RNA-seq and ATAC-seq analysis of 5-azacytidine-treated HepG2 cells reveals epigenetic reactivation of BFL-1 and SQOR in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) remains a major therapeutic challenge with poor prognosis due to treatment resistance. Epigenetic silencing of tumor suppressor genes through promoter hypermethylation contributes to oncogenesis and resistance to cell death stimuli. We employed low-concentration 5-azacytidine (5-AZA) treatment to identify epigenetically silenced genes that modulate cell death susceptibility in HepG2 hepatocellular carcinoma cells without inducing baseline cytotoxicity. HepG2 cells were treated with 0, 2, and 10 μM 5-azacytidine for 4 days, followed by integrative RNA-seq and ATAC-seq analysis to characterize transcriptomic changes and chromatin accessibility patterns. This approach revealed coordinated promoter opening and transcriptional reactivation of methylation-silenced genes, particularly BFL-1 (BCL2A1) and SQOR, whose reactivation enhanced cell death susceptibility to TNF-α/CHX and sorafenib treatments. Our findings provide mechanistic insights into epigenetic vulnerabilities in HCC and demonstrate the utility of multi-omics approaches for identifying therapeutically tractable targets for precision epigenetic editing strategies.