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Hopp MT, Ugurlar D, Pezeshkpoor B, Biswas A, Ramoji A, Neugebauer U, Oldenburg J, Imhof D. In-depth structure-function profiling of the complex formation between clotting factor VIII and heme. Thromb Res 2024; 237:184-195. [PMID: 38631156 DOI: 10.1016/j.thromres.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND AND AIMS Blood disorders, such as sickle cell disease, and other clinical conditions are often accompanied by intravascular hemolytic events along with the development of severe coagulopathies. Hemolysis, in turn, leads to the accumulation of Fe(II/III)-protoporphyrin IX (heme) in the intravascular compartment, which can trigger a variety of proinflammatory and prothrombotic reactions. As such, heme binding to the blood coagulation proteins factor VIII (FVIII), fibrinogen, and activated protein C with functional consequences has been demonstrated earlier. METHODS We herein present an in-depth characterization of the FVIII-heme interaction at the molecular level and its (patho-)physiological relevance through the application of biochemical, biophysical, structural biology, bioinformatic, and diagnostic tools. RESULTS FVIII has a great heme-binding capacity with seven heme molecules associating with the protein. The respective binding sites were identified by investigating heme binding to FVIII-derived peptides in combination with molecular docking and dynamic simulation studies of the complex as well as cryo-electron microscopy, revealing three high-affinity and four moderate heme-binding motifs (HBMs). Furthermore, the relevance of the FVIII-heme complex formation was characterized in physiologically relevant assay systems, revealing a ~ 50 % inhibition of the FVIII cofactor activity even in the protein-rich environment of blood plasma. CONCLUSION Our study provides not only novel molecular insights into the FVIII-heme interaction and its physiological relevance, but also strongly suggests the reduction of the intrinsic pathway and the accentuation of the final clotting step (by, for example, fibrinogen crosslinking) in hemolytic conditions as well as a future perspective in the context of FVIII substitution therapy of hemorrhagic events in hemophilia A patients.
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Affiliation(s)
- Marie-T Hopp
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany; Department of Chemistry, Institute for Integrated Natural Sciences, University of Koblenz, Koblenz, Germany.
| | - Deniz Ugurlar
- Center for Electron Microscopy, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Arijit Biswas
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Anuradha Ramoji
- Leibniz Institute of Photonic Technology, Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Ute Neugebauer
- Leibniz Institute of Photonic Technology, Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany; Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Bonn, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, Bonn, Germany.
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Ricotti S, Garay AS, Etcheverrigaray M, Amadeo GI, De Groot AS, Martin W, Mufarrege EF. Development of IFNβ-1a versions with reduced immunogenicity and full in vitro biological activity for the treatment of multiple sclerosis. Clin Immunol 2023; 257:109831. [PMID: 37931868 DOI: 10.1016/j.clim.2023.109831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
IFNβ (recombinant interferon Beta) has been widely used for the treatment of Multiple sclerosis for the last four decades. Despite the human origin of the IFNβ sequence, IFNβ is immunogenic, and unwanted immune responses in IFNβ-treated patients may compromise its efficacy and safety in the clinic. In this study, we applied the DeFT (De-immunization of Functional Therapeutics) approach to producing functional, de-immunized versions of IFNβ-1a. Two de-immunized versions of IFNβ-1a were produced in CHO cells and designated as IFNβ-1a(VAR1) and IFNβ-1a(VAR2). First, the secondary and tertiary protein structures were analyzed by circular dichroism spectroscopy. Then, the variants were also tested for functionality. While IFNβ-1a(VAR2) showed similar in vitro antiviral activity to the original protein, IFNβ-1a(VAR1) exhibited 40% more biological potency. Finally, in vivo assays using HLA-DR transgenic mice revealed that the de-immunized variants showed a markedly reduced immunogenicity when compared to the originator.
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Affiliation(s)
- Sonia Ricotti
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Alberto Sergio Garay
- Laboratory of Molecular Modeling, FBCB (School of Biochemistry and Biological Sciences), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Marina Etcheverrigaray
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Gabriel Ignacio Amadeo
- Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI 02903, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | | | - Eduardo Federico Mufarrege
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina.
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3
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De Groot AS, Roberts BJ, Mattei A, Lelias S, Boyle C, Martin WD. Immunogenicity risk assessment of synthetic peptide drugs and their impurities. Drug Discov Today 2023; 28:103714. [PMID: 37467878 DOI: 10.1016/j.drudis.2023.103714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Peptide drugs play an important part in medicine owing to their many therapeutic applications. Of the 80 peptide drugs approved for use in humans, at least five are now off-patent and are consequently being developed as generic alternatives to the originator products. To accelerate access to generic products, the FDA has proposed new regulatory pathways that do not require direct comparisons of generics to originators in clinical trials. The 'Abbreviated New Drug Application' (ANDA) pathway recommends that sponsors provide information on any new impurities in the generic drug, compared with the originator product, because the impurities can have potential to elicit unwanted immune responses owing to the introduction of T-cell epitopes. This review describes how peptide drug impurities can elicit unexpected immunogenicity and describes a framework for performing immunogenicity risk assessment of all types of bioactive peptide products. Although this report primarily focuses on generic peptides and their impurities, the approach might also be of interest for developers of novel peptide drugs who are preparing their products for an initial regulatory review.
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Affiliation(s)
- Anne S De Groot
- EpiVax, 188 Valley Street, Suite 424, Providence, RI, USA; University of Georgia, Center for Vaccines and Immunology, Athens, GA USA.
| | | | - Aimee Mattei
- EpiVax, 188 Valley Street, Suite 424, Providence, RI, USA
| | - Sandra Lelias
- EpiVax, 188 Valley Street, Suite 424, Providence, RI, USA
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Gokemeijer J, Wen Y, Jawa V, Mitra-Kaushik S, Chung S, Goggins A, Kumar S, Lamberth K, Liao K, Lill J, Phung Q, Walsh R, Roberts BJ, Swanson M, Singh I, Tourdot S, Kroenke MA, Rup B, Goletz TJ, Gupta S, Malherbe L, Pattijn S. Survey Outcome on Immunogenicity Risk Assessment Tools for Biotherapeutics: an Insight into Consensus on Methods, Application, and Utility in Drug Development. AAPS J 2023; 25:55. [PMID: 37266912 DOI: 10.1208/s12248-023-00820-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/12/2023] [Indexed: 06/03/2023] Open
Abstract
A survey conducted by the Therapeutic Product Immunogenicity (TPI) community within the American Association of Pharmaceutical Scientists (AAPS) posed questions to the participants on their immunogenicity risk assessment strategies prior to clinical development. The survey was conducted in 2 phases spanning 5 years, and queried information about in silico algorithms and in vitro assay formats for immunogenicity risk assessments and how the data were used to inform early developability effort in discovery, chemistry, manufacturing and control (CMC), and non-clinical stages of development. The key findings representing the trends from a majority of the participants included the use of high throughput in silico algorithms, human immune cell-based assays, and proteomics based outputs, as well as specialized assays when therapeutic mechanism of action could impact risk assessment. Additional insights into the CMC-related risks could also be gathered with the same tools to inform future process development and de-risk critical quality attributes with uncertain and unknown risks. The use of the outputs beyond supporting early development activities was also noted with participants utilizing the risk assessments to drive their clinical strategy and streamline bioanalysis.
