Japanese scientists develop affordable test detecting epigenetic changes from environmental toxins

A team of researchers at Chiba University in Japan has created a simple cell-based reporter tool to detect epigenetic alterations caused by environmental chemicals. Unlike traditional methods that rely on costly sequencing, this new cost-effective “epi-TK” assay evaluates gene expression changes by tracking methylation and acetylation at a key gene site. 

Where traditional sequencing techniques often require complex equipment and training, this new test offers a practical way to evaluate the long-term safety of substances used in food, agriculture, and other industries.

Enhancing current safety assessments, this method pinpoints gene activation and silencing effects from carcinogenic compounds, offering a practical solution for widespread use, especially in developing countries.

“Our research can enhance the understanding of the impact of chemicals on public health and disease prevention, thereby promoting safer management and use of chemicals,” says associate professor Akira Sassa of the study.

“Understanding the relationship between environmental chemicals and diseases and improving chemical safety evaluations can aid the implementation of measures to reduce the exposure to harmful chemicals in both work and living environments.”

Health hazards from everyday items

Chemicals used as food preservatives, flavoring agents, dyes, pesticides, cosmetics, cleaners, and other industrial materials are increasingly recognized as health hazards. Their widespread use has increased the prevalence of various chemical toxicity-induced diseases, including hormonal disruption, cancer, neurological disorders, skin conditions, and occupational poisoning.

Genotoxicity assays help assess the effect of potential carcinogens on epigenetic changes.Numerous chemicals are known to trigger “carcinogenesis” or cancer development by exerting genotoxic effects (direct or indirect interference with DNA replication and damage repair processes resulting in mutations and chromosomal aberrations).

Genotoxicity assays help assess the effect of potential carcinogens on epigenetic changes — subtle shifts in gene activity that don’t alter the DNA sequence itself but can still influence disease risk.

“In addition to genotoxicity, epigenetic alterations — reversible changes to DNA and chromatin (packaged DNA-protein complexes) — have been implicated in chemically induced carcinogenesis,” highlights the Chiba University research team.

“Typically, DNA methylation (the addition of methyl groups to DNA) silences gene expression. Conversely, acetylation (the addition of acetyl groups) of histones, the proteins that bind DNA, opens up the chromatin structure, making DNA accessible for transcription.”

These dynamic epigenetic alterations in DNA and histones regulate gene expression in a cell- and tissue-specific manner, note the researchers.

“Notably, environmental chemicals such as bisphenol A, arsenic, cadmium, benzene, pesticides, and other carcinogens have been reported to induce aberrant epigenetic changes in various diseases,” they warn.

Unraveling mechanisms of environmental toxins

Scientists assess how chemicals might impact our health over time, observing how the gene’s activity changes — whether it becomes more active or switches off.

Previously, researchers designed cell-based assays to detect epigenetic changes in a unidirectional manner (inactivation/reactivation of gene expression) based on the baseline status of the reporter gene. This did not capture the full picture of chemical-induced epigenetic alterations.

A flexible, bidirectional assay needed to be developed to effectively detect diverse epigenetic impacts of chemical exposure in human cells.

“In the field of genome biology, mastering epigenetic analysis techniques is both challenging and costly, making it difficult to use in the safety assessment of chemicals,” explains Sassa.

“This led us to consider developing a universally accessible method through collaborative research across academia, industry, and government. Elucidation of previously unknown epigenetic mechanisms of chemical carcinogenesis can aid safer chemical use worldwide, including in developing countries.”

The thymidine kinase (TK) gene mutation test is a standard lab tool used to detect DNA mutations. The TK gene is active in all cell types, making it useful for assessing chemical safety.

The Chiba University team developed a new “epi-TK” version of the test that can also detect epigenetic changes. They modified the gene’s on-off switch, exposing the cells to specific chemicals. They did this by adding methyl groups to the TK gene’s control region and observing how cells responded to certain chemical treatments.

When treated with DNA methylation inhibitors, cells showed more active TK genes and formed colonies, indicating gene reactivation. In contrast, a known non-genotoxic chemical, TPA, reduced both gene activity and histone acetylation, showing the assay can pick up both gene activation and silencing.

Unlike traditional methods that require complex equipment and expertise, this new assay offers a simpler and more affordable way to study how chemicals may influence long-term health through epigenetic mechanisms.