Sequencing-based fine-mapping and in silico functional characterization of the 10q24.32 arsenic metabolism efficiency locus across multiple arsenic-exposed populations

• Published in: PLOS Genetics Vol. 19; no. 1; p. e1010588
• Main Authors: Chernoff, Meytal Batya, Delgado, Dayana, Tong, Lin, Chen, Lin, Oliva, Meritxell, Tamayo, Lizeth I., Best, Lyle G., Cole, Shelley, Jasmine, Farzana, Kibriya, Muhammad G., Nelson, Heather, Huang, Lei, Haack, Karin, Kent, Jack, Umans, Jason G., Graziano, Joseph, Navas-Acien, Ana, Karagas, Margaret R., Ahsan, Habib, Pierce, Brandon L.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science (PLoS) 20.01.2023; Public Library of Science
• Subjects: Acids; Analysis; Arsenic; Arsenic - metabolism; Arsenic - toxicity; Arsenic Poisoning; Arsenic Poisoning - genetics; Arsenicals; Arsenicals - metabolism; Biology and Life Sciences; Cancer; Chromosome mapping; Chromosomes, Human, Pair 10; DNA Methylation; DNA sequencing; Drinking water; Environmental aspects; Estimates; Gene frequency; Gene mapping; Genetic aspects; Genetic diversity; Genetics; Genomes; Health aspects; Humans; Linkage disequilibrium; Longitudinal studies; Medical research; Medicine and Health Sciences; Medicine, Experimental; Metabolic regulation; Metabolism; Methods; Methylation; Methyltransferase; Methyltransferases; Methyltransferases - genetics; Methyltransferases - metabolism; Native Americans; Nucleotide sequencing; Physical Sciences; Physiological aspects; Polymorphism, Single Nucleotide; Polymorphism, Single Nucleotide - genetics; Population genetics; QH426-470; Regulatory sequences; Research and Analysis Methods; Research Article; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Skin; Skin cancer; United States; Bangladesh; New Hampshire; India; United States > US
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1010588

Inorganic arsenic is highly toxic and carcinogenic to humans. Exposed individuals vary in their ability to metabolize arsenic, and variability in arsenic metabolism efficiency (AME) is associated with risks of arsenic-related toxicities. Inherited genetic variation in the 10q24.32 region, near the arsenic methyltransferase ( AS3MT ) gene, is associated with urine-based measures of AME in multiple arsenic-exposed populations. To identify potential causal variants in this region, we applied fine mapping approaches to targeted sequencing data generated for exposed individuals from Bangladeshi, American Indian, and European American populations (n = 2,357, 557, and 648 respectively). We identified three independent association signals for Bangladeshis, two for American Indians, and one for European Americans. The size of the confidence sets for each signal varied from 4 to 85 variants. There was one signal shared across all three populations, represented by the same SNP in American Indians and European Americans (rs191177668) and in strong linkage disequilibrium (LD) with a lead SNP in Bangladesh (rs145537350). Beyond this shared signal, differences in LD patterns, minor allele frequency (MAF) (e.g., rs12573221 ~13% in Bangladesh ~0.2% among American Indians), and/or heterogeneity in effect sizes across populations likely contributed to the apparent population specificity of the additional identified signals. One of our potential causal variants influences AS3MT expression and nearby DNA methylation in numerous GTEx tissue types (with rs4919690 as a likely causal variant). Several SNPs in our confidence sets overlap transcription factor binding sites and cis-regulatory elements (from ENCODE). Taken together, our analyses reveal multiple potential causal variants in the 10q24.32 region influencing AME, including a variant shared across populations, and elucidate potential biological mechanisms underlying the impact of genetic variation on AME.