Epigenome analysis of alcohol consumption in whole blood (WB) samples
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ABSTRACT:
PROVIDER: PRJNA432606 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome wide DNA methylation profiling of drinkers and non-drinkers in WB samples. The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across 485,577 CpGs in WB samples that oevrlapped with CpGs from Illumina Infinium450k Human DNA methylation Beadchip. Samples included 47 drinkers (cases) and 47 non-drinkers (controls).
2018-04-01 | GSE110043 | GEO
Project description:Genome-wide DNA methylation profiling of individuals consuming alcohol and controls in LC samples. Individuals consuming alcohol were profiled at time of intake (T1) into treatment facility and four weeks into treatment (T2). Controls were profiled once. The Illumina Infinium 450k Human DNA Methylation BeadChip v1.0 was used to obtain DNA methylation profiles across 485,577 CpGs in LC samples. Samples included 33 case subjects at T1, 26 case subjects at T2 and 33 controls.
2014-09-24 | GSE57853 | GEO
Project description:Genome-wide DNA methylation profiling of individuals consuming alcohol and controls in LC samples. Individuals consuming alcohol were profiled at time of intake (T1) into treatment facility and four weeks into treatment (T2). Controls were profiled once. The Illumina Infinium 450k Human DNA Methylation BeadChip v1.0 was used to obtain DNA methylation profiles across 485,577 CpGs in LC samples. Samples included 33 case subjects at T1, 26 case subjects at T2 and 33 controls. Bisulfite-converted DNA from 92 samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip v1.0.
2014-09-24 | E-GEOD-57853 | biostudies-arrayexpress
Project description:Microglia are fundamentally important immune cells within the central nervous system (CNS) that respond to environmental challenges to maintain normal physiological processes. Alterations in steady-state cellular function and over-activation of microglia can facilitate the initiation and progression of neuropathological conditions such as Alzheimer’s disease, Multiple Sclerosis, and Major Depressive Disorder. Alcohol consumption disrupts signaling pathways including both innate and adaptive immune responses that are necessary for CNS homeostasis. Unbiased RNA-Seq profiling was used to identify gene expression changes in isolated microglia in response to recurring bouts of voluntary alcohol drinking behavior. Gene coexpression analysis identified a coordinately regulated group of genes, unique to microglia, that collectively are associated with alcohol consumption. Several genes in this group were involved in toll-like receptor signaling and production of the inflammatory cytokine interferon-gamma. Coordinate expression of these genes is not ascertained from an admixture of CNS cell-types, underscoring the importance of examining isolated cellular populations to reveal systematic gene expression changes arising from mature microglia. We identified a distinctive microglial gene expression signature for neuroimmune responses related to alcohol consumption that provides valuable insight into microglia-specific changes underlying the development of substance abuse, as well as related CNS disorders.
2016-12-10 | GSE91387 | GEO
Project description:Action of alcohol on synaptic mRNA in the amygdala of mice Chronic alcohol consumption induces changes in gene expression, causing persistent long-term neuro-adaptations and the remodeling of synaptic structures. These alcohol-induced synaptic changes may rely specifically on the local translation of mRNAs in the synaptic compartments of the cell. We profiled the transcriptome from synaptoneurosomes (SN) and paired total homogenates (TH) of amygdala to analyze the synaptic adaptations induced by chronic voluntary alcohol consumption in mice. In the SN both the number of alcohol-responsive mRNAs and the magnitude of fold-change were greater than in the TH. Accordingly, the SN detected many genes with coordinated patterns of expression producing a highly connected mRNA network in gene co-expression analysis. The greater sensitivity of the SN preparation allowed for improved cell-type specificity analysis, revealing an up-regulation of alcohol-responsive astrocytic and microglial modules that correlated with alcohol consumption. Alcohol was found to induce changes in the SN functionally important biological pathways, including long-term potentiation, long-term potentiation depression, glutamate pathway, neuro-immune, RNA-processing and translational machineries and provided overlap with changes seen in human alcoholic brain. Transposable elements were responsive to alcohol and found in the down-regulated neuronal mRNA module, which may underlie some of the coordinated gene expression changes associated with alcohol. We provide evidence that enrichment of synaptic components reveals a more intricate network of coordinated gene expression. Increased resolution captures the molecular effects of synaptic manipulations and provides an improved technique for identifying therapeutic targets for alcohol abuse. Synaptoneurosomes (SN) and Paired total homogenates (TH) were prepared from the same homogenate. 42 microarrays were used in total for the alcohol-control analysis (8 alcohol treated mice and 13 controls), 21 SN and 21 paired TH. 2 TH (control) samples were found outliers and were removed from the analysis. For the SN vs. TH analysis, the 2 TH samples found outliers were removed with the 2 paired SN samples.
