Chemicals used in everyday products—ranging from food preservatives and dyes to pesticides, cosmetics, and industrial materials—are increasingly recognized for their role in a wide spectrum of health issues. These include cancer, hormonal imbalances, neurological disorders, skin conditions, and occupational toxicities. Many of these compounds are known to induce carcinogenesis either by directly damaging DNA (genotoxicity) or by altering gene expression through epigenetic modifications—heritable, reversible changes to DNA and chromatin that do not involve mutations.

While traditional genotoxicity assays can detect DNA damage and mutations, they fall short in capturing the epigenetic impacts of chemical exposure. Current methods to study epigenetic changes, such as DNA methylation or histone modification profiling, rely heavily on advanced sequencing technologies. These methods, while powerful, are expensive, time-consuming, and require specialized expertise—limiting their use in widespread safety testing, particularly in low-resource settings.

To bridge this gap, a team of researchers from Chiba University and the National Institute of Health Sciences, Japan, led by Associate Professor Akira Sassa, Professor Kiyoe Ura, Manabu Yasui, and Kei-ichi Sugiyama, have developed a novel and practical alternative: the epi-TK reporter assay. Their findings, published in Scientific Reports on March 5, 2025, introduce a cost-effective, cell-based, bidirectional assay capable of quantifying epigenetic changes caused by chemical exposure.

Building on the well-established thymidine kinase gene mutation assay, the team engineered a version with site-specific methylation of the TK promoter, enabling detection of both gene silencing and reactivation. This improved assay accurately reflects global epigenetic changes by tracking the expansion of revertant cell colonies following chemical treatment.

The researchers validated the assay using known DNA methyltransferase (DNMT) inhibitors, which caused demethylation and reactivation of the TK gene. Interestingly, they also tested 12-O-tetradecanoylphorbol-13-acetate, a non-genotoxic carcinogen, which led to a reduction in gene reactivation and histone acetylation, demonstrating the assay’s ability to detect epigenetic suppression.

Unlike sequencing-based approaches, the epi-TK assay is simpler, faster, and more affordable, making it a valuable tool for screening environmental, pharmaceutical, and industrial chemicals for epigenetic toxicity. As Assoc. Prof. Sassa notes, Mastering epigenetic analysis has traditionally been costly and complex. Our goal was to develop a universally accessible assay to support safer chemical usage worldwide, including in developing countries.

This innovative approach could revolutionize chemical safety assessments by providing a practical solution for detecting epigenetic toxicity, potentially guiding regulations and reducing exposure to harmful compounds in daily life.

Source: https://www.chiba-u.ac.jp/e/news/research/simple_and_cost-effective_reporter_assay_for_evaluating_chemical-induced_epigenetic_changes.html