Extended Data Fig. 3: CD8+ T cell states and TCR clonality in melanoma clinical samples.
From: Tumour-reactive heterotypic CD8 T cell clusters from clinical samples
a, scRNA-seq UMAP of all sequenced cells from melanoma lymph node metastases (n = 5 patients), coloured by cell type. b, Expression of representative tumour cell, T cell and APC markers projected on UMAP of (a). Colour scale indicates gene-weighted density. c, Dotplot showing gene expression of a panel of T cell-related genes indicating different CD8+ T cell states. Rows labelled by annotated cell states of Fig. 3b. Colours, average expression of gene; dot size, percentage of cells expressing the gene. d, Absolute number of CD8+ T cells per annotated cell state subdivided by patient. e, Absolute number of CD8+ T cells per annotated cell state stratified by origin: single T cells, T cells from tumour clusters or T cells from APC clusters. f, Distribution of single T cells and T cells from tumour or APC clusters on the UMAP of sequenced T cells in Fig. 3b. g, Frequency of CD8+ T cell states in single and clustered T cells per patient (n = 5). FDR-adjusted Fisher’s exact test was used. Significantly enriched cell states in clustered versus single T cells indicated. h, Frequency of top 15 TCR clonotypes in single or clustered T cells per patient (n = 5) analysed as in (g). *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.
