Dissecting the immune compartment of the melanoma ecosystem under immunotherapy pressure. A, Schematic describing the design of the SPECIAL clinical study, the timing of sample collection, number of patients enrolled, and samples collected, and single-cell (spatial) methodologies deployed for their in-depth characterization. B, UMAP of the CD8+ T cells and NK cells identified by unsupervised Louvain clustering of the subset of CD8+ T/NK cells including samples from both time points. C, Dotplot of the top representative discriminatory marker genes of the cells presented in B including samples from both time points. Size of the dot represents the number of cells expressing the gene and color reflects the expression level. D, UMAP of all immune cell types and states identified by summarizing unsupervised Louvain clustering and subclustering of myeloid and CD8+T/NK cells including samples from both time points. E, Percentage of CD8+ T-cell subsets and NK cells of all immune cells compared among Before treatment (BT) and On treatment (OT) samples and both response groups (two-sided Wilcoxon test, bold text points to significant differences = P F, Dotplot showing expression of NK-related genes, oxidative phosphorylation (OXPHOS), and chemokines/cytokine genes (highly discriminating group 1, 2, and 3 of NK cells) acquired from Netskar and colleagues (29) and NK functional genes acquired from Tang and colleagues (8) and other genes within NK cell population across response and time point groups. Size of the dot represents the number of cells expressing the gene and color reflects the expression level. G, Violin plot showing log2-transformed gene score (AUCell) ratios (chemokine/cytokine signature vs. NK cytotoxicity signature), calculated based on genes shown in E. cDC1, conventional type 1 DCs; cDC2, conventional type 2 DCs; R, responder; NR, Non-responder; UMAP, Uniform Manifold Approximation and Projection. (A, Created with BioRender.com.)
Poźniak et al. (Thu,) studied this question.