Fig. 6

Macrophage- and immune checkpoint-related differences across pan-urologic genomic subtypes. a Average expression similarity correlation (Pearson’s t-statistic, based on genes in Fig. 1b; pink, positive or similar; blue, negative or dissimilar) between TCGA urologic cancer subtypes (columns) and fantom²⁷ cell types or tissues in selected categories (rows): “immune,” immune cell types or blood or related tissues; “CNS,” related to central nervous system including brain; “macrophage,” “mesenchymal,” “epithelial,” denoting fantom profiles for samples including one of these keywords. Results shown for both fantom human and fantom mouse data sets. For “immune,” “macrophage”, and “mesenchymal” correlations, differences are significant with P < 1E-10 (t-test), when comparing c5 with c6 cases, comparing c8 with c1 cases, and comparing c9 with c2 cases. b Heat maps of differential expression, for genes encoding immunotherapeutic targets (top panels) and for gene expression-based signatures³⁴ of immune cell infiltrates (bottom panels), across TCGA urologic cancer subtypes (expression values normalized within cancer type). TREG cells regulatory T cells, TGD cells T gamma delta cells, Tcm cells T central memory cells, Tem cells T effector memory cells, Tfh cells T follicular helper cells, NK cells natural killer cells, DC dendritic cells, iDC immature DCs, aDC activated DCs, P-DC plasmacytoid DCs, APM1/APM2 antigen presentation on MHC class I/class II, respectively. c Diagram of tumor-associated macrophage roles in the tumor microenvironment³⁵, with differential expression patterns represented, comparing tumors in groups c5, c8, or c9 with tumors in groups c6, c1, or c2, respectively (red, significantly higher in c5/c8/c9). P-values by t-test. d Diagram of immune checkpoint pathway (featuring interactions between T cells and antigen-presenting cells, including tumor cells), with differential expression patterns represented, comparing tumors in groups c5, c8, or c9 with tumors in groups c6, c1, or c2, respectively (red, significantly higher in c5/c8/c9). P-values by t-test. See also Supplementary Fig. 6