Affymetrix Microarray Suite Research Articles

Cyclin D1 Is a Selective Modifier of Androgen-dependent Signaling and Androgen Receptor Function

D-type cyclins regulate cellular outcomes in part through cyclin-dependent, kinase-independent mechanisms that modify transcription factor action, and recent in vivo studies showed that cyclin D1 associates with a large number of transcriptional regulators in cells of the retina and breast. Given the frequency of cyclin D1 alterations in cancer, it is imperative to delineate the molecular mechanisms by which cyclin D1 controls key transcription factor networks in human disease. Prostate cancer was used as a paradigm because this tumor type is reliant at all stages of the disease on androgen receptor (AR) signaling, and cyclin D1 has been shown to negatively modulate AR-dependent expression of prostate-specific antigen (KLK3/PSA). Strategies were employed to control cyclin D1 expression under conditions of hormone depletion, and the effect of cyclin D1 on subsequent androgen-dependent gene expression was determined using unbiased gene expression profiling. Modulating cyclin D1 conferred widespread effects on androgen signaling and revealed cyclin D1 to be a selective effector of hormone action. A subset of androgen-induced target genes, known to be directly regulated by AR, was strongly suppressed by cyclin D1. Analyses of AR occupancy at target gene regulatory loci of clinical relevance demonstrated that cyclin D1 limits AR residence after hormone stimulation. Together, these findings reveal a new function for cyclin D1 in controlling hormone-dependent transcriptional outcomes and demonstrate a pervasive role for cyclin D1 in regulating transcription factor dynamics.

Abstract 4655: Gene expression signatures of microsatellite-stable stage III colorectal adenocarcinomas based on the p53 status

Abstract Background: Microsatellite (MS) instability and p53 mutations have been implicated in development, progression and metastasis of colorectal cancer (CRCs). Thus, to identify aggressive tumor subsets, the gene expression profiles of Stage- III MS-stable (MSS), sporadic CRCs were analyzed based on their p53 gene status. Methods: DNA samples extracted from 136 Stage-III formalin-fixed paraffin embedded CRC tissues were analyzed for MSS and for p53 mutations. Further, mRNA samples extracted from 20 (10 each of p53-mutated and wild-type) corresponding snap-frozen Stage-III-MSS-CRCs were profiled for differential gene expression. Affymetrix Human Genome U133 Plus 2.0 arrays were used for gene expression profiling; and Affymetrix Microarray Suite (MAS 5.0), gene ontology annotation, and KEGG pathways were used for data analysis. Differentially expressed (DE) genes were confirmed by measuring mRNA levels by RT-PCR and by the quantitative nuclease protection assay. Results: A higher incidence of p53 mutations was found in MSS (65 of 113, 58%) than in MSI (6 of 23, 30%) phenotypes. Kaplan-Meier analyses demonstrated that patients with MSS-CRCs exhibiting p53 mutations had poor overall survival when compared to p53-wt-phenotypes (log rank, p=0.031). Gene expression analyses identified 116 DE genes (73 down-regulated and 43 up-regulated). All of these passed the stringent background filter (intensity p-value ≤0.001 and intensity ≥3 SD above mean background) and DE ratio (χ2 p-value ≤0.01 & fold change ≥2.0). GBP1, PSMB9, TRIM29, BST2 and TFF1, that have prognostic value in CRCs, were up-regulated in p53-mutated-MSS-CRCs but down-regulated in p53-wt-MSS-CRCs. Further, genes that regulate cell-cycle arrest (CDKN1B) and tumor growth suppression (ACVR1B, SESN1, WFDC1 and IRF7) were down-regulated in p53-mutated-MSS-CRCs, but up-regulated in p53-wt-MSS-CRCs. The genes presented here are the top-ranked (top-5) genes in their respective groups. The mRNA expression levels of these DE genes in all 136 CRCs were confirmed on two different platforms. Conclusion: Our findings suggest that mutant- and wt-p53 Stage-III-MSS-CRCs have distinct gene expression profiles and appear to be useful in identifying aggressive Stage III subsets and for the assessment of clinical outcomes. These studies are supported by grants from the National Institute of Health/National Cancer Institute (U54-CA118948, RO1-CA98932, and R03CA139629). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4655.

Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

We have observed extensive interindividual differences in DNA methylation of 8590 CpG sites of 6229 genes in 153 human adult cerebellum samples, enriched in CpG island "shores" and at further distances from CpG islands. To search for genetic factors that regulate this variation, we performed a genome-wide association study (GWAS) mapping of methylation quantitative trait loci (mQTLs) for the 8590 testable CpG sites. cis association refers to correlation of methylation with SNPs within 1 Mb of a CpG site. 736 CpG sites showed phenotype-wide significant cis association with 2878 SNPs (after permutation correction for all tested markers and methylation phenotypes). In trans analysis of methylation, which tests for distant regulation effects, associations of 12 CpG sites and 38 SNPs remained significant after phenotype-wide correction. To examine the functional effects of mQTLs, we analyzed 85 genes that were with genetically regulated methylation we observed and for which we had quality gene expression data. Ten genes showed SNP-methylation-expression three-way associations-the same SNP simultaneously showed significant association with both DNA methylation and gene expression, while DNA methylation was significantly correlated with gene expression. Thus, we demonstrated that DNA methylation is frequently a heritable continuous quantitatively variable trait in human brain. Unlike allele-specific methylation, genetic polymorphisms mark both cis- and trans-regulatory genetic sites at measurable distances from their CpG sites. Some of the genetically regulated DNA methylation is directly connected with genetically regulated gene expression variation.

Scavenger Chemokine (CXC Motif) Receptor 7 (CXCR7) Is a Direct Target Gene of HIC1 (Hypermethylated in Cancer 1)

The tumor suppressor gene HIC1 (Hypermethylated in Cancer 1) that is epigenetically silenced in many human tumors and is essential for mammalian development encodes a sequence-specific transcriptional repressor. The few genes that have been reported to be directly regulated by HIC1 include ATOH1, FGFBP1, SIRT1, and E2F1. HIC1 is thus involved in the complex regulatory loops modulating p53-dependent and E2F1-dependent cell survival and stress responses. We performed genome-wide expression profiling analyses to identify new HIC1 target genes, using HIC1-deficient U2OS human osteosarcoma cells infected with adenoviruses expressing either HIC1 or GFP as a negative control. These studies identified several putative direct target genes, including CXCR7, a G-protein-coupled receptor recently identified as a scavenger receptor for the chemokine SDF-1/CXCL12. CXCR7 is highly expressed in human breast, lung, and prostate cancers. Using quantitative reverse transcription-PCR analyses, we demonstrated that CXCR7 was repressed in U2OS cells overexpressing HIC1. Inversely, inactivation of endogenous HIC1 by RNA interference in normal human WI38 fibroblasts results in up-regulation of CXCR7 and SIRT1. In silico analyses followed by deletion studies and luciferase reporter assays identified a functional and phylogenetically conserved HIC1-responsive element in the human CXCR7 promoter. Moreover, chromatin immunoprecipitation (ChIP) and ChIP upon ChIP experiments demonstrated that endogenous HIC1 proteins are bound together with the C-terminal binding protein corepressor to the CXCR7 and SIRT1 promoters in WI38 cells. Taken together, our results implicate the tumor suppressor HIC1 in the transcriptional regulation of the chemokine receptor CXCR7, a key player in the promotion of tumorigenesis in a wide variety of cell types.

ZAC1 Is Up-regulated by Hypertonicity and Decreases Sorbitol Dehydrogenase Expression, Allowing Accumulation of Sorbitol in Kidney Cells

Affymetrix GeneChip technology was employed to detect differentially expressed genes in inner medullary collecting duct (IMCD3) cells grown under isotonic and hypertonic conditions. A marked up-regulation was found for the zinc-finger protein ZAC1 under hypertonic stress (219-fold, p < 0.001). Changes in expression for ZAC1 were verified by quantitative PCR for message and Western blotting for protein. In mouse and human kidney tissues, ZAC1 expression was substantial in the papilla and was absent in the cortex. Furthermore, ZAC1 expression significantly increased in the papilla of mice following 36 h of fluid restriction and decreased in polyuric mice consuming sucrose in water. Because ZAC1 has been described to be a potential negative regulator of sorbitol dehydrogenase (SDH) in hippocampal cells, we examined whether this relationship also occurs in kidney cells under hypertonic stress. We found that stable IMCD3 clones silenced for ZAC1 to varying levels demonstrated an inverse effect on SDH expression. ZAC1 binds to a consensus repression site within the promoter of SDH, pointing to a mechanism whereby ZAC1 acts by repressing SDH transcriptional activity during hypertonic conditions. Taken together, these data strongly suggest that ZAC1 is up-regulated under hypertonic stress and negatively regulates expression of SDH, allowing for accumulation of sorbitol as a compatible organic osmolyte.

