Fig. 6

Immunoediting correlates with stroma and myeloid signatures. A) WGCNA identifies gene expression modules associated with inflammation (“JAVELIN-like”), angiogenesis, and Immune Escape. Gene dendrogram was first generated and then modules were extracted using dynamic tree cutting (top). Modules were annotated by comparing the correlation between the module eigengenes and previously known gene signatures describing different phenotypes (bottom). B Modules 7 (black), 4 (salmon), and 16 (magenta) are associated with previously described signatures, JAVELIN, angiogenesis, and myeloid/stroma. C scRNAseq demonstrates the cell type enrichment of Immune Escape signature in ccRCC patients. Different colors represent different cell types inferred from scRNAseq data. UMAP plot illustrates single cells collected from all 6 patients including treated and untreated patients. Computational extracted clusters were annotated as previously described [15]. D, E Association between ITH groups, Immune Escape signature, and N/S/ES pathologies. F These regions demonstrate an elevated Immune Escape gene signature in NIVO21. RA, RB, RC, RD, and RE denote different regions of a tumor sample