Histone methyl-transferase G9a inhibition boosts the efficacy of immune checkpoint inhibitors in experimental hepatocellular carcinoma

Immune checkpoint inhibitors (ICIs) have improved cancer therapy, but their efficacy in hepatocellular carcinoma (HCC) remains limited, partly associated with tumor-intrinsic mechanisms of immune evasion. To investigate potential epigenetic drivers of immune resistance, this study evaluated transcriptional changes following pharmacological inhibition of the histone methyltransferase G9a (EHMT2). Bulk RNA sequencing was performed on the murine NM53 and human PLC/PRF/5 HCC cell lines treated with G9a inhibitors. NM53 cells were treated with CM272 with or without interferon gamma (IFN-gamma), and PLC/PRF/5 cells were treated with EZM8266. Gene-level expression was quantified for both cell lines, and transposable element (TE) family-level expression was quantified for NM53 samples. Overall design: Bulk RNA sequencing was performed on the NM53 mouse hepatocellular carcinoma (HCC) cell line, derived from MYC-driven tumors, and the human HCC cell line PLC/PRF/5. NM53 cells were treated with the epigenetic inhibitor CM272 (400 nM, 24 h), followed by IFN-gamma (75 U/mL, 24 h) or vehicle control. PLC/PRF/5 cells were treated with EZM8266 (5 uM, 48 h) or vehicle control. Three technical replicates were generated for each condition.