Tumor hepatitis B virus RNA identifies a clinically and molecularly distinct subset of hepatocellular carcinoma

Hepatitis B virus (HBV) infection contributes to hepatocellular carcinoma (HCC) initiation and is associated with worse outcomes. Many prior studies of HBV-related HCC have not accounted for potential heterogeneity among HBV-related tumors by assessing whether HBV activity is present in tumor tissue. Here, we measured tumor HBV RNA, a proxy for viral activity, and investigated the association between HBV RNA status and several clinicogenomic characteristics. We obtained clinical, mutation, RNA-Seq and survival data for 439 HCC tumors from The Cancer Genome Atlas and International Cancer Genome Consortium. Tumors were classified as HBV RNA positive if they harbored >1 HBV RNA read per million human reads. We investigated the association between HBV RNA status and nonsynonymous somatic mutations, gene set expression, homologous recombination deficiency (HRD) score and mutation-specific survival. HBV RNA positive status was associated with higher nonsynonymous mutation rates of multiple genes, including TP53 and CDKN2A, while HBV RNA negative status was associated with higher nonsynonymous BAP1 mutation rate. HBV RNA positive status was also associated with increased transcription of genes involved in multiple DNA damage repair pathways, genes upregulated by MYC and mTORC1, and genes overexpressed in several HCC subclasses associated with a proliferative phenotype. Further, HBV RNA positive status was associated with increased three-biomarker HRD score (22.2 for HBV RNA+ vs. 16.0 for HBV RNA-). Finally, HBV RNA status was associated with multiple mutation-specific survival differences, including decreased survival for HBV RNA positive patients with nonsynonymous KEAP1 mutations compared to those without (hazard ratio 4.26). HCC tumors harboring genomic evidence of HBV activity therefore constitute a distinct HCC subset characterized by specific differences in nonsynonymous mutations, gene set expression, three-biomarker HRD score and mutation-specific survival. Author summary Hepatocellular carcinoma, the most common type of liver cancer, is the second leading cause of cancer death worldwide and is most commonly caused by hepatitis B virus infection. Currently, scientists have an incomplete understanding of the genomic basis of hepatocellular carcinoma associated with hepatitis B virus infection, because prior studies have been limited by imprecision in assessing hepatitis B virus infection status and heterogeneity in hepatitis B virus activity levels in liver tumors. This has limited scientists' ability to devise new diagnostic and therapeutic options for hepatocellular carcinoma. In this study, we used computational genomics to directly measure hepatitis B virus RNA levels and activity in a large dataset of hepatocellular carcinoma tumors, and found that tumors with measurable hepatitis B virus activity are associated with a specific set of clinical and genomic characteristics. These characteristics have not previously been reported and harbor implications for future clinical and genomics research in hepatocellular carcinoma, as well as computational genomics efforts in other cancer types.