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Clinical and Developmental Immunology
Volume 2013 (2013), Article ID 467852, 7 pages
Evaluating the Immunogenicity of Protein Drugs by Applying In Vitro MHC Binding Data and the Immune Epitope Database and Analysis Resource
La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, San Diego, CA 92037, USA
Received 6 May 2013; Accepted 3 September 2013
Academic Editor: Pedro A. Reche
Copyright © 2013 Sinu Paul et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- H. Kropshofer and T. Singer, “Overview of cell-based tools for pre-clinical assessment of immunogenicity of biotherapeutics,” Journal of Immunotoxicology, vol. 3, no. 3, pp. 131–136, 2006.
- G. J. Wolbink, L. A. Aarden, and B. A. C. Dijkmans, “Dealing with immunogenicity of biologicals: assessment and clinical relevance,” Current Opinion in Rheumatology, vol. 21, no. 3, pp. 211–215, 2009.
- V. Brinks, W. Jiskoot, and H. Schellekens, “Immunogenicity of therapeutic proteins: the use of animal models,” Pharmaceutical Research, vol. 28, no. 10, pp. 2379–2385, 2011.
- Guidance for industry: Immunogenicity assessment for therapeutic protein products. Food and Drug Administration, U.S. Department of Health and Human Services, 2013.
- K. Murphy, Janeway’s Immunobiology, Garland Science, New York, NY, USA, 8th edition, 2011.
- W. E. Paul, Fundamental Immunology, Lippincott Williams & Wilkins, Philadelphia, Pa, USA, 7th edition, 2013.
- C. O. Benoist, D. J. Mathis, M. R. Kanter, et al., “Regions of allelic hypervariability in the murine Aα immune response gene,” Cell, vol. 34, no. 1, pp. 169–177, 1983.
- J. H. Brown, T. S. Jardetzky, J. C. Gorga et al., “Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1,” Nature, vol. 364, no. 6432, pp. 33–39, 1993.
- J. Greenbaum, J. Sidney, J. Chung, C. Brander, B. Peters, and A. Sette, “Functional classification of class II human leukocyte antigen (HLA) molecules reveals seven different supertypes and a surprising degree of repertoire sharing across supertypes,” Immunogenetics, vol. 63, no. 6, pp. 325–335, 2011.
- D. M. McKinney, S. Southwood, D. Hinz et al., “A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population,” Immunogenetics, vol. 65, no. 5, pp. 357–370, 2013.
- M. Nielsen, C. Lundegaard, and O. Lund, “Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method,” BMC Bioinformatics, vol. 8, article 238, 2007.
- A. Sette, S. Buus, E. Appella et al., “Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 9, pp. 3296–3300, 1989.
- V. Brusic, G. Rudy, G. Honeyman, J. Hammer, and L. Harrison, “Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network,” Bioinformatics, vol. 14, no. 2, pp. 121–130, 1998.
- S. Tangri, B. R. Mothé, J. Eisenbraun et al., “Rationally engineered therapeutic proteins with reduced immunogenicity,” The Journal of Immunology, vol. 174, no. 6, pp. 3187–3196, 2005.
- Y. Kim, J. Ponomarenko, Z. Zhu, et al., “Immune epitope database analysis resource,” Nucleic Acids Research, vol. 40, pp. W525–W530, 2008.
- J. A. Bristol, A. Gallo-Penn, J. Andrews, N. Idamakanti, M. Kaleko, and S. Connelly, “Adenovirus-mediated factor VIII gene expression results in attenuated anti-factor VIII-specific immunity in hemophilia A mice compared with factor VIII protein infusion,” Human Gene Therapy, vol. 12, no. 13, pp. 1651–1661, 2001.
- R. Kulkarni, L. M. Aledort, E. Berntorp et al., “Therapeutic choices for patients with hemophilia and high-titer inhibitors,” American Journal of Hematology, vol. 67, no. 4, pp. 240–246, 2001.
- J. Y. Reginster, S. Gaspar, R. Deroisy, B. Zegels, and P. Franchimont, “Prevention of osteoporosis with nasal salmon calcitonin: effect of anti-salmon calcitonin antibody formation,” Osteoporosis International, vol. 3, no. 5, pp. 261–264, 1993.
- A. Grauer, R. Ziegler, and F. Raue, “Clinical significance of antibodies against calcitonin,” Experimental and Clinical Endocrinology & Diabetes, vol. 103, no. 6, pp. 345–351, 1995.
- N. Casadevall, J. Nataf, B. Viron et al., “Pure red-cell aplasia and antierythropoietin antibodies in patients treated with recombinant erythropoietin,” The New England Journal of Medicine, vol. 346, no. 7, pp. 469–475, 2002.
- S. K. Gershon, H. Luksenburg, T. R. Coté et al., “Pure red-cell aplasia and recombinant erythropoietin,” The New England Journal of Medicine, vol. 346, no. 20, pp. 1584–1586, 2002.
