Gliadin-specific CD4+ T cells exhibit functional diversity independent of TCR usage or epitope specificity.

Celiac disease (CeD) is driven by pathogenic CD4+ T cell responses, primarily targeting four HLA-DQ2.5-restricted immunodominant epitopes derived from α-gliadin and ω-gliadin. While gliadin-specific CD4+ T cells have been investigated, how transcriptional and effector phenotypes in CeD vary across distinct epitope specificities remains unclear, as do the signature TCR motifs governing gliadin epitope specificity and cross-reactivity. Single-cell transcriptomic and TCR profiling of gliadin epitope-specific peripheral blood CD4+ T cells from patients with CeD after gluten challenge revealed T cells with an activated TH1 effector, conventional regulatory T cell (Treg cell) or cytotoxic phenotypes across specificities, with no evidence of functional specialization driven by specific epitopes. Moreover, we identified core TCR motifs that dictate gliadin epitope specificity and cross-reactivity and elucidated the structural basis of their cognate pMHC recognition. These motifs enabled accurate prediction of gliadin specificity from unassigned TCRs. Collectively, these findings advance our understanding of immune responses in CeD and provide a foundation for tracking disease-relevant T cells.