Fig. 6: Immune exclusion, reduced T cell fraction and clonality, and increased T cell dysfunction in the prostate ICC/IDC TME.

a Quantification of percent CD45⁺ cells by flow cytometry from paired samples of benign-enriched and ICC/IDC-enriched prostate. Graph shown as mean ± SEM analyzed by paired two-tailed t-test; n = 4 biologically independent samples. FACS gating strategies shown in Supplementary Fig. 10a. b Representative images of inflammatory cells (red arrow) in benign-enriched regions and IDC/ICC-enriched regions by H & E at 100x, bar = 50 µm, (n = 7 biologically independent samples). c, d Percent T cells of the immune fraction by individual patient (c) and collectively (d) for benign-enriched and ICC/IDC-enriched prostate. Graph in d shown as mean ± SEM analyzed by Wilcoxon matched-pair signed rank two-tailed test; n = 7 biologically independent samples. e, f Simpson Clonality by individual patient (e) and collective (f) for benign-enriched and ICC/IDC-enriched prostate. Graph in f shown as mean ± SEM analyzed by Wilcoxon matched-pair signed rank two-tailed test; n = 7 biologically independent samples. g Percentage of T cells contracted or expanded between benign-enriched and ICC/IDC-enriched prostate. h Clonotype frequency between benign-enriched and ICC/IDC-enriched prostate. i Unsupervised graph-based clustering of all samples visualized by UMAP highlighted for T cell clusters 1, 3, 7, 9, 17, and 23 delineated by benign-enriched and ICC/IDC-enriched prostate. j, k Violin (j) and feature plots (k) of clusters 1, 3, 7, 9, 17, and 23 for immune and T cell markers. l Violin plots of markers in ICC/IDC-enriched prostate compared to benign-enriched prostate in clusters 1, 3, 7, 9, 17, and 23. m PssGSEA of hallmark pathways in ICC/IDC-enriched prostate compared to benign-enriched prostate in T cell clusters. n Pseudotime trajectory analysis for clusters 1, 3, 7, 9, 17, and 23. o Representative clonotype cluster location in benign-enriched and ICC/IDC-enriched prostate and quantification. The graph is shown as mean ± SEM analyzed by Wilcoxon matched-pair signed rank two-tailed test; n = 7 biologically independent samples. Source data are provided as a Source Data file.