Rare, Protein-Altering Variants in AS3MT and Arsenic Metabolism Efficiency: A Multi-Population Association Study

Abstract

Background: Common genetic variation in the arsenic methyltransferase (AS3MT) gene region is known to be associated with arsenic metabolism efficiency (AME), measured as the percentage of dimethylarsinic acid (DMA%) in the urine. Rare, protein-altering variants in AS3MT could have even larger effects on AME, but their contribution to AME has not been investigated.

Objectives: We estimated the impact of rare, protein-coding variation in AS3MT on AME using a multi-population approach to facilitate the discovery of population-specific and shared causal rare variants.

Methods: We generated targeted DNA sequencing data for the coding regions of AS3MT for three arsenic-exposed cohorts with existing data on arsenic species measured in urine: Health Effects of Arsenic Longitudinal Study (HEALS, $n=\mathrm{2,434}$), Strong Heart Study (SHS, $n=868$), and New Hampshire Skin Cancer Study (NHSCS, $n=666$). We assessed the collective effects of rare (allele frequency $<1\%$), protein-altering AS3MT variants on DMA%, using multiple approaches, including a test of the association between rare allele carrier status (yes/no) and DMA% using linear regression (adjusted for common variants in 10q24.32 region, age, sex, and population structure).

Results: We identified 23 carriers of rare-protein-altering AS3MT variant across all cohorts (13 in HEALS and 5 in both SHS and NHSCS), including 6 carriers of predicted loss-of-function variants. DMA% was 6-10% lower in carriers compared with noncarriers in HEALS [$\beta =-9.4$ (95% CI: $-13.9$, $-4.8$)], SHS [$\beta =-6.9$ (95% CI: $-13.6$, $-0.2$)], and NHSCS [$\beta =-8.7$ (95% CI: $-15.6$, $-2.2$)]. In meta-analyses across cohorts, DMA% was 8.7% lower in carriers [$\beta =-8.7$ (95% CI: $-11.9$, $-5.4$)].

Discussion: Rare, protein-altering variants in AS3MT were associated with lower mean DMA%, an indicator of reduced AME. Although a small percentage of the population (0.5-0.7%) carry these variants, they are associated with a 6-10% decrease in DMA% that is consistent across multiple ancestral and environmental backgrounds. https://doi.org/10.1289/EHP8152.

Figure 1.

Average aligned read depth (depth of coverage) of AS3MT exons. Nine of 11 exons (excluding Exons 5 and 10) in AS3MT were sequenced with an average depth of coverage across all cohorts ranging from $173\times \text{to\hspace{0.17em}}729\times$ ($30\times$ is deemed high quality). Rare, protein-altering variants were identified across all cohorts: five variants in HEALS in Exons 4 and 6, four variants in SHS in Exons 4, 8, 9, and 11, and five in NHSCS in Exons 6, 7, 9, and 11. Note: CCDS, Consensus Coding Sequence project; chr, chromosome; Human Feb. 2009, February 2009 Human reference sequence; HEALS, Health Effects of Arsenic Longitudinal Study; NHSCS, New Hampshire Skin Cancer Study; Rfam, RNA families; SHS, Strong Heart Study; UCSC, University of California, Santa Cruz.

Figure 2.

Percentage of arsenic metabolites by carrier status of rare, protein-altering variants in AS3MT across cohorts. Measures of arsenic metabolites within each box range from the 25th to the 75th percentile. The 50th percentile (or median) is depicted by the horizontal line within each box. Data in the upper and lower whiskers of the box represent measures below and above the 25th and 75th percentiles, respectively. Individual data points for all noncarriers are shown to the left of the box plot and to the right of the box plot for carriers. There were a total of 13, 5, and 5 rare variant carriers in HEALS, NHSCS, and SHS, respectively. (A) Carriers of rare, protein-altering variants have reduced DMA% (on y-axis) compared with noncarriers, across all cohorts. Carriers of loss of function (pLoF) variants, labeled accordingly by cohort and shown by arrows, fall in the bottom 10th and 20th percentiles of DMA%. (B) MMA% (on y-axis) is higher among carriers of rare, protein-altering variants across all cohorts. (C) iAs% (on y-axis) is higher among carriers of rare, protein-altering variants across all cohorts. Note: DMA%, percentage of dimethylarsinic acid; HEALS, Health Effects of Arsenic Longitudinal Study; MMA%, percentage of monomethylated arsenic; NHSCS, New Hampshire Skin Cancer Study; SHS, Strong Heart Study.