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Affiliation(s)
- Jochem Gokemeijer
- Bristol Myers Squibb, 100 Binney Street, Cambridge, Massachusetts, 02143, USA.
| | - Yi Wen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, 46285, USA
| | - Vibha Jawa
- Bristol Myers Squibb, Lawrenceville, New Jersey, 08540, USA
| | | | - Shan Chung
- Genentech Inc., South San Francisco, California, 94080, USA
| | - Alan Goggins
- Merck & Co., Inc., South San Francisco, California, 94080, USA
| | - Seema Kumar
- EMD Serono Research & Development Institute, (A Business of Merck KGaA, Darmstadt, Germany), Billerica, Massachusetts, 01826, USA
| | | | - Karen Liao
- Merck & Co., Inc., West Point, Pennsylvania, 19486, USA
| | - Jennie Lill
- Genentech Inc., South San Francisco, California, 94080, USA
| | - Qui Phung
- Genentech Inc., South San Francisco, California, 94080, USA
| | - Robin Walsh
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, 46285, USA
| | | | - Michael Swanson
- Janssen R&D LLC., 1400 McKean Road, Spring House, Pennsylvania, 19477, USA
| | | | - Sophie Tourdot
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, 01810, USA
| | - Mark A Kroenke
- Clinical Immunology, Amgen, Thousand Oaks, California, 91320, USA
| | - Bonita Rup
- Bonnie Rup Consulting, LLC, 42 Commonwealth Ave, Boston, Massachusetts, 02116, USA
| | | | | | - Laurent Malherbe
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, 46285, USA
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Mufarrege EF, Peña LC, Etcheverrigaray M, De Groot AS, Martin W. Specific sequence mutations in a long-lasting rhIFN-α2b version reduce in vitro and in vivo immunogenicity and increase in vitro protein stability. Heliyon 2023; 9:e14670. [PMID: 37020947 PMCID: PMC10068115 DOI: 10.1016/j.heliyon.2023.e14670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
For decades, recombinant human interferon alpha (rhIFN-α2b) has been used to treat emerging and chronic viral diseases. However, rhIFN-α2b is immunogenic and has a short in vivo half-life. To solve these limitations, two long-lasting hyperglycosylated proteins with reduced immunogenicity were developed and designated as 4N-IFN(VAR1) and 4N-IFN(VAR3). Here, we continue to study the relevant characteristics of these therapeutic candidates. Thus, we demonstrated that both de-immunized IFN versions elicited significantly lower neutralizing antibody responses than the original molecule in HLA-DR1 transgenic mice, confirming our previous in vitro protein immunogenicity data. Also, we found that these biobetters exhibited remarkable stability when exposed to different physical factors that the protein product may encounter during its production process and storage, such as low pH, thermal stress, and repeated freezing/thawing cycles. Taking into consideration our previous and present results, 4N-IFN(VAR1) and 4N-IFN-4N(VAR3) appear to be valuable candidates for the treatment of human viral diseases.
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Affiliation(s)
- Eduardo Federico Mufarrege
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, S3000ZAA, Santa Fe, Argentina
- Corresponding author. Ciudad Universitaria, Paraje “El Pozo” – c.c 242, S3000ZAA, Santa Fe, Argentina.
| | - Lucía Carolina Peña
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, S3000ZAA, Santa Fe, Argentina
| | - Marina Etcheverrigaray
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, S3000ZAA, Santa Fe, Argentina
| | - Anne S. De Groot
- EpiVax, Inc., Providence, RI, 02903, USA
- Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, 02903, USA
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Giorgetti SI, Etcheverrigaray M, Terry F, Martin W, De Groot AS, Ceaglio N, Oggero M, Mufarrege EF. Development of highly stable and de-immunized versions of recombinant alpha interferon: Promising candidates for the treatment of chronic and emerging viral diseases. Clin Immunol 2021; 233:108888. [PMID: 34798238 PMCID: PMC8595249 DOI: 10.1016/j.clim.2021.108888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/04/2021] [Accepted: 11/13/2021] [Indexed: 12/23/2022]
Abstract
Human interferon alpha (hIFN-α) administration constitutes the current FDA approved therapy for chronic Hepatitis B and C virus infections. Additionally, hIFN-α treatment efficacy was recently demonstrated in patients with COVID-19. Thus, hIFN-α constitutes a therapeutic alternative for those countries where vaccination is inaccessible and for people who did not respond effectively to vaccination. However, hIFN-α2b exhibits a short plasma half-life resulting in the occurrence of severe side effects. To optimize the cytokine's pharmacokinetic profile, we developed a hyperglycosylated IFN, referred to as GMOP-IFN. Given the significant number of reports showing neutralizing antibodies (NAb) formation after hIFN-α administration, here we applied the DeFT (De-immunization of Functional Therapeutics) approach to develop functional, de-immunized versions of GMOP-IFN. Two GMOP-IFN variants exhibited significantly reduced ex vivo immunogenicity and null antiproliferative activity, while preserving antiviral function. The results obtained in this work indicate that the new de-immunized GMOP-IFN variants constitute promising candidates for antiviral therapy.
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Affiliation(s)
- Sofía Inés Giorgetti
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 Km 472.4, C.C. 242. (S3000ZAA), Santa Fe, Argentina
| | - Marina Etcheverrigaray
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 Km 472.4, C.C. 242. (S3000ZAA), Santa Fe, Argentina
| | | | | | - Anne Searls De Groot
- EpiVax, Inc., Providence, RI, USA; Institute for Immunology and Informatics, University of Rhode Island, RI, USA
| | - Natalia Ceaglio
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 Km 472.4, C.C. 242. (S3000ZAA), Santa Fe, Argentina
| | - Marcos Oggero
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 Km 472.4, C.C. 242. (S3000ZAA), Santa Fe, Argentina
| | - Eduardo Federico Mufarrege
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168 Km 472.4, C.C. 242. (S3000ZAA), Santa Fe, Argentina.
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7
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Winterling K, Martin WD, De Groot AS, Daufenbach J, Kistner S, Schüttrumpf J. Development of a novel fully functional coagulation factor VIII with reduced immunogenicity utilizing an in silico prediction and deimmunization approach. J Thromb Haemost 2021; 19:2161-2170. [PMID: 34060724 PMCID: PMC8456792 DOI: 10.1111/jth.15413] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/17/2021] [Accepted: 04/19/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Up to 30% of hemophilia A patients develop inhibitory antibodies against the infused factor VIII (FVIII). The development of a deimmunized FVIII is an unmet high medical need. Although improved recombinant FVIII (rFVIII) products evolved within the last years, the immunogenicity has not been solved. A deimmunized FVIII could reduce the probability of inhibitor development, providing safer therapy. OBJECTIVE To develop a deimmunized FVIII molecule by modifying major histocompatibility complex (MHC) class II presentation, leading to a functional but less immunogenic molecule. METHODS We performed (1) in silico prediction of potentially immunogenic T cell epitopes and their modification by amino acid substitutions in the FVIII sequence, (2) evaluation of functional and structural similarity of the modified rFVIII to unmodified FVIII and registered products, and (3) confirmation of the reduced immunogenicity by in vitro testing. RESULTS A partially deimmunized fully functional FVIII molecule incorporating 19 amino acid substitutions was generated. The substitutions led to a reduction of the immunogenicity score, indicating a reduced immunogenicity based on in silico calculations. This was confirmed in an in vitro dendritic cell (DC)--T cell assay. Using this assay, cells from healthy donors proved the significantly reduced immunogenicity of the modified FVIII variant by revealing less proliferation of T helper cells to this variant than to the unmodified FVIII. CONCLUSION In silico predictions resulted in a partially deimmunized FVIII. This FVIII is fully functional and was demonstrated to be less immunogenic in in vitro testing. This approach may result in a reduction of the inhibitor risk for patients with hemophilia A.
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Affiliation(s)
| | | | - Anne S. De Groot
- EpiVax, Inc.ProvidenceRhode IslandUSA
- Center for Vaccines and ImmunologyUniversity of GeorgiaAthensGeorgiaUSA
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Rezaieyazdi Z, Mansouritorghabeh H. Clinical Care of Bone Health in Patients on the Immune Tolerance Induction's Protocols With an Immunosuppressive Agent for Inhibitor Eradication in Hemophilia. Clin Appl Thromb Hemost 2021; 26:1076029620913951. [PMID: 32598171 PMCID: PMC7427025 DOI: 10.1177/1076029620913951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Nowadays, the development of factor VIII and IX inhibitors in patients with hemophilia is considered as the most challenging in the treatment of hemophilia. Immune tolerance induction (ITI) therapy is an approach for eradication of inhibitors. Some ITI protocols are routinely in use for the eradication of inhibitors in patients with hemophilia. Moreover, such a therapeutic regimen may facilitate the tendency to reduced bone density in patients with inhibitor. This study scheduled to investigate whether that predisposing role of ITI protocols with an immunosuppressive agent has considered or not. By a literature review, published ITI protocols in hemophilia with inhibitors were evaluated. Among them, 51 papers found and studied thoroughly. None of them had performed the bone mineral examination in patients with hemophilia and inhibitor under treatment. Since there are 2 coexisting facilitating factors in these protocols, considering the bone mineral density study for patients with inhibitor who are undergoing ITI protocols with an immunosuppressive agent is recommended.
