Chromatin accessibility module identified by single-cell sequencing underlies the diagnosis and prognosis of hepatocellular carcinoma

BACKGROUND Hepatocellular carcinoma (HCC) is notorious for its aggressive progression and dismal prognosis, with chromatin accessibility dynamics emerging as pivotal yet poorly understood drivers. AIM To dissect how multilayered chromatin regulation sustains oncogenic transcription and tumor-stroma crosstalk in HCC, we combined multiomics single cell analysis. METHODS We integrated single-cell RNA sequencing and paired single-cell assay for transposase-accessible chromatin with sequencing data of HCC samples, complemented by bulk RNA sequencing validation across The Cancer Genome Atlas, Liver Cancer Institute, and GSE25907 cohorts. Cell type-specific chromatin architectures were resolved via ArchR, with regulatory hubs identified through peak-to-gene linkages and coaccessibility networks. Functional validation employed A485-mediated histone 3 lysine 27 acetylation suppression and small interfering RNA targeting DGAT1 . RESULTS Malignant hepatocytes exhibited expanded chromatin accessibility profiles, characterized by increased numbers of accessible peaks and larger physical regions despite reduced peak intensity. Enhancer-like peaks enriched in malignant regulation, forming long-range hubs. Eighteen enhancer-like peak-related genes showed tumor-specific overexpression and diagnostic accuracy, correlating with poor prognosis. Intercellular coaccessibility analysis revealed tumor-stroma symbiosis via shared chromatin states. Pharmacological histone 3 lysine 27 acetylation inhibition paradoxically downregulated DGAT1 , the hub gene most strongly regulated by chromatin accessibility. DGAT1 knockdown suppressed cell proliferation. CONCLUSION Multilayered chromatin reprogramming sustains HCC progression through tumor-stroma crosstalk and DGAT1 -related oncogenic transcription, defining targetable epigenetic vulnerabilities.