Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis

J Proteome Res. 2017 Jan 6;16(1):122-136. doi: 10.1021/acs.jproteome.6b00386. Epub 2016 Nov 7.


Human leukocyte antigen-antigen D related (HLA-DR) molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory forms of arthritis. Here, we used LC-MS/MS to identify HLA-DR-presented self-peptides in cells taken directly from clinical samples: ST, synovial fluid mononuclear cells (SFMC), or peripheral blood mononuclear cells (PBMC) from five patients with rheumatoid arthritis (RA) and eight with Lyme arthritis (LA). We identified 1593 non-redundant HLA-DR-presented peptides, derived from 870 source proteins. A total of 67% of the peptides identified in SFMC and 55% of those found in PBMC were found in ST, but analysis of SFMC/PBMC also revealed new antigen-presented peptides. Peptides were synthesized and examined for reactivity with the patients' PBMC. To date, three autoantigens in RA and four novel autoantigens in LA, presented in ST and/or PBMC, were shown to be targets of T- and B-cell responses in these diseases; ongoing analyses may add to this list. Thus, immunoprecipitation and LC-MS/MS can now identify hundreds of HLA-DR-presented self-peptides from individual patients' tissues or fluids with mixed cell populations. Importantly, identification of HLA-DR-presented peptides from SFMC or PBMC allows testing of more patients, including those early in the disease. Direct analysis of clinical samples facilitates identification of novel immunogenic T-cell epitopes.

Keywords: HLA-DR; Lyme arthritis; autoantigens; peripheral blood mononuclear cells; rheumatoid arthritis; synovial fluid mononuclear cells; synovial tissue.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Antigen Presentation
  • Arthritis, Rheumatoid / genetics
  • Arthritis, Rheumatoid / immunology*
  • Arthritis, Rheumatoid / pathology
  • Autoantigens / chemistry
  • Autoantigens / genetics
  • Autoantigens / immunology
  • B-Lymphocytes / immunology
  • B-Lymphocytes / pathology
  • Gene Expression
  • Gene Ontology
  • HLA-DR Antigens / chemistry
  • HLA-DR Antigens / genetics
  • HLA-DR Antigens / immunology*
  • Humans
  • Lyme Disease / genetics
  • Lyme Disease / immunology*
  • Lyme Disease / pathology
  • Middle Aged
  • Molecular Sequence Annotation
  • Peptides / chemical synthesis
  • Peptides / immunology*
  • Peptides / isolation & purification
  • Synovial Fluid / chemistry
  • Synovial Fluid / immunology*
  • Synovial Membrane / chemistry
  • Synovial Membrane / immunology*
  • Synovial Membrane / pathology
  • T-Lymphocytes / immunology
  • T-Lymphocytes / pathology


  • Autoantigens
  • HLA-DR Antigens
  • Peptides