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Affiliation(s)
- Zahra Rezaieyazdi
- Rheumatic Diseases Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hassan Mansouritorghabeh
- Rheumatic Diseases Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
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Jawa V, Terry F, Gokemeijer J, Mitra-Kaushik S, Roberts BJ, Tourdot S, De Groot AS. T-Cell Dependent Immunogenicity of Protein Therapeutics Pre-clinical Assessment and Mitigation-Updated Consensus and Review 2020. Front Immunol 2020; 11:1301. [PMID: 32695107 PMCID: PMC7338774 DOI: 10.3389/fimmu.2020.01301] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/22/2020] [Indexed: 01/01/2023] Open
Abstract
Immune responses to protein and peptide drugs can alter or reduce their efficacy and may be associated with adverse effects. While anti-drug antibodies (ADA) are a standard clinical measure of protein therapeutic immunogenicity, T cell epitopes in the primary sequences of these drugs are the key drivers or modulators of ADA response, depending on the type of T cell response that is stimulated (e.g., T helper or Regulatory T cells, respectively). In a previous publication on T cell-dependent immunogenicity of biotherapeutics, we addressed mitigation efforts such as identifying and reducing the presence of T cell epitopes or T cell response to protein therapeutics prior to further development of the protein therapeutic for clinical use. Over the past 5 years, greater insight into the role of regulatory T cell epitopes and the conservation of T cell epitopes with self (beyond germline) has improved the preclinical assessment of immunogenic potential. In addition, impurities contained in therapeutic drug formulations such as host cell proteins have also attracted attention and become the focus of novel risk assessment methods. Target effects have come into focus, given the emergence of protein and peptide drugs that target immune receptors in immuno-oncology applications. Lastly, new modalities are entering the clinic, leading to the need to revise certain aspects of the preclinical immunogenicity assessment pathway. In addition to drugs that have multiple antibody-derived domains or non-antibody scaffolds, therapeutic drugs may now be introduced via viral vectors, cell-based constructs, or nucleic acid based therapeutics that may, in addition to delivering drug, also prime the immune system, driving immune response to the delivery vehicle as well as the encoded therapeutic, adding to the complexity of assessing immunogenicity risk. While it is challenging to keep pace with emerging methods for the preclinical assessment of protein therapeutics and new biologic therapeutic modalities, this collective compendium provides a guide to current best practices and new concepts in the field.
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Affiliation(s)
- Vibha Jawa
- Predictive and Clinical Immunogenicity, PPDM, Merck & Co., Kenilworth, NJ, United States
| | | | - Jochem Gokemeijer
- Discovery Biotherapeutics, Bristol-Myers Squibb, Cambridge, MA, United States
| | | | | | - Sophie Tourdot
- BioMedicine Design, Pfizer Inc., Andover, MA, United States
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
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10
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Peptides identified on monocyte-derived dendritic cells: a marker for clinical immunogenicity to FVIII products. Blood Adv 2020; 3:1429-1440. [PMID: 31053570 DOI: 10.1182/bloodadvances.2018030452] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
The immunogenicity of protein therapeutics is an important safety and efficacy concern during drug development and regulation. Strategies to identify individuals and subpopulations at risk for an undesirable immune response represent an important unmet need. The major histocompatibility complex (MHC)-associated peptide proteomics (MAPPs) assay directly identifies the presence of peptides derived from a specific protein therapeutic on a donor's MHC class II (MHC-II) proteins. We applied this technique to address several questions related to the use of factor VIII (FVIII) replacement therapy in the treatment of hemophilia A (HA). Although >12 FVIII therapeutics are marketed, most fall into 3 categories: (i) human plasma-derived FVIII (pdFVIII), (ii) full-length (FL)-recombinant FVIII (rFVIII; FL-rFVIII), and (iii) B-domain-deleted rFVIII. Here, we investigated whether there are differences between the FVIII peptides found on the MHC-II proteins of the same individual when incubated with these 3 classes. Based on several observational studies and a prospective, randomized, clinical trial showing that the originally approved rFVIII products may be more immunogenic than the pdFVIII products containing von Willebrand factor (VWF) in molar excess, it has been hypothesized that the pdFVIII molecules yield/present fewer peptides (ie, potential T-cell epitopes). We have experimentally tested this hypothesis and found that dendritic cells from HA patients and healthy donors present fewer FVIII peptides when administered pdFVIII vs FL-rFVIII, despite both containing the same molar VWF excess. Our results support the hypothesis that synthesis of pdFVIII under physiological conditions could result in reduced heterogeneity and/or subtle differences in structure/conformation which, in turn, may result in reduced FVIII proteolytic processing relative to FL-rFVIII.
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11
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Kovalova N, Boyles J, Wen Y, Witcher DR, Brown-Augsburger PL, Wroblewski VJ, Chlewicki LK. Validation of a de-immunization strategy for monoclonal antibodies using cynomolgus macaque as a surrogate for human. Biopharm Drug Dispos 2020; 41:111-125. [PMID: 32080869 DOI: 10.1002/bdd.2222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/21/2020] [Accepted: 02/10/2020] [Indexed: 12/19/2022]
Abstract
The immunogenicity of biotherapeutics presents a major challenge during the clinical development of new protein drugs including monoclonal antibodies. To address this, multiple humanization and de-immunization techniques that employ in silico algorithms and in vitro test systems have been proposed and implemented. However, the success of these approaches has been variable and to date, the ability of these techniques to predict immunogenicity has not been systematically tested in humans or other primates. This study tested whether antibody humanization and de-immunization strategies reduce the risk of anti-drug antibody (ADA) development using cynomolgus macaque as a surrogate for human. First human-cyno chimeric antibodies were constructed by grafting the variable domains of the adalimumab and golimumab monoclonal antibodies onto cynomolgus macaque IgG1 and Igκ constant domains followed by framework germlining to cyno to reduce the xenogenic content. Next, B and T cell epitopes and aggregation-prone regions were identified using common in silico methods to select domains with an ADA risk for additional modification. The resultant engineered antibodies had a comparable affinity for TNFα, demonstrated similar biophysical properties, and exhibited significantly reduced ADA levels in cynomolgus macaque compared with the parental antibodies, with a corresponding improvement in the pharmacokinetic profile. Notably, plasma concentrations of the engineered antibodies were quantifiable through 504 hours (chimeric) and 840 hours (germlined/de-immunized), compared with only 336 hours (adalimumab) or 336-672 hours (golimumab). The results point to the significant value in the investment in these engineering strategies as an important guide for monoclonal antibody optimization that can contribute to improved clinical outcomes.
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Affiliation(s)
- Natalia Kovalova
- Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Jeffrey Boyles
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Technology Center, Indianapolis, IN, USA
| | - Yi Wen
- Lilly Biotechnology Center, Lilly Research Laboratories, Eli Lilly and Company, San Diego, CA, USA
| | - Derrick R Witcher
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Technology Center, Indianapolis, IN, USA
| | - Patricia L Brown-Augsburger
- Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | | | - Lukasz K Chlewicki
- Department of Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
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12
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Abstract
Therapeutic protein drugs have significantly improved the management of many severe and chronic diseases. However, their development and optimal clinical application are complicated by the induction of unwanted immune responses. Therapeutic protein-induced antidrug antibodies can alter drug pharmacokinetics and pharmacodynamics leading to impaired efficacy and occasionally serious safety issues. There has been a growing interest over the past decade in developing methods to assess the risk of unwanted immunogenicity during preclinical drug development, with the aim to mitigate the risk during the molecular design phase, clinical development and when products reach the market. Here, we discuss approaches to therapeutic protein immunogenicity risk assessment, with attention to assays and in vivo models used to mitigate this risk.
