Identification of an epigenetic classification for hepatocellular carcinoma and biological relevance with cancer cells

Abstract Background: Hepatocellular carcinoma (HCC) is an extensive heterogeneous disease where epigenetic factors contribute to its pathogenesis. Polycomb group (PcG) proteins are a group of subunits constituting various macro molecular machines to regulate the epigenetic landscape, which contribute to cancer phenotype and have potential to develop molecular classification of HCC. Results: Here, based on multi-omics data analysis of DNA methylation, mRNA expression and copy number of PcG-related genes, we established an epigenetic classification system of HCC, which divides the HCC patients into two subgroups with a significantly different outcome. Comparing these two epigenetic subgroups, we identified different metabolic features, which were related to epigenetic regulation of Polycomb Repressive Complex 1/2 (PRC1/2). Furthermore, we experimentally proved that inhibition of PcG complexes enhanced lipid metabolism and reduced the capacity of HCC cells against glucose shortage. In addition, we validated the low chemotherapy sensitivity of HCC in Group A, and found inhibition of PRC1/2 promoted HCC cells sensitivity to oxaliplatin in vitro and in vivo. Finally, we found that aberrant upregulation CBX2 in Group A and upregulation of CBX2 was associated with poor prognosis in HCC patients. Furthermore, we found manipulation of CBX2 affected the levels of H3K27me3 and H2AK119ub. Conclusions: Our study provided a novel molecular classification system based on PcG-related genes data, and experimentally validated the biological features of HCC in two subgroups. Our founding supported the polycomb complex targeting strategy to inhibit HCC progression where CBX2 could be a feasible therapeutic target.