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

Abstract 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 up-regulated in exhausted CD8+ T cell subpopulations. Besides, a dynamic transcript landscape of immune checkpoints among different subpopulations was also depicted in this study. Moreover, we identified three overexpressed genes (PMEL, TYRP1, EDNRB) 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 PMEL, TYRP1, EDNRB could serve as potential targets for melanoma therapy.