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Association of Environmental Exposure to Chromium with Differential DNA Methylation: An Epigenome-Wide Study

ABSTRACT: Association of Environmental Exposure to Chromium with Differential DNA Methylation: An Epigenome-Wide Study

PROVIDER: PRJNA850623 | ENA |

REPOSITORIES: ENA

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Association of Environmental Exposure to Chromium with Differential DNA Methylation: An Epigenome-Wide Study

Project description:To identified the differential methylation of genes and regions to elucidate the mechanisms of toxicity related to environmental chromium exposure. Fasting whole blood samples were collected by clinicians in ethylenediaminetetraacetic acid (EDTA) anticoagulant tubes, and stored them at −80 °C. A DNeasy Blood and Tissue Kit (Qiagen) was used to isolate DNA from whole blood. The purity and concentration of DNA were estimated using Nanodrop 2000 (ThermoScietific). Approximately 500 ng of genomic DNA from each sample was used for sodium bisulfite conversion with the EZ DNA methylation Gold Kit (Zymo Research, USA) in accordance with the manufacturer’s standard protocol. Genome-wide DNA methylation was performed using the Illumina Infinium HumanMethylation850K (EPIC) BeadChip (Illumina Inc, USA) in accordance with the manufacturer’s instructions.

2022-12-13 | GSE206418 | GEO

Association of environmental exposure to chromium with differential DNA methylation: An epigenome-wide study.

Project description:Introduction: Previous studies have reported that chromium (Cr)-induced epigenetic alterations and DNA methylation play a vital role in the pathogenesis of diseases induced by chromium exposure. Epigenomic analyses have been limited and mainly focused on occupational chromium exposure; their findings are not generalizable to populations with environmental Cr exposure. Methods: We identified the differential methylation of genes and regions to elucidate the mechanisms of toxicity related to environmental chromium exposure. DNA methylation was measured in blood samples collected from individuals in Cr-contaminated (n = 10) and unexposed areas (n = 10) by using the Illumina Infinium HumanMethylation850K array. To evaluate the relationship between chromium levels in urine and CpG methylation at 850 thousand sites, we investigated differentially methylated positions (DMPs) and differentially methylated regions (DMRs) by using linear models and DMRcate method, respectively. The model was adjusted for biologically relevant variables and estimated cell-type compositions. Results: At the epigenome-wide level, we identified five CpGs [cg20690919 (p FDR =0.006), cg00704664 (p FDR =0.024), cg10809143 (p FDR =0.043), cg27057652 (p FDR =0.047), cg05390480 (p FDR =0.024)] and one DMR (chr17: 19,648,718-19,648,972), annotated to ALDH3A1 genes (p < 0.05) as being significantly associated with log2 transformed urinary chromium levels. Discussion: Environmental chromium exposure is associated with DNA methylation, and the significant DMPs and DMR being annotated to cause DNA damage and genomic instability were found in this work. Research involving larger samples is required to further explore the epigenetic effect of environmental chromium exposure on health outcomes through DNA methylation.

| S-EPMC9845398 | biostudies-literature

Epigenome-wide association study in peripheral white blood cells: Methyl Epigenome Network Association (MENA) project

Project description:Epigenome-wide association study in peripheral white blood cells: Methyl Epigenome Network Association (MENA) project

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Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology

Project description:Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology

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Epigenome wide association study of post-mortem Alzheimer’s Disease samples

Project description:Samples from 72 AD patients and 62 age-matched cognitively normal controls were assayed using Illumina© Infinium MethylationEPIC BeadChip. We performed an epigenome-wide association study (EWAS) to evaluate the epigenetic differences using post-mortem superior temporal gyrus (STG) and inferior frontal gyrus (IFG) samples. We performed an epigenome-wide association study (EWAS) to evaluate the epigenetic differences using post-mortem superior temporal gyrus (STG) and inferior frontal gyrus (IFG) samples.

2020-10-20 | GSE156984 | GEO

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Response of marine Staphylococcus cohnii strain to Chromium

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2019-12-02 | PXD012993 | Pride

Epigenome-wide Association Study of Obesity Susceptibility in Human Twins

Project description:The purpose of the current study was to use an epigenome-wide association approach (EWAS) to identify a potential DNA methylation alterations associated with obesity using twins discordant on obesity status. Buccal cells (from a cheek swab) were used as a purified marker cell for the epigenetic analysis. Analysis of differential DNA methylation regions (DMRs) was used to identify epigenetic associations with metabolic and dietary measures in obesity parameters discordant twins. An edgeR analysis provided a DMR signature with p<1e-04, but a false discovery rate analysis demonstrated a lack of significance due to low sample size and known multivariant origins of obesity.

2023-02-18 | GSE218363 | GEO

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DNA methylation alternations in the offspring liver from chromium restriction diet dams

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