Effect of 1.8 GHz radiofrequency electromagnetic fields on gene expression of rat neurons

To investigate the changes of gene expression in rat neuron induced by 1.8 GHz radiofrequency electromagnetic fields (RF EMF) to screen for RF EMF-responsive genes and the effect of different exposure times and modes on the gene expression in neuron. Total RNA was extracted immediately and purified from the primary culture of neurons after intermittent exposed or sham-exposed to a frequency of 1.8 GHz RF EMF for 24 hours at an average special absorption rate (SAR) of 2 W/kg. Affymetrix Rat Neurobiology U34 array was applied to investigate the changes of gene expression in rat neuron. Differentially expressed genes (Egr-1, Mbp and Plp) were further confirmed by semi-quantitative revere transcription polymerase chain reaction (RT PCR). The expression levels of Egr-1, Mbp and Plp were observed at different exposure times (6, 24 h) and modes (intermittent and continuous exposure). Among 1200 candidate genes, 24 up-regulated and 10 down-regulated genes were found by using Affymetrix microarray suite software 5.0 which are associated with multiple cellular functions (cytoskeleton, signal transduction pathway, metabolism, etc.) after functional classification. Under 24 h and 6 h intermittent exposure, Egr-1 and Plp in experiment groups showed statistic significance (P < 0.05) compared with the control groups, while expression of Mbp did not change significantly (P > 0.05). After 24 h continuous exposure, Egr-1 and Mbp in experiment groups showed statistic significance (P < 0.05) compared with the control group, while expression of Plp did not change significantly (P > 0.05). Under the same exposure mode 6 h, expression of all the 3 genes did not change significantly. Different times (6, 24 h) and modes (intermittent and continuous exposure) of exposure exerted remarkable different influences on the expression of Egr-1, Mbp, Plp genes (P < 0.01). The changes of many genes transcription were involved in the effect of 1.8 GHz RF EMF on rat neurons; Down-regulation of Egr-1 and up-regulation of Mbp, Plp indicated the negative effects of RF EMF on neurons; The effect of RF intermittent exposure on gene expression was more obvious than that of continuous exposure; The effect of 24 h RF exposure (both intermittent and continuous) on gene expression was more obvious than that of 6 h (both intermittent and continuous).

Imatinib Mesilate Modifies Genes Involved in Hematopoiesis in Non Clonal Bone Marrow Cells from CML Patients in Complete Cytogenetic Response.

Imatinib mesilate (IM) is the standard treatment for newly diagnosed patients with chronic phase (CP) CML. Bcr-Abl signaling has a wide range of biological activities, mainly mediated through activation of Ras/mitogen-activated protein kinase (MAPK) pathways, with broad effects on changes in cell adhesion (through Rho), proliferation (MAPK pathway) and apoptosis (through Akt). IM's efficacy results from a blockade of these effects. Extensive work on the gene-expression profiling of CML cell lines under IM therapy has been published in order to predict disease transformation or IM resistance. Nevertheless, information on the effects of IM on the residual non clonal bone marrow (BM) hematopoietic compartment is scarce, and this is an important issue, since most responding patients will require long term treatment with IM. Therefore, in the present work we have assessed the gene expression profile (GEP) of whole BM hematopoietic cells from 20 patients with CP-CML in CCR after 6 to 12 months on IM therapy and compared it with that of 6 normal BM donors. Total RNA (100-500 ng) was amplified and labeled using the “GeneChip Two-Cycle cDNA Synthesis Kit” and hybridized to “Human Genome U133A” microarray (Affymetrix). Processing of genechip data was carried out using the Robust Multi-chip Average (RMA) and the Affymetrix Microarray Suite v.5 (MAS5) gene expression algorithms. The Significance Analysis of Microarrays (SAM) algorithm identified gene expression changes in a total of 490 genes (125 up and 365 down-regulated) when samples from CCR CML patients were compared to normal BM samples. Differential genes were grouped in 4 different areas, based on their function: proliferation, apoptosis, ubiquitination and adhesion. In CCR CML samples, there was a lower expression of genes involved in cell proliferation (e.g. C6ORF108, CENPE, CENP5, ESPL1 or GAS6) and cell cycle progression (e.g. PLCB1, ZW10, CUL4A or FOSB). There was an upregulation of genes involved in the induction of apoptosis (e.g. CDC2L2, FOXO3A, ING2, ING3, RYBP or TNFRSF1B) and in the ubiquitination of proteins (e.g. ARIH1, FBXW7, RKHD2, RNF7, SUMO1, UBA2 or UBE2W). Regarding cell-to-cell adhesion, several genes involved in this processes were downregulated (e.g. ITGBL1, CTNNA1, PCDHGA1, TROAP, FLOT2, IGSF4B, SELP, SIGLEC6, ADAM22 and STAB1). In addition, in all CML samples the erythropoietin receptor (Epo-R) gene was downregulated. This is of interest since many patients on IM therapy display a slightly low Hb level, regardless of circulating Epo levels. In summary, IM induces a decrease in proliferation and increase in apoptosis and ubiquitination in residual non clonal BM cells from CCR CML patients. In addition, IM diminishes cell-to-cell adhesion and downregulates the expression of the Epo receptor in the hematopoietic compartment of these patients.

