Naturally processed and presented epitopes of the islet cell autoantigen IA-2 eluted from HLA-DR4

J Clin Invest. 1999 Nov;104(10):1449-57. doi: 10.1172/JCI7936.


During immune responses, antigen-presenting cells (APCs) process antigens and present peptide epitopes complexed with human leukocyte antigen (HLA) molecules. CD4 cells recognize these naturally processed and presented epitopes (NPPEs) bound to HLA class II molecules. Epitope identification is important for developing diagnostic and therapeutic tools for immune-mediated diseases and providing insight into their etiology, but current approaches overlook effects of natural processing on epitope selection. We have developed a technique to identify NPPEs using mass spectrometry (MS) after antigen is targeted onto APCs using a lectin-based antigen delivery system (ADS). We applied the technique to identify NPPEs of the intracellular domain of the type 1 diabetes mellitus-associated (type 1 DM-associated) autoantigen insulinoma-associated-2 (IA-2ic), presented by HLA-DR4 (0401). IA-2ic-derived NPPEs eluted from HLA-DR4 constitute 6 sets of peptides nested around distinct core regions. Synthetic peptides based on these regions bind HLA-DR4 and elicit primary T-cell proliferation frequently in HLA-DR4-positive type 1 DM patients, but rarely in non-HLA-DR4 patients, and in none of the HLA-DR4 nondiabetic controls we tested. This flexible, direct approach identifies an HLA allele-specific map of NPPEs for any antigen, presented by any HLA class II molecule. This method should enable a greater understanding of epitope selection and lead to the generation of sensitive and specific reagents for detecting autoreactive T cells.

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Amino Acid Sequence
  • Antigen-Presenting Cells / immunology*
  • Arthritis, Rheumatoid / genetics
  • Arthritis, Rheumatoid / immunology*
  • Autoantibodies / analysis
  • Autoantigens / immunology*
  • B-Lymphocytes
  • Cell Line
  • Cell Membrane / immunology
  • Child
  • Diabetes Mellitus, Type 1 / genetics
  • Diabetes Mellitus, Type 1 / immunology*
  • Epitopes / chemistry
  • Epitopes / immunology*
  • Epitopes / isolation & purification
  • Europe
  • European Continental Ancestry Group
  • Genotype
  • HLA-DR4 Antigen / immunology*
  • Humans
  • Islets of Langerhans / immunology*
  • Lymphocyte Activation
  • Membrane Proteins / chemistry
  • Membrane Proteins / immunology*
  • Middle Aged
  • Molecular Sequence Data
  • Peptide Fragments / chemistry
  • Peptide Fragments / immunology
  • Protein Tyrosine Phosphatase, Non-Receptor Type 1
  • Protein Tyrosine Phosphatases / chemistry
  • Protein Tyrosine Phosphatases / immunology*
  • Receptor-Like Protein Tyrosine Phosphatases, Class 8
  • T-Lymphocytes / immunology
  • United States


  • Autoantibodies
  • Autoantigens
  • Epitopes
  • HLA-DR4 Antigen
  • Membrane Proteins
  • Peptide Fragments
  • PTPRN protein, human
  • Protein Tyrosine Phosphatase, Non-Receptor Type 1
  • Protein Tyrosine Phosphatases
  • Receptor-Like Protein Tyrosine Phosphatases, Class 8