induced activation of the FAS promoter. Finally, activation of Akt induces an increase in the concentration of cellular fatty acids as well as phosphoglycerides, the components of cellular membranes. Our data indicate that activation of SREBP by Akt leads to the induction of key enzymes of the cholesterol and fatty acid biosynthesis pathways, and thus membrane lipid biosynthesis. | [Thomas Porstmann, Beatrice Griffiths, Yuen-Li Chung, Oona Delpuech, John R Griffiths, Julian Downward, Almut Schulze] | Oncogene | 2005-06-27 | |
| naturepublishinggroup10.1038/sj.onc.1208858 | Two subclasses of lung squamous cell carcinoma with different gene expression profiles and prognosis identified by hierarchical clustering and non-negative matrix factorization | Current clinical and histopathological criteria used to define lung squamous cell carcinomas (SCCs) are insufficient to predict clinical outcome. To make a clinically useful classification by gene expression profiling, we used a 40 386 element cDNA microarray to analyse 48 SCC, nine adenocarcinoma, and 30 normal lung samples. Initial analysis by hierarchical clustering (HC) allowed division of SCCs into two distinct subclasses. An additional independent round of HC induced a similar partition and consensus clustering with the non-negative matrix factorization approach indicated the robustness of this classification. Kaplan–Meier analysis with the log-rank test pointed to a nonsignificant difference in survival (P=0.071), but the likelihood of survival to 6 years was significantly different between the two groups (40.5 vs 81.8%, P=0.014, Z-test). Biological process categories characteristic for each subclass were identified statistically and upregulation of cell-proliferation-related genes was evident in the subclass with poor prognosis. In the subclass with better survival, genes involved in differentiated intracellular functions, such as the MAPKKK cascade, ceramide metabolism, or regulation of transcription, were upregulated. This work represents an important step toward the identification of clinically useful classification for lung SCC. | [Kentaro Inamura, Takeshi Fujiwara, Yujin Hoshida, Takayuki Isagawa, Michael H Jones, Carl Virtanen, Miyuki Shimane, Yukitoshi Satoh, Sakae Okumura, Ken Nakagawa, Eiju Tsuchiya, Shumpei Ishikawa, Hiroyuki Aburatani, Hitoshi Nomura, Yuichi Ishikawa] | Oncogene | 2005-06-27 | |
| naturepublishinggroup10.1038/sj.emboj.7600728 | Regulation of hepatic metabolic pathways by the orphan nuclear receptor SHP | SHP (small heterodimer partner) is an important component of the feedback regulatory cascade, which controls the conversion of cholesterol to bile acids. In order to identify the bona fide molecular targets of SHP, we performed global gene expression profiling combined with chromatin immunoprecipitation assays in transgenic mice constitutively expressing SHP in the liver. We demonstrate that SHP affects genes involved in diverse biological pathways, and in particular, several key genes involved in consecutive steps of cholesterol degradation, bile acid conjugation, transport and lipogenic pathways. Sustained expression of SHP leads to the depletion of hepatic bile acid pool and a concomitant accumulation of triglycerides in the liver. The mechanism responsible for this phenotype includes SHP-mediated direct repression of downstream target genes and the bile acid sensor FXR, and an indirect activation of PPAR and SREBP-1c genes. We present evidence for the role of altered chromatin configurations in defining distinct gene-specific mechanisms by which SHP mediates differential transcriptional repression. The multiplicity of genes under its control suggests that SHP is a pleiotropic regulator of diverse metabolic pathways. | [Konstantinos Boulias, Nitsa Katrakili, Krister Bamberg, Peter Underhill, Andy Greenfield, Iannis Talianidis] | The EMBO Journal | 2005-06-23 | |
| naturepublishinggroup10.1038/sj.leu.2403832 | Dlk1 in normal and abnormal hematopoiesis | Dlk1 (Pref-1) is a transmembrane and secreted protein, which is a member of the epidermal growth factor-like family, homologous to Notch/Delta/Serrate. We have found by real-time RT-PCR that Dlk1 mRNA levels were high in CD34+ cells in 10 of 12 MDS samples compared with CD34+ cells from 11 normals. Also, Dlk1 mRNA was elevated in mononuclear, low density bone marrow cells from 11/38 MDS patients, 5/11 AML M6 and 2/4 AML M7 samples. Furthermore, 5/6 erythroleukemia and 2/2 megakaryocytic leukemia cell lines highly expressed Dlk1 mRNA. Levels of Dlk1 mRNA markedly increased during megakaryocytic differentiation of both CMK megakaryoblasts as well as normal CD34+ hematopoietic stem cells. High serum levels of Dlk1 occurred in RA (4/10) and essential thrombocythemia (2/10) patients. Functional studies showed that forced expression of Dlk1 enhanced proliferation of K562 cells growing in 1% fetal bovine serum. Analysis of hematopoiesis of Dlk1 knockout mice suggested that Dlk1 contributed to granulocyte, megakaryocyte and B-cell clonogenic growth and was needed for generation of splenic B-cells. In summary, Dlk1 is overexpressed in selected samples of MDS (especially RA and RAEB) and AML (particularly M6, M7), and it appears to be associated with normal development of megakaryocytes and B cells. | [S Sakajiri, J O'Kelly, D Yin, C W Miller, W K Hofmann, K Oshimi, L-Y Shih, K-H Kim, H S Sul, C H Jensen, B Teisner, N Kawamata, H P Koeffler] | Leukemia | 2005-06-16 | |
| naturepublishinggroup10.1111/j.1523-1755.2005.00330.x | Progression of secondary hyperparathyroidism involves deregulation of genes related to DNA and RNA stability | Progression of secondary hyperparathyroidism involves deregulation of genes related to DNA and RNA stability. | [S, D , R J, J P, J M, J C] | Kidney International | 2005-06-01 | |
| naturepublishinggroup10.1038/sj.onc.1208214 | Discrimination between serous low malignant potential and invasive epithelial ovarian tumors using molecular profiling | Tumors of low malignant potential (LMP) represent 20% of epithelial ovarian cancers (EOCs) and are associated with a better prognosis than the invasive tumors (TOV). Defining the relationship between LMPs and TOVs remains an important goal towards understanding the molecular pathways that contribute to prognosis, as well as providing molecular markers, for these EOCs. To this end, DNA microarray analyses were performed either in a primary culture or a tumor tissue model system and selected candidate genes showing a distinctive expression profile between LMPs and TOVs were identified using a class prediction approach based on three statistical methods of analysis. Both model systems appear relevant as candidate genes identified by either model allowed the proper reclassification of samples as either LMPs or TOVs. Selected candidate genes (CAS, CCNE1, LGALS8, ITG3, ATP1B1, FLIP, KRT7 and KRT19) were validated by real-time quantitative PCR analysis and show differential expression between LMPs and TOVs. Immunohistochemistry analyses showed that the two tumor classes were distinguishable by their expression of CAS, TNFR1A, FLIP, CKS1 and CCNE1. These results define signature patterns for gene expression of LMPs and TOVs and identify gene candidates that warrant further study to deepen our understanding of the biology of EOC. | [V|[eacute]|ronique Ouellet, Diane M Provencher, Christine M Maugard, C|[eacute]|cile Le Page, Fengge Ren, Christian Lussier, Jaroslav Novak, Bing Ge, Thomas J Hudson, Patricia N Tonin, Anne-Marie Mes-Masson] | Oncogene | 2005-05-30 | |
| naturepublishinggroup10.1038/sj.leu.2403819 | Gene expression profiling of normal hematopoietic progenitor cells under treatment with imatinib in vitro | | [S Balabanov, K Bartolovic, M Komor, L Kanz, W K Hofmann, T H Br|[uuml]|mmendorf] | Leukemia | 2005-05-26 | |
| naturepublishinggroup10.1038/nature03555 | A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity | Despite the sequencing of the human and mouse genomes, few genetic mechanisms for protecting against autoimmune disease are currently known. Here we systematically screen the mouse genome for autoimmune regulators to isolate a mouse strain, sanroque, with severe autoimmune disease resulting from a single recessive defect in a previously unknown mechanism for repressing antibody responses to self. The sanroque mutation acts within mature T cells to cause formation of excessive numbers of follicular helper T cells and germinal centres. The mutation disrupts a repressor of ICOS, an essential co-stimulatory receptor for follicular T cells, and results in excessive production of the cytokine interleukin-21. sanroque mice fail to repress diabetes-causing T cells, and develop high titres of autoantibodies and a pattern of pathology consistent with lupus. The causative mutation is in a gene of previously unknown function, roquin (Rc3h1), which encodes a highly conserved member of the RING-type ubiquitin ligase protein family. The Roquin protein is distinguished by the presence of a CCCH zinc-finger found in RNA-binding proteins, and localization to cytosolic RNA granules implicated in regulating messenger RNA translation and stability. | [Carola G. Vinuesa, Matthew C. Cook, Constanza Angelucci, Vicki Athanasopoulos, Lixin Rui, Kim M. Hill, Di Yu, Heather Domaschenz, Belinda Whittle, Teresa Lambe, Ian S. Roberts, Richard R. Copley, John I. Bell, Richard J. Cornall, Christopher C. Goodnow] | Nature | 2005-05-26 | |
| naturepublishinggroup10.1038/ng1577 | Xlr3b is a new imprinted candidate for X-linked parent-of-origin effects on cognitive function in mice | | [William Davies, Anthony Isles, Rachel Smith, Delicia Karunadasa, Doreen Burrmann, Trevor Humby, Obah Ojarikre, Carol Biggin, David Skuse, Paul Burgoyne, Lawrence Wilkinson] | Nature Genetics | 2005-05-22 | |
| naturepublishinggroup10.1038/sj.onc.1208692 | Gene expression responses to DNA damage are altered in human aging and in Werner Syndrome | The accumulation of DNA damage and mutations is considered a major cause of cancer and aging. While it is known that DNA damage can affect changes in gene expression, transcriptional regulation after DNA damage is poorly understood. We characterized the expression of 6912 genes in human primary fibroblasts after exposure to three different kinds of cellular stress that introduces DNA damage: 4-nitroquinoline-1-oxide (4NQO), -irradiation, or UV-irradiation. Each type of stress elicited damage specific gene expression changes of up to 10-fold. A total of 85 genes had similar changes in expression of 3–40-fold after all three kinds of stress. We examined transcription in cells from young and old individuals and from patients with Werner syndrome (WS), a segmental progeroid condition with a high incidence of cancer, and found various age-associated transcriptional changes depending upon the type of cellular stress. Compared to young individuals, both WS and old individuals had similarly aberrant transcriptional responses to - and UV-irradiation, suggesting a role for Werner protein in stress-induced gene expression. Our results suggest that aberrant DNA damage-induced gene regulation may contribute to the aging process and the premature aging in WS. | [Kasper J Kyng, Alfred May, Tinna Stevnsner, Kevin G Becker, Steen K|[oslash]|lvr|[aring]|, Vilhelm A Bohr] | Oncogene | 2005-05-16 | |
| naturepublishinggroup10.1038/sj.onc.1208712 | Gene expression profiling of cancer progression reveals intrinsic regulation of transforming growth factor-|[beta]| signaling in ErbB2|[sol]|Neu-induced tumors from transgenic mice | Upregulation of HER2/ErbB2/Neu occurs in 15–30% of human breast cancers and correlates with poor prognosis. Identification of ErbB2/Neu transcriptional targets should facilitate development of novel therapeutic approaches. Development of breast cancer is a multistep process; thus, to identify the transcriptomes associated with different stages of progression of tumorigenesis, we compared expression profiles of mammary tumors and preneoplastic mammary tissue from MMTV-Neu transgenic mice to expression profiles of wild-type mammary glands using Affymetrix microarrays. We identified 324 candidate genes that were unique to ErbB2/Neu-induced tumors relative to normal mammary gland tissue from wild-type controls. Expression of a subset of these genes (82) was also changed in the preneoplastic mammary glands compared to wild-type controls, indicating that they may play a pivotal role during early events of ErbB2/Neu-initiated mammary tumorigenesis. Further analysis of the microarray data revealed that expression of several known transforming growth factor (TGF)- target genes was altered, suggesting that the TGF- signaling cascade is downregulated in ErbB2/Neu-induced tumors. Western blot analysis for TGF--Receptor-I/ALK5 and immunohistochemistry for TGF--Receptor-I/ALK5 and phosphorylated/activated Smad2 confirmed that the Smad-dependent TGF- signaling cascade was inactive in these tumors. Although absent in most of the tumor, phosphorylated Smad2 was present in the periphery of tumors. Interestingly, presence of phosphorylated/activated Smad2 correlated with expression of Activin-Receptor-IB/ALK4, suggesting that although Smad-dependent TGF- signaling is absent in ErbB2/Neu-induced tumors, Activin signaling may be active at the leading edge of these tumors. Cumulatively, these data indicate that the TGF- pathway is intrinsically suppressed in ErbB2/Neu tumors via a mechanism involving loss of TGF--Receptor-I/ALK5. | [Melissa D Landis, Darcie D Seachrist, Marjorie E Monta|[ntilde]|ez-Wiscovich, David Danielpour, Ruth A Keri] | Oncogene | 2005-05-09 | |
| naturepublishinggroup10.1038/sj.onc.1208727 | G1|[sol]|S transcriptional networks modulated by the HOX11|[sol]|TLX1 oncogene of T-cell acute lymphoblastic leukemia | The HOX11/TLX1 homeobox gene is aberrantly expressed in a subset of T-cell acute lymphoblastic leukemia (T-ALL). Here, we employed oligonucleotide microarrays to compare the expression profiles of the K3P and Sil leukemic cell lines originating from patients with HOX11+ T-ALL to that of Jurkat cells, which originated from a distinct subtype of T-ALL (TAL1+). To distinguish potential HOX11 target genes from those characteristic of the stage of HOX11 leukemic arrest, we also performed gene expression analysis on Jurkat cells, genetically engineered to express exogenous HOX11. The resulting HOX11 gene expression signature, which was validated for representative signaling pathways by transient transfection of reporter constructs, was characterized by elevated expression of transcriptional programs involved in cell proliferation, including those regulated by E2F, c-Myc and cAMP response element-binding protein. We subsequently showed that ectopic HOX11 expression resulted in hyperphosphorylation of the retinoblastoma protein (Rb), which correlated with inhibition of the major Rb serine/threonine phosphatase PP1. HOX11 also inhibited PP2A serine/threonine phosphatase activity concomitant with stimulation of the AKT/PKB signaling cascade. These results suggest that transcriptional deregulation of G1/S growth-control genes, mediated in large part through blockade of PP1/PP2A phosphatase activity, plays an important role in HOX11 pathobiology. | [Irene Riz, Robert G Hawley] | Oncogene | 2005-05-09 | |
