title: Peptidomic analysis of type 1 diabetes associated HLA-DQ molecules and the impact of HLA-DM on peptide repertoire editing.
abstract: 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.
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.
authors.forename: Zemin
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Reyes-Vargas
authors.affiliation: ARUP Laboratories, University of Utah, Salt Lake City, UT, USA.
authors.forename: Hernando
authors.initials: H
authors.lastname: Escobar
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan.
authors.forename: Kuan Y
authors.initials: KY
authors.lastname: Chang
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.|ARUP Laboratories, University of Utah, Salt Lake City, UT, USA.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Barker
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.|ARUP Laboratories, University of Utah, Salt Lake City, UT, USA.
authors.forename: Alan L
authors.initials: AL
authors.lastname: Rockwood
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.|ARUP Laboratories, University of Utah, Salt Lake City, UT, USA.
authors.forename: Julio C
authors.initials: JC
authors.lastname: Delgado
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: He
authors.affiliation: Department of Pathology, University of Utah, Salt Lake City, UT, USA.
authors.forename: Peter E
authors.initials: PE
authors.lastname: Jensen
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D017951:Antigen Presentation; D000941:Antigens / Q000378:metabolism; D000944:Antigens, Differentiation, B-Lymphocyte / Q000378:metabolism; D003198:Computer Simulation; D003922:Diabetes Mellitus, Type 1 / Q000276:immunology*; D018984:Epitopes, T-Lymphocyte / Q000235:genetics; D057809:HEK293 Cells; D006681:HLA-D Antigens / Q000378:metabolism*; D006683:HLA-DQ Antigens / Q000378:metabolism*; D000949:Histocompatibility Antigens Class II / Q000378:metabolism; D006801:Humans; D010455:Peptides / Q000378:metabolism; D011485:Protein Binding; D055550:Protein Stability; D053719:Tandem Mass Spectrometry
chemical_list: D000941:Antigens; D000944:Antigens, Differentiation, B-Lymphocyte; D018984:Epitopes, T-Lymphocyte; D006681:HLA-D Antigens; C084245:HLA-DM antigens; D006683:HLA-DQ Antigens; D000949:Histocompatibility Antigens Class II; D010455:Peptides; C045084:invariant chain
keywords: Antigen presentation; Antigen processing; HLA-DM; MHC; Peptidomic analysis