Groundwater Arsenic Leaves Fingerprints in DNA Repair Genes of Exposed Women

In the arsenic-burdened districts of Bihar, India, the poison does not announce itself. It seeps silently from contaminated groundwater into rice paddies, wheat fields, kitchen wells and, ultimately, into human bodies. A new study published in Discover Toxicology has now traced that silent journey all the way into the genome, combining precise measurements of arsenic in blood, urine and breast milk with whole exome sequencing of women chronically exposed to the metalloid. The findings, while preliminary, offer a striking molecular portrait of environmental poisoning and raise urgent questions about heritable cancer risk in one of the world’s most severely affected regions.

The research team, led by scientists at the Mahavir Cancer Sansthan and Research Centre in Patna along with collaborators across several Indian institutions, enrolled nine women from the arsenic-endemic districts of Saran, Buxar and Bhojpur. These participants were selected on the basis of the highest blood arsenic concentrations recorded in earlier surveys conducted in the region. Each woman provided samples of blood, urine and breast milk, which were acid-digested in the laboratory and analyzed for total arsenic using graphite furnace atomic absorption spectrometry, a technique sensitive enough to detect the element at concentrations below one-tenth of a microgram per liter.

The exposure data were sobering. Every one of the nine women carried blood arsenic levels above the ten micrograms per liter reference threshold, with the highest measured value reaching an extraordinary 491.2 micrograms per liter. Six of the nine exceeded the CDC’s permissible limit of fifty micrograms per liter in urine, peaking at 921.4 micrograms per liter, a pattern consistent with ongoing exposure through drinking water and locally grown food. Most alarming for public health was the breast milk analysis: eight of the nine lactating women showed arsenic concentrations above the one microgram per liter reference level set by a joint WHO/IAEA collaborative study, with a maximum of 438.6 micrograms per liter. Because breast milk represents a direct exposure pathway for nursing infants, the authors highlight this as evidence of potential maternal-to-infant transfer during a uniquely vulnerable window of development.

To probe what such sustained toxic burden might be doing at the genomic level, the team turned to whole exome sequencing, a next-generation sequencing approach that captures and reads all protein-coding regions of the genome. This strategy is well suited to the task because more than eighty-five percent of known disease-causing variants reside in exons. DNA extracted from each participant’s peripheral blood was prepared using targeted capture libraries and sequenced on an Illumina platform with paired-end chemistry, achieving mean coverage depths above eighty-five to one hundred times. Variants were called following the Genome Analysis Toolkit best-practices framework, aligned to the GRCh38 human reference genome, and classified according to the American College of Medical Genetics and Genomics guidelines using population frequency databases such as gnomAD and the 1000 Genomes Project alongside computational prediction tools including SIFT, PolyPhen-2, MutationTaster and Mutation Assessor.

Out of the nine women sequenced, two carried notable variants in genes that sit at the heart of genomic maintenance. Subject 1 harbored a novel heterozygous missense variant in the MSH6 gene, designated c.3716 T>C (p.Ile1239Thr), located in exon 8 on chromosome 2. The substitution replaces isoleucine with threonine at codon 1239 within a protein that, together with MSH2, forms the MutSα complex responsible for recognizing replication errors during DNA synthesis. Computational algorithms predicted the change to be damaging, and the affected nucleotide showed strong evolutionary conservation across one hundred vertebrate species, yet the variant is absent from all individuals in gnomAD and the 1000 Genomes Project. Under ACMG criteria it was classified as a variant of uncertain significance, a label reflecting both its suspicious features and the current limits of scientific evidence.

Subject 2 carried an even more concerning alteration: a heterozygous missense variant in the ATM gene, c.590G>A (p.Gly197Glu), in exon 6 on chromosome 11. This change, swapping glycine for glutamic acid at codon 197, was predicted damaging by both SIFT and PolyPhen-2, with the glycine residue conserved across all mammalian species examined. The variant is extremely rare, observed in only seven of 30,766 South Asian alleles in gnomAD and absent entirely from the 1000 Genomes cohort. Critically, it was classified as likely pathogenic under ACMG guidelines. The ATM gene encodes a master checkpoint kinase of the PI3/PI4-kinase family that orchestrates the cellular response to DNA double-strand breaks, phosphorylating tumor suppressors such as p53 and BRCA1, the checkpoint kinase CHK2, and the DNA repair protein NBS1. Variants in ATM have been associated with hereditary cancer susceptibility, and the remaining seven participants showed no clinically notable exomic alterations.

