code_and_files_for_fig.zip

Hepatocellular Carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. HCC morbidity is the highest in individuals with chronic liver diseases (CLDs); however, the effects of cell composition on the progression of CLDs to HCC remains unknown. Using gene biomarkers of 20 distinct cell types derived from healthy liver single cell RNA-seq (scRNA-seq) data, we estimated the cell compositions of a total of six CLDs and HCC based on their RNA-seq profiles. We observed distinct changes of normal cell type enrichment landscape among liver fibrosis, non-alcoholic fatty liver disease, and HCC. Compared to the healthy state, liver fibrosis and HCC present higher enrichment of γδ2 T cells and lower enrichment of central venous liver sinusoidal endothelial cells. High enrichment of γδ2 T cells was strongly predominant in HCC with underlying chronic hepatitis B or C virus infections, as well as in advanced HCC, and was associated with poor prognosis in the patients with higher alpha-fetoprotein level or with underlying virus infection. The enrichment scores of γδ2 T cells remarkably classified dysplastic nodules, early-stage HCC and advanced stage HCC from the healthy state (AUC: 0.87, 0.89, 0.98, respectively). Immunofluorescence staining of liver tissues confirmed a monotonic elevation of γδ2 T cells from healthy, inflammation, cirrhosis to HCC. Furthermore, fluorescence-activated cell sorting of PBMC samples revealed that more than 45% of HCC patients presented abnormal elevated level of γδ2 T cells circulating in the blood. Together, we identified γδ2 T cells as a potential marker in HCC development.<b></b>