Comprehensive Analysis and Drug Modulation of Human Endogenous Retrovirus in Hepatocellular Carcinomas

SIMPLE SUMMARY: Human endogenous retrovirus (HERV) plays important roles in the development of cancer, and most studies use data from The Cancer Genome Atlas to analyze the whole HERV alterations in cancer cells. For HCCs, most studies have focused on LINE-1 and specific HERVs to explore their importance. In this study, we used our total RNA sequencing data from 254 Taiwanese HCCs and many bioinformatic tools to analyze HERV alterations, and then explored the correlations between HERV activation and pathways and certain gene panels. Unique pathways for a higher expression of survival-related HERVs including immunity and infection, lipid and atherosclerosis, MAPK and NF-kB signaling, and cytokine-cytokine receptor interaction pathways were activated; the mRNA surveillance pathway, nucleocytoplasmic transport, ribosome biogenesis, and transcriptional misregulation in cancer pathways were suppressed. We found that many overexpressed HERV-related nearby genes were correlated with high HERV activation and poor survival. The implementation of comprehensive and integrated approaches to assess HERV expression and their association with specific pathways is poised to offer novel companion diagnostics and therapeutic strategies for HCC. ABSTRACT: Background: Human endogenous retroviruses (HERVs) play an important role in the development of cancer and many diseases. Here, we comprehensively explored the impact of HERVs on hepatocellular carcinomas (HCCs). Methods: We employed Telescope to identify HERVs and quantify their expression in the total RNA sequencing data obtained from 254 HCC samples, comprising 254 tumor tissues and 34 matched normal tissues. Results: In total, 3357 locus-specific activations of HERVs were differentially expressed, and 180 were correlated with patient survival. Using these 180 HERVs for classification, we found four subgroups with survival correlation. Higher expression levels of the 180 HERVs were correlated with poorer survival, while age, AFP, some mutations, and copy and structural variants differed among subgroups. The differential expression of host genes in high expression of these 180 HERVs primarily involved the activation of pathways related to immunity and infection, lipid and atherosclerosis, MAPK and NF-kB signaling, and cytokine–cytokine receptor interactions. Conversely, there was a suppression of pathways associated with RNA processing, including nucleocytoplasmic transport, surveillance and ribosome biogenesis, and transcriptional misregulation in cancer pathways. Almost all genes involved in HERV activation restriction, KRAB zinc finger proteins, RNA nucleocytoplasmic transport, stemness, HLA and antigen processing and presentation, and immune checkpoints were overexpressed in cancerous tissues, and many over-expressed HERV-related nearby genes were correlated with high HERV activation and poor survival. Twenty-three immune and stromal cells showed higher expression in non-cancerous than cancerous tissues, and seven were correlated with HERV activation. Small-molecule modulation of alternative splicing (AS) altered the expression of survival-related HERVs and their activation-related genes, as well as nearby genes. Conclusion: Comprehensive and integrated approaches for evaluating HERV expression and their correlation with specific pathways have the potential to provide new companion diagnostics and therapeutic strategies for HCC.