UMMS Affiliation

Department of Pathology; Proteomics and Mass Spectometry Facility; Department of Biochemistry and Molecular Pharmacology; Graduate School of Biomedical Sciences

Publication Date


Document Type

Article Postprint


Amino Acids, Peptides, and Proteins | Biochemistry | Cell Biology | Cells | Computational Biology | Genomics | Immunity | Immunopathology | Molecular Biology


Presentation of antigenic peptides on MHC-II molecules is essential for tolerance to self and for initiation of immune responses against foreign antigens. DO (HLA-DO in humans, H2-O in mice) is a non-classical MHC-II protein that has been implicated in control of autoimmunity and regulation of neutralizing antibody responses to viruses. These effects likely are related to a role of DO in selecting MHC-II epitopes, but previous studies examining the effect of DO on presentation of selected CD4 T cell epitopes have been contradictory. To understand how DO modulates MHC-II antigen presentation, we characterized the full spectrum of peptides presented by MHC-II molecules expressed by DO-sufficient and DO-deficient antigen-presenting cells in vivo and in vitro using quantitative mass spectrometry approaches. We found that DO controlled the diversity of the presented peptide repertoire, with a subset of peptides presented only when DO was expressed. Antigen-presenting cells express another non-classical MHC-II protein, DM, which acts as a peptide editor by preferentially catalyzing the exchange of less stable MHC-II peptide complexes, and which is inhibited when bound to DO. Peptides presented uniquely in the presence of DO were sensitive to DM-mediated exchange, suggesting that decreased DM editing was responsible for the increased diversity. DO-deficient mice mounted CD4 T cell responses against wild-type antigen-presenting cells, but not vice versa, indicating that DO-dependent alterations in the MHC-II peptidome could be recognized by circulating T cells. These data suggest that cell-specific and regulated expression of HLA-DO serves to fine-tune MHC-II peptidomes, to enhance self-tolerance to a wide spectrum of epitopes while allowing focused presentation of immunodominant epitopes during an immune response.


Absolute quantification, Immunoaffinity, Immunology, Label-free quantification, Mass Spectrometry, Peptidomics

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Published under license by The American Society for Biochemistry and Molecular Biology, Inc. Accepted manuscript posted as allowed by the publisher's copyright policy at

DOI of Published Version



Mol Cell Proteomics. 2018 Dec 20. pii: mcp.RA118.000956. doi: 10.1074/mcp.RA118.000956. [Epub ahead of print] Link to article on publisher's site

Journal/Book/Conference Title

Molecular and cellular proteomics : MCP

Related Resources

Link to Article in PubMed

PubMed ID