Extended Data Fig. 5: Desert, excluded or inflamed phenotypes are infiltrated by similar proportions of T cell subsets and clonotypes.
From: In situ tumour arrays reveal early environmental control of cancer immunity
a, UMAP embedding of tdTomato+ T cell subclusters (indicated by colours) from pooled STAMP tumour biopsies. b, Dot plot showing the relative expression of important marker genes within T cell subclusters. Relative expression level indicated by colour, and percent of cells expressing the transcript indicated by circle size. c, Relative abundance for each T cell subcluster separated by immune phenotype. d, Flow cytometry-based T-lymphoid immune cell profiling of rejected, inflamed, excluded and desert tumours at day 10. Absolute frequency of CD3, CD4 and CD8 T cells (upper plot) and proportion of naive, activated/resident, effector memory, and central memory of CD4 or CD8 T cells (lower plot). n = 6 animals with 3 tumours pooled per phenotype per animal. Data are mean +/−s.d. Statistical analysis was performed using a two-tailed t-test. P values are shown at the top of the graph. e, TCR clonotype diversity indices for each immune phenotype. f, Cell number of each T cell clonotype with cluster identification. g, Pathway analysis comparing excluded vs inflamed for combined top clonotypes. p-values were fdr adjusted and reported if p-value adjusted < 0.1.