- F. Deisenhammer, I. Mayringer, J. Harvey et al., “A comparative study of the relative bioavailability of different interferon beta preparations,” Neurology, vol. 54, no. 11, pp. 2055–2060, 2000.
- L. J. Stern, J. H. Brown, T. S. Jardetzky et al., “Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide,” Nature, vol. 368, no. 6468, pp. 215–221, 1994.
- A. Y. Rudensky, P. Preston-Hurlburt, S. Hong, A. Barlow, and C. A. Janeway, “Sequence analysis of peptides bound to MHC class II molecules,” Nature, vol. 353, no. 6345, pp. 622–627, 1991.
- R. M. Chicz, R. G. Urban, W. S. Lane et al., “Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size,” Nature, vol. 358, no. 6389, pp. 764–768, 1992.
- F. Castellino, G. Zhong, and R. N. Germain, “Antigen presentation by MHC class II molecules: invariant chain function, protein trafficking, and the molecular basis of diverse determinant capture,” Human Immunology, vol. 54, no. 2, pp. 159–169, 1997.
- H. Rammensee, T. Friede, and S. Stevanović, “MHC ligands and peptide motifs: first listing,” Immunogenetics, vol. 41, no. 4, pp. 178–228, 1995.
- P. A. Reche, J.-P. Glutting, H. Zhang, and E. L. Reinherz, “Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles,” Immunogenetics, vol. 56, no. 6, pp. 405–419, 2004.
- O. Rotzschke, K. Falk, S. Stevanovic, G. Jung, P. Walden, and H. G. Rammensee, “Exact prediction of a natural T cell epitope,” European Journal of Immunology, vol. 21, no. 11, pp. 2891–2894, 1991.
- H. H. Bui, J. Sidney, B. Peters et al., “Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications,” Immunogenetics, vol. 57, no. 5, pp. 304–314, 2005.
- M. Nielsen, O. Lund, S. Buus, and C. Lundegaard, “MHC Class II epitope predictive algorithms,” Immunology, vol. 130, no. 3, pp. 319–328, 2010.
- C. Lundegaard, I. Hoof, O. Lund, and M. Nielsen, “State of the art and challenges in sequence based T-cell epitope prediction,” Immunome Research, vol. 6, supplement 2, article S3, 2010.
- P. Wang, J. Sidney, C. Dow, B. Mothé, A. Sette, and B. Peters, “A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach,” PLoS Computational Biology, vol. 4, no. 4, Article ID e1000048, 2008.
- H. H. Lin, G. L. Zhang, S. Tongchusak, E. L. Reinherz, and V. Brusic, “Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research,” BMC Bioinformatics, vol. 9, supplement 12, article S22, 2008.
- M. Nielsen and O. Lund, “NN-align, an artificial neural network-based alignment algorithm for MHC class II peptide binding prediction,” BMC Bioinformatics, vol. 10, article 296, 2009.
- M. Nielsen, S. Justesen, O. Lund, C. Lundegaard, and S. Buus, “NetMHCIIpan-2.0—improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure,” Immunome Research, vol. 6, article 9, 2010.
- N. Salimi, W. Fleri, B. Peters, and A. Sette, “The immune epitope database: a historical retrospective of the first decade,” Immunology, vol. 137, no. 2, pp. 117–123, 2012.
- P. Wang, J. Sidney, Y. Kim et al., “Peptide binding predictions for HLA DR, DP and DQ molecules,” BMC Bioinformatics, vol. 11, article 568, 2010.
- T. Sturniolo, E. Bono, J. Ding et al., “Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices,” Nature Biotechnology, vol. 17, no. 6, pp. 555–561, 1999.
- J. A. Swets, “Measuring the accuracy of diagnostic systems,” Science, vol. 240, no. 4857, pp. 1285–1293, 1988.
- S. Southwood, J. Sidney, A. Kondo et al., “Several common HLA-DR types share largely overlapping peptide binding repertoires,” The Journal of Immunology, vol. 160, no. 7, pp. 3363–3373, 1998.
- C. Oseroff, J. Sidney, M. F. Kotturi et al., “Molecular determinants of T cell epitope recognition to the common timothy grass allergen,” The Journal of Immunology, vol. 185, no. 2, pp. 943–955, 2010.
- C. Oseroff, J. Sidney, V. Tripple et al., “Analysis of T cell responses to the major allergens from german cockroach: epitope specificity and relationship to IgE production,” The Journal of Immunology, vol. 189, no. 2, pp. 679–688, 2012.
- C. Oseroff, J. Sidney, R. Vita et al., “T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts,” The Journal of Immunology, vol. 189, no. 4, pp. 1800–1811, 2012.
- V. Schulten, J. A. Greenbaum, M. Hauser et al., “Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals,” Proceedings of the National Academy of Sciences, vol. 110, no. 9, pp. 3459–3464, 2013.
- C. S. L. Arlehamn, A. Gerasimova, F. Mele et al., “Memory T cells in latent mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset,” PLoS Pathogens, vol. 9, no. 1, Article ID e1003130, 2013.