| naturepublishinggroup10.1038/sj.onc.1208662 | Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor |[alpha]|, in response to deacetylase inhibition by valproic acid and trichostatin A | Valproate (VPA) and trichostatin A (TSA), inhibitors of zinc-dependent deacetylase activity, induce reduction in the levels of mRNA encoding oestrogen receptor- (ER), resulting in subsequent clearance of ER protein from breast and ovarian cell lines. Inhibition of oestrogen signalling may account for the endocrine disorders, menstrual abnormalities, osteoporosis and weight gain that occur in a proportion of women treated with VPA for epilepsy or for bipolar mood disorder. Transcriptome profiling revealed that VPA and TSA also modulate the expression of, among others, key regulatory components of the cell cycle. Meta-analysis of genes directly responsive to oestrogen indicates that VPA and TSA have a generally antioestrogenic profile in ER positive cells. Concomitant treatment with cycloheximide prevented most of these changes in gene expression, including downregulation of ER mRNA, indicating that a limited number of genes signal a hyperacetylated state within cells. Three members of the NAD-dependent deacetylases, the sirtuins, are upregulated by VPA and by TSA and sirtuin activity contributes to loss of ER expression. However, prolonged inhibition of the sirtuins by sirtinol also induces loss of ER from cells. Mechanistically, we show that VPA invokes reversible promoter shutoff of the ER, pS2 and cyclin D1 promoters, by inducing recruitment of methyl cytosine binding protein 2 (MeCP2) with concomitant exclusion of the maintenance methylase DNMT1. Furthermore, we demonstrate that, in the presence of VPA, local DNA methylation, deacetylation and demethylation of activated histones and recruitment of inhibitory complexes occurs on the pS2 promoter. | [George Reid, Rapha|[euml]|l M|[eacute]|tivier, Chin-Yo Lin, Stefanie Denger, David Ibberson, Tomi Ivacevic, Heike Brand, Vladimir Benes, Edison T Liu, Frank Gannon] | Oncogene | 2005-05-02 | |
| naturepublishinggroup10.1016/j.ymthe.2005.07.279 | 739. Impact of Activation, Transduction/Selection Steps on the Gene Expression Profile of Ex-Vivo Retrovirally Transduced CD8+ T Cells, Using High Density DNA Microarrays | Suicide gene therapy clinical approaches using retrovirally transduced donor T-lymphocytes (GMTC) have led to successful alloreactivity modulation following bone marrow transplantation. We have previously shown that our GMTC production method: 12 day ex-vivo culture in the presence of IL-2, entails phenotypical and functional alterations. Such alterations can be limited partly by CD3/CD28 activation before retroviral transduction, plus immunomagnetic selection based on cell surface membrane gene expression, i.e truncated Nerve Growth Factor (|[Delta]|NGFR). | [Marina Deschamps, Jean Marie Certoux, John de Vos, Nicolas Montcuquet, Thierry Reme, Mark Bonyhadi, Eric Robinet, Pierre Tiberghien, Christophe Ferrand] | Molecular Therapy | 2005-05-01 | |
| naturepublishinggroup10.1038/nature03449 | The genome sequence of the rice blast fungus Magnaporthe grisea | Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation. | [Ralph A. Dean, Nicholas J. Talbot, Daniel J. Ebbole, Mark L. Farman, Thomas K. Mitchell, Marc J. Orbach, Michael Thon, Resham Kulkarni, Jin-Rong Xu, Huaqin Pan, Nick D. Read, Yong-Hwan Lee, Ignazio Carbone, Doug Brown, Yeon Yee Oh, Nicole Donofrio, Jun Seop Jeong, Darren M. Soanes, Slavica Djonovic, Elena Kolomiets, Cathryn Rehmeyer, Weixi Li, Michael Harding, Soonok Kim, Marc-Henri Lebrun, Heidi Bohnert, Sean Coughlan, Jonathan Butler, Sarah Calvo, Li-Jun Ma, Robert Nicol, Seth Purcell, Chad Nusbaum, James E. Galagan, Bruce W. Birren] | Nature | 2005-04-21 | |
| naturepublishinggroup10.1038/ng1543 | A gene expression map of Arabidopsis thaliana development | | [Markus Schmid, Timothy S Davison, Stefan R Henz, Utz J Pape, Monika Demar, Martin Vingron, Bernhard Sch|[ouml]|lkopf, Detlef Weigel, Jan U Lohmann] | Nature Genetics | 2005-04-03 | |
| naturepublishinggroup10.1111/j.0022-202X.2005.23616.x | Differential Activation Profiles of Multiple Transcription Factors During Dendritic Cell Maturation | Immature dendritic cells (DC) at the environmental interfaces, such as the skin, constantly survey the tissue for the emergence of microbial products and pro-inflammatory mediators. Upon recognition of such "danger" signals, they undergo dynamic reprogramming of gene expression and functions, the process known as DC maturation, which plays critical roles in both innate and adaptive immune responses. Although DC have been shown to discriminate different maturation stimuli by expressing stimulus-specific signature genes and unique phenotypic and functional properties, underlying mechanisms for this extraordinary plasticity remain relatively unclear. We hypothesized that DC might activate unique sets of transcription factors (TF) upon sensing different stimuli. To test this hypothesis, we transduced a mouse epidermal-derived DC line XS106 to express the luciferase reporter gene under the control of each of 15 different cis-enhancer elements. The resulting DC panels were then exposed to 14 different microbial, endogenous, environmental, and pharmacological agents that produced unique maturational changes. This approach allowed systematic determination of TF activation profiles in DC. Our results revealed striking diversity, with different classes of stimuli triggering preferential activation of distinct sets of TF. We propose that differential TF usage represents a previously unrecognized mechanism regulating the direction of DC maturation. | [Norikatsu Mizumoto, Francis Hui, Dale Edelbaum, M Ryan Weil, Jonathan D Wren, David Shalhevet, Hiroyuki Matsue, Lei Liu, Harold R Garner, Akira Takashima] | Journal of Investigative Dermatology | 2005-04-01 | |
| naturepublishinggroup10.1038/modpathol.3800270 | Increased expression of osteopontin gene in atypical teratoid|[sol]|rhabdoid tumor of the central nervous system | The atypical teratoid/rhabdoid tumor, primary to the central nervous system, is a highly malignant and aggressive neoplasm of infancy and childhood. Although having distinct biological features and clinical outcomes, it is frequently misdiagnosed as primitive neuroectodermal tumor/medulloblastoma. To further distinguish the underlying pathogenesis and to identify biological markers for clinical use, an atypical teratoid/rhabdoid tumor-derived cell line was established and its gene expression pattern analyzed in comparison to the human astrocyte SVG12 cell line and the human DAOY medulloblastoma cell line using a complementary DNA microarray method. The osteopontin gene was found specifically upregulated in atypical teratoid/rhabdoid tumor cells. This specificity was confirmed by immunohistochemistry in pathological sections of tissues from atypical teratoid/rhabdoid tumor patients. Even though the role of osteopontin in the cytopathogenesis of atypical teratoid/rhabdoid tumor still needs to be determined, our data support that overexpressed osteopontin is a potential diagnostic marker for atypical teratoid/rhabdoid tumor. | [Chung-Lan Kao, Shih-Hwa Chiou, Yann-Jang Chen, Sher Singh, Han-Tso Lin, Ren-Shyan Liu, Chih-Wen Lo, Chi-Chang Yang, Chin-Wen Chi, Chen-hsen Lee, Tai-Tong Wong] | Modern Pathology | 2005-03-18 | |
| naturepublishinggroup10.1038/sj.npp.1300680 | Repeated Cocaine Administration Induces Gene Expression Changes through the Dopamine D1 Receptors | Drug addiction involves compulsive drug-seeking and drug-taking despite known adverse consequences. The enduring nature of drug addiction suggests that repeated exposure to abused drugs leads to stable alterations that likely involve changes in gene expression in the brain. The dopamine D1 receptor has been shown to mediate the long-term behavioral effects of cocaine. To examine how the persistent behavioral effects of cocaine correlate with underlying changes in gene expression, we have used D1 receptor mutant and wild-type mice to identify chronic cocaine-induced gene expression changes mediated via the D1 receptors. We focused on the caudoputamen and nucleus accumbens, two key brain regions that mediate the long-term effects of cocaine. Our analyses demonstrate that repeated cocaine administration induces changes in the expression of 109 genes, including those encoding the stromal cell-derived factor 1, insulin-like growth factor binding protein 6, sigma 1 receptor, regulators of G-protein signaling protein 4, Wnt1 responsive Cdc42 homolog, Ca2+/calmodulin-dependent protein kinase II subunit, and cyclin D2, via the D1 receptors. Moreover, the seven genes contain AP-1 binding sites in their promoter regions. These results suggest that genes encoding certain extracellular factors, membrane receptors and modulators, and intracellular signaling molecules, among others, are regulated by cocaine via the D1 receptor, and these AP-1 transcription complex-regulated genes might contribute to persistent cocaine-induced behavioral changes. | [Dongsheng Zhang, Lu Zhang, Yang Tang, Qi Zhang, Danwen Lou, Frank R Sharp, Jianhua Zhang, Ming Xu] | Neuropsychopharmacology | 2005-03-16 | |
| naturepublishinggroup10.1038/sj.leu.2403678 | Differential gene expression in hematopoietic progenitors from paroxysmal nocturnal hemoglobinuria patients reveals an apoptosis|[sol]|immune response in |[lsquo]|normal|[rsquo]| phenotype cells | Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired stem cell disorder characterized clinically by intravascular hemolysis, venous thrombosis, and bone marrow failure. Despite elucidation of the biochemical and molecular defects in PNH, the pathophysiology of clonal expansion of glycosylphosphatidylinositol-anchored protein (GPI-AP)-deficient cells remains unexplained. In pursuit of evidence of differences between GPI-AP-normal and -deficient CD34 cells, we determined gene expression profiles of isolated marrow CD34 cells of each phenotype from PNH patients and healthy donors, using DNA microarrays. Pooled and individual patient samples revealed consistent gene expression patterns relative to normal controls. GPI-AP-normal cells from PNH patients showed upregulation of genes involved in apoptosis and the immune response. Conversely, genes associated with antiapoptotic function and hematopoietic cell proliferation and differentiation were downregulated in these cells. In contrast, the PNH clone of GPI-AP-deficient cells appeared more similar to CD34 cells of healthy individuals. Gene chip data were confirmed by other methods. Similar gene expression patterns were present in PNH that was predominantly hemolytic as in PNH associated with aplastic anemia. Our results implicate an environmental influence on hematopoietic cell proliferation, in which the PNH clone evades immune attack and destruction, while normal cells suffer a stress response followed by programmed cell death. | [G Chen, W Zeng, J P Maciejewski, K Kcyvanfar, E M Billings, N S Young] | Leukemia | 2005-03-10 | |
| naturepublishinggroup10.1038/nbt1075 | Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks | A major challenge in drug discovery is to distinguish the molecular targets of a bioactive compound from the hundreds to thousands of additional gene products that respond indirectly to changes in the activity of the targets1, 2, 3, 4, 5, 6, 7, 8. Here, we present an integrated computational-experimental approach for computing the likelihood that gene products and associated pathways are targets of a compound. This is achieved by filtering the mRNA expression profile of compound-exposed cells using a reverse-engineered model of the cell's gene regulatory network. We apply the method to a set of 515 whole-genome yeast expression profiles resulting from a variety of treatments (compounds, knockouts and induced expression), and correctly enrich for the known targets and associated pathways in the majority of compounds examined. We demonstrate our approach with PTSB, a growth inhibitory compound with a previously unknown mode of action, by predicting and validating thioredoxin and thioredoxin reductase as its target. | [Diego di Bernardo, Michael J Thompson, Timothy S Gardner, Sarah E Chobot, Erin L Eastwood, Andrew P Wojtovich, Sean J Elliott, Scott E Schaus, James J Collins] | Nature Biotechnology | 2005-03-04 | |
| naturepublishinggroup10.1038/sj.onc.1208546 | Transcriptional repression of WEE1 by Kruppel-like factor 2 is involved in DNA damage-induced apoptosis | Human Kruppel-like factor 2 (KLF2) is a Cys2/His2 zinc-finger-containing transcriptional factor, which is involved in multiple cellular pathways. Utilizing gene expression profiling to identify aberrantly expressed genes in ovarian cancer, we found that KLF2 was significantly and specifically downregulated in ovarian tumors. After reintroducing KLF2 into ovarian cancer cell lines, we observed decreased cell growth and increased sensitivity to DNA damage-induced apoptosis. Analysis of genes that could be potential targets of KLF2 revealed that KLF2 negatively regulated WEE1 expression. WEE1 encodes a tyrosine kinase that regulates the G2/M cell cycle transition. Expression of KLF2 markedly repressed the transcription of WEE1 by directly binding to an SP1/CPBP motif located between -252 bp and the start codon of the WEE1 promoter. Both activation and zinc-finger domains of KLF2 were required for this suppression of Wee1 expression. In addition, we demonstrated that Wee1 expression prevents cancer cells from undergoing apoptosis in response to DNA damage; however, this resistance was abolished by coexpression of KLF2, which inhibits WEE1 transcription. Thus, the level of WEE1 is regulated by KLF2 and enhanced KLF2 expression sensitizes cells to DNA damage-induced apoptosis. | [Fang Wang, Yu Zhu, Yan Huang, Sarah McAvoy, William B Johnson, Tak Hong Cheung, Tony Kwok Hung Chung, Keith Wing Kit Lo, So Fan Yim, May M Y Yu, Hextan Y S Ngan, Yick Fu Wong, David I Smith] | Oncogene | 2005-02-28 | |
| naturepublishinggroup10.1038/sj.onc.1208498 | Molecular signature of retinoic acid treatment in acute promyelocytic leukemia | Acute promyelocytic leukemia (APL) is a distinct subtype of acute myeloid leukemia characterized by a block of differentiation at the promyelocytic stage. APL patients respond to pharmacological concentrations of all-trans retinoic acid (RA) and disease remission correlates with terminal differentiation of leukemic blasts. The PML/RAR oncogenic transcription factor is responsible for both the pathogenesis of APL and for its sensitivity to RA. In order to identify physiological targets of RA therapy, we analysed gene expression profiles of RA-treated APL blasts and found 1056 common target genes. Comparing these results to those obtained in RA-treated U937 cell lines revealed that transcriptional response to RA is largely dependent on the expression of PML/RAR. Several genes involved in the control of differentiation and stem cell renewal are early targets of RA regulation, and may be important effectors of RA response. Modulation of chromatin modifying genes was also observed, suggesting that specific structural changes in local chromatin domains may be required to promote RA-mediated differentiation. Computational analysis of upstream genomic regions in RA target genes revealed nonrandom distribution of transcription factor binding sites, indicating that specific transcriptional regulatory complexes may be involved in determining RA response. | [Natalia Meani, Simone Minardi, Silvia Licciulli, Vania Gelmetti, Francesco Lo Coco, Clara Nervi, Pier Giuseppe Pelicci, Heiko M|[uuml]|ller, Myriam Alcalay] | Oncogene | 2005-02-21 | |
