Flagellin-specific CD4+T cells can be detected in IBD patients’ peripheral blood. (A) Gating strategy and representative flow cytometry data for cohort 1. (B) The percentage of CD25+OX40+ cells within CD4+ T cells after stimulation of whole blood with FliC or Fla2 for 44 hours (CD, n = 55; UC, n = 7). (C) Anti-FliC and anti-Fla2 IgG levels in plasma measured using an enzyme-linked immunosorbent assay (ELISA); concentrations are in arbitrary units based on high-titer pooled plasma standards. (D) Correlations between FliC– and Fla2–specific CD4+ T cells and IgG levels and (E) correlations between FliC- and Fla2-specific CD4+ T cells and IgG levels. FliC- and Fla2-specific CD4+ T-cell responses were compared between CD patients based on (F) current treatments (untreated, n = 5; glucocorticoids or mesalamine, (n = 9 for FliC and n = 8 for Fla2); Fla2, antimetabolites n = 26 and biologics n = 19) and (G) clinical phenotype of disease: perianal (n = 5), luminal (n = 20), or stricturing/penetrating (n = 9). Statistical analyses used (B and C) Mann–Whitney U tests, (D and E) calculated Spearman Rho (r), and (F and G) Kruskal–Wallis tests. APC, allophycocyanin; PECy7, phycoerythrin-cyanine 7.