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This article is part of the supplement: APBioNet – Fifth International Conference on Bioinformatics (InCoB2006)

Open Access Proceedings

Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris

Joo Chuan Tong12, Tin Wee Tan1, Animesh A Sinha3* and Shoba Ranganathan14*

Author Affiliations

1 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore

2 Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore

3 Center for Investigative Dermatology, Division of Dermatology and Cutaneous Sciences, College of Human Medicine, Michigan State University, 4120 Biomedical and Physical Sciences Building, East Lansing, MI 48824, USA

4 Department of Chemistry and Biomolecular Sciences & Biotechnology Research Institute, Macquarie University, Sydney NSW 2109, Australia

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BMC Bioinformatics 2006, 7(Suppl 5):S7  doi:10.1186/1471-2105-7-S5-S7

Published: 18 December 2006

Abstract

Background

Pemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles DRB1*0402 and DQB1*0503. The target antigen of PV, desmoglein 3 (Dsg3), is crucial for initiating T-cell response in early disease. Although a number of T-cell specificities within Dsg3 have been reported, the number is limited and the role of T-cells in the pathogenesis of PV remains poorly understood. We report here a structure-based model for the prediction of peptide binding to DRB1*0402 and DQB1*0503. The scoring functions were rigorously trained, tested and validated using experimentally verified peptide sequences.

Results

High predictivity is obtained for both DRB1*0402 (r2 = 0.90, s = 1.20 kJ/mol, q2 = 0.82, spress = 1.61 kJ/mol) and DQB1*0503 (r2 = 0.95, s = 1.20 kJ/mol, q2 = 0.75, spress = 2.15 kJ/mol) models, compared to experimental data. We investigated the binding patterns of Dsg3 peptides and illustrate the existence of multiple immunodominant epitopes that may be responsible for both disease initiation and propagation in PV. Further analysis reveals that DRB1*0402 and DQB1*0503 may share similar specificities by binding peptides at different binding registers, thus providing a molecular mechanism for the dual HLA association observed in PV.

Conclusion

Collectively, the results of this study provide interesting new insights into the pathology of PV. This is the first report illustrating high-level of cross-reactivity between both PV-implicated alleles, DRB1*0402 and DQB1*0503, as well as the existence of a potentially large number of T-cell epitopes throughout the entire Dsg3 extracellular domain (ECD) and transmembrane region. Our results reveal that DR4 and DR6 PV may initiate in the ECD and transmembrane region respectively, with implications for immunotherapeutic strategies for the treatment of this autoimmune disease.