| naturepublishinggroup10.1038/ng1515 | Widespread and nonrandom distribution of DNA palindromes in cancer cells provides a structural platform for subsequent gene amplification | | [Hisashi Tanaka, Donald A Bergstrom, Meng-Chao Yao, Stephen J Tapscott] | Nature Genetics | 2005-02-13 | |
| naturepublishinggroup10.1038/labinvest.3700233 | Downregulation of major histocompatibility complex antigens in invading glioma cells: stealth invasion of the brain | Invasion into surrounding brain tissue is a fundamental feature of gliomas and the major reason for treatment failure. The process of brain invasion in gliomas is not well understood. Differences in gene expression and/or gene products between invading and noninvading glioma cells may identify potential targets for new therapies. To look for genes associated with glioma invasion, we first employed Affymetrix microarray Genechip® technology to identify genes differentially expressed in migrating glioma cells in vitro and in invading glioma cells in vivo using laser capture microdissection. We observed upregulation of a variety of genes, previously reported to be linked to glioma cell migration and invasion. Remarkably, major histocompatiblity complex (MHC) class I and II genes were significantly downregulated in migrating cells in vitro and in invading cells in vivo. Decreased MHC expression was confirmed in migrating glioma cells in vitro using RT-PCR and in invading glioma cells in vivo by immunohistochemical staining of human and murine glioblastomas for 2 microglobulin, a marker of MHC class I protein expression. To the best of our knowledge, this report is the first to describe the downregulation of MHC class I and II antigens in migrating and invading glioma cells, in vitro and in vivo, respectively. These results suggest that the very process of tumor invasion is associated with decreased expression of MHC antigens allowing glioma cells to invade the surrounding brain in a 'stealth'-like manner. | [David Zagzag, Konstantin Salnikow, Luis Chiriboga, Herman Yee, Li Lan, M Aktar Ali, Roberto Garcia, Sandra Demaria, Elizabeth W Newcomb] | Laboratory Investigation | 2005-01-31 | |
| naturepublishinggroup10.1038/sj.gene.6364160 | Transcriptional response signature of human lymphoid cells to staphylococcal enterotoxin B | Two shock-inducing toxins that result in similar eventual outcome of disease were studied to determine host gene expression responses, for correlation of both similar and unique gene patterns. We initially used differential display (DD)-PCR and identified 859 cDNA fragments that were differentially expressed after 16 h of in vitro exposure of human peripheral blood mononuclear cells (PBMC) to staphylococcal enterotoxin B (SEB). Upon further examination using custom cDNA microarrays and RT-PCR analysis, we found unique set of genes to each toxin (SEB or lipopolysaccharide (LPS)), especially at early time periods. By 16 h, there was a convergence of some gene expression responses and many of those genes code for proteins such as proteinases, transcription factors, vascular tone regulators, and respiratory distress. In an attempt to replicate the findings in vivo, monkeys were challenged with SEB and the resultant gene expression responses indicated a pattern typical of SEB exposure when compared to LPS, with a similar outcome. We provide evidence that vastly diverse global gene analysis techniques used in unison can not only effectively identify pathogen-specific genomic markers and provide a solid foundation to mechanistic insights but also explain some of the toxin-related symptoms through gene functions. | [C Mendis, R Das, R Hammamieh, A Royaee, D Yang, S Peel, M Jett] | Genes and Immunity | 2005-01-20 | |
| naturepublishinggroup10.1038/sj.onc.1208393 | C|[sol]|EBP|[delta]| expression in a BCR-ABL-positive cell line induces growth arrest and myeloid differentiation | CCAAT/enhancer-binding proteins (C/EBPs) are a family of highly conserved transcription factors that have important roles in normal myelopoiesis as well as associated with myeloid disorders. The chronic myelogenous leukemia (CML) cell lines, KCL22 and K562, express exceptionally low levels of endogenous C/EBPs and provide a good model to test the effects of C/EBPs on myeloid differentiation. To explore the possibility that C/EBP can promote differentiation in BCR-ABL-positive cells, we generated stable KCL22 and K562 clones that expressed an inducible C/EBP gene. C/EBP expression resulted in G0/G1 proliferative arrest and a moderate increase in apoptosis of the KCL22 and the K562 cells. Within 4 days of inducing expression of C/EBP, myeloid differentiation of the CML blast cells occurred as shown by morphologic changes and induction of secondary granule-specific genes. We also showed that during granulocytic differentiation of KCL22 cells, the C/EBP protein was detected in immunocomplexes with both Rb and E2F1. Furthermore, expression of C/EBP was associated with downregulation of c-Myc and cyclin E and upregulation of the cyclin-dependent kinase inhibitor p27Kip1 in both the KCL22 and K562 cell lines. These results show that expression of C/EBP in BCR-ABL-positive leukemic cells in blast crisis is sufficient for neutrophil differentiation and point to the therapeutic potential of ectopic induction of C/EBP in the acute phase of CML. | [Sigal Gery, Sakae Tanosaki, Wolf-K Hofmann, Ahrin Koppel, H Phillip Koeffler] | Oncogene | 2005-01-10 | |
| naturepublishinggroup10.1038/sj.onc.1208242 | Gene expression signature for angiogenic and nonangiogenic non-small-cell lung cancer | Angiogenesis is regarded as essential for tumour growth. However, we have demonstrated that some other aggressive non-small-cell lung carcinomas (n-SCLC) do not have angiogenesis. In this study, using cDNA microarray analysis, we demonstrate that angiogenic and nonangiogenic tumour types can be distinguished by their gene expression profiles. Tissue samples from 42 n-SCLC patients were obtained with consent. In all, 12 tumours were nonangiogenic and 30 angiogenic. The two groups were matched by age, sex, smoking and tumour stage. Total RNAs were extracted followed by microarray hybridization and image scan procedure. Data were analysed using GeneSpring 5.1 software. A total of 62 genes were found to be able to separate angiogenic from nonangiogenic tumours. Nonangiogenic tumours have higher levels of genes concerned with mitochondrial metabolism, mRNA transcription, protein synthesis and the cell cycle. Angiogenic tumours have higher levels of genes coding for membrane vesicles, integrins, remodelling, angiogenesis and apoptosis. These results further support our first finding that nonangiogenic lung tumours are fast-growing tumours filling the alveoli in the absence of vascular remodelling. We raise the hypothesis that in nonangiogenic tumours, hypoxia leads to a higher activation of the mitochondrial respiratory chain, which allows tumour growth without triggering angiogenesis. | [Jiangting Hu, Fabrizio Bianchi, Mary Ferguson, Alfredo Cesario, Stefano Margaritora, Pierluigi Granone, Peter Goldstraw, Michelle Tetlow, Cathy Ratcliffe, Andrew G Nicholson, Adrian Harris, Kevin Gatter, Francesco Pezzella] | Oncogene | 2004-12-13 | |
| naturepublishinggroup10.1038/sj.emboj.7600460 | FGF-20 and DKK1 are transcriptional targets of |[beta]|-catenin and FGF-20 is implicated in cancer and development | -catenin is the major effector of the canonical Wnt signaling pathway. Mutations in components of the pathway that stabilize -catenin result in augmented gene transcription and play a major role in many human cancers. We employed microarrays to identify transcriptional targets of deregulated -catenin in a human epithelial cell line (293) engineered to produce mutant -catenin and in ovarian endometrioid adenocarcinomas characterized with respect to mutations affecting the Wnt/-catenin pathway. Two genes strongly induced in both systems—FGF20 and DKK1—were studied in detail. Elevated levels of FGF20 RNA were also observed in adenomas from mice carrying the ApcMinallele. Both XFGF20 and Xdkk-1 are expressed early in Xenopus embryogenesis under the control of the Wnt signaling pathway. Furthermore, FGF20 and DKK1 appear to be direct targets for -catenin/TCF transcriptional regulation via LEF/TCF-binding sites. Finally, by using small inhibitory RNAs specific for FGF20, we show that continued expression of FGF20 is necessary for maintenance of the anchorage-independent growth state in RK3E cells transformed by -catenin, implying that FGF-20 may be a critical element in oncogenesis induced by the Wnt signaling pathway. | [Mario N Chamorro, Donald R Schwartz, Alin Vonica, Ali H Brivanlou, Kathleen R Cho, Harold E Varmus] | The EMBO Journal | 2004-12-09 | 6.0 |
| naturepublishinggroup10.1038/nmeth1204-263 | Microarrays go mainstream | | [Diane Gershon] | Nature Methods | 2004-12-01 | |
| naturepublishinggroup10.1038/sj.jhh.1001764 | Annual Scientific Meeting of the British Hypertension Society13|[ndash]|15 September 2004St. John's College, Cambridge, UKBHS Abstracts | | [C Delles, NJ Brain, WK Lee, RE Schmieder, AF Dominiczak] | Journal of Human Hypertension | 2004-12-01 | |
| naturepublishinggroup10.1038/nature03124 | A FADD-dependent innate immune mechanism in mammalian cells | Vertebrate innate immunity provides a first line of defence against pathogens such as viruses and bacteria. Viral infection activates a potent innate immune response, which can be triggered by double-stranded (ds)RNA produced during viral replication1, 2, 3. Here, we report that mammalian cells lacking the death-domain-containing protein FADD4, 5 are defective in intracellular dsRNA-activated gene expression, including production of type I (/) interferons, and are thus very susceptible to viral infection. The signalling pathway incorporating FADD is largely independent of Toll-like receptor 3 and the dsRNA-dependent kinase PKR, but seems to require receptor interacting protein 1 as well as Tank-binding kinase 1-mediated activation of the transcription factor IRF-3. The requirement for FADD in mammalian host defence is evocative of innate immune signalling in Drosophila, in which a FADD-dependent pathway responds to bacterial infection by activating the transcription of antimicrobial genes6. These data therefore suggest the existence of a conserved pathogen recognition pathway in mammalian cells that is essential for the optimal induction of type I interferons and other genes important for host defence. | [Siddharth Balachandran, Emmanuel Thomas, Glen N. Barber] | Nature | 2004-11-18 | |
| naturepublishinggroup10.1038/sj.onc.1208228 | Transcript profiling of Wilms tumors reveals connections to kidney morphogenesis and expression patterns associated with anaplasia | Anaplasia (unfavorable histology) is associated with therapy resistance and poor prognosis of Wilms tumor, but the molecular basis for this phenotype is unclear. Here, we used a cDNA array with 9240 clones relevant to cancer biology and/or kidney development to examine the expression profiles of 54 Wilms tumors, five normal kidneys and fetal kidney. By linking genes differentially expressed between fetal kidney and Wilms tumors to kidney morphogenesis, we found that genes expressed at a higher level in Wilms tumors tend to be expressed more in uninduced metanephrogenic mesenchyme or blastema than in their differentiated structures. Conversely, genes expressed at a lower level in Wilms tumors tend to be expressed less in uninduced metanephrogenic mesenchyme or blastema. We also identified 97 clones representing 76 Unigenes or unclustered ESTs that clearly separate anaplastic Wilms tumors from tumors with favorable histology. Genes in this set provide insight into the nature of the abnormal nuclear morphology of anaplastic tumors and may facilitate identification of molecular targets to improve their responsiveness to treatment. | [Wenliang Li, Patricia Kessler, Bryan R G Williams] | Oncogene | 2004-11-08 | |
| naturepublishinggroup10.1038/nmeth1104-169 | Bioinformatics|[mdash]|from genes to pathways | | [Laura Bonetta] | Nature Methods | 2004-11-01 | |
| naturepublishinggroup10.1038/nmeth717 | Microarray-based, high-throughput gene expression profiling of microRNAs | | [Peter T Nelson, Don A Baldwin, L Marie Scearce, J Carl Oberholtzer, John W Tobias, Zissimos Mourelatos] | Nature Methods | 2004-10-21 | 6.2 |
| naturepublishinggroup10.1038/ni1126 | Amplification of IFN-|[alpha]|-induced STAT1 activation and inflammatory function by Syk and ITAM-containing adaptors | | [Ioannis Tassiulas, Xiaoyu Hu, Hao Ho, Yogita Kashyap, Paul Paik, Yongmei Hu, Clifford A Lowell, Lionel B Ivashkiv] | Nature Immunology | 2004-10-03 | |
| naturepublishinggroup10.1038/sj.onc.1208060 | Prediction of high risk Ewing's sarcoma by gene expression profiling | Ewing's sarcoma (ES) is the second most common primary malignant bone tumor in children and adolescents. Currently accepted clinical prognostic factors fail to classify ES patients' risk to relapse at diagnosis. We aimed to find a new strategy to distinguish between poor and good prognosis ES patients already at diagnosis. We analysed the gene expression profiles of 14 primary tumor specimens and six metastases from ES patients, using oligonucleotide microarray analysis. The over-expression of two genes was validated by quantitative PCR using the LightCycler system. We identified two distinct gene expression signatures distinguishing high-risk ES patients that are likely to progress from low-risk ES patients with a favorable prognosis of long-term progression-free survival. The microarray-based classification was superior to currently used prognostic parameters. Over-expressed genes in the poor prognosis patients included genes regulating the cell cycle and genes associated with invasion and metastasis, while among the downregulated genes were tumor suppressor genes and inducers of apoptosis. Our results indicate the existence of a specific gene expression signature of outcome in ES already at diagnosis, and provide a strategy to select patients who would benefit from risk-adapted improved therapy. | [Anat Ohali, Smadar Avigad, Rina Zaizov, Ron Ophir, Shirley Horn-Saban, Ian J Cohen, Isaac Meller, Yehuda Kollender, Josephine Issakov, Isaac Yaniv] | Oncogene | 2004-09-27 | |
| naturepublishinggroup10.1038/nm1099 | The 5-lipoxygenase pathway promotes pathogenesis of hyperlipidemia-dependent aortic aneurysm | | [Lei Zhao, Michael P W Moos, Rolf Gr|[auml]|bner, Fr|[eacute]|d|[eacute]|rique P|[eacute]|drono, Jinjin Fan, Brigitte Kaiser, Nicole John, Sandra Schmidt, Rainer Spanbroek, Katharina L|[ouml]|tzer, Li Huang, Jisong Cui, Daniel J Rader, Jilly F Evans, Andreas J R Habenicht, Colin D Funk] | Nature Medicine | 2004-08-22 | |
