Fig 1: Pathogenic effector CTLs enriched in PWPs compared to NSPs. a t-SNE plot of CD8B, CD103, CD69, and PDCD1 expression levels on CTLs. b Bubble plots showing significant ligand/receptor pairs between CTLs and other cell types. Point sizes indicate permutation p values (CellPhoneDB). c IF staining showing the infiltration of CD3+ CD8+ GZMB+ CTLs in PWPs. 5× magnification (right). Scale bars, 100 µm. d Volcano plots of differentially expressed genes in CTLs obtained from PWP relative to NSP. Hurdle model likelihood ratio test for differential expression, Benjamini–Hochberg multiple testing correction. All genes are given in Additional file 18: Table S9. e IF staining showing the co-expression of PRF and GZMB in CTLs. Scale bars, 100 µm. f Cell densities (number of cells/villus) of CD3+ CD8+ GZMB+ CTLs and GZMB+ PRF+ CTLs of NSPs and PWPs, according to Fig. 6c and e. ***p<0.001. Student’s t-test. Error bars: SEM (n=6). g Violin plot showing the expression of costimulatory and exhausted gene sets in CTLs of NSPs and PWPs. Wilcoxon test. *p<0.05, **p<0.01, ***p<0.001