Immunoinformatics Applied to Modifying and Improving Biological Therapeutics

  • Anne S. De Groot
  • Paul M. Knopf
  • Daniel Rivera
  • William Martin


Protein therapeutics have recently emerged as a viable means of treating chronic diseases and are beginning to rival small-molecule drugs in market share. Although their promise of targeted therapy is a major medical advance, repeated administrations in many cases lead to development of antitherapeutic antibodies that compromise treatment. Multiple sources of immunogenicity are considered in this chapter with a focus on the T-cell-dependent immune response. Development of high-affinity antibodies depends on activation of T helper cells by antigen presentation. Disruption of antigen presentation in an antigen-specific manner would be a rational solution to this problem. Here we present the powerful combination of recombinant protein expression and immunoinformatic and molecular modeling tools as a means of reducing immunogenicity by modification of T-cell epitopes. This approach promises to bring to the clinic safer protein therapeutics both as first- and second-generation products.


Human Leukocyte Antigen Human Leukocyte Antigen Class Therapeutic Protein Peptide Epitope Human Leukocyte Antigen Allele 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Braun, A., Kwee, L., Labow, M.A., and Alsenz, (1997) Protein aggregates seem to play a key role among the parameters influencing the antigenicity of interferon alpha (IFN-alpha) in normal and transgenic mice. J. Pharm. Res. 14:1472-1478.CrossRefGoogle Scholar
  2. Carroll, M.C. (2004) The complement system in B cell regulation. Mol. Immunol. 41:141-146.PubMedCrossRefGoogle Scholar
  3. Casadevall, N., Nataf, J., Viron, B., Kolta, A., Kiladjian, J.J., Martin-Dupont, P., Michaud, P., Papo, T., Ugo, V., Teyssandier, I., Varet, B., and Mayeux, P. (2002) Pure red-cell aplasia and antierythropoietin antibodies in patients treated with recombinant erythropoietin. N. Engl. J. Med. 346:469-475.PubMedCrossRefGoogle Scholar
  4. Chatenoud, L. (1993) Immunologic monitoring during OKT3 therapy. Clin. Transplant. 7(4 Pt 2):422-430.PubMedGoogle Scholar
  5. Collen, D. (1996) Fibrin-selective thrombolytic therapy for acute myocardial infarction. Circulation 93:857-865.PubMedGoogle Scholar
  6. De Groot, A.S., Jesdale, B.M., Szu, E., and Schafer, J.R. (1997) An interactive Web site providing MHC ligand predictions: Application to HIV research. AIDS Res. Hum. Retroviruses 13:539-541.Google Scholar
  7. De Groot, A.S., Bosma, A., Chinai, N., Frost, J., Jesdale, B.M., Gonzalez, M.A., Martin, W., and Saint-Aubin, C. (2001a) From genome to vaccine: In silico predictions, ex vivo verification. Vaccine 19:4385-4395.Google Scholar
  8. De Groot, A.S., Saint Aubin, C.S., Rayner, J., and Martin, W. (2001b) Rapid determination of HLA B*07- ligands from the West Nile Virus genome. Emerg. Infect. Dis. 7:706-713.CrossRefGoogle Scholar
  9. De Groot, A.S., and Martin, W. (2003a) From immunome to vaccine: Epitope mapping and vaccine design tools. Novartis Found. Symp. 254:57-72.CrossRefGoogle Scholar
  10. De Groot, A.S., Jesdale, B., Martin, W., Saint-Aubin, C., Sbai, H., Bosma, A., Lieberman, J., Skowron, G., Mansourati, F., and Mayer, K.H. (2003b) Mapping cross-clade HIV-1 vaccine epitopes using a bioinformatics approach. Vaccine 21:4486-4504.Google Scholar
  11. Diamond, B. (2003) Speculations on the immunogenicity of self-proteins. Dev. Biol. (Basel)112:29-34.Google Scholar
  12. Elvin, J., Potter, C., Elliott, T., Cerundolo, V., and Townsend, A. (1993) A method to quantify binding of unlabeled peptides to class I MHC molecules and detect their allele specificity. J. Immunol. Methods 158:161-171.PubMedCrossRefGoogle Scholar
  13. Finkelman, F.D., Lees, A., and Morris, S.C. (1992) Antigen presentation by B lymphocytes to CD4+ T lymphocytes in vivo: Importance for B lymphocyte and T lymphocyte activation. Semin. Immunol. 4:247-255.PubMedGoogle Scholar