| naturepublishinggroup10.1038/labinvest.3700160 | Chromosome 12, frequently deleted in human pancreatic cancer, may encode a tumor-suppressor gene that suppresses angiogenesis | Several lines of evidence have suggested that the long arm of chromosome 12 may carry a tumor-suppressor gene(s) that plays a role in pancreatic ductal carcinogenesis. We have previously found a significant association between loss of heterozygosity of the 12q arm and a poor prognosis in pancreatic cancer patients. In this study, we introduced a normal copy of chromosome 12 into some pancreatic ductal carcinoma cells. Both anchorage-dependent and -independent proliferations as well as invasiveness were similar throughout the hybrid clones when compared with their corresponding parental cells. In sharp contrast, significant suppression of tumorigenesis was observed after inoculation of the hybrid clones into nude mice. Measurements made up to 1 month later showed that there was a significant delay in the growth of tumors into which the introduced normal copy of chromosome 12 had been restored. More significantly, using our dorsal skin chamber and an intravital microscopy system experiment in SCID mice, we demonstrated and visualized directly that implantation of the hybrids failed to promote the angiogenic phenotype encountered in the parental cells. Gene expression profiling using the complementary DNA microarray system identified a set of 24 genes differentially expressed between the hybrids and parental cells. An additional set of 18 genes was also identified that were differentially expressed between the hybrid clone that lost its growth-suppression activity and one that retained such activity. Another set of 25 genes mapped on 12q was detected that showed high expression levels in the hybrid clones retaining growth-suppressive activity. In summary, this study provides the first functional evidence of the existence of an additional tumor-suppressor gene(s) on chromosome 12, whose absence is responsible for the pathogenesis in pancreatic ductal carcinogenesis. | [Sumitaka Yamanaka, Makoto Sunamura, Toru Furukawa, Libo Sun, Liviu P Lefter, Tadayoshi Abe, Toshimasa Yatsuoka, Hiroko Fujimura, Emiko Shibuya, Noriko Kotobuki, Mitsuo Oshimura, Akira Sakurada, Masami Sato, Takashi Kondo, Seiki Matsuno, Akira Horii] | Laboratory Investigation | 2004-08-09 | |
| naturepublishinggroup10.1038/nature02651 | Role of transposable elements in heterochromatin and epigenetic control | Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation1. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize2. These regions are repetitive and late-replicating3. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation4. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development2. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs. | [Zachary Lippman, Anne-Val|[eacute]|rie Gendrel, Michael Black, Matthew W. Vaughn, Neilay Dedhia, W. Richard McCombie, Kimberly Lavine, Vivek Mittal, Bruce May, Kristin D. Kasschau, James C. Carrington, Rebecca W. Doerge, Vincent Colot, Rob Martienssen] | Nature | 2004-07-22 | |
| naturepublishinggroup10.1038/ng1377 | Periodic gene expression program of the fission yeast cell cycle | | [Gabriella Rustici, Juan Mata, Katja Kivinen, Pietro Li|[oacute]|, Christopher J Penkett, Gavin Burns, Jacqueline Hayles, Alvis Brazma, Paul Nurse, J|[uuml]|rg B|[auml]|hler] | Nature Genetics | 2004-06-13 | |
| naturepublishinggroup10.1038/ng1367 | Essential role of Plzf in maintenance of spermatogonial stem cells | | [Jos|[eacute]| A Costoya, Robin M Hobbs, Maria Barna, Giorgio Cattoretti, Katia Manova, Meena Sukhwani, Kyle E Orwig, Debra J Wolgemuth, Pier Paolo Pandolfi] | Nature Genetics | 2004-05-23 | |
| naturepublishinggroup10.1038/nsmb759 | Genome-wide analysis of mRNAs regulated by the THO complex in Drosophila melanogaster | | [Jan Rehwinkel, Andrea Herold, Kerstin Gari, Thomas K|[ouml]|cher, Michaela Rode, Francesca L Ciccarelli, Matthias Wilm, Elisa Izaurralde] | Nature Structural & Molecular Biology | 2004-05-09 | |
| naturepublishinggroup10.1038/sj.ejhg.5201215 | TEAM: a tool for the integration of expression, and linkage and association maps | The identification of genes primarily responsible for complex genetic disorders is a daunting task. Despite the assignment of many susceptibility loci, there has only been limited success in identifying disease genes based solely on positional information from genome-wide screens. The incorporation of several complementary strategies in a single integrated approach should facilitate and further enhance the efficacy of this search for genes. To permit the integration of linkage, association and expression data, together with functional annotations, we have developed a Java-based software tool: TEAM (tool for the integration of expression, and linkage and association maps). TEAM includes a genome viewer, capable of overlaying karyobands, genes, markers, linkage graphs, association data, gene expression levels and functional annotations in one composite view. Data management, analysis and filtering functionality was implemented and extended with links to the Ensembl, Unigene and Gene Ontology databases to facilitate gene annotation. Filtering functionality can help prevent the exclusion of poorly annotated, but differentially expressed, genes that reside in candidate regions that show linkage or association. Here we demonstrate the program's functionality in our study on coeliac disease (OMIM 212750), a multifactorial gluten-sensitive enteropathy. We performed a combined data analysis of a genome-wide linkage screen in 82 Dutch families with affected siblings and the microarray expression profiles of 18 110 cDNAs in 22 intestinal biopsies. | [Lude Franke, Harm van Bakel, Bego|[ntilde]|a Diosdado, Martine van Belzen, Martin Wapenaar, Cisca Wijmenga] | European Journal of Human Genetics | 2004-04-28 | |
| naturepublishinggroup10.1038/sj.mp.4001511 | Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress | The etiology and pathophysiology of schizophrenia remain unknown. A parallel transcriptomics, proteomics and metabolomics approach was employed on human brain tissue to explore the molecular disease signatures. Almost half the altered proteins identified by proteomics were associated with mitochondrial function and oxidative stress responses. This was mirrored by transcriptional and metabolite perturbations. Cluster analysis of transcriptional alterations showed that genes related to energy metabolism and oxidative stress differentiated almost 90% of schizophrenia patients from controls, while confounding drug effects could be ruled out. We propose that oxidative stress and the ensuing cellular adaptations are linked to the schizophrenia disease process and hope that this new disease concept may advance the approach to treatment, diagnosis and disease prevention of schizophrenia and related syndromes. | [S Prabakaran, J E Swatton, M M Ryan, S J Huffaker, JT-J Huang, J L Griffin, M Wayland, T Freeman, F Dudbridge, K S Lilley, N A Karp, S Hester, D Tkachev, M L Mimmack, R H Yolken, M J Webster, E F Torrey, S Bahn] | Molecular Psychiatry | 2004-04-20 | |
| naturepublishinggroup10.1038/sj.onc.1207360 | Anlaysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol|[sol]|fatty acid synthetic pathways as a possible major target of WT1 | The Wilms' tumour suppressor gene, WT1, encodes a zinc-finger protein that is mutated in Wilms' tumours and other malignancies. WT1 is one of the earliest genes expressed during kidney development. WT1 proteins can activate and repress putative target genes in vitro, although the in vivo relevance of such target genes often remains unverified. To better understand the role of WT1 in tumorigenesis and kidney development, we need to identify downstream target genes. In this study, we have expression profiled human embryonic kidney 293 cells stably transfected to allow inducible WT1 expression and mouse mesonephric M15 cells transfected with a WT1 antisense construct to abolish endogenous expression of all WT1 isoforms to identify WT1-responsive genes. The complementary overlap between the two cell lines revealed a pronounced repression of genes involved in cholesterol biosynthesis by WT1. This pathway is transcriptionally regulated by the sterol responsive element-binding proteins (SREBPs). Here, we provide evidence that the C-terminal end of the WT1 protein can directly interact with SREBP, suggesting that WT1 may modify the transcriptional function of SREBPs via a direct protein–protein interaction. Therefore, the tumour suppressor activities of WT1 may be achieved by repressing the mevalonate pathway, thereby controlling cellular proliferation and promoting terminal differentiation. | [Fiona Kaven Rae, Gemma Martinez, Kevin Robert Gillinder, Aaron Smith, Gary Shooter, Alistair Raymond Forrest, Sean Michael Grimmond, Melissa Helen Little] | Oncogene | 2004-03-15 | |
| naturepublishinggroup10.1038/428778a | Table of suppliers | | [] | Nature a - z index | 2004-04-15 | |
| naturepublishinggroup10.1038/sj.onc.1207575 | Limited role of N-terminal phosphoserine residues in the activation of transcription by p53 | The p53 tumor suppressor is phosphorylated in response to various cellular stress signals, such as DNA damage, leading to its release from MDM2 and consequent stabilization and activation as a transcription factor. In human U2OS cells, treatment with adriamycin causes p53 to be phosphorylated on all six serine residues tested, leading to the dissociation of p53 from MDM2 and transcription of the p21 and mdm2 genes. In contrast, in these cells, IPTG-dependent induction of p14ARF, which sequesters MDM2 away from p53, does not lead to detectable phosphorylation of any of the five N-terminal serine residues tested (6, 9, 15, 20, 37). Only C-terminal serine 392 is phosphorylated. However, the increase of p21 and mdm2 mRNAs was indistinguishable following treatment with adriamycin or induction of p14ARF. By using cDNA arrays to examine global p53-dependent gene expression in response to adriamycin or p14ARF, we found that most genes were regulated similarly by the two treatments. However, a subset of p53-regulated genes whose products have proliferative roles or regulate VEGF activity, newly described here, are repressed by p14ARF much more than by adriamycin. We conclude that the phosphorylation of p53 on N-terminal serine residues is not required for increased transcription of the great majority of p53-responsive genes and that the induction of p53 by p14ARF, with little phosphorylation, leads to substantial repression of genes whose products have roles in proliferation. | [Mark W Jackson, Mukesh K Agarwal, Munna L Agarwal, Archana Agarwal, Patricia Stanhope-Baker, Bryan RG Williams, George R Stark] | Oncogene | 2004-04-05 | |
| naturepublishinggroup10.1038/sj.onc.1207563 | Microarray expression profiling in melanoma reveals a BRAF mutation signature | We have used microarray gene expression profiling and machine learning to predict the presence of BRAF mutations in a panel of 61 melanoma cell lines. The BRAF gene was found to be mutated in 42 samples (69%) and intragenic mutations of the NRAS gene were detected in seven samples (11%). No cell line carried mutations of both genes. Using support vector machines, we have built a classifier that differentiates between melanoma cell lines based on BRAF mutation status. As few as 83 genes are able to discriminate between BRAF mutant and BRAF wild-type samples with clear separation observed using hierarchical clustering. Multidimensional scaling was used to visualize the relationship between a BRAF mutation signature and that of a generalized mitogen-activated protein kinase (MAPK) activation (either BRAF or NRAS mutation) in the context of the discriminating gene list. We observed that samples carrying NRAS mutations lie somewhere between those with or without BRAF mutations. These observations suggest that there are gene-specific mutation signals in addition to a common MAPK activation that result from the pleiotropic effects of either BRAF or NRAS on other signaling pathways, leading to measurably different transcriptional changes. | [Sandra Pavey, Peter Johansson, Leisl Packer, Jennifer Taylor, Mitchell Stark, Pamela M Pollock, Graeme J Walker, Glen M Boyle, Ursula Harper, Sarah-Jane Cozzi, Katherine Hansen, Laura Yudt, Chris Schmidt, Peter Hersey, Kay AO Ellem, Michael GE O'Rourke, Peter G Parsons, Paul Meltzer, Markus Ringn|[eacute]|r, Nicholas K Hayward] | Oncogene | 2004-03-29 | |
| naturepublishinggroup10.1038/sj.tpj.6500234 | Comprehensive expression analysis of a rat depression model | Herein we report on a large-scale analysis of gene expression in the 'learned helplessness' (LH) rat model of human depression, using DNA microarrays. We compared gene expression in the frontal cortex (FC) and hippocampus (HPC) of untreated controls, and LH rats treated with saline (LH-S), imipramine or fluoxetine. A total of 34 and 48 transcripts were differentially expressed in the FC and HPC, respectively, between control and LH-S groups. Unexpectedly, only genes for NADH dehydrogenase and zinc transporter were altered in both the FC and HPC, suggesting limited overlap in the molecular processes from specific areas of the brain. Principal component analysis revealed that sets of upregulated metabolic enzyme genes in the FC and downregulated genes for signal transduction in the HPC can distinguish clearly between depressed and control animals, as well as explain the responsiveness to antidepressants. This comprehensive data could help to unravel the complex genetic predispositions involved in human depression. | [N Nakatani, H Aburatani, K Nishimura, J Semba, T Yoshikawa] | The Pharmacogenomics Journal | 2004-02-26 | |
| naturepublishinggroup10.1038/nbt950 | Capturing and profiling adult hair follicle stem cells | The hair follicle bulge possesses putative epithelial stem cells. Characterization of these cells has been hampered by the inability to target bulge cells genetically. Here, we use a Keratin1-15 (Krt1-15, also known as K15) promoter to target mouse bulge cells with an inducible Cre recombinase construct or with the gene encoding enhanced green fluorescent protein (EGFP), which allow for lineage analysis and for isolation of the cells. We show that bulge cells in adult mice generate all epithelial cell types within the intact follicle and hair during normal hair follicle cycling. After isolation, adult Krt1-15-EGFP-positive cells reconstituted all components of the cutaneous epithelium and had a higher proliferative potential than Krt1-15-EGFP-negative cells. Genetic profiling of hair follicle stem cells revealed several known and unknown receptors and signaling pathways important for maintaining the stem cell phenotype. Ultimately, these findings provide potential targets for the treatment of hair loss and other disorders of skin and hair. | [Rebecca J Morris, Yaping Liu, Lee Marles, Zaixin Yang, Carol Trempus, Shulan Li, Jamie S Lin, Janet A Sawicki, George Cotsarelis] | Nature Biotechnology | 2004-03-14 | |
