Figure S3.

T Cell Receptor Repertoire Analysis of CD4⁺ and CD8⁺ Bladder Tumor- and Non-malignant Tissue-Infiltrating T Cells, Related to Figures 3 and 4

(A) The percentage of unique paired TRA and TRB CDR3 nucleotide sequences that are expressed by one cell (blue), shared by two cells (green), or shared by three or more cells (red) is indicated for CD4⁺ T cells from individual tumor (darker shades) and non-malignant tissues (lighter shades) from anti-PD-L1-treated (“PD-L1”), untreated, and chemotherapy-treated (“chemo”) patients. Triplicate control samples from a single healthy donor’s CD4⁺ T cells sorted from peripheral blood and processed for scRNA-seq and TCR in identical fashion in separate sequencing runs is shown (“healthy 1-3”), as well as reference publicly available data from peripheral blood CD4⁺ from a healthy donor. (B) Lorenz curves showing the cumulative frequency distributions for unique CD4⁺ T cells and unique CD4⁺ T cell clonotypes for tumor, non-malignant tissues, and healthy donor blood. Mean ± SD is shown. (C) Gini coefficients for CD4⁺ T cell clonotypes from tumor, non-malignant tissues, and healthy donor blood, calculated from the Lorenz curves in (D); p = 0.009 by Wilcoxon with Benjamini-Hochberg correction for tumor versus non-malignant tissues. For (D) and (E): N = 7 tumor samples; 6 non-malignant samples, 4 healthy donor samples (3 triplicates from one healthy donor, 1 dataset from 10X Genomics). (D-F) Paired TRA/TRB clonotype sharing between cells, Lorenz curves, and Gini coefficients for CD8⁺ clonotype data as in (A-C). (G) Gini coefficients for tissue-infiltrating CD4⁺ in individual populations, separated by treatment type. (H-I) Gini coefficients for CD8⁺ T cells in individual populations, separated by tumor versus non-malignant tissue (H) and treatment type (I). All box and whisker plots are formatted as in Figure 3C.