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13
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Azam A, Gallais Y, Mallart S, Illiano S, Duclos O, Prades C, Maillère B. Healthy Donors Exhibit a CD4 T Cell Repertoire Specific to the Immunogenic Human Hormone H2-Relaxin before Injection. THE JOURNAL OF IMMUNOLOGY 2019; 202:3507-3513. [PMID: 31101669 DOI: 10.4049/jimmunol.1800856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 04/11/2019] [Indexed: 11/19/2022]
Abstract
H2-relaxin (RLN2) is a two-chain peptide hormone structurally related to insulin with a therapeutic potential in multiple indications. However, multiple injections of human RLN2 induced anti-RLN2 Abs in patients, hampering its clinical development. As T cell activation is required to produce Abs, we wondered whether T cells specific for RLN2 might be already present in the human blood before any injection. We therefore quantified the RLN2-specific T cell repertoire using PBMCs collected from healthy donors. CD4 T cells were stimulated in multiple replicates by weekly rounds of stimulation by dendritic cells loaded with RLN2, and their specificity was assessed by IFN-γ ELISPOT. The number of specific T cell lines was used to estimate the frequency of circulating T cells. In vitro T cell response was demonstrated in 18 of the 23 healthy donors, leading to the generation of 70 independent RLN2-specific T cell lines. The mean frequency of RLN2-specific CD4 T cells was similar to that of T cells specific for known immunogenic therapeutic proteins. Using overlapping peptides, we identified multiple T cell epitopes hosted in the N-terminal parts of the α- and β-chains and common to multiple donors, in agreement with their capacity to bind to multiple HLA-DR molecules. Our results provide important clues to the immunogenicity of RLN2 and highlight the weak central immune tolerance induced against this self-hormone.
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Affiliation(s)
- Aurélien Azam
- Biologics Research, Sanofi Research and Development, 94400 Vitry sur Seine, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)-Saclay, Université Paris-Saclay, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette, France
| | - Yann Gallais
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)-Saclay, Université Paris-Saclay, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette, France
| | - Sergio Mallart
- Integrated Drug Discovery, Sanofi Research and Development, 91380 Chilly Mazarin, France; and
| | - Stephane Illiano
- Cardiovascular Diseases and Metabolism, Sanofi Research and Development, 91380 Chilly Mazarin, France
| | - Olivier Duclos
- Integrated Drug Discovery, Sanofi Research and Development, 91380 Chilly Mazarin, France; and
| | - Catherine Prades
- Biologics Research, Sanofi Research and Development, 94400 Vitry sur Seine, France
| | - Bernard Maillère
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)-Saclay, Université Paris-Saclay, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette, France;
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14
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Sekiguchi N, Kubo C, Takahashi A, Muraoka K, Takeiri A, Ito S, Yano M, Mimoto F, Maeda A, Iwayanagi Y, Wakabayashi T, Takata S, Murao N, Chiba S, Ishigai M. MHC-associated peptide proteomics enabling highly sensitive detection of immunogenic sequences for the development of therapeutic antibodies with low immunogenicity. MAbs 2018; 10:1168-1181. [PMID: 30199322 DOI: 10.1080/19420862.2018.1518888] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Immunogenicity is a key factor capable of influencing the efficacy and safety of therapeutic antibodies. A recently developed method called MHC-associated peptide proteomics (MAPPs) uses liquid chromatography/mass spectrometry to identify the peptide sequences derived from a therapeutic protein that are presented by major histocompatibility complex class II (MHC II) on antigen-presenting cells, and therefore may induce immunogenicity. In this study, we developed a MAPPs technique (called Ab-MAPPs) that has high throughput and can efficiently identify the MHC II-presented peptides derived from therapeutic antibodies using magnetic nanoparticle beads coated with a hydrophilic polymer in the immunoprecipitation process. The magnetic beads could identify more peptides and sequence regions originating from infliximab and adalimumab in a shorter measurement time than Sepharose beads, which are commonly used for MAPPs. Several sequence regions identified by Ab-MAPPs from infliximab corresponded to immunogenic sequences reported by other methods, which suggests the method's high potential for identifying significant sequences involved in immunogenicity. Furthermore, our study suggests that the Ab-MAPPs method can recognize the difference of a single amino acid residue between similar antibody sequences with different levels of T-cell proliferation activity and can identify potentially immunogenic peptides with high binding affinity to MHC II. In conclusion, Ab-MAPPs is useful for identifying the immunogenic sequences of therapeutic antibodies and will contribute to the design of therapeutic antibodies with low immunogenicity during the drug discovery stage.
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Affiliation(s)
- Nobuo Sekiguchi
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Chiyomi Kubo
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Ayako Takahashi
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Kumiko Muraoka
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Akira Takeiri
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Shunsuke Ito
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Mariko Yano
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Futa Mimoto
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Atsuhiko Maeda
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Yuki Iwayanagi
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Tetsuya Wakabayashi
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Shotaro Takata
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Naoaki Murao
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Shuichi Chiba
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
| | - Masaki Ishigai
- a Research Division, Fuji Gotemba Research Labs , Chugai Pharmaceutical Co., Ltd ., Gotemba , Shizuoka , Japan
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15
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Sauna ZE, Lagassé D, Pedras-Vasconcelos J, Golding B, Rosenberg AS. Evaluating and Mitigating the Immunogenicity of Therapeutic Proteins. Trends Biotechnol 2018; 36:1068-1084. [DOI: 10.1016/j.tibtech.2018.05.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022]
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16
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Moise L, M Biron B, Boyle CM, Kurt Yilmaz N, Jang H, Schiffer C, M Ross T, Martin WD, De Groot AS. T cell epitope engineering: an avian H7N9 influenza vaccine strategy for pandemic preparedness and response. Hum Vaccin Immunother 2018; 14:2203-2207. [PMID: 30015562 PMCID: PMC6183197 DOI: 10.1080/21645515.2018.1495303] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The delayed availability of vaccine during the 2009 H1N1 influenza pandemic created a sense of urgency to better prepare for the next influenza pandemic. Advancements in manufacturing technology, speed and capacity have been achieved but vaccine effectiveness remains a significant challenge. Here, we describe a novel vaccine design strategy called immune engineering in the context of H7N9 influenza vaccine development. The approach combines immunoinformatic and structure modeling methods to promote protective antibody responses against H7N9 hemagglutinin (HA) by engineering whole antigens to carry seasonal influenza HA memory CD4+ T cell epitopes – without perturbing native antigen structure – by galvanizing HA-specific memory helper T cells that support sustained antibody development against the native target HA. The premise for this vaccine concept rests on (i) the significance of CD4+ T cell memory to influenza immunity, (ii) the essential role CD4+ T cells play in development of neutralizing antibodies, (iii) linked specificity of HA-derived CD4+ T cell epitopes to antibody responses, (iv) the structural plasticity of HA and (v) an illustration of improved antibody response to a prototype engineered recombinant H7-HA vaccine. Immune engineering can be applied to development of vaccines against pandemic concerns, including avian influenza, as well as other difficult targets.
