TCPro: an In Silico Risk Assessment Tool for Biotherapeutic Protein Immunogenicity
Most immune responses to biotherapeutic proteins involve the development of anti-drug antibodies (ADAs). New drugs must undergo immunogenicity assessments to identify potential risks at early stages in the drug development process. This immune response is T cell-dependent. Ex vivo assays that monitor T cell proliferation often are used to assess immunogenicity risk. Such assays can be expensive and time-consuming to carry out. Furthermore, T cell proliferation requires presentation of the immunogenic epitope by major histocompatibility complex class II (MHCII) proteins on antigen-presenting cells. The MHC proteins are the most diverse in the human genome. Thus, obtaining cells from subjects that reflect the distribution of the different MHCII proteins in the human population can be challenging. The allelic frequencies of MHCII proteins differ among subpopulations, and understanding the potential immunogenicity risks would thus require generation of datasets for specific subpopulations involving complex subject recruitment. We developed TCPro, a computational tool that predicts the temporal dynamics of T cell counts in common ex vivo assays for drug immunogenicity. Using TCPro, we can test virtual pools of subjects based on MHCII frequencies and estimate immunogenicity risks for different populations. It also provides rapid and inexpensive initial screens for new biotherapeutics and can be used to determine the potential immunogenicity risk of new sequences introduced while bioengineering proteins. We validated TCPro using an experimental immunogenicity dataset, making predictions on the population-based immunogenicity risk of 15 protein-based biotherapeutics. Immunogenicity rankings generated using TCPro are consistent with the reported clinical experience with these therapeutics.
KEY WORDSanti-drug antibodies (ADA) computational approaches immunogenicity protein-based therapeutics
This project was supported in part by an appointment to the Research Participation Program at CBER, US Food and Drug Administration, administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the US Department of Energy and FDA.
Conceptualization: ONY, ZES, JRM, MAT, HY.
Data curation: ONY, ZES, JRM.
Formal analysis: ONY.
Funding acquisition: HY, ZES.
Investigation: ONY, ZES.
Methodology: ONY, ZES, JRM, MAT, HY.
Project administration: HY, ZES, MAT.
Resources: HY, ZES.
Supervision: HY, ZES, MAT.
Writing—original draft: ONY, ZES, JRM.
Writing—review and editing: ONY, ZES, JRM, MAT, HY.
Compliance with Ethical Standards
Conflict of Interest
The authors declare that they have no conflict of interest.
This article reflects the views of the authors and should not be construed to represent FDA's views or policies.
- 6.DeFrancesco L. Three deaths sink Affymax: Nature Publishing Group; 2013.Google Scholar
- 14.Lamberth K, Weldingh KN, Ehrenforth S, Chéhadé MR, Østergaard H. Immunogenicity lessons learned from the clinical development of vatreptacog alfa, a recombinant activated factor VII analog, in Hemophilia with inhibitors. Protein Therapeutics: Springer; 2017. p. 123–60.Google Scholar
- 16.Rosenberg AS, Sauna ZE. Immunogenicity assessment during the development of protein therapeutics. J Pharm Pharmacol. 2017.Google Scholar
- 20.Zubler RH, editor Naive and memory B cells in T-cell-dependent and T-independent responses. Springer seminars in immunopathology. Springer; 2001.Google Scholar
- 23.La Gruta NL, Gras S, Daley SR, Thomas PG, Rossjohn J. Understanding the drivers of MHC restriction of T cell receptors. Nat Rev Immunol. 2018;1.Google Scholar
- 25.Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, et al. Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology. 2018.Google Scholar
- 26.Baker MP, Jones TD. Identification and removal of immunogenicity in therapeutic proteins. Curr Opin Drug Discov Dev. 2007;10(2):219–27.Google Scholar
