Single-Cell Sequencing Identifies the Heterogeneity of CD8+ T Cells and Novel Biomarker Genes in Hepatocellular Carcinoma.

Abstract

CD8+ T cells are required for the establishment of antitumor immunity, and their substantial infiltration is associated with a good prognosis. However, CD8+ T cell subsets in the tumor microenvironment may play distinct roles in tumor progression, prognosis, and immunotherapy. In this study, we used the scRNA-seq data of hepatocellular carcinoma (HCC) to reveal the heterogeneity of different CD8+ T cell subsets. The scRNA-seq data set GSE149614 was obtained from the GEO database, and the transcriptome and sample phenotypic data of TCGA-LIHC were obtained from the TCGA database. CD8+ T cell subtypes and metabolic gene sets were obtained from published reports. The data processing and analysis of CD8+ T cell groups was performed by R language. The PPI network was constructed to obtain the hub genes, and the KM survival curve of the hub genes was further plotted to determine the hub genes with differences in survival. CD8+ T cells in HCC were divided into 7 subsets, and the cytotoxic CD8 T cells 4 subset showed considerable differences between the TP53-mutant and nonmutant groups, as well as between different degrees of cirrhosis, HCC grades, stages, ages, and body weights. Cytotoxic CD8 T cells 4 differential genes were analyzed by TCGA-LIHC data and single-cell sequencing data set. 10 hub genes were found: FGA, ApoA1, ApoH, AHSG, FGB, HP, TTR, TF, HPX, and APOC3. Different subsets of CD8+ T cells were found to contribute to heterogeneous prognosis and pathway activity in HCC. Alterations in the cytotoxic and immune checkpoint gene expression during CD8+ T cell differentiation were also identified. We found that cytotoxic CD8 T cells 4 is closely associated with survival and prognosis of HCC and identified four differential genes that can be used as biological markers for survival, prognosis, and clinically relevant characteristics of HCC. Results of this study could help finding targets for immunotherapy of HCC and aid in the accelerated development of immunotherapy for HCC.