Comprehensive epigenomic profiling reveals diagnostic and prognostic biomarkers in oral squamous cell carcinoma

Objective The number of patients with oral cancer is increasing, and despite advances in diagnostic techniques and the development of novel therapies, survival rates have not significantly improved. Therefore, innovative approaches that serve as potential therapeutic targets and diagnostic markers are required. The epigenome plays a critical role in maintaining cellular homeostasis and regulating the expression of genes associated with cancer. Among epigenetic mechanisms, super-enhancers (SEs) are key regulatory regions that drive gene expression. However, the epigenomic landscape of oral squamous cell carcinoma (OSCC) remains relatively underexplored compared with that of other carcinomas. Methods In this study, we performed ChIP-seq analysis of histone H3 lysine 27 acetylation (H3K27ac) in OSCC cell lines to identify SE regions. The Cancer Genome Atlas (TCGA) datasets of head and neck cancer (HNC) were analyzed to examine the clinical samples. Results We detected several coding genes and non-coding RNAs that were potentially regulated by SEs. Furthermore, we identified SE-controlled genomic regions that are specific to OSCC by integrating genome-wide expression analyses. Analysis of the TCGA dataset revealed that several of these genes were upregulated in tumors and were associated with the prognosis of patients Conclusions Collectively, our findings demonstrate that ChIP-seq analysis combined with public database validation provides a novel strategy for identifying potential diagnostic markers in OSCC.