| naturepublishinggroup10.1038/nm1008 | Reduced atherosclerosis in MyD88-null mice links elevated serum cholesterol levels to activation of innate immunity signaling pathways | | [Harry Bj|[ouml]|rkbacka, Vidya V Kunjathoor, Kathryn J Moore, Stephanie Koehn, Christine M Ordija, Melinda A Lee, Terry Means, Kristen Halmen, Andrew D Luster, Douglas T Golenbock, Mason W Freeman] | Nature Medicine | 2004-03-14 | |
| naturepublishinggroup10.1016/j.ymthe.2003.11.007 | Role of Viral Vectors and Virion Shells in Cellular Gene Expression | The role of the virion shell in viral pathogenesis is relatively unknown yet the use of viral vectors in human gene transfer experiments requires an understanding of these interactions. In this study, we used DNA microarrays to identify genes modulated during pathogenic adenovirus or nonpathogenic adeno-associated virus infections. Responses to wt viruses, recombinant vectors, or empty virion particles were compared. Adeno-associated virus shells induced nearly the full complement of changes elicited by the intact virus. The cellular genes elicited a nonpathogenic response, with antiproliferative genes being induced as a cluster. In contrast, adenovirus and adenovirus empty capsid infection yielded a broader response and subset, respectively, including induction of immune and stress-response genes associated with pathogenic effects. Our studies show that the impact of the viral capsid on cellular gene expression, and potential host toxicity, must be considered independent of the vector genome for safe gene transfer in the clinic. | [Jackie L. Stilwell, Richard Jude Samulski] | Molecular Therapy | 2004-03-01 | |
| naturepublishinggroup10.1038/ng1320 | Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1) | | [P|[auml]|ivi Pajukanta, Heidi E Lilja, Janet S Sinsheimer, Rita M Cantor, Aldons J Lusis, Massimiliano Gentile, Xiaoqun Joyce Duan, Aino Soro-Paavonen, Jussi Naukkarinen, Janna Saarela, Markku Laakso, Christian Ehnholm, Marja-Riitta Taskinen, Leena Peltonen] | Nature Genetics | 2004-02-29 | |
| naturepublishinggroup10.1097/01.WCB.0000106012.33322.A2 | Genome-wide Gene Expression Analysis for Induced Ischemic Tolerance and Delayed Neuronal Death Following Transient Global Ischemia in Rats | Genome-wide gene expression analysis of the hippocampal CA1 region was conducted in a rat global ischemia model for delayed neuronal death and induced ischemic tolerance using an oligonucleotide-based DNA microarray containing 8,799 probes. The results showed that expression levels of 246 transcripts were increased and 213 were decreased following ischemia, corresponding to 5.1% of the represented probe sets. These changes were divided into seven expression clusters using hierarchical cluster analysis, each with distinct conditions and time-specific patterns. Ischemic tolerance was associated with transient up-regulation of transcription factors (c-Fos, JunB Egr-1, -2, -4, NGFI-B), Hsp70 and MAP kinase cascade-related genes (MKP-1), which are implicated cell survival. Delayed neuronal death exhibited complex long-lasting changes of expression, such as up-regulation of proapoptotic genes (GADD153, Smad2, Dral, Caspase-2 and -3) and down-regulation of genes implicated in survival signaling (MKK2, and PI4 kinase, DAG/PKC signaling pathways), suggesting an imbalance between death and survival signals. Our study provides a differential gene expression profile between delayed neuronal death and induced ischemic tolerance in a genome-wide analysis, and contributes to further understanding of the complex molecular pathophysiology in cerebral ischemia. | [Nobutaka Kawahara, Yan Wang, Akitake Mukasa, Kazuhide Furuya, Tatsuya Shimizu, Takao Hamakubo, Hiroyuki Aburatani, Tatsuhiko Kodama, Takaaki Kirino] | Journal of Cerebral Blood Flow & Metabolism | 2004-02-01 | |
| naturepublishinggroup10.1097/01.WCB.0000110532.48786.46 | Identification of Potential Stroke Targets by Lentiviral Vector Mediated Overexpression of HIF-1|[alpha]| and HIF-2|[alpha]| in a Primary Neuronal Model of Hypoxia | The identification of genes differentially regulated by ischemia will lead to an improved understanding of cell death pathways such as those involved in the neuronal loss observed following a stroke. Furthermore, the characterization of such pathways could facilitate the identification of novel targets for stroke therapy. We have used a novel approach to amplify differential gene expression patterns in a primary neuronal model of stroke by employing a lentiviral vector system to specifically bias the transcriptional activation of hypoxically regulated genes. Overexpression of the hypoxia-induced transcription factor subunits HIF-1 and HIF-2 elevated hypoxia-mediated transcription of many known HIF-regulated genes well above control levels. Furthermore, many potentially novel HIF-regulated genes were discovered that were not previously identified as hypoxically regulated. Most of the novel genes identified were activated by a combination of HIF-2 overexpression and hypoxic insult. These included several genes with particular importance in cell survival pathways and of potential therapeutic value. Hypoxic induction of HIF-2 may therefore be a critical factor in mediating protective responses against ischemic injury. Further investigation of the genes identified in this study may provide increased understanding of the neuronal response to hypoxia and may uncover novel therapeutic targets for the treatment of cerebral ischemia. | [G S Ralph, S Parham, S R Lee, G L Beard, M H Craigon, N Ward, J R White, R D Barber, W Rayner, S M Kingsman, C R Mundy, N D Mazarakis, D Krige] | Journal of Cerebral Blood Flow & Metabolism | 2004-02-01 | |
| naturepublishinggroup10.1038/sj.mp.4001437 | Molecular characterization of bipolar disorder by comparing gene expression profiles of postmortem brains of major mental disorders | We performed the oligonucleotide microarray analysis in bipolar disorder, major depression, schizophrenia, and control subjects using postmortem prefrontal cortices provided by the Stanley Foundation Brain Collection. By comparing the gene expression profiles of similar but distinctive mental disorders, we explored the uniqueness of bipolar disorder and its similarity to other mental disorders at the molecular level. Notably, most of the altered gene expressions in each disease were not shared by one another, suggesting the molecular distinctiveness of these mental disorders. We found a tendency of downregulation of the genes encoding receptor, channels or transporters, and upregulation of the genes encoding stress response proteins or molecular chaperons in bipolar disorder. Altered expressions in bipolar disorder shared by other mental disorders mainly consisted of upregulation of the genes encoding proteins for transcription or translation. The genes identified in this study would be useful for the understanding of the pathophysiology of bipolar disorder, as well as the common pathophysiological background in major mental disorders at the molecular level. In addition, we found the altered expression of LIM and HSPF1 both in the brains and lymphoblastoid cells in bipolar disorder. These genes may have pathophysiological importance and would be novel candidate genes for bipolar disorder. | [K Iwamoto, C Kakiuchi, M Bundo, K Ikeda, T Kato] | Molecular Psychiatry | 2004-01-26 | |
| naturepublishinggroup10.1038/sj.leu.2403261 | DNA microarray analysis of natural killer cell-type lymphoproliferative disease of granular lymphocytes with purified CD3|[minus]|CD56|[plus]| fractions | Natural killer (NK) cell-type lymphoproliferative disease of granular lymphocytes (LDGL) is characterized by the outgrowth of CD3-CD16/56+ NK cells, and can be further subdivided into two distinct categories: aggressive NK cell leukemia (ANKL) and chronic NK lymphocytosis (CNKL). To gain insights into the pathophysiology of NK cell-type LDGL, we here purified CD3-CD56+ fractions from healthy individuals (n=9) and those with CNKL (n=9) or ANKL (n=1), and compared the expression profiles of >12 000 genes. A total of 15 'LDGL-associated genes' were identified, and a correspondence analysis on such genes could clearly indicate that LDGL samples share a 'molecular signature' distinct from that of normal NK cells. With a newly invented class prediction algorithm, 'weighted distance method', all 19 samples received a clinically matched diagnosis, and, furthermore, a detailed cross-validation trial for the prediction of normal or CNKL status could achieve a high accuracy (77.8%). By applying another statistical approach, we could extract other sets of genes, expression of which was specific to either normal or LDGL NK cells. Together with sophisticated statistical methods, gene expression profiling of a background-matched NK cell fraction thus provides us a wealth of information for the LDGL condition. | [Y L Choi, H Makishima, J Ohashi, Y Yamashita, R Ohki, K Koinuma, J Ota, Y Isobe, F Ishida, K Oshimi, H Mano] | Leukemia | 2004-01-22 | |
| naturepublishinggroup10.1038/sj.leu.2403265 | Differentially expressed genes in adult familial myelodysplastic syndromes | The precise genetic events leading to myelodysplastic syndromes (MDSs) and leukemic transformation remain poorly defined. Even less is known about adult familial MDS. We report an adult MDS family in whom enriched tissue-specific transcripts were derived by subtractive hybridization of cDNA from the mononuclear and CD34+ cells of affected and unaffected family members. These expression libraries were then hybridized to Genome Discovery arrays containing 18 404 genes and expressed sequence tags, and several clusters of differentially expressed genes were identified. A group of 21 genes was underexpressed (>5-fold) in affected vs unaffected family members, and among these were transcription factors and genes involved in myeloid differentiation, such as ZNF140 and myeloid nuclear differentiation antigen (MNDA). Another group of 36 genes was overexpressed (>5-fold), and these encoded proteins belonging to signaling pathways, such as Ras- and Fos-related genes. The top two genes downregulated in this MDS family, ZNF140 and MNDA, were similarly altered in another MDS family, and in some cases of sporadic MDS. Our data suggest that we have identified genes differentially expressed in adult familial MDS, and that alteration of some of these genes may also be important for the evolution of different stages or severity of sporadic MDS. | [A Pradhan, A Mijovic, K Mills, P Cumber, N Westwood, G J Mufti, F V Rassool] | Leukemia | 2004-01-22 | |
| naturepublishinggroup10.1038/sj.onc.1207164 | A novel time-course cDNA microarray analysis method identifies genes associated with the development of cisplatin resistance | In recent years, most cDNA microarray studies of chemotherapeutic drug resistance have not considered the temporal pattern of gene expression. The objective of this study was to examine systematically changes in gene expression of NCI-H226 and NCI-H2170 lung cancer cells treated weekly with IC10 doses of cisplatin. NCI-H226 lung cancer cells were treated weekly with an IC10 dose of cisplatin. Candidate genes with a fold change of 2.0 or more were identified from this study. A second experiment was conducted by exposing NCI-H2170 cells to cisplatin doses that were increased in week 4 and decreased in week 5. Overall, 44 genes were differentially expressed in both the NCI-H226 and NCI-H2170 cell lines. In the NCI-H2170 cell line, 24 genes had a twofold gene expression change from weeks 3 to 4. Real-time PCR found a significant correlation of the gene expression changes for seven genes of interest. This small time-ordered series identified novel genes associated with cisplatin resistance. This kind of analysis should be viewed as a first step towards building gene-regulatory networks. | [Martin A Whiteside, Dung-Tsa Chen, Renee A Desmond, Sarki A Abdulkadir, Gary L Johanning] | Oncogene | 2004-01-22 | |
| naturepublishinggroup10.1038/ng1294 | Lamr1 functional retroposon causes right ventricular dysplasia in mice | | [Yoshihiro Asano, Seiji Takashima, Masanori Asakura, Yasunori Shintani, Yulin Liao, Tetsuo Minamino, Hiroshi Asanuma, Shoji Sanada, Jiyoong Kim, Akiko Ogai, Tomi Fukushima, Yumiko Oikawa, Yasushi Okazaki, Yasufumi Kaneda, Manabu Sato, Jun-ichi Miyazaki, Soichiro Kitamura, Hitonobu Tomoike, Masafumi Kitakaze, Masatsugu Hori] | Nature Genetics | 2004-01-18 | |
| naturepublishinggroup10.1038/sj.emboj.7600030 | Cytoprotection by pre-emptive conditional phosphorylation of translation initiation factor 2 | Transient phosphorylation of the -subunit of translation initiation factor 2 (eIF2) represses translation and activates select gene expression under diverse stressful conditions. Defects in the eIF2 phosphorylation-dependent integrated stress response impair resistance to accumulation of malfolded proteins in the endoplasmic reticulum (ER stress), to oxidative stress and to nutrient deprivations. To study the hypothesized protective role of eIF2 phosphorylation in isolation of parallel stress signaling pathways, we fused the kinase domain of pancreatic endoplasmic reticulum kinase (PERK), an ER stress-inducible eIF2 kinase that is normally activated by dimerization, to a protein module that binds a small dimerizer molecule. The activity of this artificial eIF2 kinase, Fv2E-PERK, is subordinate to the dimerizer and is uncoupled from upstream stress signaling. Fv2E-PERK activation enhanced the expression of numerous stress-induced genes and protected cells from the lethal effects of oxidants, peroxynitrite donors and ER stress. Our findings indicate that eIF2 phosphorylation can initiate signaling in a cytoprotective gene expression pathway independently of other parallel stress-induced signals and that activation of this pathway can single-handedly promote a stress-resistant preconditioned state. | [Phoebe D Lu, C|[eacute]|line Jousse, Stefan J Marciniak, Yuhong Zhang, Isabel Novoa, Donalyn Scheuner, Randal J Kaufman, David Ron, Heather P Harding] | The EMBO Journal | 2004-01-08 | |
| naturepublishinggroup10.1038/sj.bjc.6601458 | Cellular responses to ErbB-2 overexpression in human mammary luminal epithelial cells: comparison of mRNA and protein expression | Microarray analysis offers a powerful tool for studying the mechanisms of cellular transformation, although the correlation between mRNA and protein expression is largely unknown. In this study, a microarray analysis was performed to compare transcription in response to overexpression of the ErbB-2 receptor tyrosine kinase in a model mammary luminal epithelial cell system, and in response to the ErbB-specific growth factor heregulin 1. We sought to validate mRNA changes by monitoring changes at the protein level using a parallel proteomics strategy, and report a surprisingly high correlation between transcription and translation for the subset of genes studied. We further characterised the identified targets and relate differential expression to changes in the biological properties of ErbB-2-overexpressing cells. We found differential regulation of several key cell cycle modulators, including cyclin D2, and downregulation of a large number of interferon-inducible genes, consistent with increased proliferation of the ErbB-2-overexpressing cells. Furthermore, differential expression of genes involved in extracellular matrix modelling and cellular adhesion was linked to altered adhesion of these cells. Finally, we provide evidence for enhanced autocrine activation of MAPK signalling and the AP-1 transcription complex. Together, we have identified changes that are likely to drive proliferation and anchorage-independent growth of ErbB-2- overexpressing cancer cells. | [S L White, S Gharbi, M F Bertani, H-L Chan, M D Waterfield, J F Timms] | British Journal of Cancer | 2004-01-12 | |
