Extended Data Fig. 1: Phenotypic characterization of PD1 + CD45RA- CD4 T cells in kidney, bladder and prostate cancer patients.
From: Differentiation fate of a stem-like CD4 T cell controls immunity to cancer
a) ScRNAseq analysis of PD1 + CD45RA- CD4 T cells in kidney cancer patients (n = 2). Bar plot showing cluster distribution between patients. b) UMAP projections of selected genes across all clusters. c) VISION GSEA using defined human CD4 T cell lineage (Treg, Th1, Tfh) and proliferation (cell cycle) signatures. UMAP projections show the top 10% scoring cells and the enrichment score for the signature is represented as violin plots for each cluster. Means shown for every violin plot and were analyzed by one-way ANOVA with Tukey’s multiple-comparison tests. d-e) Total quantification (d) and frequency of PD1+ (e) CD4 T cell infiltration in kidney (K n = 125), prostate (P n = 6) and bladder (B n = 17) tumors. f) Frequency of activated CD4 T cell populations based on transcription factor expression in human bladder (n = 17) and prostate (n = 6) tumors. g) Representative TCF1 and KI67 expression in activated CD4 T cells infiltrating human kidney tumors (n = 21). Mean ± 95% CI are represented and were analyzed by two-sided unpaired Mann Whitney U test. h) Representative plots of various phenotypic markers expressed in activated CD4 T cells in human kidney tumors. Mean ± s.d. are represented in each summary plot and were analyzed by Kruskal-Wallis test with Dunn’s multiple-comparison tests (n = 14–125 kidney cancer patients for each marker). i) Quantification of PD1 + CD4 T cell infiltration in kidney tumor draining lymph nodes, shown as the percent of total CD4 T cells (n = 12). j-k) Representative lineage transcription factor and PD1 expression in PD1 + CD45RA- CD4 T cell populations in kidney tumor draining lymph nodes (n = 9–12). Mean ± s.d. are represented in each summary plot and were analyzed by Kruskal-Wallis test with Dunn’s multiple-comparison tests. l) Phenotype of activated CD4 T cells in kidney tumor draining lymph nodes (n = 5–12 patients per marker). Mean ± s.d. are represented in each summary plot and were analyzed by Kruskal-Wallis test with Dunn’s multiple-comparison tests. Each point represents an individual patient. The activated populations were defined based on the following gates: Tregs: CD28 + FOXP3 + TBET- EOMES-, EOMES: CD28 + FOXP3- TBET-EOMES +, TFH: CD28 + FOXP3-TBET-EOMES-TCF1 + BCL6 +, Th1: CD28- FOXP3-TBET +, TCF1+lin-: CD28 + FOXP3-TBET-EOMES-TCF1 + BCL6-.