2013-10-28 | E-GEOD-51730 | biostudies-arrayexpress
Project description:We investigated the molecular mechanisms of chronic alcohol consumption or lipopolysaccharide insult by gene expression profiling in prefrontal cortex and liver of C57BL/6J mice. We identified similar patterns of transcriptional changes in brain and liver among three different alcohol consumption tests and lipopolysaccharide injection. We also demonstrated distinct genomic consequences of different types of alcohol consumption.
2013-04-01 | GSE42789 | GEO
Project description:Accumulating evidence suggests that lifestyle-related factors may influence radiation responses and the resulting cancer risks through epigenetic mechanisms, such as miRNA regulations. Chronic alcohol consumption is a major risk factor for various pathologies, including alcoholic liver disease. We have recently shown that consumption of Japanese sake promotes glutathione metabolism and anti-oxidative activities in the liver of irradiated C57BL/6 mice. Here we show that chronic alcohol consumption resulted in elevated ciculating levels of the inflammatory cytokine TNF-α and that it triggered specific miRNA regulations (such as the upregulation of the radio-resistant miR-210) that are susceptible to influence the resulting radiation effects in the mouse liver.
2016-03-15 | GSE79186 | GEO
Project description:Accumulating evidence suggests that lifestyle-related factors may influence radiation responses and the resulting cancer risks through epigenetic mechanisms, such as miRNA regulations. Chronic alcohol consumption is a major risk factor for various pathologies, including alcoholic liver disease. We have recently shown that consumption of Japanese sake promotes glutathione metabolism and anti-oxidative activities in the liver of irradiated C57BL/6 mice. Here we show that chronic alcohol consumption resulted in elevated ciculating levels of the inflammatory cytokine TNF-α and that it triggered specific miRNA regulations (such as the upregulation of the radio-resistant miR-210) that are susceptible to influence the resulting radiation effects in the mouse liver. Japanese sake was administrated to C3H mice irradiated with 3 Gy X-rays. miRNA expression was measured in the livers of 3 mice for each experimental group.
2016-03-15 | E-GEOD-79186 | biostudies-arrayexpress
Project description:We investigated the molecular mechanisms of chronic alcohol consumption or lipopolysaccharide insult by gene expression profiling in prefrontal cortex and liver of C57BL/6J mice. We identified similar patterns of transcriptional changes in brain and liver among three different alcohol consumption tests and lipopolysaccharide injection. We also demonstrated distinct genomic consequences of different types of alcohol consumption. The microarray experiment was performed to compare gene expression changes induced by three separate paradigms of alcohol consumption and immune activation by lipopolysaccharide injection. The three tests of alcohol consumption were the continuous chronic two bottle choice (Chronic), two bottle choice available every other day (Chronic Intermittent) and limited access to one bottle of ethanol (Drinking in the Dark). All alcohol studies utilized 20% ethanol and each treatment group had it's own control group which received only water. The immune activation test consisted of 2 lipopolysaccharide injections (1 mg/kg i.p.) spaced one week apart, with animals being sacrificed one week after the last injection. Control animals received saline injections. All studies used female, adult mice.
2013-04-01 | E-GEOD-42789 | biostudies-arrayexpress
Project description:LncRNAs are important regulators of quantitative and qualitative features of the transcriptome. We have used QTL and other statistical analyses to identify a gene coexpression module associated with the phenotype of alcohol consumption. The “hub gene” of this module, Lrap (Long non-coding RNA for alcohol preference), was an unannotated transcript resembling a lncRNA. We used partial correlation analyses to establish that Lrap is a major contributor to the integrity of the coexpression module. Using CRISPR/Cas9 technology, we disrupted an exon of Lrap in Wistar rats. The genetically modified rats were assessed for alcohol consumption and brain RNA expression levels were evaluated using RNASeq. Measures of alcohol consumption in wild type, heterozygous and knockout rats demonstrated that disruption of Lrap produced increases in alcohol consumption/alcohol preference. The disruption of Lrap also produced changes in expression of over 700 other transcripts. Furthermore, it became apparent that Lrap may have a function in alternative splicing of the affected transcripts. More than 20% of the differentially expressed isoforms exhibited evidence for novel alternative splicing between Lrap+/+ and Lrap-/- rats. The GO category of “Response to Ethanol” emerged as one of the top candidates in an enrichment analysis of the differentially expressed transcripts. We validate the role of Lrap as a mediator of alcohol consumption by rats, and also implicate Lrap as a modifier of the expression and splicing of a large number of brain transcripts. A defined subset of these transcripts significantly impacts alcohol consumption by rats (and possibly humans).
2020-08-19 | GSE155709 | GEO