Extended Data Fig. 4: Clustering of CXCL13 + tumor-reactive T cells.
a, UMAP plot of 27,155 CXCL13+ CD8 T cells from N = 15 post-ICB lung tumor samples from the Caushi et al. data, color-coded by clusters. b, UMAP plots showing the expression levels of certain signature genes in different cell clusters from a. c, TOX gene expression in the tumor-specific CD8 T cell subsets from N = 20 tumor samples from 10 patients from the Liu et al. NSCLC dataset. d, UMAP plots of CXCL13+ CD8 T cells from pre- and post-ICB tumors for other immunotherapy datasets. N = 20, 22, 7, 53, 22, 7, and 4 tumor samples for the 7 datasets, respectively (from left to right and top to bottom). e, Comparison of the stem-like T cell signature scores and terminally differentiated (TD) signature scores in different cell clusters from a and d, color-coded by clusters. Precursor-like T cells were not identified in the two RCC datasets, and we therefore included the reference data as comparisons when analyzing TD cells. The reference data were from the Eberhardt et al. study and included experimentally validated stem-like and TD cells. Each dot represents one cell while the center line indicates the median value. Data were summarized from n = 13,538, 27,155, 1,944, 4,360, 3,325, 542, 7,290, 3,305 cells from the 8 datasets, respectively. The tumor sample size for each dataset is the same as in a and d. The lower and upper hinges represent the 25th and 75th percentiles, respectively, and whiskers denote 1.5× interquartile range. ***P < 2.2×10−16, two-sided t-test.
