Figure 1.

Bladder Cancer Contains Canonical CD8⁺ T Cell States

(A) Uniform manifold approximation and projection (UMAP) plots of 10,762 single sorted CD3⁺ CD8⁺ T cells obtained from bladder tumors and adjacent non-malignant tissue (N = 7 patients). Phenotypic clusters are represented in distinct colors.

(B) Relative intensity of expression of select genes superimposed on the UMAP projections in (A).

(C) Violin plots showing the relative expression of select differentially expressed genes (columns) for each cluster shown in (A) (rows) (all P_adj < 0.05).

(D) The frequency of cells expressing MAIT-associated TRAV1-2/TRAJ33⁺ TCRs within each defined CD8⁺ phenotypic cluster.

(E) The frequency of cells in individual clusters shown as a proportion of total CD8⁺ cells within tumor or non-malignant compartments across all patients (orange, tumor; blue, non-malignant). For each cluster, a box and whisker plot is shown with the median, interquartile range (IQR, a box with lower and upper bounds representing 25^th and 75^th percentiles, respectively), and 1.5 times the IQR (whiskers). Outlier points are shown if more than 1.5 times the IQR beyond the lower and upper quartiles. Statistical testing was done using an exact permutation test.

(F) Density plots showing distribution of cells in tumor or non-malignant samples.