Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of C. elegans slr-2, C2H2 Zn-finger protein mutant to normal controls at L1 stage

ABSTRACT: Our slr-2 dataset showed strong overrepresentation of genes previously identified in a serial analysis of gene expression (SAGE) intestinal library (McGhee et al., 2006) (p << 0.01); 812 genes were common to both data sets. Consistent with the deregulation of intestinal genes, we observed repression of several important metabolic pathways, including the TOR and insulin signaling networks, suggesting that slr-2(ku297) mutants experience metabolic stress. We also compared differentially regulated genes in slr-2 and lin-35 single mutants. Again, we saw a statistically significant overlap (p-value < 0.01); 261 genes were present in both data sets. Strikingly, > 75% of genes common both datasets showed expression changes in the same direction, although the common dataset contained an approximately equal mixture of up and downregulated genes. Furthermore, more than fifty genes common to the lin-35 and slr-2 datasets are known to have intestinal-associated functions. That some of these common intestinal genes were absent from the gut SAGE library could be due to differences in the developmental stage of the animals assayed (adults versus L1s) as well as experimental approaches (SAGE versus microarrays) Experiment Overall Design: We compared transcriptome profiles of slr-2 mutants and control N2 worms at L1 stage stage. Experiment Overall Design: Each comparison was done in triplicate with independently grown and isolated animals. Experiment Overall Design: Data for N2 L1 stage were from our previous experiments (Series GSE6547) Experiment Overall Design: To achieve higher accuracy, RMA values were calculated on the basis of 21 microarray experiments (including data from Series GSE6547)

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: David Fay

PROVIDER: E-GEOD-9246 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Phosphorylation of histone H3 at Serine 10 emerges as a mechanism increasing chromatin accessibility of the transcription factor NF-kB for a particular set of immune genes. Here we report that a bacterial pathogen uses this strategy to shape the transcriptional response of infected host cells. We identify the Shigella flexneri type III protein effector OspF as a Dual Specific Phosphatase. OspF dephosphorylates MAP kinases within the nucleus impairing histone H3 phosphorylation at Serine 10 in a gene-specific manner. Therefore, OspF reprograms the transcriptional response for inactivation of a subset of NF-kB responsive genes. This regulation leads to repression of polymorphonuclear leukocytes recruitment in infected tissues. Thus, pathogens have evolved the ability to precisely modulate host cell epigenetic information as a strategy to repress innate immunity. Experiment Overall Design: The wild-type (WT) invasive strain of S. flexneri serotype 5a. To construct the ospF mutant, a PCR amplified DNA fragment encompassing nucleotides 61 to 420 of ospF was cloned between the XbaI and EcoRI sites of the suicide plasmid pSW23T, giving raise to pSWOspFTr. This plasmid was transferred by conjugation to the WT strain WT-Sm. To complement the ospF mutant, we constructed pUC18-OspF containing a PCR fragment encompassing the ospF gene inserted between the EcoRI and HindIII sites of pUC18. Experiment Overall Design: Cells were infected 2 hours with the differents strains. 2 biological replicates were done for each experimental conditions. After infection, cells were washed and total RNA was extracted using Rneasy mini kit from Qiagen. After cRNA synthesis and labeling with biotin, hybridizations were performed following Affymetrix procedures. After scanning, data were normalized with RMA (Quantile normalization). Experiment Overall Design: Comparative analyses with dChip software between baseline (wild-type-infected cells) and experiment (mutant- or transcomplemented strain-infected cells) were done using an unpaired Welch t-test with a p-value threshold of 0.05 and a Signal Log Ratio (SLR) threshold of 0.6. This SLR threshold corresponds to a Fold Change of 1.5

Project description:Mdr1a-, Bcrp-, and Mrp2-knockout rats are a more practical species for ADME studies than murine models and previously demonstrated expected alterations in pharmacokinetics of various probe substrates. At present, gene expression and pathology changes were systematically studied in small intestine, liver, kidney, and brain tissue from male SAGE Mdr1a-, Bcrp-, and Mrp2-knockout rats versus wild-type Sprague Dawley controls. Gene expression data supported the relevant knockout genotype. As expected, Mrp2-knockout rats were hyperbilirubinemic and exhibited upregulation of hepatic Mrp3. Overall, few alterations were observed within 137 ADME-relevant genes. The two most consequential changes were upregulation of intestinal carboxylesterase in Mdr1a-knockouts and catechol-O-methyltransferase in all tissues of Bcrp-knockout rats. Previously reported upregulation of hepatic Mdr1b P-glycoprotein in proprietary Wistar Mdr1a-knockout rats was not observed in the SAGE counterpart investigated herein. Relative liver and kidney weights were 22-53% higher in all three knockouts, with microscopic increases in hepatocyte size in Mdr1a- and Mrp2-knockout rats, and glomerular size in Bcrp- and Mrp2-knockouts. Increased relative weight of clearing organs is quantitatively consistent with reported increases in clearance of drugs that are not substrates of the knocked-out transporter. Overall, SAGE knockout rats demonstrated modest compensatory changes, which do not preclude their general application to study transporter-mediated pharmacokinetics. However until future studies elucidate the magnitude of functional change, caution is warranted in rare instances of extensive metabolism by catechol-O-methyltransferase in Bcrp-knockouts and intestinal carboxylesterase in Mdr1a-knockout rats, specifically for molecules with free catechol groups and esters subject to gut wall hydrolysis. 3 groups of knockout animals compared to wild-type male Sprague Dawley control rats. 4 animals per group. Assayed the following tissues: brain, duodenum, ileum, jejunum, kidney (cortex-anterior pole), kidney (medulla), liver. Hybridized to Affymetrix Rat Genome 230 v2 [Rat230_2] arrays.

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Transcription profiling of C. elegans slr-2, C2H2 Zn-finger protein mutant to normal controls at L1 stage

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