Extended Data Fig. 7: Expression of regulatory T cell-associated markers on gluten-specific CD4⁺ T cells in vitro and ex vivo.

a, CD4⁺ blood T cells of a patient with UCeD were HLA-DQ2.5:gluten tet-sorted ex vivo and cultured in vitro with phytohemmagglutinin and irradiated PBMCs for 2 weeks before re-staining with HLA-DQ2.5:gluten tets to analyze for the expression of Foxp3 and CD25 (n = 2, 1 experiment). b, The same experiment as in a, only with tet-sorted CD4⁺ gut T cells from the patient in a (n = 1, 1 experiment). c, RNA-seq-derived log₂ fold-change expression of glycoprotein A repetitions predominant (GARP) in tet⁺ (<2 GARP transcripts per million) versus tet⁻ CD4⁺ gut T cells of five patients with UCeD and in tet⁺ of five patients with UCeD versus CD4⁺ gut T cells of four control subjects. GARP was differentially expressed in tet⁺ versus tet⁻ cells, but not when compared to CD4⁺ gut T cells in controls (indicated by asterisks) (differentially expressed genes in Supplementary Table 5). d,e, Ex vivo flow cytometry staining of tet⁺/⁻ CD4⁺ gut T cells from a patient with UCeD with anti-CD127, anti-CD25 and anti-Foxp3 (d) and summarized CD25/Foxp3 staining in gut biopsies of five patients with HLA-DQ2.5⁺ UCeD and one patient with UCeD HLA-DQ8⁺ (five experiments) (e). The median frequency and interquartile range are indicated. f,g, Tet⁺/⁻ CD4⁺ blood T cells from a patient with UCeD with anti-CD127, anti-CD25 and anti-Foxp3 (f) and summarized CD25/FoxP3 staining in blood of five patients with UCeD and four gluten-challenged patients with UCeD (four experiments) (g). The median frequency and interquartile range are indicated. Samples in a and b were stained with a different anti-CD25 antibody than samples in d, e, f, and g.