Figure 6 from Functionally Characterizing the Renal Cell Carcinoma Tumor-Immune Microenvironment via Patient-Derived Ex Vivo Models

Differential activation of T cell clones dependent on their prior cell state. A, The UMAP view of TCR distribution displaying clonotype frequency in CD8+ (i) and CD4+ (ii) T cell populations. B, Bar plot showing the relative abundance of clones among patients with RCC (RCC_1–RCC_8) in CD8+ (i) and CD4+ (ii) T cells. C, Average clonality of TCR repertoires at the cluster level, shown separately for CD8+ (i) and CD4+ (ii) T cells. D, Bar plot showing the relative abundance of clones among treatments (anti–PD-1, VEGFRi, anti–PD-1 + VEGFRi, and anti-CD3/CD28/CD2) in CD8+ (i) and CD4+ (ii) T cells. E, Scatter plot showing the expansion levels of T cell clones in control and different treatments. Clonal expansion or contraction is measured as the ratio of cells from a clonotype to the number of T cells. Each point represents a T cell clone from an individual patient. For each clone, Fisher exact test was performed to evaluate the statistical significance of expansion or contraction, and clones with FDR ≤0.05 were considered significantly altered and labeled in the figure. F, Gene set enrichment analysis (GSEA) of pathways upregulated or downregulated by the treatments in selected CD8+ and CD4+ clones. Heatmap shows the GSEA results at the clone level for the five largest clones of each patient (RCC_4–RCC_8). The most prevalent cell phenotype (cluster) in the control condition is indicated for each clone. Signatures with FDR ≤0.01 are highlighted within the heatmap tiles. G, A dot plot showing the proportion of cell at exhausted and activated cluster in control and each treatment condition for the largest clones, labeling those clones that are less responsive to anti-CD3/CD28/CD2. The clones are shown in the same order as in F. H, A volcano plot showing the results of Fisher exact test, identifying upregulated genes (FDR ≤0.05; log2FC ≥ 0.25; Wilcoxon rank-sum test) that are overrepresented in anti-CD3/CD28/CD2-responsive clones compared with less responsive clones. Categorization to “responsive” and “less responsive” is based on the analysis presented in G. FC, fold change.