Fig. 2: Identification of CD8⁺ Trm cells.

a UMAP embedding of the CD8⁺ T-lineage cells that passed quality control, colored by inferred cell types based on transcriptional profiles. b Expressions of selected marker genes in CD8⁺ T-cell subsets. c Fraction of CD8⁺ Trm-CXCR6 cells in CTL (n = 7) and CIP (n = 9) patients. A two-tailed Mann–Whitney U test was performed. d Box plots showing differences in the expression levels of ITGAE and ZNF683 between CTL (n = 29) and CIP (n = 7) patients based on bulk RNA-seq. P values were determined using a one-tailed Mann–Whitney U test. e Box plot showing the scoring of a Trm activation signature in CD8⁺ T cells from CTL (n = 7) and CIP (n = 9) patients. A two-tailed Mann–Whitney U test was performed. f Representative multiplex immunofluorescence images of CD8⁺ CD103⁺ T cells in CTL and CIP patients. g Box plot quantifying multiplex immunofluorescence in (f) for the CTL group (n = 5) and the CIP group (n = 5). P value was determined by a one-tailed Mann–Whitney U test. h Heatmap showing the top genes of Trm-like, Trm-ZNF683 and Trm-CXCR6 clusters. i Dot plot showing relative IFNG and STAT1 expression between CTL and CIP patients. j Representative multiplex immunofluorescence images of CD8⁺ IFN-γ⁺ T cells in CTL and CIP patients. k Box plot quantifying multiplex immunofluorescence in (j) for the CTL group (n = 3) and the CIP group (n = 3). P value was determined by a one-tailed Mann–Whitney U test. In the box plots (c–e, g and k), the centre line represents the median, the bounds of the box correspond to the 25th and 75th percentiles, the whiskers extend to the largest and smallest values within 1.5× the interquartile range from the quartiles, and individual points beyond the whiskers indicate outliers. Trm, tissue-resident memory.