Farnesoid X Receptor Agonist Reduces Serum Asymmetric Dimethylarginine Levels through Hepatic Dimethylarginine Dimethylaminohydrolase-1 Gene Regulation

The farnesoid X receptor (FXR, NR1H4) is a bile acid-responsive nuclear receptor that plays critical roles in the transcriptional regulation genes involved in cholesterol, bile acid, triglyceride, and carbohydrate metabolism. By microarray analysis of hepatic genes from female Zucker diabetic fatty (ZDF) rats treated with the FXR agonist GW4064, we have identified dimethylarginine dimethylaminohydrolase-1 (DDAH1) as an FXR target gene. DDAH1 is a key catabolic enzyme of asymmetric dimethylarginine (ADMA), a major endogenous nitric-oxide synthase inhibitor. Sequence analysis of the DDAH1 gene reveals the presence of an FXR response element (FXRE) located 90 kb downstream of the transcription initiation site and within the first intron. Functional analysis of the putative FXRE demonstrated GW4064 dose-dependent transcriptional activation from the element, and we have demonstrated that the FXRE sequence binds the FXR-RXR heterodimer. In vivo administration of GW4064 to female ZDF rats promoted a dose-dependent and >6-fold increase in hepatic DDAH1 gene expression. The level of serum ADMA was reduced concomitantly. These findings provide a mechanism by which FXR may increase endothelium-derived nitric oxide levels through modulation of serum ADMA levels via direct regulation of hepatic DDAH1 gene expression. Thus, beneficial clinical outcomes of FXR agonist therapy may include prevention of atherosclerosis and improvement of the metabolic syndrome.

Evaluation of NCAM and DKK1 Expression in Multiple Myeloma and MGUS by Gene and Tissue Microarrays: Expression Accompanies Progression.

Introduction: Expression NCAM1, a cell adhesion molecule involved in neuron-neuron adhesion, is also expressed by multiple myeloma (MM PC). Osteolytic bone lesions are a hallmark of MM and elevated expression of NCAM in MM PC has been correlated with this process (Ely and Knowles, 2003). We have previously reported that MM PC express DKK1 and MM blocks osteoblast differentiation in a DKK1-specific manner, suggesting that secretion of the Wnt signaling inhibitor plays a role in MM bone disease. Herein we used gene expression microarrays and tissue microarrays (TMAs) to investigate the simultaneous expression of DKK1 and NCAM in MM and MGUS.Methods: The study population consisted of 198 newly diagnosed MM and 44 MGUS. RNA from CD138-selected plasma cells was hybridized to Affymetrix U133Plus microarrays and data processed with Affymetrix Microarray Suite GCOS1.1 software. TMAs were constructed from formalin-fixed, paraffin embedded bone marrow biopsies. Serial sections of TMA were immunostained for CD138, NCAM and DKK1. TMAs were scanned using ScanScope using 20x lens, assessed using TMA lab software (Aperio Technologies) and scored as an average number of cells in the context of CD138 staining.Results: When put in context of a recently described molecular classification (Zhan et al., 2006), NCAM and DKK1 were found significantly co-over-expressed (DKK1+/NCAM+) in HYPERDIPLOID MM (P < 0.01); NCAM+/DKK1− was typical for MMSET-spike MM (P<0.001); NCAM−/DKK1+ DKK1 was characteristic of MM in MAF-spike disease (P < 0.001), CCND1 spikes with co-expression of CD20 (P<0.01), and the so-called MYELOID subgroup (P<0.001). In contrast, virtually all cases of MGUS were DKK1−/NCAM-. On TMAs, DKK1 expression varied in CD138-positive cells in MM, and in osteocytes and megakaryocytes in MM and MGUS, but was clearly negative in osteoblasts/lining cells. NCAM expression, was also variably expressed in PC of MM cases and in virtually 100% of osteoblasts/lining cells in both MM and MGUS. Osteocytes were distinctly negative for NCAM in both diseases. Of 195 analyzable MM biopsies, PC were DKK1+ in 1% to > 90% of PC in 191 (98%); of these, 94 were also NCAM+ in 5% to > 90% of PC; 1 case was positive for NCAM+/DKK− and 3 were NCAM−/DKK−. There was no significant difference in clinical parameters and survival in a comparison of NCAM+/DKK+ and NCAM−/DKK+ groups. DKK1 gene expression was higher in DKK1+/NCAM+ than in DKK1+/NCAM− MM (P=0.006); NCAM gene expression was higher in DKK1+/NCAM+ than in DKK+/NCAM− MM (P<0.0001) and NCAM was the number one SAM-defined gene over-expressed in DKK1+/NCAM+ relative to DKK1+/NCAM− disease. Consistent with GEP data, DKK1+/NCAM+ MM was over-represented in HYPERDIPLOID MM (32% v. 10%; P<0.001), while DKK1+/NCAM− disease was overrepresented in MAF-spike (15% v. 2%; P=0.003) and MYELOID subgroups (32% v. 18%; P=0.03). DKK1+/NCAM+ MM was completely absent in CCND1-spike /CD20-negative disease, with only 4% of DKK1+/NCAM− cases in this subgroup. No difference was observed for the other subtypes.Conclusion: DKK1 is expressed in all cases of MM with half also expressing NCAM. Neither gene is expressed in MGUS PC. These data suggests that expression of these genes in plasma cells accompanies disease progression.

