Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of hypertension disease induced by treating mice with salt water (vs plain water as control) RNA collected from 5 tissues (Brain stem, Brain, liver, kidney, and heart) of two strains (SWR and C3H)

ABSTRACT: Gene expression profiling of hypertension disease induced by treating mice with salt water (vs. plain water as control). RNA are collected from 5 tissues (Brain stem, Brain, liver, kidney, and heart) of two strains (SWR and C3H)

ORGANISM(S): Mus musculus

SUBMITTER: Yonghong Wang

PROVIDER: E-TIGR-89 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In order to understand how biochemical and genetic differences correlate with treatment response, we measured depressive-like behavior, gene expression and the levels of thirty-six neurobiochemical analytes across a panel of genetically-diverse mouse inbred lines after chronic treatment with vehicle or fluoxetine. Neurobiochemical markers were chosen based on their putative molecular function within pathways proposed to underlie depression, which include neuronal transmission, HPA-axis regulation, and neuroimmune processes. The goal of this study is to establish genetic and biochemical biomarkers that can predict treatment response and to propose a molecular pathway that is critical in mediating anti-depressant response. Thirty mouse inbred strains (129S1/SvImJ, A/J, AKR/J, BALB/cJ, BTBRT T(+) tf/J, BUB/BnJ, C3H/HeJ, C57BL/6J, C57BLKS/J, C57BR/cdJ, C58/J, CBA/J, CE/J, DBA/2J, FVB/NJ, I/LnJ, LG/J, LP/J, MA/MyJ, MRL/MpJ, NOD/LtJ, NOR/LtJ, NZB/BlNJ, NZW/LacJ, P/J, PL/J, RIIIS/J, SJL/J, SM/J, and SWR/J) aged 5-6 weeks old were obtained from The Jackson Laboratory (Bar Harbor, ME). Male mice were kept in polycarbonate cages on a 12-hour light/dark cycle (lights on at 0700h) with access to food and water ad libitum. Following one week of habituation, mice were randomized to either control or treatment group (n=12 male mice per strain per treatment group). Mean water intake for each strain was determined previously by measuring daily water consumption for three weeks (n=12 mice per strain). This information, along with average weight measurements for each strain, was used to determine the amount of fluoxetine required to provide a daily oral dose of 0 or 18 mg/kg per mouse. After chronic administration of 0 or 18 mg/kg of fluoxetine for 21 days, mice aged 9-10 weeks were tested in a tail-suspension and open field apparatus. Upon completion of the study, mice were sacrificed by cervical dislocation and decapitation between 0900h and 1300h. Trunk blood was quickly collected and allowed to clot on ice. Following centrifugation, serum samples were collected and stored at -20C for determination of fluoxetine and norfluoxetine levels using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Micro-dissections of individual regions were performed on serial coronal brain sections (approximately 10 µm) that were placed on a cold metal block. Cortex was taken from the same section for each animal and immediately snaps frozen on dry ice. Samples were stored at -80C until analysis.

Project description:Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent histone modifications) may take place at the earliest stages of carcinogenesis and their identification holds great promise for biomedical research. Here, we evaluate the sensitivity and specificity of genome-wide epigenomic and transcriptomic profiling in phenobarbital (PB)-treated B6C3F1 mice, a well-characterized rodent model of non-genotoxic liver carcinogenesis. Methylated DNA Immunoprecipitation (MeDIP)-coupled microarray profiling of 17,967 promoter regions and 4,566 intergenic CpG islands was combined with genome-wide mRNA expression profiling to identify liver tissue-specific PB-mediated DNA methylation and transcriptional alterations. Only a limited number of significant anti-correlations were observed between PB-induced transcriptional and promoter-based DNA methylation perturbations. However, the constitutive androstane receptor (CAR) target gene Cyp2b10 was found to be concomitantly hypomethylated and transcriptionally activated in a liver tissue-specific manner following PB treatment. Furthermore, analysis of active and repressive histone modifications using chromatin immunoprecipitation revealed a strong PB-mediated epigenetic switch at the Cyp2b10 promoter. Our data reveal that PB-induced transcriptional perturbations are not generally associated with broad changes in the DNA methylation status at proximal promoters and suggest that the drug-inducible CAR pathway regulates an epigenetic switch from repressive to active chromatin at the target gene Cyp2b10. This study demonstrates the utility of integrated epigenomic and transcriptomic profiling for elucidating early mechanisms and biomarkers of non-genotoxic carcinogenesis. 29M-bM-^@M-^S32 days old male B6C3F1/Crl (C57BL/6 M-bM-^YM-^B x C3H/He M-bM-^YM-^@) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups (n = 10) and phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behavior and sacrificed on the last day of dosing (day 28). Blood was withdrawn for PK analysis and target (liver) and non-target (kidney) tissues removed, split into several sections, frozen in liquid nitrogen and stored at M-bM-^HM-^R80M-BM-0C for subsequent analyses. Total RNA from liver and kidney was purified and processed for Affymetrix gene expression profiling while genomic DNA was prepared for promoter array based methylome analysis using the Methylated DNA immunoprecipitation (MeDIP) procedure. Remaining tissue material was used for chromatin immunoprecipitation (ChIP) to analyze histone modifications at individual promoters. Plasma samples were also collected to evaluate phenobarbital exposure in individual animals by LC-MS.

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Transcription profiling of hypertension disease induced by treating mice with salt water (vs plain water as control) RNA collected from 5 tissues (Brain stem, Brain, liver, kidney, and heart) of two strains (SWR and C3H)

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