Extended Data Fig. 4: Relationship between transition of T cell exhaustion state and CD160, and distribution of CD160+CD8+ T cells in different intestinal tissues.
a, Box plots showing normalized IEL signature in different clusters, ordered by decreasing values. The number of samples in each group is listed below the boxes. b, Monocle trajectory plots of TCRαβ+ IEL-T cells. Cells are colored by the Exh_Tex score (left) and MKI67 expression (right). c, Monocle trajectory reconstruction of TCRαβ+ IEL-T cells. Regression lines are fitted against pseudotime for EOMES, IL7R, TOX, REL expression of different tissue types. d, Box plots demonstrating the expression of CD160 in ileum, colon and tumor tissues from GTEx, TCGA-CRC, GSE39582, and GSE21510 datasets. e, f, Representative flow cytometry plots (e) and frequencies (f) of CD160 in CD8+ T cells among different intestinal tissues from C57BL/6 mice (n = 3 mice). g, Experimental scheme of AOM/DSS-induced CRC mouse model. h, Representative small intestine and colon images of AOM/DSS-induced CRC mouse (n = 6 mice). i, j, Representative flow cytometry plots (i) and frequencies (j) of CD160 in CD8+ T cells among ileum, colon and tumor from AOM/DSS-induced CRC mice (n = 4 mice). k, l, Representative immunofluorescence staining (k) and quantification (l) of ileum, colon and tumor from AOM/DSS induced CRC mouse. Staining for CD8 (green), CD160 (red) and DAPI (blue). Red triangles highlight CD160+CD8+ T cells. Scale bars: 50 μm (n = 4 mice). m, Box plots showing the Exh_Pex score (left) and Exh_Tex score (right) of tumoral TCRαβ+ IELs per indicated regional pattern. n, Box plots showing the Exh_Pex score (left) and Exh_Tex score (right) across CD160+ and CD160− cells in tumoral CD8+ T cells from GSE205506 dataset. o, Box plots showing the Exh_Pex score (left) and Exh_Tex score (right) of tumoral CD8+ T cells per indicated regional pattern. p, Bar plots showing the fraction of tumoral CD8+ T cells that are clonally linked with cells from other indicated tissues. Cells are divided by the cutoff 0.45 of Exh_Tex score, and only cells from clones containing at least 2 tumoral CD8+ T cells are included. P values are determined by paired two-sided Mann-Whitney test (a, d, m, n and o). Data are shown as the mean ± s.e.m, P values were determined by unpaired two-tailed Student’s t-test (f, j, and l). Box plots: center line, median; box limits, first and third quartile; whiskers, 1.5× interquartile range.