  14. Forsthuber, T.G., Shive, C.L., Wienhold, W., de Graaf, K., Spack, E.G., Sublett, R., Melms, A., Kort, J., Racke, M.K., and Weissert, R. (2001) T-cell epitopes of human myelin oligodendrocyte glycoprotein identified in HLA-DR4 (DRB1*0401) transgenic mice are encephalitogenic and are presented by human B cells. J. Immunol. 167:7119-7125.PubMedGoogle Scholar
  15. Fowell, D., and Mason, D. (1993) Evidence that the T-cell repertoire of normal rats contains cells with the potential to cause diabetes. Characterization of the CD4+ T-cell subset that inhibits this autoimmune potential. J. Exp. Med. 177:627-636.PubMedCrossRefGoogle Scholar
  16. Haselbeck, A. (2003) Epoetins: Differences and their relevance to immunogenicity. Curr. Med. Res. Opin. 19:430-432.PubMedGoogle Scholar
  17. Hill, A.V., Jepson, A., Plebanski, M., and Gilbert, S.C. (1997) Genetic analysis of host-parasite coevolution in human malaria. Philos. Trans. R. Soc. London Ser. B 352:1317-1325.CrossRefGoogle Scholar
  18. Jensen, P.B., Birkeland, S.A., Rohrp, N., Elbirk, A., and Jorgensen, K.A. (1996) Development of anti-OKT3 antibodies after OKT3 treatment. Scand. J. Urol. Nephrol. 30:227-230.PubMedCrossRefGoogle Scholar
  19. Josic, D., Buchacher, A., Kannicht, C., Lim, Y.P., Loster, K., Pock, K., Robinson, S., Schwinn, H., and Stadler, M. (1999) Degradation products of factor VIII which can lead to increased immunogenicity. Vox Sang. 77(Suppl. 1):90.PubMedCrossRefGoogle Scholar
  20. Kappler, J.W., Roehm, N., and Marrack, P. (1987) T-cell tolerance by clonal elimination in the thymus. Cell 49:273-280.PubMedCrossRefGoogle Scholar
  21. Kast, W.M., Brandt, R.M., Sidney, J., Drijfhout, J.W., Kubo, R.T., Grey, H.M., Melief, C.J., and Sette, A. (1994) Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins. J. Immunol. 152:3904-3912.PubMedGoogle Scholar
  22. Keech, C.L., Farris, A.D., Beroukas, D., Gordon, T.P., and McCluskey, J. (2001) Cognate T-cell help is sufficient to trigger anti-nuclear autoantibodies in naive mice. J. Immunol. 166:5826-5834.PubMedGoogle Scholar
  23. Kersh, G.J., Miley, M.J., Nelson, C.A., Grakoui, A., Horvath, S., Donermeyer, D.L., Kappler, J., Allen, P.M., and Fremont, D.H. (2001) Structural and functional consequences of altering a peptide MHC anchor residue. J. Immunol.166:3345-3354.PubMedGoogle Scholar
  24. Kontsek, P., Liptakova, H., and Kontsekova, E. (1999) Immunogenicity of interferon-alpha 2 in therapy: Structural and physiological aspects. Acta Virol. 43:63-70.PubMedGoogle Scholar
  25. Koren, E., Zuckerman, L.A., and Mire-Suis, A.R. (2002) Immune responses to therapeutic proteins in humans - Clinical significance, assessment and prediction. Curr. Pharm. Biotechnol. 3:349-360.PubMedCrossRefGoogle Scholar
  26. Meister, G.E., Roberts, C.G.P., Berzofsky, J.A., and De Groot, A.S. (1995) Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences. Vaccine 13:581-591.PubMedCrossRefGoogle Scholar
  27. Miller, L.L., Korn, E.L., Stevens, D.S., Janik, J.E., Gause, B.L., Kopp, W.C., Holmlund, J.T., Curti, B.D., Sznol, M., Smith, J.W., Urba, W.J., Donegan, S.E., Watson, T.M., and Longo, D.L. (1999) Abrogation of the hematological and biological activities of the interleukin-3/granulocyte-macrophage colony-stimulating factor fusion protein PIXY321 by neutralizing anti-PIXY321 antibodies in cancer patients receiving high-dose carboplatin. Blood 93:3250-3258.PubMedGoogle Scholar
  28. Mullbacher, A. (1992) Viral escape from immune recognition: Multiple strategies of adenoviruses. Immunol. Cell Biol. 70(Part 1):59-63.PubMedCrossRefGoogle Scholar
  29. Nilsson, J.B., Nilsson, T.K., Jansson, J.H., Boman, K., Soderberg, S., and Naslund, U. (2002) The effect of streptokinase neutralizing antibodies on fibrinolytic activity and reperfusion following streptokinase treatment in acute myocardial infarction. J. Intern. Med. 252:405-411.PubMedCrossRefGoogle Scholar
