Comparison of cells across BC urine, tumor, and blood, and specifically CD4 ⁺ T cells. (A) UMAP of 106,587 integrated UDCs, tumor cells, and PBMC. With a resolution of 0.5, there were 22 clusters. Cells are color-coded according to their subset and annotated based on prior studies. (B) Bar-plot comparison of cluster frequencies across tissue. (C) UMAP of 25,538 CD4⁺ T cells across tissue. With a resolution of 0.6, there were 11 CD4⁺ T clusters. Cells are colored according to subset and annotated based on prior studies. (D) UMAP of CD4⁺ T cells split by tissue. (E) Bar-plot comparison of CD4⁺ T cell cluster composition across tissue. (F) Expression level of functional markers of interest in CD4⁺ T cells across tissue. (G and H) Volcano plot displaying DEGs between CD4⁺ T cells in (G) urine versus tumor and (H) in blood versus tumor. (I) GSEA on genes upregulated in CD4⁺ T cells in tumor versus blood. (J) Volcano plot depicting DEGs between CD4⁺ T cells in urine versus blood. (K) GSEA on genes upregulated in urine versus blood CD4⁺ T cells. Cutoffs of log₂FC > |1| and P value <0.05 were for volcano plots and pathway analysis.