| naturepublishinggroup10.1038/sj.onc.1207377 | Microarray analysis identifies Autotaxin, a tumour cell motility and angiogenic factor with lysophospholipase D activity, as a specific target of cell transformation by v-Jun | We have used chicken cDNA microarrays to investigate gene-expression changes induced during transformation of chick embryo fibroblasts (CEF) by the viral Jun oncoprotein encoded by ASV17. This analysis reveals that v-Jun induces increases and decreases of varying magnitude in the expression of genes involved in diverse cellular functions, most of which have not been detected in previous screens for putative v-Jun targets. In all, 27 individual genes were identified, whose expression is increased threefold or more in v-Jun-transformed cells, including genes involved in energy generation, protein synthesis, and gene transcription. Interestingly, this group includes the hypoxia-inducible factor-1 alpha (Hif-1) transcription factor and the glycolytic enzyme enolase, suggesting that adaptation to hypoxia could play a role in tumorigenesis by v-Jun. We also identified 32 genes whose expression is decreased threefold or more, including chaperones, components of the cytoskeleton, and, unexpectedly, DNA replication factors. The gene whose expression is upregulated most dramatically (100-fold) encodes Autotaxin (ATX), a secreted tumor motility-promoting factor with lysophospholipase D activity. Strikingly, v-Jun-transformed CEF secrete catalytically active ATX and chemotactic activity, which can be detected in conditioned medium. ATX is not detectably expressed in normal CEF or CEF transformed by the v-Src or v-Myc oncoproteins, indicating that induction of this putative autocrine/paracrine factor is a specific consequence of cell transformation by v-Jun. ATX has been implicated in both angiogenesis and invasion, and could therefore play an important role in tumorigenesis by v-Jun in vivo. | [Elizabeth J Black, Timothy Clair, Jeffrey Delrow, Paul Neiman, David A F Gillespie] | Oncogene | 2003-12-22 | |
| naturepublishinggroup10.1038/nm972 | Molecular determinants of resistance to antiandrogen therapy | | [Charlie D Chen, Derek S Welsbie, Chris Tran, Sung Hee Baek, Randy Chen, Robert Vessella, Michael G Rosenfeld, Charles L Sawyers] | Nature Medicine | 2003-12-21 | |
| naturepublishinggroup10.1038/nsb1015 | Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock | | [Thomas Preiss, Julie Baron-Benhamou, Wilhelm Ansorge, Matthias W Hentze] | Nature Structural & Molecular Biology | 2003-11-09 | |
| naturepublishinggroup10.1038/ng1260 | Pyruvate kinase deficiency in mice protects against malaria | | [Gundula Min-Oo, Anny Fortin, Mi-Fong Tam, Andr� Nantel, Mary M Stevenson, Philippe Gros] | Nature Genetics | 2003-11-02 | |
| naturepublishinggroup10.1046/j.1523-1755.2003.00276.x | A catalogue of gene expression in the developing kidney | A catalogue of gene expression in the developing kidney. | [Kristopher Schwab, Larry T Patterson, Bruce J Aronow, Ruth Luckas, Hung-Chi Liang, S Steven Potter] | Kidney International | 2003-11-01 | |
| naturepublishinggroup10.1038/nn1143 | Regulation of gene expression and cocaine reward by CREB and |[Delta]|FosB | | [Colleen A McClung, Eric J Nestler] | Nature Neuroscience | 2003-10-19 | |
| naturepublishinggroup10.1038/sj.onc.1206887 | Expression profiling of epithelial plasticity in tumor progression | Epithelial-to-mesenchymal transition (EMT), a switch of polarized epithelial cells to a migratory, fibroblastoid phenotype, is increasingly considered as an important event during malignant tumor progression and metastasis. To identify molecular players involved in EMT and metastasis, we performed expression profiling of a set of combined in vitro/in vivo cellular models, based on clonal, fully polarized mammary epithelial cells. Seven closely related cell pairs were used, which were modified by defined oncogenes and/or external factors and showed specific aspects of epithelial plasticity relevant to cell migration, local invasion and metastasis. Since mRNA levels do not necessarily reflect protein levels in cells, we used an improved expression profiling method based on polysome-bound RNA, suitable to analyse global gene expression on Affymetrix chips. A substantial fraction of all regulated genes was found to be exclusively controlled at the translational level. Furthermore, profiling of the above multiple cell pairs allowed one to identify small numbers of genes by cluster analysis, specifically correlating gene expression with EMT, metastasis, scattering and/or oncogene function. A small set of genes specifically regulated during EMT was identified, including key regulators and signaling pathways involved in cell proliferation, epithelial polarity, survival and trans-differentiation to mesenchymal-like cells with invasive behavior. | [Martin Jechlinger, Stefan Grunert, Ido H Tamir, Elzbieta Janda, Susanna L|[uuml]|demann, Thomas Waerner, Peter Seither, Andreas Weith, Hartmut Beug, Norbert Kraut] | Oncogene | 2003-10-16 | |
| naturepublishinggroup10.1038/sj.leu.2403098 | DNA microarray analysis of hematopoietic stem cell-like fractions from individuals with the M2 subtype of acute myeloid leukemia | Acute myeloid leukemia (AML) may develop de novo or secondarily to myelodysplastic syndrome (MDS). Although the clinical outcome of MDS-related AML is worse than that of de novo AML, it is not easy to differentiate between these two clinical courses without a record of prior MDS. Large-scale profiling of gene expression by DNA microarray analysis is a promising approach with which to identify molecular markers specific to de novo or MDS-related AML. This approach has now been adopted with AC133-positive hematopoietic stem cell-like fractions purified from 10 individuals, each with either de novo or MDS-related AML of the M2 subtype. Sets of genes whose activity was associated with either disease course were identified. Furthermore, on the basis of the expression profiles of these genes, it was possible to predict correctly the clinical diagnosis for 17 (85%) of the 20 cases in a cross-validation trial. Similarly, different sets of genes were identified whose expression level was associated with clinical outcome after induction chemotherapy. These data suggest that, at least in terms of gene expression profiles, de novo AML and MDS-related AML are distinct clinical entities. | [Y Oshima, M Ueda, Y Yamashita, Y L Choi, J Ota, S Ueno, R Ohki, K Koinuma, T Wada, K Ozawa, A Fujimura, H Mano] | Leukemia | 2003-10-01 | |
| naturepublishinggroup10.1038/nature01874 | Chemokine receptor CXCR4 downregulated by von Hippel|[ndash]|Lindau tumour suppressor pVHL | Organ-specific metastasis is governed, in part, by interactions between chemokine receptors on cancer cells and matching chemokines in target organs. For example, malignant breast cancer cells express the chemokine receptor CXCR4 and commonly metastasize to organs that are an abundant source of the CXCR4-specific ligand stromal cell-derived factor-1 (ref. 1). It is still uncertain how an evolving tumour cell is reprogrammed to express CXCR4, thus implementing the tendency to metastasize to specific organs. Here we show that the von Hippel–Lindau tumour suppressor protein pVHL negatively regulates CXCR4 expression owing to its capacity to target hypoxia-inducible factor (HIF) for degradation under normoxic conditions. This process is suppressed under hypoxic conditions, resulting in HIF-dependent CXCR4 activation. An analysis of clear cell renal carcinoma that manifests mutation of the VHL gene in most cases revealed an association of strong CXCR4 expression with poor tumour-specific survival. These results suggest a mechanism for CXCR4 activation during tumour cell evolution and imply that VHL inactivation acquired by incipient tumour cells early in tumorigenesis confers not only a selective survival advantage but also the tendency to home to selected organs. | [Peter Staller, Jitka Sulitkova, Joanna Lisztwan, Holger Moch, Edward J. Oakeley, Wilhelm Krek] | Nature | 2003-09-18 | |
| naturepublishinggroup10.1038/425216a | Table of suppliers | | [] | Nature a - z index | 2003-09-11 | |
| naturepublishinggroup10.1038/ng1235 | Impaired feedback regulation of XBP1 as a genetic risk factor for bipolar disorder | | [Chihiro Kakiuchi, Kazuya Iwamoto, Mizuho Ishiwata, Miki Bundo, Takaoki Kasahara, Ichiro Kusumi, Takahiro Tsujita, Yuji Okazaki, Shinichiro Nanko, Hiroshi Kunugi, Tsukasa Sasaki, Tadafumi Kato] | Nature Genetics | 2003-08-31 | |
| naturepublishinggroup10.1038/ncb1038 | Activation of the interferon system by short-interfering RNAs | RNA interference (RNAi) is a powerful tool used to manipulate gene expression or determine gene function1, 2. One technique of expressing the short double-stranded (ds) RNA intermediates required for interference in mammalian systems is the introduction of short-interfering (si) RNAs3, 4, 5, 6. Although RNAi strategies are reliant on a high degree of specificity, little attention has been given to the potential non-specific effects that might be induced. Here, we found that transfection of siRNAs results in interferon (IFN)-mediated activation of the Jak–Stat pathway and global upregulation of IFN-stimulated genes. This effect is mediated by the dsRNA-dependent protein kinase, PKR, which is activated by 21-base-pair (bp) siRNAs and required for upregulation of IFN- in response to siRNAs. In addition, we show by using cell lines deficient in specific components mediating IFN action that the RNAi mechanism itself is independent of the interferon system. Thus, siRNAs have broad and complicating effects beyond the selective silencing of target genes when introduced into cells. This is of critical importance, as siRNAs are currently being explored for their potential therapeutic use7, 8. | [Carol A. Sledz, Michelle Holko, Michael J. de Veer, Robert H. Silverman, Bryan R.G. Williams] | Nature Cell Biology | 2003-08-24 | |
| naturepublishinggroup10.1038/ni960 | CIITA-regulated plexin-A1 affects T-cell|[ndash]|dendritic cell interactions | | [Athena W Wong, W June Brickey, Debra J Taxman, Hendrick W van Deventer, William Reed, Jian Xin Gao, Pan Zheng, Yang Liu, Ping Li, Janice S Blum, Karen P McKinnon, Jenny P-Y Ting] | Nature Immunology | 2003-08-10 | |
| naturepublishinggroup10.1038/ng1213 | Identification of acquired somatic mutations in the gene encoding chromatin-remodeling factor ATRX in the |[alpha]|-thalassemia myelodysplasia syndrome (ATMDS) | | [Richard J Gibbons, Andrea Pellagatti, David Garrick, William G Wood, Nicola Malik, Helena Ayyub, Cordelia Langford, Jacqueline Boultwood, James S Wainscoat, Douglas R Higgs] | Nature Genetics | 2003-07-13 | |
| naturepublishinggroup10.1038/sj.onc.1206545 | Mutant p53 and aberrant cytosine methylation cooperate to silence gene expression | p53 is an important transcriptional regulator that is frequently mutated in cancer. Gene-profiling experiments of breast cancer cells infected with wt p53 revealed both MASPIN and desmocollin 3 (DSC3) to be p53-target genes, even though both genes are silenced in association with aberrant cytosine methylation of their promoters. Despite the transcriptional repression of these genes by aberrant DNA methylation, restoration of p53 resulted in the partial reactivation of both genes. This reactivation is a result of wt p53 binding to its consensus DNA-binding sites within the MASPIN and DSC3 promoters, stimulating histone acetylation, and enhancing chromatin accessibility of their promoters. Interestingly, wt p53 alone did not affect the methylation status of either promoter, suggesting that p53 itself can partially overcome the repressive barrier of DNA methylation. Pharmacologic inhibition of DNA methylation with 5-aza-2'-deoxycytidine in combination with restoration of wt p53 status resulted in a synergistic reactivation of these genes to near-normal levels. These results suggest that cancer treatments that target both genetic and epigenetic facets of gene regulation may be a useful strategy towards the therapeutic transcriptional reprogramming of cancer cells. | [Marc M Oshiro, George S Watts, Ryan J Wozniak, Damian J Junk, Jose L Munoz-Rodriguez, Frederick E Domann, Bernard W Futscher] | Oncogene | 2003-06-05 | |
| naturepublishinggroup10.1097/01.LAB.0000073130.58435.E5 | Comparative Microarray Analysis of Gene Expression During Activation of Human Peripheral Blood T Cells and Leukemic Jurkat T Cells | Activation of T cells involves a complex cascade of signal transduction pathways linking T-cell receptor engagement at the cell membrane to the transcription of multiple genes within the nucleus. The T-cell leukemia–derived cell line Jurkat has generally been used as a model system for the activation of T cells. However, genome-wide comprehensive studies investigating the activation status, and thus the appropriateness, of this cell line for this purpose have not been performed. We sought to compare the transcriptional profiles of phenotypically purified human CD2+ T cells with those of Jurkat T cells during T-cell activation, using cDNA microarrays containing 6912 genes. About 300 genes were up-regulated by more than 2-fold during activation of both peripheral blood (PB) T cells and Jurkat T cells. The number of down-regulated genes was significantly lower than that of up-regulated genes. Only 79 genes in PB T cells and 37 genes in Jurkat T cells were down-regulated by more than 2-fold during activation. Comparison of gene expression during activation of Jurkat and PB T cells revealed a common set of genes that were up-regulated, such as Rho GTPase-activating protein 1, SKP2, CDC25A, T-cell specific transcription factor 7, cytoskeletal proteins, and signaling molecules. Genes that were commonly down-regulated in both PB T cells and Jurkat T cells included CDK inhibitors (p16, p19, p27), proapoptotic caspases, and the transcription factors c-fos and jun-B. After activation, 71 genes in PB T cells and only 3 genes in Jurkat T cells were up-regulated 4-fold or more. Of these up-regulated genes and expressed sequence tags, 44 were constitutively expressed at high levels in nonactivated Jurkat cells. Quantitative real-time RT-PCR analysis confirmed our microarray data. Our findings indicate that although there is significant overlap in the activation-associated transcriptional profiles in PB T cells compared with Jurkat T cells, there is a subset of genes showing differential expression patterns during the activation of the two cell types. | [Zhaosheng Lin, G Chris Fillmore, Tae-Hyun Um, Kojo S J Elenitoba-Johnson, Megan S Lim] | Laboratory Investigation | 2003-06-01 | |
