Supplementary Figure 1: Characterization of T_RM cells in IBD.

(a) Flow cytometry of lamina propria mononuclear cells (LPMCs). Left panels: Representative dot plots indicating the expression of the T cell markers CD4 or CD8 in total LPMCs and CD69⁺CD103⁺ LPMCs. Right panels: Quantification of T cells expressing CD4 and/or CD8 among CD69⁺CD103⁺ LPMCs in CON (n = 4), UC (n = 3) and CD (n = 8). (b) Correlation of CD69 mRNA with CXCR6 and CD101 mRNA expression as determined by qPCR in intestinal tissue from patients with IBD (n = 35). Spearman’s R and regression lines are indicated, * P < 0.05. (c, e) mRNA expression of CRTAM1 (c, n = 5) and NR4A1 (e, n = 6) in CD3⁺CD69⁺ vs. CD3⁺CD69^- T cells isolated from colonic lamina propria as determined by qPCR. Pairwise normalization to the expression in CD3⁺CD69⁺ T cells was performed. *** P < 0.001, paired two-tailed student’s t-test. (d) Quantitative flow cytometry of CD44 mean fluorescence intensity (MFI) in LPMC subsets. n = 16, *** P < 0.001, repeated-measures ANOVA with Newman-Keuls post-hoc test. (f) Analysis of T_RM-associated molecules on CD69⁺ T_RM cells from the intestinal lamina propria (LP) and T cells from the peripheral blood. Histograms of the expression of CD49a and CXCR6 representative for two independent experiments are shown. (g) Correlation of CD69 mRNA expression with mRNA expression of IFNG (n = 24), IL13 (n = 26), IL17A (n = 31), IL12A (n = 46), IL12B (n = 28) and TNF (n = 36) as determined by qPCR in intestinal tissue from patients with IBD. Spearman’s R and regression lines are indicated; * P < 0.05, ** P < 0.01, *** P < 0.001.