Epigenetic Regulation of Human γ-Glutamyl Hydrolase Activity in Acute Lymphoblastic Leukemia Cells

Gamma-glutamyl hydrolase (GGH) catalyzes degradation of the active polyglutamates of natural folates and the antifolate methotrexate (MTX). We found that GGH activity is directly related to GGH messenger RNA expression in acute lymphoblastic leukemia (ALL) cells of patients with a wild-type germline GGH genotype. We identified two CpG islands (CpG1 and CpG2) in the region extending from the GGH promoter through the first exon and into intron 1 and showed that methylation of both CpG islands in the GGH promoter (seen in leukemia cells from approximately 15% of patients with nonhyperdiploid B-lineage ALL) is associated with significantly reduced GGH mRNA expression and catalytic activity and with significantly higher accumulation of MTX polyglutamates (MTXPG(4-7)) in ALL cells. Furthermore, methylation of CpG1 was leukemia-cell specific and had a pronounced effect on GGH expression, whereas methylation of CpG2 was common in leukemia cells and normal leukocytes but did not significantly alter GGH expression. These findings indicate that GGH activity in human leukemia cells is regulated by epigenetic changes, in addition to previously recognized genetic polymorphisms and karyotypic abnormalities, which collectively determine interindividual differences in GGH activity and influence MTXPG accumulation in leukemia cells.

Global gene response to GSM 1800 MHz radiofrequency electromagnetic field in MCF-7 cells

To investigate whether GSM 1800 MHz radiofrequency electromagnetic field (RF EMF) can change the gene expression profile in MCF-7 cells and to screen RF EMF responsive genes. Subcultured MCF-7 cells were intermittently (5-minute fields on/10-minute fields off) exposed or sham-exposed to GSM 1800 MHz RF EMF, which was modulated by 217 Hz EMF, for 24 hours at an average specific absorption rate (SAR) of 2.0 W/kg or 3.5 W/kg. Immediately after RF EMF exposure or sham-exposure, total RNA was isolated from MCF-7 cells and then purified. Affymetrix Human Genome U133A Genechip was applied to examine the change of gene expression profile according to the manufacturer's instruction. Data was analyzed by Affymetrix Microarray Suite 5.0 (MAS 5.0) and Affymetrix Data Mining Tool 3.0 (DMT 3.0). Quantitative reverse transcription polymerase chain reaction (RT-PCR) was used to validate the differentially expressed genes identified by Genechip analysis. A small number of differential expression genes were found in each comparison after RF EMF exposure. Through reproducible and consistent analysis, no gene or five up-regulated genes were screened out after exposure to RF EMF at SAR of 2.0 W/kg or 3.5 W/kg, respectively. However, these five genes could not be further confirmed by RT-PCR. The present study did not provide clear evidence that RF EMF exposure might distinctly change the gene expression profile in MCF-7 cells under current experimental conditions, implying that the exposure might not affect the MCF-7 cell physiology, or this cell line might be less sensitive to the RF EMF exposure.

