Hepatitis B virus compartmentalization and single-cell differentiation in hepatocellular carcinoma

Abstract

Chronic hepatitis B virus (HBV) infection is a major cause of hepatocellular carcinoma (HCC) world-wide. The molecular mechanisms of viral hepatocarcinogenesis are still partially understood. Here, we applied two complementary single-cell RNA-sequencing protocols to investigate HBV–HCC host cell interactions at the single cell level of patient-derived HCC. Computational analyses revealed a marked HCC heterogeneity with a robust and significant correlation between HBV reads and cancer cell differentiation. Viral reads significantly correlated with the expression of HBV-dependency factors such as HLF in different tumor compartments. Analyses of virus-induced host responses identified previously undiscovered pathways mediating viral carcinogenesis, such as E2F- and MYC targets as well as adipogenesis. Mapping of fused HBV–host cell transcripts allowed the characterization of integration sites in individual cancer cells. Collectively, single-cell RNA-Seq unravels heterogeneity and compartmentalization of both, virus and cancer identifying new candidate pathways for viral hepatocarcinogenesis. The perturbation of pro-carcinogenic gene expression even at low HBV levels highlights the need of HBV cure to eliminate HCC risk.

Novel insights into HBV‐hepatocellular carcinoma at single‐cell sequencing

“…The critical role of HBV in ITH was also reflected in the interaction with the host cells. A prominent link between HBV reads and tumor cell differentiation has been noticed by a study that employed two complementary single‐cell RNA sequencing approaches 104 . Copy number alteration (CNA) due to genomic instability is another dominant contributor to ITH 105 .…”

Single-Cell Transcriptomics of Liver Cancer: Hype or Insights?

“…The previous reports are summarized in Table 1 . 2 , 3 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 The samples in these reports consisted mostly of cells from primary tumors, while circulating tumor cells were studied in a few reports. 15 , 16 In brief, scRNA-seq has been reported to allow delineation of cell type abundance, cell-cell interactions, transition in cellular status, clonal evolution, heterogeneity landscape, and lineage hierarchy in terms of marker gene expression, mutation and inferred copy number variation (CNV) status, and gene expression profiling at single-cell resolution ( Figure 3 ).…”

“…In another study, 17 by modified CEL-Seq2 platform, 938 single cells (including 420 HCC cells) of 2 HCC patients with chronic hepatitis B virus (HBV) infection were analyzed. The complementary scRNA-seq platform Smart-Seq2 was also applied to intensely cover the full-length RNA-transcripts.…”

Unraveling the Complexity of Liver Disease One Cell at a Time

“…A small study quantifying viral reads in HBV-induced HCC determined that viral read expression was correlated with the degree of hepatocyte differentiation and activation of downstream pathways associated with adipogenesis and cell stemness. 81 A more comprehensive analysis, in a large cohort of patient-derived tumor and matched adjacent tissue, is needed to further elucidate the impact of HBV infection on hepatocyte function and oncogenesis.…”