Figure 7 from Functionally Characterizing the Renal Cell Carcinoma Tumor-Immune Microenvironment via Patient-Derived Ex Vivo Models

Cell–cell communication in the RCC TME. A, Heatmap showing cell–cell communication network for selected signaling pathways in the untreated, control condition. Normalized pathway network centrality scores (importance) are visualized for galectin, NECTIN-TIGIT, CD39, and CD86–CTLA4 signaling pathways, showing signal for cell types as “sender” and “receiver.” More intense color indicates higher relative “sender” or “receiver” signal. B, Heatmap showing the average expression of selected ligands and receptors in the control for specified immune cell types. C, Ridge plot showing the pseudobulk analysis comparing each treatment with the control condition. The change in the ligand–receptor expression is expressed as mean Wald statistic, in which positive values denote increase and negative values decrease in ligand–receptor expression. D, The results of the pseudobulk analysis comparing each treatment with the control condition were visualized as a dot plot. In this plot, each row represents a ligand–receptor pair, and each column corresponds to a cell type and treatment combination. Ligand and receptor results were visualized in separate panels. Dot color indicates the log2 FC between treatment and control, whereas dot size reflects −log10 FDR. Dots with FDR ≤0.25 were highlighted with a circle, in which circle color denotes the direction of change: red for higher expression in treatment and blue for lower expression. FC, fold change.