Figure 6. Tumor-infiltrating T_eee cells are associated with immunotherapy resistance in metastatic melanoma.

The publicly available single-cell RNA-seq melanoma dataset GSE120575 was assessed for the association of tumor-infiltrating T_eee and patient outcomes. (A) A UMAP plot is shown of the CD3+CD4+ TIL concatenated across patient samples. Cells are colored by expression of the T_eee signature genes, with higher expression scores shown in red. (B) The same UMAP plot is shown, colored by clusters. (C) A dot plot is shown with each row showing a cluster and the columns showing select genes. Genes with higher average expression in a cluster are colored red, genes with lower expression are colored blue, and genes with intermediate expression are colored yellow. Larger circle size denotes expression by higher proportion of cells within that cluster. (D) A UMAP plot is shown as before. Cells from non-responding patients are colored red and cells from responding patients are colored blue. (E) The frequency of T_eee (CD38+CD39+) cells as a percentage of the CD4+ T-cell population for each baseline patient sample are plotted, comparing non-responding and responding patients. The corresponding p-value was determined by a Welch’s t-test. (F) Patients were divided based on median frequency of tumor infiltrating T_eee at baseline and survival assessed. Patients with lower than median frequency of T_eee are shown in blue and patients with higher than median frequency in red. The corresponding p-value was determined by Cox proportional hazards regression. (G-I) The frequency of T_eee as a percentage of the CD4+ T-cell population is plotted against the frequency of CD8+ T-cells expressing (G) MKI67, (H) TOX, and (I) TCF7. Non-responding patients are represented with red circles and responding patients with blue triangles. Unadjusted R² and p-values were determined by linear regression ANOVAs.