- 28.Karle A, Spindeldreher S, Kolbinger F, editors. Secukinumab, a novel anti–IL-17A antibody, shows low immunogenicity potential in human in vitro assays comparable to other marketed biotherapeutics with low clinical immunogenicity. MAbs. Taylor & Francis; 2016.Google Scholar
- 35.Rubic-Schneider T, Kuwana M, Christen B, Aßenmacher M, Hainzl O, Zimmermann F, et al. T-cell assays confirm immunogenicity of tungsten-induced erythropoietin aggregates associated with pure red cell aplasia. 2017;1(6):367–79.Google Scholar
- 36.Delluc S, Ravot G, Maillere B. Quantification of the pre-existing CD4 T cell repertoire specific for human erythropoietin reveals its immunogenicity potential. Blood. 2010:blood-2010-04-280875.Google Scholar
- 37.Casadevall N, Dobronravov V, Eckardt K-U, Ertürk S, Martynyuk L, Schmitt S, et al. Evaluation of the safety and immunogenicity of subcutaneous HX575 epoetin alfa in the treatment of anemia associated with chronic kidney disease in predialysis and dialysis patients. Clin Nephrol. 2017;88(4):190–7.PubMedPubMedCentralCrossRefGoogle Scholar
- 43.Ismael G, Hegg R, Muehlbauer S, Heinzmann D, Lum B, Kim S-B, et al. Subcutaneous versus intravenous administration of (neo) adjuvant trastuzumab in patients with HER2-positive, clinical stage I–III breast cancer (HannaH study): a phase 3, open-label, multicentre, randomised trial. Lancet Oncol. 2012;13(9):869–78.PubMedCrossRefGoogle Scholar
- 44.Cobleigh MA, Vogel CL, Tripathy D, Robert NJ, Scholl S, Fehrenbacher L, et al. Multinational study of the efficacy and safety of humanized anti-HER2 monoclonal antibody in women who have HER2-overexpressing metastatic breast cancer that has progressed after chemotherapy for metastatic disease. J Clin Oncol. 1999;17(9):2639.PubMedCrossRefGoogle Scholar
- 45.Pivot X, Bondarenko I, Nowecki Z, Dvorkin M, Trishkina E, Ahn J-H, et al. Phase III, randomized, double-blind study comparing the efficacy, safety, and immunogenicity of SB3 (trastuzumab biosimilar) and reference trastuzumab in patients treated with neoadjuvant therapy for human epidermal growth factor receptor 2–positive early breast cancer. J Clin Oncol. 2018;36(10):968–74.PubMedCrossRefGoogle Scholar
- 46.Spindeldreher S. Comparison of T cell assays: results from the ABIRISK consortium. 9th Open EIP Scientific Symposium And Final ABIRISK Open conference on Immunogenicity of Biopharmaceuticals. Lisbon, Portugal; 2017.Google Scholar
- 51.Plasencia C, Pascual-Salcedo D, Nuño L, Bonilla G, Villalba A, Peiteado D, et al. Influence of immunogenicity on the efficacy of long-term treatment of spondyloarthritis with infliximab. Ann Rheum Dis. 2012:annrheumdis-2011-200828.Google Scholar
- 54.Cohen SB, Alten R, Kameda H, Hala T, Radominski SC, Rehman MI, et al. A randomized controlled trial comparing PF-06438179/GP1111 (an infliximab biosimilar) and infliximab reference product for treatment of moderate to severe active rheumatoid arthritis despite methotrexate therapy. Arthritis Res Ther. 2018;20(1):155.PubMedPubMedCentralCrossRefGoogle Scholar
- 59.van Vollenhoven RF, Emery P, Bingham CO, Keystone EC, Fleischmann R, Furst DE, et al. Longterm safety of patients receiving rituximab in rheumatoid arthritis clinical trials. J Rheumatol. 2010:jrheum. 090856.Google Scholar
- 62.Deodhar AA, Gladman DD, McInnes IB, Strand V, Ren M, Spindeldreher S, et al. Secukinumab immunogenicity in patients with psoriatic arthritis and ankylosing spondylitis during a 52-week treatment period. Arthritis Rheumatol. 2018.Google Scholar
- 64.Gokemeijer J, Jawa V, Mitra-Kaushik S. How close are we to profiling immunogenicity risk using in silico algorithms and in vitro methods?: an industry perspective. AAPS J. 2017:1–6.Google Scholar
- 71.Ryan J. Endotoxins and cell culture. Corning Life Sciences Technical Bulletin. 2004;1–8.Google Scholar
- 77.Squibb B-M. Opdivo (nivolumab) package insert. Princeton: Bristol-Myers Squibb; 2015.Google Scholar
- 79.Chen X, Hickling T, Vicini P. A mechanistic, multiscale mathematical model of immunogenicity for therapeutic proteins: part 2—model applications. CPT Pharmacometrics Syst Pharmacol. 2014;3(9):1–10.Google Scholar