Figure 3 from Functionally Characterizing the Renal Cell Carcinoma Tumor-Immune Microenvironment via Patient-Derived Ex Vivo Models

Characterization of CD4+ T cells in control. A, UMAP of 2,136 CD4+ T cells in untreated control condition captured across eight patient samples (RCC_1–RCC_8), colored by characterized cell types. B, Bar plot showing distribution of characterized CD4+ cell types across all eight patients, ordered by the proportion of regulatory CD4+ cells in each patient. C, Dot plot showing average expression of selected genes across identified cell clusters. Each dot represents a specific gene–cluster combination, in which the size of the dot indicates the percentage of cells within the cluster expressing the gene, and the color intensity reflects the average expression level of the gene in those cells. D, CyTOF analysis of CD4+ T cells in control condition from nine patients (RCC_9–RCC_17). Marker expression patterns are visualized using t-distributed stochastic neighbor embedding (t-SNE) plots. E, Signature score for naïve, activation/effector, exhaustion, TCR signaling, cytotoxicity, cytokines, IFN response, Treg, and co-stimulation CD4+ T cell signatures plotted on CD4+ T cell UMAP. F, UMAP depicting the pseudotime inference of CD4+ T cells, showing three distinct paths. Heatmaps on the right show the top 20 genes that change their expression over the course of path progression.