Peptidomic analysis of type 1 diabetes associated HLA‐DQ molecules and the impact of HLA‐DM on peptide repertoire editing

• Published in: European journal of immunology 2017-02, Vol.47 (2), p.314-326
• Main Authors: Zhou, Zemin, Reyes‐Vargas, Eduardo, Escobar, Hernando, Chang, Kuan Y., Barker, Adam P., Rockwood, Alan L., Delgado, Julio C., He, Xiao, Jensen, Peter E.
• Format: Article
• Language: English
• Subjects: Amino Acid Motifs - genetics; Antigen Presentation; Antigen processing; Antigens - metabolism; Antigens, Differentiation, B-Lymphocyte - metabolism; Assaying; Cofactors; Computer Simulation; Diabetes; Diabetes mellitus; Diabetes Mellitus, Type 1 - immunology; Editing; Epitopes; Epitopes, T-Lymphocyte - genetics; HEK293 Cells; Histocompatibility antigen HLA; Histocompatibility Antigens Class II - metabolism; HLA-D Antigens - metabolism; HLA-DQ Antigens - metabolism; HLA‐DM; Humans; Invariant chain; Lymphocytes T; Major histocompatibility complex; Mass spectrometry; Mass spectroscopy; MHC; Peptides; Peptides - metabolism; Peptidomic analysis; Protein Binding; Protein Stability; Scientific imaging; Tandem Mass Spectrometry
• ISSN: 0014-2980; 1521-4141
• DOI: 10.1002/eji.201646656

HLA‐DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII‐bound peptides in human embryonic kidney 293T cells expressing HLA‐DQ molecules in the absence or presence of these cofactors. We found that Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative. The peptide repertoires of type 1 diabetes (T1D) associated DQ8, DQ2, and DQ8/2 are altered to a lesser degree by DM expression, and these molecules share overlapping features in their peptide binding motifs that are distinct from control DQ1 and DQ6 molecules. Peptides were categorized into DM‐resistant, DM‐dependent, or DM‐sensitive groups based on the mass spectrometry data, and representative peptides were tested in competitive binding assays and peptide dissociation rate experiments with soluble DQ6. Our data support the conclusion that high intrinsic stability of DQ‐peptide complexes is necessary but not sufficient to confer resistance to DM editing, and provide candidate parameters that may be useful in predicting the sensitivity of T‐cell epitopes to DM editing. DM editing favors the enrichment of stable DQ–peptide complexes. Unstable complexes are universally sensitive to DM. DM‐resistant complexes are stable, but a subset of stable complexes is sensitive to DM. The peptide repertoires of type 1 diabetes associated DQ molecules are impacted less by DM than control DQ molecules.