GPNMB+Gal‐3+ hepatic parenchymal cells promote immunosuppression and hepatocellular carcinogenesis

Hepatocellular carcinoma (HCC) formation is a multi‐step pathological process that involves evolution of a heterogeneous immunosuppressive tumor microenvironment. However, the specific cell populations involved and their origins and contribution to HCC development remain largely unknown. Here, comprehensive single‐cell transcriptome sequencing was applied to profile rat models of toxin‐induced liver tumorigenesis and HCC patients. Specifically, we identified three populations of hepatic parenchymal cells emerging during HCC progression, termed metabolic hepatocytes (HCMeta), Epcam+ population with differentiation potential (EP+Diff) and immunosuppressive malignant transformation subset (MTImmu). These distinct subpopulations form an oncogenic trajectory depicting a dynamic landscape of hepatocarcinogenesis, with signature genes reflecting the transition from EP+Diff to MTImmu. Importantly, GPNMB+Gal‐3+ MTImmu cells exhibit both malignant and immunosuppressive properties. Moreover, SOX18 is required for the generation and malignant transformation of GPNMB+Gal‐3+ MTImmu cells. Enrichment of the GPNMB+Gal‐3+ MTImmu subset was found to be associated with poor prognosis and a higher rate of recurrence in patients. Collectively, we unraveled the single‐cell HCC progression atlas and uncovered GPNMB+Gal‐3+ parenchymal cells as a major subset contributing to the immunosuppressive microenvironment thus malignance in HCC. Synopsis Malignant transformation is the major driver of liver cancer, but the molecular and cellular bases for its induction remain poorly understood. Here, in‐depth profiling of hepatocellular carcinoma (HCC) initiation and progression defines new molecular markers involved and emerging malignant cell populations counteracting immune surveillance. Longitudinal single‐cell RNA‐sequencing of toxin‐induced liver tumorigenesis in rats reveals a dynamic composition and transformation of hepatic parenchymal cells. Complementary analyses of four HCC patients show conservation of HCC cell dynamics. GPNMB+Gal‐3+ parenchymal cells arise from EPCAM+ cells during HCC progression and exhibit immunosuppressive and malignant properties in vivo. The transcription factor SOX18 is required for the GPNMB+Gal‐3+ cell stemness and immunosuppressive capacity. Enrichment of GPNMB+Gal‐3+ cells is associated with poor prognosis in HCC patients. Longitudinal single‐cell profiling of liver cancer in rats and patients unveils an emerging aggressive parenchymal cell populati