Biotin Sensing in Saccharomyces cerevisiae Is Mediated by a Conserved DNA Element and Requires the Activity of Biotin-Protein Ligase

Biotin is a water-soluble vitamin that functions as a prosthetic group in carboxylation reactions. In addition to its role as a cofactor, biotin has multiple roles in gene regulation. We analyzed biotin effects on gene expression in the yeast Saccharomyces cerevisiae and demonstrated by microarray, Northern, and Western analyses that all yeast genes encoding proteins involved in biotin metabolism are up-regulated following biotin depletion. Many of these genes contain a palindromic promoter element that is necessary and sufficient for mediating the biotin response and functions as an upstream-activating sequence. Mutants lacking the plasma membrane biotin transporter Vht1p display constitutively high expression levels of biotin-responsive genes. However, they react normally to biotin precursors that do not require Vht1p for uptake. The biotin-like effect of precursors with regard to gene expression requires their intracellular conversion to biotin. This demonstrates that Vht1p does not act as a sensor for biotin and that intracellular biotin is crucial for gene expression. Mutants with defects in biotin-protein ligase, similar to vht1delta mutants, also display aberrantly high expression of biotin-responsive genes. Like vht1delta cells, they have reduced levels of protein biotinylation, but unlike vht1delta mutants, they possess normal levels of free intracellular biotin. This indicates that free intracellular biotin is irrelevant for gene regulation and identifies biotin-protein ligase as an important element of the biotin-sensing pathway in yeast.

Functional Genomic Responses to Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and CFTRΔ508 in the Lung

Cystic fibrosis (CF), a common lethal pulmonary disorder in Caucasians, is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) that disturbs fluid homeostasis and host defense in target organs. The effects of CFTR and delta508-CFTR were assessed in transgenic mice that 1) lack CFTR expression (Cftr-/-); 2) express the human delta508 CFTR (CFTR(delta508)); 3) overexpress the normal human CFTR (CFTR(tg)) in respiratory epithelial cells. Genes were selected from Affymetrix Murine Gene-Chips analysis and subjected to functional classification, k-means clustering, promoter cis-elements/modules searching, literature mining, and pathway exploring. Genomic responses to Cftr-/- were not corrected by expression of CFTR(delta508). Genes regulating host defense, inflammation, fluid and electrolyte transport were similarly altered in Cftr-/- and CFTR(delta508) mice. CFTR(delta508) induced a primary disturbance in expression of genes regulating redox and antioxidant systems. Genomic responses to CFTR(tg) were modest and were not associated with lung pathology. CFTR(tg) and CFTR(delta508) induced genes encoding heat shock proteins and other chaperones but did not activate the endoplasmic reticulum-associated degradation pathway. RNAs encoding proteins that directly interact with CFTR were identified in each of the CFTR mouse models, supporting the hypothesis that CFTR functions within a multiprotein complex whose members interact at the level of protein-protein interactions and gene expression. Promoters of genes influenced by CFTR shared common regulatory elements, suggesting that their co-expression may be mediated by shared regulatory mechanisms. Genes and pathways involved in the response to CFTR may be of interest as modifiers of CF.

Myocyte Enhancer Factors 2A and 2C Induce Dilated Cardiomyopathy in Transgenic Mice

Cardiac hypertrophy and dilation are mediated by neuroendocrine factors and/or mitogens as well as through internal stretch- and stress-sensitive signaling pathways, which in turn transduce alterations in cardiac gene expression through specific signaling pathways. The transcription factor family known as myocyte enhancer factor 2 (MEF2) has been implicated as a signal-responsive mediator of the cardiac transcriptional program. For example, known hypertrophic signaling pathways that utilize calcineurin, calmodulin-dependent protein kinase, and MAPKs can each affect MEF2 activity. Here we demonstrate that MEF2 transcription factors induced dilated cardiomyopathy and lengthening of myocytes. Specifically, multiple transgenic mouse lines with cardiac-specific overexpression of MEF2A or MEF2C presented with cardiomyopathy at base line or were predisposed to more fulminant disease following pressure overload stimulation. The cardiomyopathic response associated with MEF2A and MEF2C was not further altered by activated calcineurin, suggesting that MEF2 functions independently of calcineurin in this response. In cultured cardiomyocytes, MEF2A, MEF2C, and MEF2-VP16 overexpression induced sarcomeric disorganization and focal elongation. Mechanistically, MEF2A and MEF2C each programmed similar profiles of altered gene expression in the heart that included extracellular matrix remodeling, ion handling, and metabolic genes. Indeed, adenoviral transfection of cultured cardiomyocytes with MEF2A or of myocytes from the hearts of MEF2A transgenic adult mice showed reduced transient outward K(+) currents, consistent with the alterations in gene expression observed in transgenic mice and partially suggesting a proximal mechanism underlying MEF2-dependent cardiomyopathy.