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Affiliation(s)
- Leonard Moise
- a EpiVax, Inc ., Providence , RI , USA.,b Institute for Immunology and Informatics , University of Rhode Island , Providence , RI , USA.,c Department of Cell and Molecular Biology , University of Rhode Island , Providence , RI , USA
| | | | | | - Nese Kurt Yilmaz
- d Department of Biochemistry and Molecular Pharmacology , UMass Medical School , Worcester , MA , USA
| | - Hyesun Jang
- e Center for Vaccines and Immunology , University of Georgia , Athens , GA , USA
| | - Celia Schiffer
- d Department of Biochemistry and Molecular Pharmacology , UMass Medical School , Worcester , MA , USA
| | - Ted M Ross
- e Center for Vaccines and Immunology , University of Georgia , Athens , GA , USA.,f Department of Infectious Diseases , University of Georgia , Athens , GA , USA
| | | | - Anne S De Groot
- a EpiVax, Inc ., Providence , RI , USA.,b Institute for Immunology and Informatics , University of Rhode Island , Providence , RI , USA.,c Department of Cell and Molecular Biology , University of Rhode Island , Providence , RI , USA
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17
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Gutiérrez AH, Rapp-Gabrielson VJ, Terry FE, Loving CL, Moise L, Martin WD, De Groot AS. T-cell epitope content comparison (EpiCC) of swine H1 influenza A virus hemagglutinin. Influenza Other Respir Viruses 2018; 11:531-542. [PMID: 29054116 PMCID: PMC5705686 DOI: 10.1111/irv.12513] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2017] [Indexed: 02/03/2023] Open
Abstract
Background Predicting vaccine efficacy against emerging pathogen strains is a significant problem in human and animal vaccine design. T‐cell epitope cross‐conservation may play an important role in cross‐strain vaccine efficacy. While influenza A virus (IAV) hemagglutination inhibition (HI) antibody titers are widely used to predict protective efficacy of 1 IAV vaccine against new strains, no similar correlate of protection has been identified for T‐cell epitopes. Objective We developed a computational method (EpiCC) that facilitates pairwise comparison of protein sequences based on an immunological property—T‐cell epitope content—rather than sequence identity, and evaluated its ability to classify swine IAV strain relatedness to estimate cross‐protective potential of a vaccine strain for circulating viruses. Methods T‐cell epitope relatedness scores were assessed for 23 IAV HA sequences representing the major H1 swine IAV phylo‐clusters circulating in North American swine and HA sequences in a commercial inactivated vaccine (FluSure XP®). Scores were compared to experimental data from previous efficacy studies. Results Higher EpiCC scores were associated with greater protection by the vaccine against strains for 23 field IAV strain vaccine comparisons. A threshold for EpiCC relatedness associated with full or partial protection in the absence of cross‐reactive HI antibodies was identified. EpiCC scores for field strains for which FluSure protective efficacy is not yet available were also calculated. Conclusion EpiCC thresholds can be evaluated for predictive accuracy of protection in future efficacy studies. EpiCC may also complement HI cross‐reactivity and phylogeny for selection of influenza strains in vaccine development.
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Affiliation(s)
- Andres H Gutiérrez
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA
| | | | | | - Crystal L Loving
- Virus and Prion Diseases Research Unit, NADC, USDA ARS, Ames, IA, USA
| | - Leonard Moise
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA.,EpiVax Inc., Providence, RI, USA
| | | | - Anne S De Groot
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA.,EpiVax Inc., Providence, RI, USA
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18
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Bartholdy C, Reedtz-Runge SL, Wang J, Hjerrild Zeuthen L, Gruhler A, Gudme CN, Lamberth K. In silico and in vitro immunogenicity assessment of B-domain-modified recombinant factor VIII molecules. Haemophilia 2018; 24:e354-e362. [DOI: 10.1111/hae.13555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2018] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - J. Wang
- Novo Nordisk A/S; Copenhagen Denmark
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19
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Mazor R, King EM, Pastan I. Strategies to Reduce the Immunogenicity of Recombinant Immunotoxins. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1736-1743. [PMID: 29870741 DOI: 10.1016/j.ajpath.2018.04.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/19/2018] [Accepted: 04/06/2018] [Indexed: 12/23/2022]
Abstract
Recombinant immunotoxins (RITs) are genetically engineered proteins being developed to treat cancer. They are composed of an Fv that targets a cancer antigen and a fragment of a bacterial toxin that kills tumor cells. Because the toxin is a foreign protein, it is immunogenic. The clinical success of RITs in patients with a normal immune system is limited by their immunogenicity. In this review, we discuss our progress in therapeutic protein deimmunization and the balancing act between immunogenicity and therapeutic potency. One approach is to prevent the activation of B cells by mapping and elimination of B-cell epitopes. A second approach is to prevent helper T-cell activation by interfering with major histocompatibility complex II presentation or T-cell recognition. Immunizing mice with RITs that were deimmunized by elimination of the murine B- or T-cell epitopes showed that both approaches are effective. Another approach to control immunogenicity is to modify the host immune system. Nanoparticles containing synthetic vaccine particles encapsulating rapamycin can induce immune tolerance and prevent anti-drug antibody formation. This treatment restores RIT anti-tumor activity that is otherwise neutralized because of immunogenicity.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Emily M King
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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20
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Faraji F, Karjoo Z, Moghaddam MV, Heidari S, Emameh RZ, Falak R. Challenges related to the immunogenicity of parenteral recombinant proteins: Underlying mechanisms and new approaches to overcome it. Int Rev Immunol 2018; 37:301-315. [PMID: 29851534 DOI: 10.1080/08830185.2018.1471139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Immune response elicited by therapeutic proteins is an important safety and efficacy issue for regulatory agencies, drug manufacturers, clinicians, and patients. Administration of therapeutic proteins can potentially induce the production of anti-drug antibodies or cell-mediated immune responses. At first, it was speculated that the immunogenicity is related to the non-human origin of these proteins. Later on, it was confirmed that the human proteins may also show immunogenicity. In this review article, we will focus on a number of factors, which play crucial roles in the human protein immunogenicity. These factors are related to the patient's status (or intrinsic properties) and molecular characteristics of the therapeutic protein's (or extrinsic properties). Furthermore, we will discuss available in silico, in vitro, and in vivo methods for the prediction of sequences, which may generate an immune response following parenteral administration of these proteins. In summary, nowadays, it is possible for drug manufacturers to evaluate the risk of immunogenicity of therapeutic proteins and implement a management plan to overcome the problems prior to proceeding to human clinical trials.
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Affiliation(s)
- Fatemeh Faraji
- a Immunology Research Center , Iran University of Medical Sciences (IUMS) , Tehran , Iran.,b Department of Immunology, School of Medicine , Iran University of Medical Sciences (IUMS) , Tehran , Iran
| | - Zahra Karjoo
- a Immunology Research Center , Iran University of Medical Sciences (IUMS) , Tehran , Iran
| | | | - Sahel Heidari
- a Immunology Research Center , Iran University of Medical Sciences (IUMS) , Tehran , Iran.,b Department of Immunology, School of Medicine , Iran University of Medical Sciences (IUMS) , Tehran , Iran
| | - Reza Zolfaghari Emameh
- c Department of Energy and Environmental Biotechnology, Division of Industrial & Environmental Biotechnology , National Institute of Genetic Engineering and Biotechnology (NIGEB) , Tehran , Iran
| | - Reza Falak
- a Immunology Research Center , Iran University of Medical Sciences (IUMS) , Tehran , Iran.,b Department of Immunology, School of Medicine , Iran University of Medical Sciences (IUMS) , Tehran , Iran
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21
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Anti-Drug Antibodies: Emerging Approaches to Predict, Reduce or Reverse Biotherapeutic Immunogenicity. Antibodies (Basel) 2018; 7:antib7020019. [PMID: 31544871 PMCID: PMC6698869 DOI: 10.3390/antib7020019] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
The development of anti-drug antibodies (ADAs) following administration of biotherapeutics to patients is a vexing problem that is attracting increasing attention from pharmaceutical and biotechnology companies. This serious clinical problem is also spawning creative research into novel approaches to predict, avoid, and in some cases even reverse such deleterious immune responses. CD4+ T cells are essential players in the development of most ADAs, while memory B-cell and long-lived plasma cells amplify and maintain these responses. This review summarizes methods to predict and experimentally identify T-cell and B-cell epitopes in therapeutic proteins, with a particular focus on blood coagulation factor VIII (FVIII), whose immunogenicity is clinically significant and is the subject of intensive current research. Methods to phenotype ADA responses in humans are described, including T-cell stimulation assays, and both established and novel approaches to determine the titers, epitopes and isotypes of the ADAs themselves. Although rational protein engineering can reduce the immunogenicity of many biotherapeutics, complementary, novel approaches to induce specific tolerance, especially during initial exposures, are expected to play significant roles in future efforts to reduce or reverse these unwanted immune responses.
