FIGURE 6.

Expanded clonotypes between the pre-REP TILs and REP TILs show distinct phenotypic differences within the tumor. A, UMAPs comparing the size of the T cell clonotypes found in the sc-RNAseq+TCRαβ-seq and TCRβ-seq data from 2 patients (pt115 and pt616). Each dot represents a clone in which the color corresponds to the size of the clone in the sc-RNAseq+TCRαβ-seq (left column), TCRβ-seq data from the pre-REP TILs (middle column), and TCRβ-seq data from the REP TILs (right column). Representations for all samples, including the available tumor and healthy kidney samples are found in Supplementary Fig. S10C). B, UMAPs showing the expanded pre-REP TIL and REP TIL clones in pt115 and pt616 (Benjamini-Hochberg–corrected two-sided Fisher’s exact test, P_adjusted < 0.05). In both patients, more pre-REP TIL clonotypes were expanded in the CD8⁺ T_PRE-EXH (pt115) and CD8⁺ T_EXH (pt616) phenotypes, whereas expanded REP TIL clonotypes were mainly characterized by the CD4⁺ T_CYTOTOXIC cell phenotype. C, Volcano plots showing the DEGs in the expanded REP TIL samples (right) compared with those in the pre-REP TILs (left) in pt115 and pt616. In pt115, genes that were most upregulated (right) in the expanded REP TIL clonotypes were NKG7, CCL5, and CD8A, together with those related to cytotoxicity, such as GZMB, GZMH, and GZMK. In pt616, genes related to activation such as HLA-DRB1, HLA-DRA, chemokines such as CCL3 and CCL4L2, as well as LAG-3 were upregulated in the expanded REP TIL clonotypes. In both patients, IL7R was among the DEGs in the expanded pre-REP TIL clonotypes. D, UMAP showing T cells carrying the RCC-associated motifs found in the sc-RNAseq+TCRαβ-seq tumor patients (n = 3). T cells carrying the RCC-associated motifs showed distinct T cell phenotypes in each individual sample.