| naturepublishinggroup10.1093/emboj/cdg233 | Genome-wide analysis of nuclear mRNA export pathways in Drosophila | NXF1, p15 and UAP56 are essential nuclear mRNA export factors. The fraction of mRNAs exported by these proteins or via alternative pathways is unknown. We have analyzed the relative abundance of nearly half of the Drosophila transcriptome in the cytoplasm of cells treated with the CRM1 inhibitor leptomycin-B (LMB) or depleted of export factors by RNA interference. While the vast majority of mRNAs were unaffected by LMB, the levels of most mRNAs were significantly reduced in cells depleted of NXF1, p15 or UAP56. The striking similarities of the mRNA expression profiles in NXF1, p15 and UAP56 knockdowns show that these proteins act in the same pathway. The broad effect on mRNA levels observed in these cells indicates that the functioning of this pathway is required for export of most mRNAs. Nonetheless, a set of mRNAs whose export was unaffected by the depletions and some requiring NXF1:p15 but not UAP56 were identified. In addition, our analysis revealed a feedback loop by which a block to mRNA export triggers the upregulation of genes involved in this process. | [Andrea Herold, Luis Teixeira, Elisa Izaurralde] | The EMBO Journal | 2003-05-15 | |
| naturepublishinggroup10.1038/nbt0503-581 | Cell & tissue culture and Gene & protein expression | | [] | Nature a - z index | 2003-05-01 | |
| naturepublishinggroup10.1038/sj.onc.1206349 | cDNA microarray analysis of genes associated with ERBB2 (HER2|[sol]|neu) overexpression in human mammary luminal epithelial cells | To investigate changes in gene expression associated with ERBB2, expression profiling of immortalized human mammary luminal epithelial cells and variants expressing a moderate and high level of ERBB2 has been carried out using cDNA microarrays corresponding to approximately 6000 unique genes/ESTs. A total of 61 significantly up- or downregulated (2.0-fold) genes were identified and further validated by RT–PCR analysis as well as microarray comparisons with a spontaneously ERBB2- overexpressing breast cancer cell line and ERBB2-positive primary breast tumors. The expression and clinical relevance of proteins predicted to be associated with ERBB2 overexpression in breast cancers were analysed together with their clinical relevance by antibody screening using a tissue array. Differentially regulated genes include those involved in cell–matrix interactions including proline 4-hydroxylase (P4HA2), galectin 1 (LGALS1) and galectin 3 (LGALS3), fibronectin 1 (FN1) and p-cadherin (CDH3), and cell proliferation (CRIP1, IGFBP3) and transformation (S100P, S100A4). A number of genes associated with MYC signalling were also differentially expressed, including NDRG1, USF2 and the epithelial membrane proteins 1 and 3 (EMP1, EMP3). These data represent profiles of the transcriptional changes associated with ERBB2-related pathways in the breast, and identify novel and potentially useful targets for prognosis and therapy. | [Alan Mackay, Chris Jones, Tim Dexter, Ricardo L A Silva, Karen Bulmer, Allison Jones, Peter Simpson, Robert A Harris, Parmjit S Jat, A Munro Neville, Luiz F L Reis, Sunil R Lakhani, Michael J O'Hare] | Oncogene | 2003-05-01 | |
| naturepublishinggroup10.1038/sj.gene.6363966 | Analysis of gene expression profiles in human systemic lupus erythematosus using oligonucleotide microarray | Epidemiologic studies suggest a strong genetic component for susceptibility to systemic lupus erythematosus (SLE). To investigate the genetic mechanism of pathogenesis of SLE, we studied the difference in gene expression of peripheral blood cells between 10 SLE patients and 18 healthy controls using oligonucleotide microarray. When gene expression for patients was compared to the mean of normal controls, among the 3002 target genes, 61 genes were identified with greater than a two-fold change difference in expression level. Of these genes, 24 were upregulated and 37 downregulated in at least half of the patients. By the Welch's ANOVA/Welch's t-test, all these 61 genes were significantly different (P<0.05) between SLE patients and normal controls. Among these genes with differential expression, IFN- and Ly6E (TSA-1/Sca-2) may play an important role in the mechanism of SLE pathogenesis. TSA-1 antigens may represent an important alternative pathway for T-cell activation that may be involved in IFN-mediated immunomodulation. Hierarchical clustering showed that patient samples were clearly separated from controls based on their gene expression profile. These results demonstrate that high-density oligonucleotide microarray has the potential to explore the mechanism of pathogenesis of systemic lupus erythematosus. | [G-M Han, S-L Chen, N Shen, S Ye, C-D Bao, Y-Y Gu] | Genes and Immunity | 2003-04-01 | |
| naturepublishinggroup10.1038/nature01545 | The BMP antagonist noggin regulates cranial suture fusion | During skull development, the cranial connective tissue framework undergoes intramembranous ossification to form skull bones (calvaria). As the calvarial bones advance to envelop the brain, fibrous sutures form between the calvarial plates1. Expansion of the brain is coupled with calvarial growth through a series of tissue interactions within the cranial suture complex2. Craniosynostosis, or premature cranial suture fusion, results in an abnormal skull shape, blindness and mental retardation3. Recent studies have demonstrated that gain-of-function mutations in fibroblast growth factor receptors (fgfr) are associated with syndromic forms of craniosynostosis4, 5. Noggin, an antagonist of bone morphogenetic proteins (BMPs), is required for embryonic neural tube, somites and skeleton patterning6, 7, 8. Here we show that noggin is expressed postnatally in the suture mesenchyme of patent, but not fusing, cranial sutures, and that noggin expression is suppressed by FGF2 and syndromic fgfr signalling. Since noggin misexpression prevents cranial suture fusion in vitro and in vivo, we suggest that syndromic fgfr-mediated craniosynostoses may be the result of inappropriate downregulation of noggin expression. | [Stephen M. Warren, Lisa J. Brunet, Richard M. Harland, Aris N. Economides, Michael T. Longaker] | Nature | 2003-04-10 | 4.2 |
| naturepublishinggroup10.1038/sj.tpj.6500147 | Analysis of gene expression in carbon tetrachloride-treated rat livers using a novel bioarray technology | The present study successfully utilizes a new ADME Rat Expression Bioarray, containing 1040 metabolism- and toxicology-linked genes, to monitor gene expression from the livers of rats treated with carbon tetrachloride (CCl4). Histopathological analysis, hierarchical clustering methods, and gene expression profiling are compared between the control and CCl4-treated animals. A total of 44 transcripts were found to be altered in response to the hepatotoxin, 19 of which were upregulated and 25 were downregulated. Some of these gene expression changes were expected and concurred with previously published data while others were novel findings. | [M B Young, M R DiSilvestro, T J Sendera, J Freund, A Kriete, S R Magnuson] | The Pharmacogenomics Journal | 2003-01-01 | |
| naturepublishinggroup10.1097/01.WCB.0000048518.34839.DE | Blood Genomic Expression Profile for Neuronal Injury | This study determined whether stroke and other types of insults produced a gene expression profile in blood that correlated with the presence of neuronal injury. Adult rats were subjected to ischemic stroke, intracerebral hemorrhage, status epilepticus, and insulin-induced hypoglycemia and compared with untouched, sham surgery, and hypoxia animals that had no brain injury. One day later, microarray analyses showed that 117 genes were upregulated and 80 genes were downregulated in mononuclear blood cells of the "injury" (n = 12) compared with the "no injury" (n = 9) animals. A second experiment examined the whole blood genomic response of adult rats after global ischemia and kainate seizures. Animals with no brain injury were compared with those with brain injury documented by TUNEL and PANT staining. One day later, microarray analyses showed that 37 genes were upregulated and 67 genes were downregulated in whole blood of the injury (n = 4) animals compared with the no-injury (n = 4) animals. Quantitative reverse transcription–polymerase chain reaction confirmed that the vesicular monoamine transporter-2 increased 2.3- and 1.6-fold in animals with severe and mild brain injury, respectively, compared with no-injury animals. Vascular tyrosine phosphatase-1 increased 2.0-fold after severe injury compared with no injury. The data support the hypothesis that there is a peripheral blood genomic response to neuronal injury, and that this blood response is associated with a specific blood mRNA gene expression profile that can be used as a marker of the neuronal damage. | [Yang Tang, Alex C Nee, Aigang Lu, Ruiqiong Ran, Frank R Sharp] | Journal of Cerebral Blood Flow & Metabolism | 2003-03-01 | |
| naturepublishinggroup10.1038/sj.onc.1206187 | The transcriptional response after oxidative stress is defective in Cockayne syndrome group B cells | Cockayne syndrome (CS) is a human hereditary disease belonging to the group of segmental progerias, and the clinical phenotype is characterized by postnatal growth failure, neurological dysfunction, cachetic dwarfism, photosensitivity, sensorineural hearing loss, and retinal degradation. CS-B cells are defective in transcription-coupled DNA repair, base excision repair, transcription, and chromatin structural organization. Using array analysis, we have examined the expression profile in CS complementation group B (CS-B) fibroblasts after exposure to oxidative stress (H2O2) before and after complete complementation with the CSB gene. The following isogenic cell lines were compared: CS-B cells (CS-B null), CS-B cells complemented with wild-type CSB (CS-B wt), and a stably transformed cell line with a point mutation in the ATPase domain of CSB (CS-B ATPase mutant). In the wt rescued cells, we detected significant induction (two-fold) of 112 genes out of the 6912 analysed. The patterns suggested an induction or upregulation of genes involved in several DNA metabolic processes including DNA repair, transcription, and signal transduction. In both CS-B mutant cell lines, we found a general deficiency in transcription after oxidative stress, suggesting that the CSB protein influenced the regulation of transcription of certain genes. Of the 6912 genes, 122 were differentially regulated by more than two-fold. Evidently, the ATPase function of CSB is biologically important as the deficiencies seen in the ATPase mutant cells are very similar to those observed in the CS-B-null cells. Some major defects are in the transcription of genes involved in DNA repair, signal transduction, and ribosomal functions. | [Kasper J Kyng, Alfred May, Robert M Brosh, Wen-Hsing Cheng, Catheryne Chen, Kevin G Becker, Vilhelm A Bohr] | Oncogene | 2003-02-27 | |
| naturepublishinggroup10.1038/ni903 | Transcriptional profiling identifies Id2 function in dendritic cell development | | [Christine Hacker, Ralf D. Kirsch, Xin-Sheng Ju, Thomas Hieronymus, Tatjana C. Gust, Christiane Kuhl, Thorsten Jorgas, Steffen M. Kurz, Stefan Rose-John, Yoshifumi Yokota, Martin Zenke] | Nature Immunology | 2003-02-24 | |
| naturepublishinggroup10.1038/sj.onc.1206070 | Functional genomic analysis reveals distinct neoplastic phenotypes associated with c-myb mutation in the bursa of Fabricius | Avian retroviral integration into the c-myb locus is casually associated with the development of lymphomas in the bursa of Farbricius of chickens; these arise with a shorter latency than bursal lymphomas caused by deregulation of c-myc. This study indicates that c-myb mutation in embryonic bursal precursors leads to an oligoclonal population of developing bursal follicles, showing a variable propensity to form a novel lesion, the neoplastic follicle (NF). About half of such bursas rapidly developed lymphomas. Detection of changes in gene expression, during the development of neoplasms, was carried out by cDNA microarray analysis. The transcriptional signature of lymphomas with mutant c-myb was more limited than, and only partially shared with, those of bursal lymphomas caused by Myc or Rel oncogenes. The c-myb-associated lymphomas frequently showed overexpression of c-myc and altered expression of other genes involved in cell cycle control and proliferation-related signal transduction. Oligoclonal, NF-containing bursas lacked detectable c-myc overexpression and demonstrated a pattern of gene expression distinct from that of normal bursa and partially shared with the short-latency lymphomas. This functional genomic analysis uncovered several different pathways of lymphomagenesis by oncogenic transcription factors acting in a B-cell lineage. | [Paul E Neiman, Jovana J Grbi|[ccedil]|, Tatjana S Polony, Robert Kimmel, Sandra J Bowers, Jeffrey Delrow, Karen L Beemon] | Oncogene | 2003-02-20 | |
| naturepublishinggroup10.1038/sj.bjc.6600766 | Molecular classification of synovial sarcomas, leiomyosarcomas and malignant fibrous histiocytomas by gene expression profiling | In this study, we have used genome-wide expression profiling to categorise synovial sarcomas, leiomyosarcomas and malignant fibrous histiocytomas (MFHs). Following hierarchical clustering analysis of the expression data, the best match between tumour clusters and conventional diagnosis was observed for synovial sarcomas. Eight of nine synovial sarcomas examined formed a cluster that was characterised by higher expression of a set of 48 genes. In contrast, sarcomas conventionally classified as leiomyosarcomas and MFHs did not match the clusters defined by hierarchical clustering analysis. One major cluster contained a mixture of both leiomyosarcomas and MFHs and was defined by the lower expression of a set of 202 genes. A cluster containing a subgroup of MFHs was also detected. These results may have implications for the classification of soft tissue sarcomas, and are consistent with the view that sarcomas conventionally defined as MFHs do not represent a separate diagnostic category. | [Y-F Lee, M John, S Edwards, J Clark, P Flohr, K Maillard, M Edema, L Baker, D C Mangham, R Grimer, R Wooster, J M Thomas, C Fisher, I Judson, C S Cooper] | British Journal of Cancer | 2003-02-24 | |
