Discriminative T-cell receptor recognition of highly homologous HLA-DQ2-bound gluten epitopes

Celiac disease (CeD) provides an opportunity to study the specificity underlying human T-cell responses to an array of similar epitopes presented by the same human leukocyte antigen II (HLA-II) molecule. Here, we investigated T-cell responses to the two immunodominant and highly homologous HLA-DQ2.5-restricted gluten epitopes, DQ2.5-glia-alpha 1a (PFPQPELPY) and DQ2.5-glia-omega 1 (PFPQPEQPF). Using HLA-DQ2.5-DQ2.5-glia-alpha 1a and HLA-DQ2.5-DQ2.5-glia-omega 1 tetramers and single-cell alpha beta T-cell receptor (TCR) sequencing, we observed that despite similarity in biased variable-gene usage in the TCR repertoire responding to these nearly identical peptide-HLA-II complexes, most of the T cells are specific for either of the two epitopes. To understand the molecular basis of this exquisite fine specificity, we undertook Ala substitution assays revealing that the p7 residue (Leu/Gln) is critical for specific epitope recognition by both DQ2.5-glia-alpha 1a- and DQ2.5-glia-omega 1-reactive T-cell clones. We determined high-resolution binary crystal structures of HLA-DQ2.5 bound to DQ2.5-glia-alpha 1a (2.0 A) and DQ2.5-glia-omega 1 (2.6 A). These structures disclosed that differences around the p7 residue subtly alter the neighboring substructure and electrostatic properties of the HLA-DQ2.5-peptide complex, providing the fine specificity underlying the responses against these two highly homologous gluten epitopes. This study underscores the ability of TCRs to recognize subtle differences in the peptide-HLA-II landscape in a human disease setting.