Exposure of rat brain to 915 MHz GSM microwaves induces changes in gene expression but not double stranded DNA breaks or effects on chromatin conformation

We investigated whether exposure of rat brain to microwaves (MWs) of global system for mobile communication (GSM) induces DNA breaks, changes in chromatin conformation and in gene expression. An exposure installation was used based on a test mobile phone employing a GSM signal at 915 MHz, all standard modulations included, output power level in pulses 2 W, specific absorption rate (SAR) 0.4 mW/g. Rats were exposed or sham exposed to MWs during 2 h. After exposure, cell suspensions were prepared from brain samples, as well as from spleen and thymus. For analysis of gene expression patterns, total RNA was extracted from cerebellum. Changes in chromatin conformation, which are indicative of stress response and genotoxic effects, were measured by the method of anomalous viscosity time dependencies (AVTD). DNA double strand breaks (DSBs) were analyzed by pulsed-field gel electrophoresis (PFGE). Effects of MW exposure were observed on neither conformation of chromatin nor DNA DSBs. Gene expression profiles were obtained by Affymetrix U34 GeneChips representing 8800 rat genes and analyzed with the Affymetrix Microarray Suite (MAS) 5.0 software. In cerebellum from all exposed animals, 11 genes were upregulated in a range of 1.34-2.74 fold and one gene was downregulated 0.48-fold (P < .0025). The induced genes encode proteins with diverse functions including neurotransmitter regulation, blood-brain barrier (BBB), and melatonin production. The data shows that GSM MWs at 915 MHz did not induce PFGE-detectable DNA double stranded breaks or changes in chromatin conformation, but affected expression of genes in rat brain cells.

Selective Loss of Fine Tuning of Gq/11 Signaling by RGS2 Protein Exacerbates Cardiomyocyte Hypertrophy

Alterations in cardiac G protein-mediated signaling, most prominently G(q/11) signaling, are centrally involved in hypertrophy and heart failure development. Several RGS proteins that can act as negative regulators of G protein signaling are expressed in the heart, but their functional roles are still poorly understood. RGS expression changes have been described in hypertrophic and failing hearts. In this study, we report a marked decrease in RGS2 (but not other major cardiac RGS proteins (RGS3-RGS5)) that occurs prior to hypertrophy development in different models with enhanced G(q/11) signaling (transgenic expression of activated Galpha(q)(*) and pressure overload due to aortic constriction). To assess functional consequences of selective down-regulation of endogenous RGS2, we identified targeting sequences for effective RGS2 RNA interference and used lipid-based transfection to achieve uptake of fluorescently labeled RGS2 small interfering RNA in >90% of neonatal and adult ventricular myocytes. Endogenous RGS2 expression was dose-dependently suppressed (up to 90%) with no major change in RGS3-RGS5. RGS2 knockdown increased phenylephrine- and endothelin-1-induced phospholipase Cbeta stimulation in both cell types and exacerbated the hypertrophic effect (increase in cell size and radiolabeled protein) in neonatal myocytes, with no major change in G(q/11)-mediated ERK1/2, p38, or JNK activation. Taken together, this study demonstrates that endogenous RGS2 exerts functionally important inhibitory restraint on G(q/11)-mediated phospholipase Cbeta activation and hypertrophy in ventricular myocytes. Our findings point toward a potential pathophysiological role of loss of fine tuning due to selective RGS2 down-regulation in G(q/11)-mediated remodeling. Furthermore, this study shows the feasibility of effective RNA interference in cardiomyocytes using lipid-based small interfering RNA transfection.

Genome-wide Transcriptional Profile of Escherichia coli in Response to High Levels of the Second Messenger 3′,5′-Cyclic Diguanylic Acid

Cyclic diguanylic acid (c-di-GMP; cGpGp) is a global second messenger controlling motility and adhesion in bacterial cells. Intracellular concentrations of c-di-GMP depend on two opposite activities: diguanylate cyclase, recently assigned to the widespread GGDEF domain, and c-di-GMP-specific phosphodiesterase, associated with proteins harboring the EAL domain. To date, little is known about the targets of c-di-GMP in the cell or if it affects transcriptional regulation of certain genes. In order to expand our knowledge of the effect of this molecule on the bacterial metabolism, here we report on the Escherichia coli transcriptional profile under high levels of c-di-GMP. We show that an important number of genes encoding cell surface and membrane-bound proteins are altered in their transcriptional activity. On the other hand, genes encoding several transcriptional factors, such as Fur, RcsA, SoxS, and ZraR, are up-regulated, and others, such as GadE, GadX, GcvA, and MetR, are down-regulated. Transcription of motility and cell division genes were altered, and consistent with this was the physiological analysis of cells overexpressing yddV, a diguanylate cyclase; these cells displayed an abnormal cell division process when high levels of c-di-GMP were present. We also show evidence that the diguanylate cyclase gene yddV is co-transcribed with dos, a heme base oxygen sensor with c-di-GMP-specific phosphodiesterase activity. A delta dos::kan mutation rendered the cells unable to divide properly, suggesting that dos and yddV may be part of a fine-tuning mechanism for regulating the intracellular levels of c-di-GMP.

