Locus-Specific Differential DNA Methylation and Urinary Arsenic: An Epigenome-Wide Association Study in Blood among Adults with Low-to-Moderate Arsenic Exposure

Abstract

BACKGROUND: Chronic exposure to arsenic (As), a human toxicant and carcinogen, remains a global public health problem. Health risks persist after As exposure has ended, suggesting epigenetic dysregulation as a mechanistic link between exposure and health outcomes. OBJECTIVES: We investigated the association between total urinary As and locus-specific DNA methylation in the Strong Heart Study, a cohort of American Indian adults with low-to-moderate As exposure [total urinary As, mean ð±SDÞ lg=g creatinine: 11.7 (10.6)]. METHODS: DNA methylation was measured in 2,325 participants using the Illumina MethylationEPIC array. We implemented linear models to test differentially methylated positions (DMPs) and the DMRcate method to identify regions (DMRs) and conducted gene ontology enrichment analysis. Models were adjusted for estimated cell type proportions, age, sex, body mass index, smoking, education, estimated glomerular filtration rate, and study center. Arsenic was measured in urine as the sum of inorganic and methylated species. RESULTS: In adjusted models, methylation at 20 CpGs was associated with urinary As after false discovery rate (FDR) correction (FDR < 0:05). After Bonferroni correction, 5 CpGs remained associated with total urinary As (p Bonferroni < 0:05), located in SLC7A11, ANKS3, LINGO3, CSNK1D, ADAMTSL4. We identified one DMR on chromosome 11 (chr11:2,322,050-2,323,247), annotated to C11orf2; TSPAN32 genes. DISCUSSION: This is one of the first epigenome-wide association studies to investigate As exposure and locus-specific DNA methylation using the Illumina MethylationEPIC array and the largest epigenome-wide study of As exposure. The top DMP was located in SLC7A11A, a gene involved in cystine/glutamate transport and the biosynthesis of glutathione, an antioxidant that may protect against As-induced oxidative stress. Additional DMPs were located in genes associated with tumor development and glucose metabolism. Further research is needed, including research in more diverse populations, to investigate whether As-related DNA methylation signatures are associated with gene expression or may serve as biomarkers of disease development.

Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes

“…HNRNPUL1 , annotated to the DVP cg26384602, was also found to be differentially methylated with maternal urinary arsenic in cord blood in a Taiwanese birth cohort [ 17 ]. We also compared our DMPs and DVPs to all nominally significant DMPs previously associated with urinary arsenic levels among adults in the US ( p < 0.05) [ 9 ]. Notably, HDAC4 included 38 DMPs, SNTG2 included 9 DMPs, and TOLLIP included 8 DMPs identified by Bozack et al in the Strong Heart Study, a cohort of American Indian adults from the Great Plains and the Southwest [ 9 ] ( p < 0.05).…”

“…A greater number of DMPs was also identified among males in an EWAS of prenatal arsenic exposure on DNAm measured at age 9 in Bangladesh ( N = 113): 9, 57, and 15 CpGs were associated with exposure among children overall, males, and females, respectively ( FDR < 0.05), with no overlap between CpGs identified in sex-stratified analyses [ 14 ]. However, in an EWAS of arsenic exposure in the Strong Heart Study ( N = 2,325), substantial sex-specific effects in stratified analyses were not observed with all FDR-significant CpGs achieving nominal significance in sex-stratified analyses ( p < 0.05) [ 9 ]. Further, in our study, there is insufficient evidence to conclude that prenatal exposure is associated with sex in the Chile study’s datasets (Pearson’s chi-squared test p = 1, 0.88 in the PBMC and the buccal studies, respectively).…”

“…To assess the consistency of our results with those of previous studies, we searched the Comparative Toxicogenomics Database [ 51 ] for interactions between arsenic and the genes containing DMPs and DVPs. We also compared our identified DMPs and DVPs with nominally significant DMPs reported by Bozack et al [ 9 ] and DMPs significant after adjustment for multiple comparisons reported by EWAS of arsenic exposure [ 10 – 21 , 52 , 53 ].…”

“…Previous EWAS have commonly studied prenatal arsenic exposure and DNAm measured in cord blood and placenta samples among birth cohorts in the United States (US) (N = 136; 343) [10,11], Bangladesh (N = 44; 45; 113; 127) [12][13][14][15], Mexico (N = 38) [16], and Taiwan (N = 64) [17]. Studies of exposure later in the life course have measured DNAm in blood samples, including adults with low (N = 46) [18] or low-to-moderate exposure in the US (N = 2325) [9], moderate-to-high exposure in Bangladesh (N = 400; 396) [19,20], and women in Argentina (N = 96) [21].…”

“…In epidemiological studies, arsenic exposure has been associated with changes in global levels of DNAm [ 7 ]. Arsenic-induced changes in the DNA methylome have also been studied in epigenome-wide association studies (EWAS), which had previously been reviewed and summarized [ 8 , 9 ]. EWAS most commonly measure DNAm on the individual-locus level using the Illumina HumanMethylation BeadChip (450K) or Illumina Infinium MethylationEPIC BeadChip (850K) which interrogate > 450,000 and > 850,000 methylation sites, respectively.…”