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22
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Schubert B, Schärfe C, Dönnes P, Hopf T, Marks D, Kohlbacher O. Population-specific design of de-immunized protein biotherapeutics. PLoS Comput Biol 2018; 14:e1005983. [PMID: 29499035 PMCID: PMC5851651 DOI: 10.1371/journal.pcbi.1005983] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 03/14/2018] [Accepted: 01/15/2018] [Indexed: 11/19/2022] Open
Abstract
Immunogenicity is a major problem during the development of biotherapeutics since it can lead to rapid clearance of the drug and adverse reactions. The challenge for biotherapeutic design is therefore to identify mutants of the protein sequence that minimize immunogenicity in a target population whilst retaining pharmaceutical activity and protein function. Current approaches are moderately successful in designing sequences with reduced immunogenicity, but do not account for the varying frequencies of different human leucocyte antigen alleles in a specific population and in addition, since many designs are non-functional, require costly experimental post-screening. Here, we report a new method for de-immunization design using multi-objective combinatorial optimization. The method simultaneously optimizes the likelihood of a functional protein sequence at the same time as minimizing its immunogenicity tailored to a target population. We bypass the need for three-dimensional protein structure or molecular simulations to identify functional designs by automatically generating sequences using probabilistic models that have been used previously for mutation effect prediction and structure prediction. As proof-of-principle we designed sequences of the C2 domain of Factor VIII and tested them experimentally, resulting in a good correlation with the predicted immunogenicity of our model.
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Affiliation(s)
- Benjamin Schubert
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Dept. of Computer Science, Tübingen, Germany
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| | - Charlotta Schärfe
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Dept. of Computer Science, Tübingen, Germany
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pierre Dönnes
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- SciCross AB, Skövde, Sweden
| | - Thomas Hopf
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Debora Marks
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Dept. of Computer Science, Tübingen, Germany
- Quantitative Biology Center, Tübingen, Germany
- Faculty of Medicine, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
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23
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Qiu J, Qiu T, Huang Y, Cao Z. Identifying the Epitope Regions of Therapeutic Antibodies Based on Structure Descriptors. Int J Mol Sci 2017; 18:E2457. [PMID: 29186775 PMCID: PMC5751102 DOI: 10.3390/ijms18122457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 11/16/2022] Open
Abstract
Therapeutic antibodies are widely used for disease detection and specific treatments. However, as an exogenous protein, these antibodies can be detected by the human immune system and elicit a response that can lead to serious illnesses. Therapeutic antibodies can be engineered through antibody humanization, which aims to maintain the specificity and biological function of the original antibodies, and reduce immunogenicity. However, the antibody drug effect is synchronously reduced as more exogenous parts are replaced by human antibodies. Hence, a major challenge in this area is to precisely detect the epitope regions in immunogenic antibodies and guide point mutations of exogenous antibodies to balance both humanization level and drug effect. In this article, the latest dataset of immunoglobulin complexes was collected from protein data bank (PDB) to discover the spatial features of immunogenic antibody. Furthermore, a series of structure descriptors were generated to characterize and distinguish epitope residues from non-immunogenic regions. Finally, a computational model was established based on structure descriptors, and results indicated that this model has the potential to precisely predict the epitope regions of therapeutic antibodies. With rapid accumulation of immunoglobulin complexes, this methodology could be used to improve and guide future antibody humanization and potential clinical applications.
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Affiliation(s)
- Jingxuan Qiu
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (J.Q.); (Y.H.)
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Tianyi Qiu
- The Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China;
| | - Yin Huang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (J.Q.); (Y.H.)
| | - Zhiwei Cao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (J.Q.); (Y.H.)
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24
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Dhanda SK, Grifoni A, Pham J, Vaughan K, Sidney J, Peters B, Sette A. Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity. Immunology 2017; 153:118-132. [PMID: 28833085 DOI: 10.1111/imm.12816] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/27/2017] [Accepted: 08/14/2017] [Indexed: 12/13/2022] Open
Abstract
Unwanted immune responses against protein therapeutics can reduce efficacy or lead to adverse reactions. T-cell responses are key in the development of such responses, and are directed against immunodominant regions within the protein sequence, often associated with binding to several allelic variants of HLA class II molecules (promiscuous binders). Herein, we report a novel computational strategy to predict 'de-immunized' peptides, based on previous studies of erythropoietin protein immunogenicity. This algorithm (or method) first predicts promiscuous binding regions within the target protein sequence and then identifies residue substitutions predicted to reduce HLA binding. Further, this method anticipates the effect of any given substitution on flanking peptides, thereby circumventing the creation of nascent HLA-binding regions. As a proof-of-principle, the algorithm was applied to Vatreptacog α, an engineered Factor VII molecule associated with unintended immunogenicity. The algorithm correctly predicted the two immunogenic peptides containing the engineered residues. As a further validation, we selected and evaluated the immunogenicity of seven substitutions predicted to simultaneously reduce HLA binding for both peptides, five control substitutions with no predicted reduction in HLA-binding capacity, and additional flanking region controls. In vitro immunogenicity was detected in 21·4% of the cultures of peptides predicted to have reduced HLA binding and 11·4% of the flanking regions, compared with 46% for the cultures of the peptides predicted to be immunogenic. This method has been implemented as an interactive application, freely available online at http://tools.iedb.org/deimmunization/.
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Affiliation(s)
- Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Kerrie Vaughan
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
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Addressing the Immunogenicity of the Cargo and of the Targeting Antibodies with a Focus on Demmunized Bacterial Toxins and on Antibody-Targeted Human Effector Proteins. Biomedicines 2017; 5:biomedicines5020028. [PMID: 28574434 PMCID: PMC5489814 DOI: 10.3390/biomedicines5020028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 12/22/2022] Open
Abstract
Third-generation immunotoxins are composed of a human, or humanized, targeting moiety, usually a monoclonal antibody or an antibody fragment, and a non-human effector molecule. Due to the non-human origin of the cytotoxic domain, these molecules stimulate potent anti-drug immune responses, which limit treatment options. Efforts are made to deimmunize such immunotoxins or to combine treatment with immunosuppression. An alternative approach is using the so-called “human cytotoxic fusion proteins”, in which antibodies are used to target human effector proteins. Here, we present three relevant approaches for reducing the immunogenicity of antibody-targeted protein therapeutics: (1) reducing the immunogenicity of the bacterial toxin, (2) fusing human cytokines to antibodies to generate immunocytokines and (3) addressing the immunogenicity of the targeting antibodies.
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Mufarrege EF, Giorgetti S, Etcheverrigaray M, Terry F, Martin W, De Groot AS. De-immunized and Functional Therapeutic (DeFT) versions of a long lasting recombinant alpha interferon for antiviral therapy. Clin Immunol 2017; 176:31-41. [PMID: 28089609 DOI: 10.1016/j.clim.2017.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/05/2017] [Accepted: 01/07/2017] [Indexed: 11/18/2022]
Abstract
Interferon α (IFN-α) exerts potent antiviral, immunomodulatory, and antiproliferative activity and have proven clinical utility in chronic hepatitis B and C virus infections. However, repeated IFN-α administration induces neutralizing antibodies (NAb) against the therapeutic in a significant number of patients. Associations between IFN-α immunogenicity and loss of efficacy have been described. So as to improve the in vivo biological efficacy of IFN-α, a long lasting hyperglycosylated protein (4N-IFN) derived from IFN-α2b wild type (WT-IFN) was developed. However, in silico analysis performed using established in silico methods revealed that 4N-IFN had more T cell epitopes than WT-IFN. In order to develop a safer and more efficient IFN therapy, we applied the DeFT (De-immunization of Functional Therapeutics) approach to producing functional, de-immunized versions of 4N-IFN. Using the OptiMatrix in silico tool in ISPRI, the 4N-IFN sequence was modified to reduce HLA binding potential of specific T cell epitopes. Following verification of predictions by HLA binding assays, eight modifications were selected and integrated in three variants: 4N-IFN(VAR1), (VAR2) and (VAR3). Two of the three variants (VAR1 and VAR3) retained anti-viral function and demonstrated reduced T-cell immunogenicity in terms of T-cell proliferation and Th1 and Th2 cytokine levels, when compared to controls (commercial NG-IFN (non-glycosylated), PEG-IFN, WT-IFN and 4N-IFN). It was previously demonstrated that N-glycosylation improved IFN-α pharmacokinetic properties. Here, we further reduce immunogenicity as measured in vitro using T cell assays and cytokine profiling by modifying the T cell epitope content of a protein (de-immunizing). Taking into consideration the present results and previously reported immunogenicity data for commercial IFN-α2b variants, 4N-IFN(VAR1) and 4N-IFN-4N(VAR3) appear to be promising candidates for improved IFN-α therapy of HCV and HBV.
