Figure 5 from Functionally Characterizing the Renal Cell Carcinoma Tumor-Immune Microenvironment via Patient-Derived Ex Vivo Models

The effects of anti–PD-1 (pembrolizumab), VEGFRi (axitinib), and their combination on immune cell functionality in the RCC TME. A, Volcano plot illustrating changes in cytokine secretion in response to anti–PD-1, VEGFRi, or anti–PD-1 + VEGFRi combination. Each point represents a cytokine, and upregulated and statistically significant cytokines are highlighted in dark red, whereas downregulated and statistically significant cytokines are colored in dark blue [−log10(P) > −log10(0.05) or P > 0.05]. B, Heatmap comparing change in immune effector markers expression between control, anti–PD-1, VEGFRi, or anti–PD-1 + VEGFRi combination in CD8+ and CD4+ T cells. C, Volcano plot illustrating changes in gene expression in response to anti–PD-1, VEGFRi, or anti–PD-1 + VEGFRi combination in CD8+ T cells (i) or CD4+ T cells (ii). Each point represents a gene, the upregulated genes are colored dark red, whereas downregulated genes are dark blue. Only significant genes are labeled [adjusted P value < 0.05 and abs(avg_log2FC) > 0.5, and in the case of anti–PD-1 adjusted P value < 0.05 and abs(avg_log2FC) > 0.3]. D, Dot plot of selected immunology-related hallmark pathways, comparing anti–PD-1, VEGFRi, or anti–PD-1 + VEGFRi to control condition. Genes were identified using the FindMarkers method and included if the P value was < 0.05. Circle size represents the logP value, whereas color indicates the percentage of genes in our dataset that are upregulated (+) or downregulated (−). E, Volcano plot illustrating changes in relative cluster size in response to anti–PD-1, VEGFRi, or anti–PD-1 + VEGFRi combination treatments. Each point represents a T cell cluster (CD8+ T cells and CD4+ T cells). Cell populations that are enriched in treatment and statistically significant (adjusted P value < 0.05 and log2FC > 0) are highlighted in dark red, and cell populations that are diminished in treatments and statistically significant (adjusted P value < 0.05 and log2FC < 0) are colored in dark blue. FC, fold change. F, Signature score distributions for terminally exhausted, progenitor exhausted and IFN CD8+ T cell signatures comparing control with anti–PD-1, VEGFRi, anti–PD-1 + VEGFRi, and anti-CD3/CD28/CD2. Statistical significance of differential signature enrichment (P value) between subtypes was determined by two-sided Wilcoxon rank-sum test (ns, P > 0.05; ****, P ≤ 0.0001).