Definition of Naturally Processed Peptides Reveals Convergent Presentation of Autoantigenic Topoisomerase I Epitopes in Scleroderma

Arthritis Rheumatol. 2020 Aug;72(8):1375-1384. doi: 10.1002/art.41248. Epub 2020 Jun 26.


Objective: Autoimmune responses to DNA topoisomerase I (topo I) are found in a subset of scleroderma patients who are at high risk for interstitial lung disease (ILD) and mortality. Anti-topo I antibodies (ATAs) are associated with specific HLA-DRB1 alleles, and the frequency of HLA-DR-restricted topo I-specific CD4+ T cells is associated with the presence, severity, and progression of ILD. Although this strongly implicates the presentation of topo I peptides by HLA-DR in scleroderma pathogenesis, the processing and presentation of topo I has not been studied.

Methods: We developed a natural antigen processing assay (NAPA) to identify putative CD4+ T cell epitopes of topo I presented by monocyte-derived dendritic cells (mo-DCs) from 6 ATA-positive patients with scleroderma. Mo-DCs were pulsed with topo I protein, HLA-DR-peptide complexes were isolated, and eluted peptides were analyzed by mass spectrometry. We then examined the ability of these naturally presented peptides to induce CD4+ T cell activation in 11 ATA-positive and 11 ATA-negative scleroderma patients.

Results: We found that a common set of 10 topo I epitopes was presented by Mo-DCs from scleroderma patients with diverse HLA-DR variants. Sequence analysis revealed shared peptide-binding motifs within the HLA-DRβ chains of ATA-positive patients and a subset of topo I epitopes with distinct sets of anchor residues capable of binding to multiple different HLA-DR variants. The NAPA-derived epitopes elicited robust CD4+ T cell responses in 73% of ATA-positive patients (8 of 11), and the number of epitopes recognized correlated with ILD severity (P = 0.025).

Conclusion: These findings mechanistically implicate the presentation of a convergent set of topo I epitopes in the development of scleroderma.

Publication types

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

MeSH terms

  • Adult
  • Alleles
  • Autoantibodies / immunology
  • Autoantigens / immunology
  • CD4-Positive T-Lymphocytes / immunology
  • DNA Topoisomerases, Type I / immunology*
  • Dendritic Cells / immunology
  • Epitopes, T-Lymphocyte / immunology*
  • Female
  • HLA-DRB1 Chains / immunology
  • Humans
  • Lung Diseases, Interstitial / immunology*
  • Lymphocyte Activation / immunology
  • Male
  • Peptides / immunology*
  • Scleroderma, Systemic / immunology*
  • Severity of Illness Index


  • Autoantibodies
  • Autoantigens
  • Epitopes, T-Lymphocyte
  • HLA-DRB1 Chains
  • Peptides
  • DNA Topoisomerases, Type I
  • TOP1 protein, human