Single-cell RNA-sequencing analyses identify heterogeneity of CD8 T cell subpopulations and novel therapy targets in melanoma.

CD8 T cells are crucial to establish antitumor immunity, and their high infiltration associates with favorable prognoses. However, several CD8 T cell subpopulations in the tumor microenvironment may play different roles in prognosis, progression, and immunotherapy. Here, we analyzed prior published single-cell RNA-sequencing (scRNA-seq) melanoma data to explore the heterogeneity of CD8 T cell subpopulations and identified 7 major subpopulations. We found that high infiltration of exhausted CD8 T cell subpopulation 2 would contribute to unfavorable prognoses. In contrast, a large proportion of naive/memory cells and cytotoxic CD8 T cell subpopulation 3 would lead to favorable prognoses. Notably, the proportion of the cytotoxic CD8 T cell subpopulation 3 would decrease in later-stage melanoma samples, while that of the exhausted CD8 T cell subpopulation 2 would increase. We also found that high abnormal activities of metabolic pathways existed in exhausted CD8 T cell subpopulation 1. Significantly, immunosuppressive checkpoints PD-1 and CTLA-4 signaling pathways were upregulated in exhausted CD8 T cell subpopulations. In addition, a dynamic transcript landscape of immune checkpoints among different subpopulations was also depicted in this study. Moreover, we identified three overexpressed genes (, , and ) that were significantly correlated to poor prognoses and only expressed in exhausted CD8 T cell subpopulation 2. Importantly, they showed the highest expression in melanoma samples compared to other tumors. In general, we characterized the CD8 T cell subpopulations in melanoma and identified that not only genes of immunosuppressive checkpoints but also , , and could serve as potential targets for melanoma therapy.