Integrated RNA-seq and ATAC-seq profiling for assessing chemically induced inflammatory responses in human TK6 cells

Abstract Background Chemical exposure can exert biological effects not only through genetic alterations but also by changing gene regulation and chromatin states. Inflammation is a key cellular response to diverse chemical stresses, and immune cells control activation and inflammatory gene programs through dynamic chromatin remodeling; moreover, chronic inflammation and immunosuppression are recognized key characteristics of carcinogens. However, how chemically induced transcriptional responses are coordinated with changes in chromatin accessibility remains incompletely understood. Here, we investigated whether integrating transcriptomic and chromatin accessibility profiling could provide a molecular framework for assessing chemically induced inflammatory responses. To do so, human TK6 cells, an immune-lineage cell line widely used in regulatory genotoxicity testing, were exposed for 24h to the non-genotoxic tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA), allowed to recover for up to 7 days before being analyzed by RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq). Results TPA induced time-dependent transcriptional changes that persisted after chemical removal. Upregulated genes were enriched in immune- and inflammation-related processes, including leukocyte and lymphocyte activation and cytokine production. ATAC-seq revealed extensive chromatin remodeling that increased progressively during the post-exposure period: the total number of differentially accessible regions rose from 6,488 immediately after exposure to 11,364 and 12,710 on Days 3 and 7, respectively. Integrated RNA-seq and ATAC-seq analysis showed that the proportion of upregulated genes accompanied by increased chromatin accessibility rose from 32.7% on Day 0 to 50.1% and 46.3% on Days 3 and 7, respectively. Concordance among downregulated genes increased more markedly, from 8.7% on Day 0 to 26.1% on Day 3 and 39.6% on Day 7. Concordant changes included inflammation-related genes associated with susceptibility to human disease, including TNFSF4, CSF2, and SELL. Conclusions These findings show that TPA induces sustained transcriptional and chromatin states that continue to remodel after chemical removal. Integrated RNA-seq and ATAC-seq profiling identifies coordinated molecular responses that transcriptomic analysis alone does not capture. These concordant RNA–ATAC changes, particularly at disease-associated inflammatory genes, may provide candidate molecular indicators for mechanistically informed assessment of chemically induced inflammatory and non-genotoxic effects.