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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 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 (PMEL, TYRP1, and 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, and EDNRB could serve as potential targets for melanoma therapy.

SUBMITTER: Deng W

PROVIDER: S-EPMC7851490 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe regulatory functions of microRNAs (miRNAs) in anti-tumour immunity have been mainly described in immune effector cells. Since little is known about miRNA effects on the susceptibility of target cells during T cell-target cell interaction, this study focused on the identification of miRNAs expressed in tumour cells controlling their susceptibility to CD8+ T cell-mediated cytotoxicity.MethodsLuciferase expressing B16F10 melanoma (B16F10 Luci+ ) cells transfected with individual miRNAs covering a comprehensive murine miRNA library were screened for their susceptibility to lysis by an established cytotoxic T lymphocyte (CTL) line (5a, clone Nβ) specific for the melanoma-associated antigen tyrosinase-related protein 2. miRNAs with the most pronounced effects on T cell-mediated lysis were validated and stably expressed in B16F10 cells. In silico analyses identified common targets of miRNA sets determined by the screen, which were further confirmed by small interfering RNA (siRNA)-mediated silencing experiments modulating immune surveillance. The Ingenuity Pathway Analysis (IPA) software and RNA sequencing (RNA-seq) data from miRNA-overexpressing cell lines were applied to investigate the underlying mechanisms. The Cancer Genome Atlas (TCGA)-derived miRNA sequencing data were used to assess the correlation of miRNA expression with melanoma patients' survival.ResultsThe miRNA screen resulted in the selection of seven miRNAs enhancing CTL-mediated melanoma cell killing in vitro. Upon stable overexpression of selected miRNAs, hsa-miR-320a-3p, mmu-miR-7037-5p and mmu-miR-666-3p were determined as most effective in enhancing susceptibility to CTL lysis. In silico analyses and subsequent siRNA-mediated silencing experiments identified Psmc3 and Ndufa1 as common miRNA targets possibly involved in the functional effects observed. The analyses of RNA-seq data with IPA showed pathways, networks, biological functions and key molecules potentially involved in the miRNA-mediated functional effects. Finally, based on TCGA data analysis, a positive correlation of the conserved miRNAs among the panel of the seven identified miRNAs with overall survival of melanoma patients was determined.ConclusionsFor the first time, this study uncovered miRNA species that affect the susceptibility of melanoma cells to T cell-mediated killing. These miRNAs might represent attractive candidates for novel therapy approaches against melanoma and other tumour entities.

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

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

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

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OmicsDI is part of the ELIXIR infrastructure

Tweets

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