A missense variant in FTCD is associated with arsenic metabolism and toxicity phenotypes in Bangladesh

Abstract

Inorganic arsenic (iAs) is a carcinogen, and exposure to iAs via food and water is a global public health problem. iAs-contaminated drinking water alone affects >100 million people worldwide, including ~50 million in Bangladesh. Once absorbed into the blood stream, most iAs is converted to mono-methylated (MMA) and then di-methylated (DMA) forms, facilitating excretion in urine. Arsenic metabolism efficiency varies among individuals, in part due to genetic variation near AS3MT (arsenite methyltransferase; 10q24.32). To identify additional arsenic metabolism loci, we measured protein-coding variants across the human exome for 1,660 Bangladeshi individuals participating in the Health Effects of Arsenic Longitudinal Study (HEALS). Among the 19,992 coding variants analyzed exome-wide, the minor allele (A) of rs61735836 (p.Val101Met) in exon 3 of FTCD (formiminotransferase cyclodeaminase) was associated with increased urinary iAs% (P = 8x10-13), increased MMA% (P = 2x10-16) and decreased DMA% (P = 6x10-23). Among 2,401 individuals with arsenic-induced skin lesions (an indicator of arsenic toxicity and cancer risk) and 2,472 controls, carrying the low-efficiency A allele (frequency = 7%) was associated with increased skin lesion risk (odds ratio = 1.35; P = 1x10-5). rs61735836 is in weak linkage disequilibrium with all nearby variants. The high-efficiency/major allele (G/Valine) is human-specific and eliminates a start codon at the first 5´-proximal Kozak sequence in FTCD, suggesting selection against an alternative translation start site. FTCD is critical for catabolism of histidine, a process that generates one-carbon units that can enter the one-carbon/folate cycle, which provides methyl groups for arsenic metabolism. In our study population, FTCD and AS3MT SNPs together explain ~10% of the variation in DMA% and support a causal effect of arsenic metabolism efficiency on arsenic toxicity (i.e., skin lesions). In summary, this work identifies a coding variant in FTCD associated with arsenic metabolism efficiency, providing new evidence supporting the established link between one-carbon/folate metabolism and arsenic toxicity.

Fig 1. FTCD SNP rs61735836 is associated with the all three arsenic species measured in urine (iAs%, MMA%, and DMA%).

Quantile-quantile plots (A-C) for all 19,992 post-QC exome chip variants and scatterplots (D-F) depicting the association between rs61735836 (301G>A, Val101Met) and arsenic species percentages (iAs% on left, MMA% center, and DMA% right) among 1,660 HEALS participants.

Fig 2. Regional association plots for the FTCD region (21q22.3).

The vertical axes show the–log₁₀(P-value) for the association of SNP allele counts with (A) DMA%, (B) MMA%, (C) iAs% (A-C based on 1,660 HEALs participants), and (D) arsenic induced skin lesions (2,401 cases, 2,472 controls).

Fig 3. The minor allele of missense variant rs61735836 changes a valine to a methionine.

The minor allele (A, MAF = 0.07) changes a valine (V, circled) codon (GTG, red box) to a methionine (M) codon (ATG/AUG) at a site that is highly conserved across vertebrates. This change introduces a potential start codon in exon 3 which is the first 5´-proximal Kozak consensus sequence ([A/G]xxAUGG) in the FTCD gene.

Fig 4. The role of FTCD in histidine catabolism and the one-carbon/folate cycle, which provides methyl groups for arsenic methylation (by AS3MT) via the methionine cycle.

The formininotranserase domain of FTCD catalyzes the transfer of a formimino group from N-formimino-L-glutamate (FIGLU) (or a formyl group from N-formyl-L-glutamate) to tetrahydrofolate (THF) producing formimino-THF. The cyclodeaminase domain of FTCD then catalyzes the removal of ammonia from formimino-THF, generating 5,10-methenyl THF, which can then be converted to 5:10 methylene-THF or THF, both key components of the canonical one-carbon/folate cycle (shown in bold). The folate cycle contributes one-carbon groups to the methionine cycle, which in turn supplies these groups to methyltransferases (such as AS3MT) involved in methylation of arsenic, DNA, and other substrates. DHF, dihydrofolate; dUTP, deoxyuridine triphosphate.

Fig 5. Mendelian randomization supports a causal effect of arsenic metabolism efficiency on arsenic-induced skin lesion risk.

Horizontal and vertical error bars for each SNP correspond to the 95% CI for the beta coefficient for its association with DMA% and skin lesion risk, respectively. The slope of the diagonal line (-0.013) is the inverse-variance-weighted estimate of the causal effect (i.e., the ln(OR), corresponding to OR = 0.89 for a 10% increase in DMA%; P = 6x10^-8).