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Affiliation(s)
- Eduardo F Mufarrege
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Cultivos Celulares, FBCB, UNL, Santa Fe, Argentina.
| | - Sofía Giorgetti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Cultivos Celulares, FBCB, UNL, Santa Fe, Argentina
| | - Marina Etcheverrigaray
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Cultivos Celulares, FBCB, UNL, Santa Fe, Argentina
| | | | | | - Anne S De Groot
- EpiVax, Inc., Providence, RI, USA; Institute for Immunology and Informatics, University of Rhode Island, RI, USA
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EpiSweep: Computationally Driven Reengineering of Therapeutic Proteins to Reduce Immunogenicity While Maintaining Function. Methods Mol Biol 2017; 1529:375-398. [PMID: 27914063 DOI: 10.1007/978-1-4939-6637-0_20] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Therapeutic proteins are yielding ever more advanced and efficacious new drugs, but the biological origins of these highly effective therapeutics render them subject to immune surveillance within the patient's body. When recognized by the immune system as a foreign agent, protein drugs elicit a coordinated response that can manifest a range of clinical complications including rapid drug clearance, loss of functionality and efficacy, delayed infusion-like allergic reactions, more serious anaphylactic shock, and even induced auto-immunity. It is thus often necessary to deimmunize an exogenous protein in order to enable its clinical application; critically, the deimmunization process must also maintain the desired therapeutic activity.To meet the growing need for effective, efficient, and broadly applicable protein deimmunization technologies, we have developed the EpiSweep suite of protein design algorithms. EpiSweep seamlessly integrates computational prediction of immunogenic T cell epitopes with sequence- or structure-based assessment of the impacts of mutations on protein stability and function, in order to select combinations of mutations that make Pareto optimal trade-offs between the competing goals of low immunogenicity and high-level function. The methods are applicable both to the design of individual functionally deimmunized variants as well as the design of combinatorial libraries enriched in functionally deimmunized variants. After validating EpiSweep in a series of retrospective case studies providing comparisons to conventional approaches to T cell epitope deletion, we have experimentally demonstrated it to be highly effective in prospective application to deimmunization of a number of different therapeutic candidates. We conclude that our broadly applicable computational protein design algorithms guide the engineer towards the most promising deimmunized therapeutic candidates, and thereby have the potential to accelerate development of new protein drugs by shortening time frames and improving hit rates.
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Berntorp E. Plasma-derived versus recombinant factor concentrates in PUPs: a never ending debate? Hamostaseologie 2016; 37:53-57. [PMID: 27878207 DOI: 10.5482/hamo-16-10-0040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/14/2016] [Indexed: 01/03/2023] Open
Abstract
Inhibitor development in haemophilia is a serious complication to treatment with factor concentrates. Since the advent of more pure products, especially developed using recombinant DNA technology, some studies have shown an increased incidence of inhibitors in previously untreated patients (PUPs) receiving recombinant products whereas plasma-derived concentrates sometimes have been claimed to have a protective role, probably due to the content of von Willebrand factor (VWF). In fact, experiments indicate that the VWF may block uptake of factor VIII into macrophages for further processing to the immune system. Also, a competition between VWF and inhibitor binding to the C2 domain of factor VIII has been suggested. Recently, large cohort and surveillance studies have created a vigorous debate about the role of product class for inhibitor development as results have been conflicting. The only randomised prospective study, the SIPPET study, was published in 2016, and substantiated previous reports claiming that plasma derived concentrates give less inhibitors in patients with severe haemophilia A, previously not exposed to factor VIII. The debate will continue.
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Affiliation(s)
- Erik Berntorp
- Prof. Erik Berntorp, Centre for Thrombosis and Hemostasis, Lund University, Skane University Hospital, Jan Waldenströms gata 14, SE-205 02, Malmö, Sweden, Tel: +46705752496, E-Mail:
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Tabriznia-Tabrizi S, Gholampour M, Mansouritorghabeh H. A close insight to factor VIII inhibitor in the congenital hemophilia A. Expert Rev Hematol 2016; 9:903-13. [PMID: 27367203 DOI: 10.1080/17474086.2016.1208554] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Hemophilia A (HA) has an X-linked pattern of inheritance and is the most common of the hemorrhagic disorders. HA is caused by a decreased or deficiency of the functional clotting factor VIII (FVIII) and effects 1 in 5000-10,000 male births. The common treatment for hemophilia is replacement therapy by plasma-derived or recombinant FVIII. Approximately 20-30% of people with a severe type of HA develop an inhibitor and this phenomenon is the main challenge in the management of these patients. Genetic factors and environmental determinants contribute to inhibitor development. Here, the roles of various genetic and environmental factors such as the type of FVIII concentrate used, the number of exposure days, and peak treatment time will be discussed in detail. It seems this information is helpful for hematologists. AREAS COVERED A literature review was done in January 2016 on PubMed and Scopus using the following keywords:' h(a)emophilia A & factor VIII inhibitor', 'h(a)emophilia A & factor VIII alloantibody', 'h(a)emophilia A & inhibitor'. There was no time limitation; however, there was an English language limitation placed on the articles selected. Expert commentary: Influential genetic and environmental factors in developing inhibitors have been discussed. Most of the risk factors are related to previously untreated patients with hemophili.
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Affiliation(s)
| | - Marzie Gholampour
- a Haematology , Mashhad University of Medical sciences (MUMS) , Mashhad , Iran
| | - Hassan Mansouritorghabeh
- b Allergy Research Center, Ghaem hospital, School of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
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T cells from hemophilia A subjects recognize the same HLA-restricted FVIII epitope with a narrow TCR repertoire. Blood 2016; 128:2043-2054. [PMID: 27471234 DOI: 10.1182/blood-2015-11-682468] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 07/18/2016] [Indexed: 12/15/2022] Open
Abstract
Factor VIII (FVIII)-neutralizing antibodies ("inhibitors") are a serious problem in hemophilia A (HA). The aim of this study was to characterize HLA-restricted T-cell responses from a severe HA subject with a persistent inhibitor and from 2 previously studied mild HA inhibitor subjects. Major histocompatibility complex II tetramers corresponding to both of the severe HA subject's HLA-DRA-DRB1 alleles were loaded with peptides spanning FVIII-A2, C1, and C2 domains. Interestingly, only 1 epitope was identified, in peptide FVIII2194-2213, and it was identical to the HLA-DRA*01-DRB1*01:01-restricted epitope recognized by the mild HA subjects. Multiple T-cell clones and polyclonal lines having different avidities for the peptide-loaded tetramer were isolated from all subjects. Only high- and medium-avidity T cells proliferated and secreted cytokines when stimulated with FVIII2194-2213 T-cell receptor β (TCRB) gene sequencing of 15 T-cell clones from the severe HA subject revealed that all high-avidity clones expressed the same TCRB gene. High-throughput immunosequencing of high-, medium-, and low-avidity cells sorted from a severe HA polyclonal line revealed that 94% of the high-avidity cells expressed the same TCRB gene as the high-avidity clones. TCRB sequencing of clones and lines from the mild HA subjects also identified a limited TCRB gene repertoire. These results suggest a limited number of epitopes in FVIII drive inhibitor responses and that the T-cell repertoires of FVIII-responsive T cells can be quite narrow. The limited diversity of both epitopes and TCRB gene usage suggests that targeting of specific epitopes and/or T-cell clones may be a promising approach to achieve tolerance to FVIII.