The biological significance of these two genes makes their disruption in arsenic-exposed individuals particularly noteworthy. MSH6 is a cornerstone of the mismatch repair pathway, working in concert with MSH2, MLH1 and PMS2 to excise mispaired bases and preserve fidelity during cell division. Germline MSH6 mutations are a recognized cause of Lynch syndrome, the most common hereditary colorectal cancer predisposition condition, and a meta-analysis of twenty-seven studies found MSH6 mutations in roughly seven percent of colorectal and nearly ten percent of endometrial cancer cases. Prior experimental work has shown that MSH6 also interacts with Ku70 to regulate non-homologous end joining of double-strand breaks, and that Msh6-deficient mice accumulate mutation frequencies up to five-fold higher than controls, particularly after ionizing radiation. Arsenic’s toxicological mechanism, meanwhile, is known to generate reactive oxygen species that inflict oxidative DNA damage, including 8-oxoG lesions that mismatch repair helps to process in cooperation with the SETD2 methyltransferase and the ATM signaling pathway.

The authors are careful to frame the findings as hypothesis-generating rather than conclusive. With only nine participants, no unexposed control group, and no matched tissue samples to distinguish somatic from germline variants, the study cannot establish a causal or dose-response relationship between arsenic burden and DNA repair gene mutation. Indeed, several women with equally severe arsenic exposure showed no detectable genomic alterations, hinting that individual genetic background, arsenic metabolism profiles and hormonal factors may shape who develops molecular damage. Sex-specific differences in arsenic methylation capacity, reflected in varying ratios of methylated metabolites, could help explain why women represent a potentially under-recognized high-risk group for environmentally driven cancers, including colorectal cancer, which the researchers identify as a particular concern in chronically exposed populations.

Even within those limits, the study’s integrated design, pairing multi-matrix toxicology with exome-wide sequencing, points toward a new model for environmental health surveillance. The detection of potentially pathogenic variants that conventional screening would miss underscores the value of genomic approaches in exposed communities, and the breast milk findings add an urgent transgenerational dimension, since arsenic has been shown in animal models to induce epigenetic alterations that can be inherited across generations. The research team calls for larger cohort studies incorporating matched controls, functional validation of the identified variants through mismatch repair assays, ATM kinase signaling measurements and CRISPR-based modeling, and exploration of epigenetic silencing in ATM and MSH6. If validated, these molecular markers could serve as early-warning biomarkers of arsenic-induced carcinogenesis, enabling targeted screening and precision public health interventions for the estimated ten million people in Bihar alone who live with poisoned groundwater, and millions more worldwide who share the same invisible exposure.

Beyond the immediate findings, the study sits within a broader epidemiological landscape. Chronic arsenic exposure through groundwater is estimated to affect well over one hundred million people worldwide, with South Asia bearing a disproportionate share of the burden. The metalloid is classified as a Group 1 human carcinogen, and epidemiological work across Bangladesh, India and parts of South America has linked prolonged exposure not only to cancers of the skin, bladder, lung and colorectum, but also to cardiovascular disease and reproductive toxicity. What distinguishes the present research is its attempt to move from population-level risk statistics toward the individual molecular events that may underlie them.

The choice of sequencing platform also merits attention. Unlike targeted gene panels, which interrogate a predefined set of loci, whole exome sequencing permits the discovery of rare, novel or compound variants that no a priori hypothesis would have flagged. It additionally opens the door to mutational signature analysis, in which distinctive patterns of base substitution can be matched to specific mutagenic processes, including the oxidative stress that arsenic is known to induce through reactive oxygen species generation. Such signatures, once validated, could serve as fingerprints of environmental carcinogenesis within a tumor or normal tissue genome.

The breast milk results carry particular weight for regional health policy. Arsenic is efficiently methylated in the body to mono- and dimethylated species, and interindividual variation in this metabolism is thought to influence both retention in tissues and excretion into milk. If lactational transfer proves to be a consistent pathway, interventions such as provision of arsenic-safe drinking water to nursing mothers, nutritional supplementation, and routine screening of breast milk in endemic districts could become practical priorities alongside existing water decontamination programs.

Ultimately, the work illustrates how environmental toxicology and clinical genomics can be woven together at small scale to generate testable hypotheses. Larger cohorts with matched unexposed controls, longitudinal sampling and functional assays will be needed to determine whether the DNA repair variants observed here are truly arsenic-driven, incidental, or markers of broader genomic instability in exposed communities.

Subject of Research: Whole exome sequencing of women chronically exposed to arsenic through contaminated groundwater to identify DNA repair gene variants

Article Title: Whole exome sequencing reveals DNA repair gene variants in women exposed to chronic arsenic poisoning

Article References: Agarwal, R., Kumar, A., Pandey, T., Verma, D., Kumar, K., Chayal, N. K., Ali, M., Srivastava, A., Verma, K. S., Kumar, D., Sharma, A., Singh, M., & Ghosh, A. K. (2026). Whole exome sequencing reveals DNA repair gene variants in women exposed to chronic arsenic poisoning. Discover Toxicology, 3(1), Article 15. https://doi.org/10.1007/s44339-026-00059-9

Image Credits: AI Generated

DOI: 10.1007/s44339-026-00059-9

Keywords: arsenic poisoning, whole exome sequencing, DNA repair genes, MSH6, ATM, groundwater contamination, breast milk arsenic, Bihar India, colorectal cancer risk, genotoxicity, mismatch repair, environmental health