Citation:

Carswell, G., J. Chamberlin, B. Bennett, P. Bushel, AND B. Chorley. Persistent gene expression and DNA methylation alterations linked to carcinogenic effects of dichloroacetic acid. Frontiers in Oncology. Frontiers, Lausanne, Switzerland, 14:1389634, (2024). https://doi.org/10.3389/fonc.2024.1389634

Impact/Purpose:

The manuscript describes the results of an archived rodent case study demonstrating the value of genomic and epigenomic measures to help establish the mechanism of early-life non-genotoxic carcinogenic exposures. This study is latest of a series of EPA-funded publications on the water disinfection byproduct, dichloroacetic acid (DCA), that dates back to the late 1980's and most recently 2022 on describing the mechanism of action of rodent liver tumorigenesis of this environmental compound. Relevance to Agency to help establish biomarkers of effect for chemical screening hazard ID and also relevance to human health risk assessment to identify key events of tumorigenesis linked to early-life exposures. The use of archived rodent tissues to measure DNA methylation alterations is also novel to the Agency and could be utilized in future studies using biobanked tissue samples.  Early-life environmental factors can influence later-life susceptibility to cancer. Previously, we showed that exposure to water disinfection byproduct, dichloroacetic acid (DCA), increased liver cancer in mice following transient early life exposure. Earlier studies did not support direct cytotoxic, mitogenic, or genotoxic modes of action. Here, we proposed that prior DCA exposure mediates carcinogenic activity through persistent epigenetic effects.

Description:

Background: Mechanistic understanding of transient exposures that lead to adverse health outcomes will enhance our ability to recognize biological signatures of disease. Here, we measured the transcriptomic and epigenomic alterations due to exposure to the metabolic reprogramming agent, dichloroacetic acid (DCA). Previously, we showed that exposure to DCA increased liver tumor incidence in B6C3F1 mice after continuous or early life exposures significantly over background level. Methods: Using archived formalin-fixed liver samples, we utilized modern methodologies to measure gene expression and DNA methylation levels to link to previously generated phenotypic measures. Gene expression was measured by targeted RNA sequencing (TempO-seq 1500+ toxicity panel: 2754 total genes) in liver samples collected from 10-, 32-, 57-, and 78-week old mice exposed to deionized water (controls), 3.5 g/L DCA continuously in drinking water (“Direct” group), or DCA for 10-, 32-, or 57-weeks followed by deionized water until sample collection (“Stop” groups). Genome-scaled alterations in DNA methylation were measured by Reduced Representation Bisulfite Sequencing (RRBS) in 78-week liver samples for control, Direct, 10-week Stop DCA exposed mice.   Results: Transcriptomic changes were most robust with concurrent or adjacent timepoints after exposure was withdrawn. We observed a similar pattern with DNA methylation alterations where we noted attenuated differentially methylated regions (DMRs) in the 10-week Stop DCA exposure groups compared to the Direct group at 78-weeks. Gene pathway analysis indicated cellular effects linked to increased oxidative metabolism, a primary mechanism of action for DCA, closer to exposure windows especially early in life. Conversely, many gene signatures and pathways reversed patterns later in life and reflected more pro-tumorigenic patterns for both current and prior DCA exposures. DNA methylation patterns correlated to early gene pathway perturbations, such as cellular signaling, regulation and metabolism, suggesting persistence in the epigenome and possible regulatory effects.   Conclusion: Liver metabolic reprogramming effects of DCA interacted with normal age mechanisms, increasing tumor burden with both continuous and prior DCA exposure in the male B6C3F1 rodent model.  

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