Extended Data Fig. 10: Cells with profile of gluten-specific CD4⁺ T cells in celiac, autoimmune and viral disease identified with manual gating.

a, Manual gating strategy with markers giving a well-defined shift in staining intensity that define gluten-specific T cells, encompassing 41% and 48% of HLA-DQ2.5:gluten tet-binding CD4⁺ T cells in the gut and CD4⁺ effector memory T cells in the blood, respectively, in patients with UCeD (although the gluten-specific cells were phenotypically similar, not all of the cells had a staining intensity for all ten markers above or below the manually set threshold, as also visualized in Figs. 1c and 2c). Here, visualized in the peripheral blood of a patient with UCeD. b–d, Frequency of cells gated as in a in the gut (b) and in the blood (c) (pre-tet-enriched sample) of patients with UCeD, TCeD (gluten-free diet) and healthy controls, and in patients with TCeD before and following gluten challenge (differing from gating encountering gluten-specific cells in patients with UCeD chiefly by lower CD39 expression, as also visualized in Fig. 2f) (d). Blood and gut samples analyzed in 12 and six experiments, respectively. Gluten challenge samples were analyzed in two experiments. e,f, Frequency of cells gated as in a within patients with the indicated autoimmune disorders and different set as in b of control subjects (seven experiments in total) (e), and within a cohort during and after influenza infection (f) (three experiments in total). Statistics: an unpaired, two-tailed t-test was used and the median frequency and interquartile range are indicated in b, c and e. *A paired, two-tailed t-test was used and the lines indicate paired samples in d and f.