| naturepublishinggroup10.1097/01.LAB.0000053913.85892.E9 | Gene Expression Profile of Serial Samples of Transformed B-Cell Lymphomas | Follicular lymphoma (FL) is characterized by a continuous rate of relapse and transformation to a high-grade lymphoma, usually diffuse large B-cell lymphoma (DLBCL), associated with a dismal prognosis and a poor response to conventional chemotherapy. The progression of indolent to aggressive FL is accompanied by the successive accumulation of recurrent chromosomal defects, but the resultant alterations of gene expression are largely unknown. To expand the understanding of the pathogenesis of FL transformation, we initially performed oligonucleotide microarray analyses using Affymetrix HuFL chips on five cases with matched snap-frozen lymph nodes before and after transformation. Expression data were analyzed using the Affymetrix Microarray Suite 4.0 and Genespring 4.0. Thirty-six genes with increased expression and 66 genes with decreased expression associated with transformation were identified and functionally classified. The expression of differentially expressed genes was confirmed by real-time quantitative RT-PCR (QRT-PCR) using a total of seven matched pairs and an additional five FL and five unrelated DLBCL. In addition, selected genes were further analyzed by QRT-PCR or immunohistochemistry using a large, unrelated series of FL (grades 1 to 3) as well as transformed and de novo DLBCL (total of 51 samples). The microarray results correlated with the protein expression data obtained from samples at the time of initial diagnosis and transformation. Furthermore, the expression of 25 candidate genes was evaluated by QRT-PCR with a 78% confirmation rate. Some of the identified genes, such as nucleobindin, interferon regulatory factor 4, and tissue inhibitor of metalloproteinases 1, are already known to be associated with high-grade non-Hodgkin's lymphoma. Novel candidate genes with confirmed increased and decreased expression in transformed DLBCL include ABL2 and NEK2, and PDCD1 and VDUP1, respectively. In summary, this study shows that transformation of FL to DLBCL is associated with a distinct set of differentially expressed genes of potential functional importance. | [Sven de Vos, Wolf-Karsten Hofmann, Thomas M Grogan, Utz Krug, Mathew Schrage, Thomas P Miller, Jonathan G Braun, William Wachsman, H Phillip Koeffler, Jonathan W Said] | Laboratory Investigation | 2003-02-01 | |
| naturepublishinggroup10.1038/sj.onc.1206131 | Distinct changes in gene expression induced by A-Myb, B-Myb and c-Myb proteins | The c-Myb, A-Myb and B-Myb transcription factors have nearly identical DNA-binding domains, activate the same reporter gene constructs in animal cells, but have different biological roles. The Myb proteins are often coexpressed in the same cells, raising questions about whether they activate similar or distinct gene expression profiles, and whether they cooperate or compete in regulating the same promoters. Here, recombinant adenoviruses were used to express each protein in human mammary cells, and then microarray assays were used to assess global changes in gene expression. Each Myb protein induced a unique and specific set of changes, displaying activities far more complex than revealed by standard reporter gene assays. These results have important implications for the roles of various Myb proteins in normal and transformed human cells, for regulatory pathways that might modify their activities and for the importance of acquired mutations that may qualitatively alter their functions in tumors. | [John J Rushton, Lisa M Davis, Wanli Lei, Xianming Mo, Achim Leutz, Scott A Ness] | Oncogene | 2003-01-16 | |
| naturepublishinggroup10.1038/nm820 | Reciprocal regulation of inflammation and lipid metabolism by liver X receptors | | [Sean B. Joseph, Antonio Castrillo, Bryan A. Laffitte, David J. Mangelsdorf, Peter Tontonoz] | Nature Medicine | 2003-01-13 | |
| naturepublishinggroup10.1038/nature01204 | Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX | Plant cells coordinately regulate the expression of nuclear and plastid genes that encode components of the photosynthetic apparatus. Nuclear genes that regulate chloroplast development and chloroplast gene expression provide part of this coordinate control. There is evidence that information also flows in the opposite direction, from chloroplasts to the nucleus1, 2. Until now, at least three different signalling pathways have been identified that originate in the plastid and control nuclear gene expression3, 4 but the molecular nature of these signals has remained unknown. Here we show that the tetrapyrrole intermediate Mg-protoporphyrin (Mg-ProtoIX) acts as a signalling molecule in one of the signalling pathways between the chloroplast and nucleus. Accumulation of Mg-ProtoIX is both necessary and sufficient to regulate the expression of many nuclear genes encoding chloroplastic proteins associated with photosynthesis. | [|[Aring]|sa Strand, Tadao Asami, Jose Alonso, Joseph R. Ecker, Joanne Chory] | Nature | 2003-01-02 | |
| naturepublishinggroup10.1038/sj.onc.1205992 | Androgen-induced expression of endoplasmic reticulum (ER) stress response genes in prostate cancer cells | | [] | | 2002-12-12 | |
| naturepublishinggroup10.1038/ng1030 | Options available|[mdash]|from start to finish|[mdash]|for obtaining data from DNA microarrays II | | [Andrew J. Holloway, Ryan K. van Laar, Richard W. Tothill, David D.L. Bowtell] | Nature Genetics | 2002-12-01 | |
| naturepublishinggroup10.1038/sj.onc.1205975 | Novel genes regulated by Sonic Hedgehog in pluripotent mesenchymal cells | | [] | | 2002-11-21 | |
| naturepublishinggroup10.1093/emboj/cdf600 | Nutrient control of gene expression in Drosophila: microarray analysis of starvation and sugar-dependent response | We have identified genes regulated by starvation and sugar signals in Drosophila larvae using whole-genome microarrays. Based on expression profiles in the two nutrient conditions, they were organized into different categories that reflect distinct physiological pathways mediating sugar and fat metabolism, and cell growth. In the category of genes regulated in sugar-fed, but not in starved, animals, there is an upregulation of genes encoding key enzymes of the fat biosynthesis pathway and a downregulation of genes encoding lipases. The highest and earliest activated gene upon sugar ingestion is sugarbabe, a zinc finger protein that is induced in the gut and the fat body. Identification of potential targets using microarrays suggests that sugarbabe functions to repress genes involved in dietary fat breakdown and absorption. The current analysis provides a basis for studying the genetic mechanisms underlying nutrient signalling. | [Ingo Zinke, Christina S. Sch|[uuml]|tz, J|[ouml]|rg D. Katzenberger, Matthias Bauer, Michael J. Pankratz] | The EMBO Journal | 2002-11-15 | |
| naturepublishinggroup10.1038/sj.onc.1205979 | Expression profiling of primary non-small cell lung cancer for target identification | | [] | | 2002-10-31 | |
| naturepublishinggroup10.1038/419759a | table of suppliers | | [] | Nature a - z index | 2002-10-17 | |
| naturepublishinggroup10.1046/j.1523-1747.2002.00694.x | Pimecrolimus Identifies a Common Genomic Anti-inflammatory Profile, is Clinically Highly Effective in Psoriasis and is Well Tolerated | The ascomycin macrolactam pimecrolimus is a novel inflammatory cytokine release inhibitor that so far has not been administered systemically to humans. In this phase I/II randomized double-blind, placebo-controlled, multiple rising dose proof of concept study psoriasis patients were treated with oral pimecrolimus or placebo. Gene profiling identified a common genomic profile with a downregulation of genes associated with inflammation but no changes in gene expression linked to drug-related side-effects. A steady state of pimecrolimus was reached after 5–10 d, Cmax, and area under the curve (0–24) was 54.5 ng per ml and 589.9 ng h per ml, respectively, at steady state at the highest dose. There was clear clinical efficacy in patients receiving 20 mg pimecrolimus twice daily and 30 mg twice daily with a reduction of Psoriasis Area and Severity Index by 60% and 75%, respectively. Histopatho logically and immunopathologically there was a reversion of the psoriatic phenotype towards normal. There were no notable clinical, laboratory, kidney function, or immunologic side-effects. We conclude that pimecrolimus taken orally is highly effective in a concentration-dependent manner in patients with psoriasis and on a short-term basis it is well tolerated and this is confirmed by its pharmacogenomic profile. The latter also indicates that pimecrolimus should be equally effective in other inflammatory skin diseases. | [Klemens Rappersberger, Michael Komar, Marie-Eve Ebelin, Graham Scott, Pascale Burtin, Gerard Greig, Jeanne Kehren, Salah-Dine Chibout, Andre Cordier, Wolfgang Holter, Leo Richter, Rainer Oberbauer, Anton Stuetz, Klaus Wolff] | Journal of Investigative Dermatology | 2002-10-01 | |
| naturepublishinggroup10.1038/nbt728 | Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays | We have used DNA microarrays to follow Neisseria meningitidis serogroup B (MenB) gene regulation during interaction with human epithelial cells. Host-cell contact induced changes in the expression of 347 genes, more than 30% of which encode proteins with unknown function. The upregulated genes included transporters of iron, chloride, amino acids, and sulfate, many virulence factors, and the entire pathway of sulfur-containing amino acids. Approximately 40% of the 189 upregulated genes coded for peripherally located proteins, suggesting that cell contact promoted a substantial reorganization of the cell membrane. This was confirmed by fluorescence activated cell sorting (FACS) analysis on adhering bacteria using mouse sera against twelve adhesion-induced proteins. Of the 12 adhesion-induced surface antigens, 5 were able to induce bactericidal antibodies in mice, demonstrating that microarray technology is a valid approach for identifying new vaccine candidates and nicely complements other genome mining strategies used for vaccine discovery. | [Renata Grifantini, Erika Bartolini, Alessandro Muzzi, Monia Draghi, Elisabetta Frigimelica, Joel Berger, Giulio Ratti, Roberto Petracca, Giuliano Galli, Mauro Agnusdei, Marzia Monica Giuliani, Laura Santini, Brunella Brunelli, Herv|[eacute]| Tettelin, Rino Rappuoli, Filippo Randazzo, Guido Grandi] | Nature Biotechnology | 2002-08-12 | |
| naturepublishinggroup10.1038/ng951 | The transcriptional program of meiosis and sporulation in fission yeast | | [Juan Mata, Rachel Lyne, Gavin Burns, J|[uuml]|rg B|[auml]|hler] | Nature Genetics | 2002-08-05 | |
| naturepublishinggroup10.1038/ng929 | Systematic screen for human disease genes in yeast | | [Lars M. Steinmetz, Curt Scharfe, Adam M. Deutschbauer, Dejana Mokranjac, Zelek S. Herman, Ted Jones, Angela M. Chu, Guri Giaever, Holger Prokisch, Peter J. Oefner, Ronald W. Davis] | Nature Genetics | 2002-07-22 | |
| naturepublishinggroup10.1038/sj.onc.1205495 | Distinction in gene expression profiles of oligodendrogliomas with and without allelic loss of 1p | | [] | | 2002-06-05 | |
| naturepublishinggroup10.1038/416893a | table of suppliers | | [] | Nature a - z index | 2002-04-25 | |
| naturepublishinggroup10.1038/sj.onc.1205048 | TRAIL and inhibitors of apoptosis are opposing determinants for NF-|[kappa]|B-dependent, genotoxin-induced apoptosis of cancer cells | | [] | | 2002-01-11 | |
| naturepublishinggroup10.1038/sj.onc.1205029 | Characterization of stage progression in chronic myeloid leukemia by DNA microarray with purified hematopoietic stem cells | | [] | | 2001-12-13 | |
| naturepublishinggroup10.1038/sj.onc.1204935 | Gene expression profiles of pancreatic cancer and stromal desmoplasia | | [] | | 2001-11-02 | |
| naturepublishinggroup10.1038/nm0901-1067 | On the market | | [] | Nature a - z index | 2001-09-01 | |
| naturepublishinggroup10.1038/35090638 | Try the soft option | | [] | Nature a - z index | 2001-08-23 | 4.0 |
| naturepublishinggroup10.1038/35089143 | Peptides and proteins | | [] | Nature a - z index | 2001-08-16 | |
| naturepublishinggroup10.1038/sj.tpj.6500022 | Genes that co-cluster with estrogen receptor alpha in microarray analysis of breast biopsies | The estrogen receptor plays a critical role in the pathogenesis and clinical behavior of breast cancer. To better understand the molecular basis of estrogen-dependent forms of this disease we studied gene expression profiles from 53 primary breast cancer biopsies. Gene expression data for more than 7000 genes were generated from each tumor sample with oligo microarrays. A standard correlation-clustering algorithm identified 18 genes that co-clustered with estrogen receptor alpha. Eleven of these genes had previously been associated with estrogen regulation or breast tumorigenesis including trefoil factor 1 and estrogen regulated LIV-1. Additional study of these 18 genes may further delineate the role of estrogen receptor in breast cancer, generate new predictive biomarkers for response to endocrine therapies and identify novel therapeutic targets. | [M A Dressman, T M Walz, C Lavedan, L Barnes, S Buchholtz, I Kwon, M J Ellis, M H Polymeropoulos] | The Pharmacogenomics Journal | 2001-01-01 | |
| naturepublishinggroup10.1038/35087138 | Navigating gene expression using microarrays |[mdash]| a technology review | Parallel quantification of large numbers of messenger RNA transcripts using microarray technology promises to provide detailed insight into cellular processes involved in the regulation of gene expression. This should allow new understanding of signalling networks that operate in the cell and of the molecular basis and classification of disease. But can the technology deliver such far-reaching promises? | [Almut Schulze, Julian Downward] | Nature Cell Biology | 2001-08-01 | |
| naturepublishinggroup10.1038/82539 | The core meiotic transcriptome in budding yeasts | | [Michael Primig, Roy M. Williams, Elizabeth A. Winzeler, Gela G. Tevzadze, Andrew R. Conway, Seung Y. Hwang, Ronald W. Davis, Rochelle Easton Esposito] | Nature Genetics | 2000-12-01 | |
| naturepublishinggroup10.1038/35020701 | Microarrays on the slide | | [] | Nature a - z index | 2000-08-10 | |
| naturepublishinggroup10.1038/78711 | On the market | | [] | Nature a - z index | 2000-08-01 | |
| naturepublishinggroup10.1038/35015701 | Genomics, gene expression and DNA arrays | Experimental genomics in combination with the growing body of sequence information promise to revolutionize the way cells and cellular processes are studied. Information on genomic sequence can be used experimentally with high-density DNA arrays that allow complex mixtures of RNA and DNA to be interrogated in a parallel and quantitative fashion. DNA arrays can be used for many different purposes, most prominently to measure levels of gene expression (messenger RNA abundance) for tens of thousands of genes simultaneously. Measurements of gene expression and other applications of arrays embody much of what is implied by the term 'genomics'; they are broad in scope, large in scale, and take advantage of all available sequence information for experimental design and data interpretation in pursuit of biological understanding. | [David J. Lockhart, Elizabeth A. Winzeler] | Nature | 2000-06-15 | |
| naturepublishinggroup10.1038/44407 | Genes amplified, detected, visualized | | [] | Nature a - z index | 1999-10-14 | |
| naturepublishinggroup10.1038/12734 | Autumn's picks | | [] | Nature Genetics | 1999-09-01 | |
| naturepublishinggroup10.1038/10948 | New products | | [] | Nature a - z index | 1999-07-01 | |
| naturepublishinggroup10.1038/10571 | ON THE MARKET | | [] | Nature a - z index | 1999-07-01 | |
| naturepublishinggroup10.1038/4455 | Options available |[mdash]| from start to finish |[mdash]| for obtaining expression data by microarray | | [David D.L. Bowtell] | Nature Genetics | 1999-01-01 | |
| naturepublishinggroup10.1038/4478 | Gene expression informatics |[mdash]|it's all in your mine | | [Douglas E. Bassett, Michael B. Eisen, Mark S. Boguski] | Nature Genetics | 1999-01-01 | |
| naturepublishinggroup | | | [] | | | |
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