A Comparative Analysis of the Peptide Repertoires of HLA-DR Molecules Differentially Associated With Rheumatoid Arthritis

Arthritis Rheumatol. 2016 Oct;68(10):2412-21. doi: 10.1002/art.39736.


Objective: To evaluate similarity of the peptide repertoires bound to HLA-DR molecules that are differentially associated with rheumatoid arthritis (RA), and to define structural features of the shared peptides.

Methods: Peptide pools bound to HLA-DRB1*01:01, HLA-DRB1*04:01, and HLA-DRB1*10:01 (RA associated) and those bound to HLA-DRB1*15:01 (non-RA-associated) were purified and analyzed by liquid chromatography (LC) matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MS) and LC-ion-trap MS. Peptide pools from each allotype were compared in terms of size, protein origin, composition, and affinity (both theoretical and experimental with some peptides). Finally, 1 peptide sequenced from DR1, DR4, and DR10, but not from DR15, was modeled in complex with all 4 HLA-DRB1 molecules and HLA-DRB5*01:01.

Results: A total of 6,309 masses and 962 unique peptide sequences were compared. DR10 shared 29 peptides with DR1, 9 with DR4, and 1 with DR15; DR1 shared 6 peptides with DR4 and 9 with DR15; and DR4 and DR15 shared 4 peptides. The direct identification of peptide ligands indicated that DR1 and DR10 were the most similar molecules regarding the peptides that they could share. The peptides common to these molecules contained a high proportion of Leu at P4 and basic residues at P8 binding core positions.

Conclusion: The degree of overlap between peptide repertoires associated with different HLA-DR molecules is low. The repertoires associated with DR1 and DR10 have the highest similarity among the molecules analyzed (∼10% overlap). Among the peptides shared between DR1 and DR10, a high proportion contained Leu(4) and basic residues at the P8 position of the binding core.

Publication types

  • Comparative Study

MeSH terms

  • Amino Acid Sequence
  • Arthritis, Rheumatoid / metabolism*
  • Carrier Proteins / metabolism
  • Cell Line
  • Chromatography, Liquid
  • HLA-DR Serological Subtypes / metabolism
  • HLA-DR1 Antigen / metabolism
  • HLA-DR4 Antigen / metabolism
  • HLA-DRB1 Chains / metabolism*
  • HLA-DRB5 Chains / metabolism
  • HSP70 Heat-Shock Proteins / metabolism
  • Humans
  • Intracellular Signaling Peptides and Proteins
  • Lysosome-Associated Membrane Glycoproteins / metabolism
  • Peptides / metabolism*
  • Receptors, LDL / metabolism
  • Receptors, Lipoprotein / metabolism
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization


  • Carrier Proteins
  • HLA-DR Serological Subtypes
  • HLA-DR1 Antigen
  • HLA-DR10 antigen
  • HLA-DR4 Antigen
  • HLA-DRB1 Chains
  • HLA-DRB1*01:01 antigen
  • HLA-DRB1*04:01 antigen
  • HLA-DRB1*15:01 antigen
  • HLA-DRB5 Chains
  • HSP70 Heat-Shock Proteins
  • Intracellular Signaling Peptides and Proteins
  • LAMTOR1 protein, human
  • Lysosome-Associated Membrane Glycoproteins
  • Peptides
  • Receptors, LDL
  • Receptors, Lipoprotein
  • lipolysis-stimulated receptor