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In Silico Prediction of Peptides Binding to Multiple HLA-DR Molecules Accurately Identifies Immunodominant Epitopes from gp43 of Paracoccidioides brasiliensis Frequently Recognized in Primary Peripheral Blood Mononuclear Cell Responses from Sensitized Individuals

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Abstract

One of the major drawbacks limiting the use of synthetic peptide vaccines in genetically distinct populations is the fact that different epitopes are recognized by T cells from individuals displaying distinct major histocompatibility complex molecules. Immunization of mice with peptide (181–195) from the immunodominant 43 kDa glycoprotein of Paracoccidioides brasiliensis (gp43), the causative agent of Paracoccidioidomycosis (PCM), conferred protection against infectious challenge by the fungus. To identify immunodominant and potentially protective human T-cell epitopes in gp43, we used the TEPITOPE algorithm to select peptide sequences that would most likely bind multiple HLA-DR molecules and tested their recognition by T cells from sensitized individuals. The 5 most promiscuous peptides were selected from the gp43 sequence and the actual promiscuity of HLA binding was assessed by direct binding assays to 9 prevalent HLA-DR molecules. Synthetic peptides were tested in proliferation assays with peripheral blood mononuclear cells (PBMC) from PCM patients after chemotherapy and healthy controls. PBMC from 14 of 19 patients recognized at least one of the promiscuous peptides, whereas none of the healthy controls recognized the gp43 promiscuous peptides. Peptide gp43(180–194) was recognized by 53% of patients, whereas the other promiscuous gp43 peptides were recognized by 32% to 47% of patients. The frequency of peptide binding and peptide recognition correlated with the promiscuity of HLA-DR binding, as determined by TEPITOPE analysis. In silico prediction of promiscuous epitopes led to the identification of naturally immunodominant epitopes recognized by PBMC from a significant proportion of a genetically heterogeneous patient population exposed to P. brasiliensis. The combination of several such epitopes may increase the frequency of positive responses and allow the immunization of genetically distinct populations.

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Acknowledgments

We would like to thank Dr Maria Lúcia Marin who helped us with determining the HLA of patients, Dr Simone Gonçalves da Fonseca and Renata Cristina Ferreira who helped with FACS acquisition, and Washington Robert da Silva for technical assistance. This study was supported by grant 00-08404-3 and LKI was supported by fellowship grant 99/15319-6 from São Paulo State Science Funding Agency (FAPESP). ECN is the recipient of productivity grant 520533/97-6 from the Brazilian National Research Council (CNPq). AS and JS are supported by National Institutes of Health contracts N01-AI-95362 and HHSN266200400006C.

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Authors and Affiliations

  1. Laboratory of Immunology-Heart Institute (Incor), Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo Medical School, Av. Dr. Eneas de Carvalho Aguiar 44, Bloco 2, 9° andar, São Paulo, SP, 05403-000, Brazil

    Leo Kei Iwai, Anna Carla Goldberg, Jorge Kalil & Edecio Cunha-Neto

  2. Division of Clinical Immunology and Allergy, Millenium Institutes, São Paulo, Brazil

    Jorge Kalil & Edecio Cunha-Neto

  3. Institute for Investigation in Immunology, Millenium Institutes, São Paulo, Brazil

    Leo Kei Iwai, Anna Carla Goldberg, Jorge Kalil & Edecio Cunha-Neto

  4. Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil

    Márcia Yoshida & Maria Aparecida Shikanai-Yasuda

  5. Department of Biophysics, Federal University of São Paulo, UNIFESP, São Paulo, Brazil

    Leo Kei Iwai, Maria Aparecida Juliano & Luiz Juliano

  6. Discipline of Cell Biology, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, UNIFESP, São Paulo, Brazil

    Luiz Rodolpho Travassos

  7. Department of Genomic and Information Sciences, Hoffmann-La Roche Inc, Nutley, New Jersey, USA

    Jurgen Hammer

  8. La Jolla Institute for Allergy and Immunology, San Diego, California, USA

    John Sidney & Alessandro Sette

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  1. Leo Kei Iwai
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  2. Márcia Yoshida
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Correspondence to Edecio Cunha-Neto.

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Iwai, L.K., Yoshida, M., Sidney, J. et al. In Silico Prediction of Peptides Binding to Multiple HLA-DR Molecules Accurately Identifies Immunodominant Epitopes from gp43 of Paracoccidioides brasiliensis Frequently Recognized in Primary Peripheral Blood Mononuclear Cell Responses from Sensitized Individuals. Mol Med 9, 209–219 (2003). https://doi.org/10.1007/BF03402131

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