Inhibition of EZH2 restores normal expression of genes associated with cysteine metabolism and ferroptosis in hepatocellular carcinoma [CUT&Tag]

Epigenetic dysregulation is closely associated with the pathogenesis of hepatocellular carcinoma (HCC). Enhancer of zeste homolog 2 (EZH2) is a key protein involved in the exacerbation of various cancers, including HCC. Despite several clinical trials of epigenetic therapies targeting EZH2, the mechanisms underlying EZH2-mediated gene suppression in HCC are not fully understood. In this study, we investigated EZH2-mediated transcriptional programs under EZH2-selective inhibition through an integrative analysis of epigenomic (ATAC-seq) and transcriptomic (RNA-seq) approaches. To determine the impact of EZH2 dysfunction, we measured the levels of H3K27me3 and EZH2 expression using flow cytometry and reverse transcription quantitative real-time PCR (RT-qPCR), respectively. Notably, we found that higher expression of EZH2 was significantly correlated with poorer survival among HCC patients by reanalyzing transcriptomes in the cancer genome atlas (TCGA). Inhibition of EZH2 with Tazemetostat (EPZ-6438), a selective inhibitor of EZH2, showed that EZH2 regulates genes involved in lipid homeostasis, and cysteine-methionine metabolism. Among the 13 EZH2 target genes identified by transcriptomic and epigenomic profiling, we selected BHMT and CDO1, which were significantly associated with poor survival in HCC patients. When HCC cells were treated with Tazemetostat, the expression levels of the BHMT and CDO1 genes increased, while the expression levels of ferroptosis marker genes, such as FSP1, NFS1, and SLC7A11, decreased. This suggests that inhibiting EZH2 may have potential therapeutic benefits in HCC by regulating the expression of genes involved in important biological processes. Our study suggests that EZH2 epigenetically regulates ferroptosis by controlling cysteine metabolism in HCC.