  30. Nissenson, A.R. (2001) Novel erythropoiesis stimulating protein for managing the anemia of chronic kidney disease. Am. J. Kidney Dis. 38:1390-1397.PubMedGoogle Scholar
  31. Panina-Bordignon, P., Tan, A., Termijtelen, A., Demotz, S., Corradin, G., and Lanzavecchia, A. (1989) Universally immunogenic T cell epitopes: Promiscuous binding to human MHC class II and promiscuous recognition by T cells. Eur. J. Immunol. 19:2237-2242.PubMedCrossRefGoogle Scholar
  32. Pevear, D.C., Luo, M., and Lipton, H.L. (1988) Three-dimensional model of the capsid proteins of two biologically different Theiler virus strains: Clustering of amino acid difference identifies possible locations of immunogenic sites on the virion. Proc. Natl. Acad. Sci. USA 85:4496-4500.PubMedCrossRefGoogle Scholar
  33. Prabhakar, S.S., and Muhlfelder, T. (1997) Antibodies to recombinant human erythropoietin causing pure red cell aplasia. Clin. Nephrol. 47:331-335.PubMedGoogle Scholar
  34. Reijonen, H., Novak, E.J., Kochik, S., Heninger, A., Liu, A.W., Kwok, W.W., and Nepom, G.T. (2002) Detection of GAD65-specific T-cells by major histocompatibility complex class II tetramers in type 1 diabetic patients and at-risk subjects. Diabetes 51:1375-1382.PubMedCrossRefGoogle Scholar
  35. Rosenberg, A.S. (2003) Immunogenicity of biological therapeutics: A hierarchy of concerns. Dev. Biol. (Basel) 112:15-21.Google Scholar
  36. Ryff, J.C., and Schellekens, H. (2002) Immunogenicity of rDNA-derived pharmaceuticals. Trends Pharmacol. Sci. 23:254-256.PubMedCrossRefGoogle Scholar
  37. Scanlan, M.J., and Jager, D. (2001) Challenges to the development of antigen-specific breast cancer vaccines. Breast Cancer Res. 3:95-98.PubMedCrossRefGoogle Scholar
  38. Schafer, J.A., Jesdale, B.M., George, J.A., Kouttab, N.M., and De Groot, A.S. (1998) Prediction of well conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix. Vaccine 16:1880-1884.PubMedCrossRefGoogle Scholar
  39. So, T., Ito, H.-O., Koga, T., Watanabe, S., Ueda, T., and Imoto, T. (1997) Depression of T-cell epitope generation by stabilizing hen lysozyme. J. Biol. Chem. 272:32136-32140.PubMedCrossRefGoogle Scholar
  40. Stein, K.E. (2002) Immunogenicity: Concepts/issues/concerns. Dev. Biol. (Basel) 109:15-23.Google Scholar
  41. Sturniolo, T., Bono, E., Ding, J., Raddrizzani, L., Tuereci, O., Sahin, U., Braxenthaler, M., Gallazzi, F., Protti, M.P., Sinigaglia, F., and Hammer, J. (1999) Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nature Biotech. 17:555-561.CrossRefGoogle Scholar
  42. Tompkins, S.M., Rota, P.A., Moore, J.C., and Jensen, P.E. (1993) A europium fluoroimmunoassay for measuring binding of antigen to class II MHC glycoproteins. J. Immunol. Methods 163:209-216.PubMedCrossRefGoogle Scholar
  43. Vossen, M.T., Westerhout, E.M., Soderberg-Naucler, C., and Wiertz, E.J. (2002) Viral immune evasion: A masterpiece of evolution. Immunogenetics 54:527-542.PubMedCrossRefGoogle Scholar
  44. Vuong, K.D., and Jankovic, J. (2005) Long-term botulinum toxin efficacy, safety, and immunogenicity. Mov. Disord. 20:592-597.PubMedCrossRefGoogle Scholar
  45. Wadhwa, M., Mellstedt, H., Small, E., and Thorpe, R. (2003) Immunogenicity of GM-CSF products in cancer patients following immunostimulatory therapy with GM-CSF. Dev. Biol. (Basel) 12:61-67.CrossRefGoogle Scholar
  46. Warmerdam, P.A., Plaisance, S., Vanderlick, K., Vandervoort, P., Brepoels, K., Collen, D., and De Maeyer, M. (2002) Elimination of a human T-cell region in staphylokinase by T-cell screening and computer modeling. Thromb. Haemost. 87:666-673.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC. 2008

Authors and Affiliations

  • Anne S. De Groot
    • 1
    • 2
  • Paul M. Knopf
    • 1
    • 2
  • Daniel Rivera
    • 2
  • William Martin
    • 2
  1. 1.Department of MedicineBrown UniversityProvidenceUSA
  2. 2.EpiVax, IncProvidenceUSA

Personalised recommendations