Fig. 5: Immune phenotyping demonstrates enrichment of Inflamed tumors in Ba/Sq subtype.

a FFPE slides were stained with anti-CD8 and Masson’s Trichrome and the pattern of CD8 + cells were evaluated. Samples were either called as “Desert”, “Excluded”, or “Inflamed”. Representative images of the three phenotypes are shown at a total magnification of ×40 (left) and ×200 (right). The area shown at ×200 is boxed within the ×40 image (Desert = yellow, Excluded = green, Inflamed = blue). The area within the box on left is the tumor portion at right. b the distribution of immune phenotypes within UC-GENOME (n = 155 samples). c Boxplots of Ayer’s T cells inflamed, d Bindea T cells, and e Ayer’s INFG signatures by immune phenotype. Wilcoxon p-values are shown above the comparison groups (n = 155 samples). All boxplots are shown with boxes representing the IQR and midline at the median. Error bars represent Q1/Q3  ±  1.5 × IQR. f Stacked barplots of the immune phenotype distribution across the consensus subtypes and g clinical benefit to ICI are shown with the number of samples within each bar at center. Lines at top represent the comparison groups, with p-values calculated using fisher’s exact test. h Group boxplot of the Ayer’s T cells inflamed z-score by immune phenotype and response status (n = 84 samples). Two-sided Wilcoxon p-values for responders versus non-responders for each phenotype is shown at top. Source data are provided as a Source Data file.