A new summarization method for affymetrix probe level data

We propose a new model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. The new summarization method is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise. Thereafter, the RNA concentration is estimated from the model. In contrast to previous methods our new method called 'Factor Analysis for Robust Microarray Summarization (FARMS)' supplies both P-values indicating interesting information and signal intensity values. We compare FARMS on Affymetrix's spike-in and Gene Logic's dilution data to established algorithms like Affymetrix Microarray Suite (MAS) 5.0, Model Based Expression Index (MBEI), Robust Multi-array Average (RMA). Further, we compared FARMS with 43 other methods via the 'Affycomp II' competition. The experimental results show that FARMS with default parameters outperforms previous methods if both sensitivity and specificity are simultaneously considered by the area under the receiver operating curve (AUC). We measured two quantities through the AUC: correctly detected expression changes versus wrongly detected (fold change) and correctly detected significantly different expressed genes in two sets of arrays versus wrongly detected (P-value). Furthermore FARMS is computationally less expensive then RMA, MAS and MBEI. The FARMS R package is available from http://www.bioinf.jku.at/software/farms/farms.html. http://www.bioinf.jku.at/publications/papers/farms/supplementary.ps

AMarge

AMarge is a web tool for the automatic quality assessment of Affymetrix GeneChip data. It is essential to have a trustworthy set of chips in order to derive gene expression data for phenotypic analysis, and AMarge provides a complete and rigorous web-accessible tool to fulfill this need. The quality assessment steps include image plots of weights derived from a robust linear model fit of the data, a 3'/5' RNA digestion plot, and Affymetrix Microarray Suite version 5.0 (MAS 5.0) quality standard procedures. Furthermore, robust multi-array average expression values are generated in order to have a start-up expression set for the subsequent analysis. The results of the complete analysis are summarised and returned as an HTML report. The AMarge web interface is accessible at http://nin.crg.es/cgi-binf/AMargeWeb.cgi. A mirror server is also available at http://bioinformatics.istge.it/AMarge-bin/AMargeWeb.cgi. The software implementing all these methods is part of the Bioconductor project (http://www.bioconductor.org).

Increased small GTPases- the fundamental molecular mechanism underlying decreased myometrial responsiveness during quiescence

UNDERLYING DECREASED MYOMETRIAL RESPONSIVENESS DURING QUIESCENCE CLIFFORD MASON, PETER W. SWAAN, CARL P. WEINER, University of Maryland at Baltimore, Pharmaceutical Sciences, Baltimore, Maryland, University of Maryland at Baltimore, Physiology and Obstetrics, Gynecology and Reproductive Sciences, Baltimore, Maryland OBJECTIVE: The proposed mechanisms of myometrial quiescence include progesterone, fewer gap junctions, altered receptor density, etc. We showed that guinea pig (GP) myometrial quiescence was associated with increased GTPase activity. Given their pivotal role modulating secondary effector responses after receptor activation, we speculated the increased GTPase activity could provide a unifying pathway for decreased receptor mediated responses by reducing the half-life of the activated receptor complex. The object of this study was to identify the mechanism for increased myometrial GTPase activity. STUDY DESIGN: Gene profiling was performed with myometrial RNA obtained from nonpregnant, midpregnant (MP, w0.67 gestation), termpregnant (TP, w0.96 gestation), castrate and estradiol-treated castrate GPs (Affymetrix Human Genome U133A). Gene expression was normalized using Affymetrix Microarray Suite 5.0. Fold-changes in levels were calculated from the mean signals during MP and TP vs. their NP controls. Cluster analysis was performed by separating the genes into those upand down-regulated during each time period using MetaCore . Each category was further subdivided into genes specific for quiescence and activation. RESULTS: The impact of pregnancy on G-protein related mRNA was modest. Only the small GTPase Rap1b showed altered expression O2 fold (up 3! during quiescence) across gestation. But network analyses revealed that only Rab7, another small GTPase was exclusively upregulated (80%) during quiescence. In contrast, network analysis showed G-protein as the only component exclusively upregulated during late pregnancy. Estradiol mimicked the effects of pregnancy on some but not all potentially relevant G-protein family genes (including Rap1). CONCLUSION: The increased MP myometrial GTPase activity appears at least in part secondary to increased transcription of the small GTPases Rap1b and Rab7. The application of computer annotated databases allowed for the visualization of ‘pregnancy’ and ‘estradiol’ networks and universes that provide a basis for future investigation.