Environmental Exposure study with Bisulfite-Seq data on dbGaP (80 participants)

phs003392 — Epigenetic Changes in Immune Response and Oncogenesis Related Genes    Caused by Heavy Metal Long-Term Exposure

Our study investigated methylation changes in CpG islands located in immune response and oncogenesis related genes in humans induced by long-term environmental heavy metal exposure. We assessed the methylation levels of 654 CpG sites located on <a href="https://www.ncbi.nlm.nih.gov/gene/4790">NFKB1</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/1029">CDKN2A</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/2099">ESR1</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/116519">APOA5</a><a href="https://www.ncbi.nlm.nih.gov/gene/116519"> </a>and <a href="https://www.ncbi.nlm.nih.gov/gene/3481">IGF2/H19</a> genes by targeted bisulfite sequencing (target enrichment by 48.48 Access Array Integrated Fluidic Circuit (Fluidigm, USA) in a cohort of 40 subjects living near a metal mining area (the Kapan mining region, Armenia) and 40 unexposed subjects. We performed linear regression on our data to find differentially methylated positions with adjustment for gender, age, BMI class, smoking, and plasma concentrations of 21 essential and non-essential metals detected by ICP-MS. Our study showed hypomethylation of five CpG sites in the NFKB1 promoter region in the exposed group. According to our findings, the methylation changes of CpG sites in <a href="https://www.ncbi.nlm.nih.gov/gene/4790">NFKB1</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/1029">CDKN2A</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/3481">IGF2</a><a href="https://www.ncbi.nlm.nih.gov/gene/3481"> </a>and <a href="https://www.ncbi.nlm.nih.gov/gene/2099">ESR1</a><a href="https://www.ncbi.nlm.nih.gov/gene/2099"> </a>genes are associated with multiple and specific metal exposures. Targeted bisulfite sequencing data obtained for 80 subjects who participated in this study are available through dbGaP. The tables contain information about age, sex, BMI, smoking and exposure status, as well as race and ethnicity of the study participants.