Viral-Track integrated single-cell RNA-sequencing reveals HBV lymphotropism and immunosuppressive microenvironment in HBV-associated hepatocellular carcinoma

The tumor microenvironment (TME) is a crucial mediator of tumor progression and treatment response. Here, we compare the immune microenvironments of HBV and non-HBV-HCC and investigate the reason for the persistence of HBV infection in the liver. We combine the Viral-Track method with single-cell RNA sequencing and profile the transcriptomes of 71,466 cells from HBV and non-HBV-HCC patients. In addition to hepatocytes and macrophages, HBV transcripts were also detected in T and B cells using the Viral-Track method, confirming the HBV-lymphotropic nature for the first time in scRNA-sequencing data. HBV-HCC tumors have reduced levels of CD4+ Tregs, NK, macrophages, dendritic cells (DCs), and increased malignant hepatocytes compared with non-HBV tumors. Notably, we explicitly reported the enrichment of metallothioneins (MTs), particularly MT1G expression in HBV-related HCC TAMs, which was associated with a worse prognosis. HBV-tumor-infiltrated CD8+ T cells exhibited a cytotoxic dysfunctional T cell phenotype, characterized by upregulated MDK and CTLA4 expression and reduced IFN-γ production, unlike the non-HBV-HCC. Additionally, HBV-HCC exhibited immunosuppressive ligand-receptor interactions, whereas non-HBV-HCC exhibited antitumor ligand-receptor interactions. Our comprehensive understanding of the HBV HCC ecosystem by viral-track integrated scRNA sequencing analysis provides deeper insights into immune evasion mechanisms and HBV lymphotropism associated with viral persistence.