Fig. 1: Altered CD4⁺ T cell reactivity against fungal microorganisms in CD patients.

a, Frequencies of reactive CD154⁺CD45RA⁻CD4⁺ T_mem cells against whole microbial lysates in healthy donors and patients with an IBD: healthy donors (HD, black dots), CD (red dots) and UC (gray dots). The letter n indicates the number of individual donors specified below each group. The P values are given at the top of each figure. b, Dot plot examples for the ex vivo detection of microorganism-reactive CD4⁺ T cells by ARTE. Absolute cell counts after magnetic CD154⁺ enrichment from 1× 10⁷ PBMCs are indicated. w/o, without. c, ITS-seq and analysis of stool samples from patients with CD (n = 38). The relative abundance of the top 12 fungal species identified by this analysis is shown. Less abundant or less represented fungal species are grouped under ‘other’. d, Serum anti-IgG and IgA ASCA concentrations in healthy donors and patients with IBD (HD, n = 46; CD, n = 88; UC, n = 73). Sera were considered positive if their activity was >20 relative units (RU) per ml. Both single-positive IgA or IgG samples and double-positive samples classified donors who are ASCA⁺. e, Frequencies of fungus-reactive CD4⁺ T cells in patients with CD, according to their ASCA status. f, Total CD4⁺ T_mem cells isolated from biopsies of inflamed and uninflamed intestinal tissue of patients with CD who are ASCA⁺ (n = 5). Cells were seeded at 200 cells per well in multiple wells, and expanded and restimulated with fungal lysates in the presence of autologous APCs. Mean frequencies of reactive CD154⁺ cells for all wells per patient are shown. g, Dot plot examples for restimulation of expanded CD4⁺ T_mem cells from an inflamed biopsy. The percentage of CD154⁺ TNF⁺ cells within CD4⁺ is indicated. Each symbol in a, d, e and f represents one individual donor and horizontal lines in a and e indicate the mean. Box-and-whisker plots are shown in c with center lines representing the median, box limits 25% (lower) and 75% (upper) quartiles and whiskers the minimum/maximum. Truncated violin plots with quartiles and range are shown in f. Statistical differences were obtained using the Kruskal–Wallis test with Dunn’s post hoc test in a with only significant differences shown; the two-tailed Mann–Whitney U-test was used in e.