Extended Data Fig. 6: Prophylactic effect of uPAR-targeting CAR T cells on intestinal crypts.

a, Experimental scheme for b-h: Young (3 months) mice were treated with 0.5x10^6 untransduced T cells (UT) or uPAR CAR T cells (m.uPAR-m.28z). Mice were harvested 15 months after infusion at the age of 18 months and scRNAseq was performed from whole small intestine: duodenum, jejunum and ileum. (n=1 per group). b, UMAP visualization of small intestinal cell types generated by 10X chromium protocol. Colors indicate the 10 different identified populations. c, Dot plot showing the 40 signature gene expressions across the 10 cellular clusters. The size of the dots represents the proportion of cells expressing a particular marker, and the color scale indicates the mean expression levels of the markers (log1p transformed). d, Volcano plot of differentially expressed genes between young mice treated with UT or m.uPAR-m.28z cells 15 months after treatment. x-axis displays log2 fold change while y axis is the -log10 adjusted p-value as calculated by MAST. e, UMAP visualization from pseudotime trajectory analysis of cells from UT or m.uPAR-m.28z treated young mice 15 months after treatment. Arrows highlight predicted trajectories within cell clusters. Color scale represents pseudotime. f, Density plot from pseudotime trajectory analysis demonstrating density differences along pseudotime of all cells between UT or m.uPAR-m.28z treated young mice 15 months after treatment. g, Line plot showing the expression levels of stemness signature score in UT or m.uPAR-m.28z treated young mice 15 months after treatment along the indicated pseudotime axis. h, Dot plot showing Log2 fold change in the functional scores for the different terms across Paneth, goblet, enteroendocrine and enterocytes of young mice treated with UT or m.uPAR-m.28z cells 15 months after treatment. Results of 1 independent experiment (a-h). Two-tailed Fisher test (f). Two-tailed Wilcoxon rank-sum test *P<0.05,**P<0.01, ***P<0.001, ****P<0.0001 (g-h). MAST method: two-sided, p-values adjusted for multiple comparisons using the Benjamini-Hochberg method (d). Illustration created with Biorender.com (a).