Fig. 2

Identification of an EBV-imprinted intratumoural CD8⁺ T-cell compartment. a UMAP visualization of 61,348 T cells identifying 28 subpopulations. b Stacked violin plot showing the marker genes expression of major T-cell subpopulations. c Heatmap showing the expression of T-cell-related function genes including naÏve markers, cytokines and effector molecules, co-stimulatory molecules, tissue retention markers, exhaustion markers and transcription factors. d Heatmap representing the EBV state preferences and treatment stage of major T-cell subpopulations. Center number indicates the Ro/e value. e Scatter plot showing the expansion scores of T-cell subpopulations. Variation of expansion scores for different treatment stages and EBV infection states are shown on the x-axis and y-axis. f KEGG pathways enriched in the GZMK⁺ T cells (CD8.C12 cluster), ranked by gene ratio which is the ratio of genes related to signature to total number of genes in signature. g UMAP visualization of 3616 GZMK⁺ T cells (CD8.C12 cluster) identifying six subpopulations. h Shannon diversity index (SDI) of six subpopulations from GZMK⁺ T cells (CD8.C12 cluster). i The KEGG pathways enriched in the ISG-15⁺ T cells (CD8.C12.2 cluster), ranked by gene ratio which is the ratio of genes related to signature to total number of genes in signature. j Gene set variation analysis (GSVA) of ISG-15⁺ T cells (CD8.C12.2 cluster), using TCGA-STAD (n = 228), ACRG cohort (n = 300) and Yonsei cohort (n = 433). The horizontal line shows the median, the box comprises the interquartile range and the whiskers extend to the 5th and 95th percentiles. P values were computed using a two-sided Wilcoxon test