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Abstract
Recombinant immunotoxins (RITs) are chimeric proteins designed to treat cancer. They are made up of an Fv or Fab that targets an antigen on a cancer cell fused to a 38-kDa portion of Pseudomonas exotoxin A (PE38). Because PE38 is a bacterial protein, it is highly immunogenic in patients with solid tumors that have normal immune systems, but much less immunogenic in patients with hematologic malignancies where the immune system is suppressed. RITs have shown efficacy in refractory hairy cell leukemia and in some children with acute lymphoblastic leukemia, but have been much less effective in solid tumors, because neutralizing antibodies develop and prevent additional treatment cycles. In this paper we will (i) review data from clinical trials describing the immunogenicity of PE38 in different patient populations; (ii) review results from clinical trials using different immunosuppressive drugs; and (iii) describe our efforts to make new less-immunogenic RITs by identifying and removing T- and B-cell epitopes to hide the RIT from the immune system.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Masanori Onda
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Hartholt RB, Peyron I, Voorberg J. Hunting down factor VIII in the immunopeptidome. Cell Immunol 2016; 301:59-64. [DOI: 10.1016/j.cellimm.2015.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 01/24/2023]
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Pratt KP. Engineering less immunogenic and antigenic FVIII proteins. Cell Immunol 2015; 301:12-7. [PMID: 26566286 DOI: 10.1016/j.cellimm.2015.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/22/2015] [Indexed: 01/03/2023]
Abstract
The development of neutralizing antibodies against blood coagulation factor VIII (FVIII), referred to clinically as "inhibitors", is the most challenging and deleterious adverse event to occur following intravenous infusions of FVIII to treat hemophilia A. Inhibitors occlude FVIII surfaces that must bind to activated phospholipid membranes, the serine proteinase factor IXa, and other components of the 'intrinsic tenase complex' in order to carry out its important role in accelerating blood coagulation. Inhibitors develop in up to one of every three patients, yet remarkably, a substantial majority of severe hemophilia A patients, who circulate no detectable FVIII antigen or activity, acquire immune tolerance to FVIII during initial infusions or else after intensive FVIII therapy to overcome their inhibitor. The design of less immunogenic FVIII proteins through identification and modification ("de-immunization") of immunodominant T-cell epitopes is an important goal. For patients who develop persistent inhibitors, modification of B-cell epitopes through substitution of surface-exposed amino acid side chains and/or attachment of bulky moieties to interfere with FVIII attachment to antibodies and memory B cells is a promising approach. Both experimental and computational methods are being employed to achieve these goals. Future therapies for hemophilia A, as well as other monogenic deficiency diseases, are likely to involve administration of less immunogenic proteins in conjunction with other novel immunotherapies to promote a regulatory cellular environment promoting durable immune tolerance.
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Affiliation(s)
- Kathleen P Pratt
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.
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34
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Elimination of murine and human T-cell epitopes in recombinant immunotoxin eliminates neutralizing and anti-drug antibodies in vivo. Cell Mol Immunol 2015; 14:432-442. [PMID: 26477977 DOI: 10.1038/cmi.2015.91] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/22/2015] [Accepted: 09/22/2015] [Indexed: 12/16/2022] Open
Abstract
Antibodies against the toxin portion of recombinant immunotoxins (RIT) reduce their efficacy and pose a potential safety risk. To overcome this problem we mutated the very immunogenic immunotoxin SS1P to produce LMB-T20, a de-immunized RIT that has the eight human T-cell epitopes in SS1P modified or removed. To determine the effect of T-cell epitope removal in vivo we mapped the T-cell epitopes in immune-competent BALB/c mice and found that these mice recognize two epitopes. One corresponds to the human immunodominant T-cell epitope and the other to a human subdominant epitope; both were eliminated in LMB-T20. We found that mice immunized with LMB-T20 did not have T-cell activation and did not develop anti-drug antibodies (ADA), whereas mice immunized with SS1P, showed T-cell activation, and developed ADA detected by both ELISA and drug neutralizing assays. The ability of the mice treated with LMB-T20 to respond to other antigens was not compromised. We conclude that elimination of T-cell epitopes is sufficient to prevent formation of antibodies to an immunogenic foreign protein.
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Mazor R, Tai CH, Lee B, Pastan I. Poor correlation between T-cell activation assays and HLA-DR binding prediction algorithms in an immunogenic fragment of Pseudomonas exotoxin A. J Immunol Methods 2015; 425:10-20. [PMID: 26056938 PMCID: PMC4604018 DOI: 10.1016/j.jim.2015.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 12/20/2022]
Abstract
The ability to identify immunogenic determinants that activate T-cells is important for the development of new vaccines, allergy therapy and protein therapeutics. In silico MHC-II binding prediction algorithms are often used for T-cell epitope identification. To understand how well those programs predict immunogenicity, we computed HLA binding to peptides spanning the sequence of PE38, a fragment of an anti-cancer immunotoxin, and compared the predicted and experimentally identified T-cell epitopes. We found that the prediction for individual donors did not correlate well with the experimental data. Furthermore, prediction of T-cell epitopes in an HLA heterogenic population revealed that the two strongest epitopes were predicted at multiple cutoffs but the third epitope was predicted negative at all cutoffs and overall 4/9 epitopes were missed at several cutoffs. We conclude that MHC class-II binding predictions are not sufficient to predict the T-cell epitopes in PE38 and should be supplemented by experimental work.
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Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Chin-Hsien Tai
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Byungkook Lee
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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36
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He L, De Groot AS, Bailey-Kellogg C. Hit-and-run, hit-and-stay, and commensal bacteria present different peptide content when viewed from the perspective of the T cell. Vaccine 2015; 33:6922-9. [PMID: 26428457 DOI: 10.1016/j.vaccine.2015.08.099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/10/2015] [Accepted: 08/24/2015] [Indexed: 01/02/2023]
Abstract
Different types of bacteria face different pressures from the immune system, with those that persist ("hit-and-stay") potentially having to adapt more in order to escape than those prone to short-lived infection ("hit-and-run"), and with commensal bacteria potentially different from both due to additional physical mechanisms for avoiding immune detection. The Janus Immunogenicity Score (JIS) was recently developed to assess the likelihood of T cell recognition of an antigen, using an analysis that considers both binding of a peptide within the antigen by major histocompatability complex (MHC) and recognition of the peptide:MHC complex by cognate T cell receptor (TCR). This score was shown to be predictive of T effector vs. T regulatory or null responses in experimental data, as well as to distinguish viruses representative of the hit-and-stay vs. hit-and-run phenotypes. Here, JIS-based analyses were conducted in order to characterize the extent to which the pressure to avoid T cell recognition is manifested in genomic differences among representative hit-and-run, hit-and-stay, and commensal bacteria. Overall, extracellular proteins were found to have different JIS profiles from cytoplasmic ones. Contrasting the bacterial groups, extracellular proteins were shown to be quite different across the groups, much more so than intracellular proteins. The differences were evident even at the level of corresponding peptides in homologous protein pairs from hit-and-run and hit-and-stay bacteria. The multi-level analysis of patterns of immunogenicity across different groups of bacteria provides a new way to approach questions of bacterial immune camouflage or escape, as well as to approach the selection and optimization of candidates for vaccine design.
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Affiliation(s)
- Lu He
- Dartmouth Computer Science, Hanover, NH 03755, United States
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI 02903, United States; Institute for Immunology and Informatics, University of Rhode Island, Providence, RI 02903, United States
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Salvat RS, Choi Y, Bishop A, Bailey-Kellogg C, Griswold KE. Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads. Biotechnol Bioeng 2015; 112:1306-18. [PMID: 25655032 PMCID: PMC4452428 DOI: 10.1002/bit.25554] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/09/2015] [Accepted: 01/18/2015] [Indexed: 12/31/2022]
Abstract
Anti-drug immune responses are a unique risk factor for biotherapeutics, and undesired immunogenicity can alter pharmacokinetics, compromise drug efficacy, and in some cases even threaten patient safety. To fully capitalize on the promise of biotherapeutics, more efficient and generally applicable protein deimmunization tools are needed. Mutagenic deletion of a protein's T cell epitopes is one powerful strategy to engineer immunotolerance, but deimmunizing mutations must maintain protein structure and function. Here, EpiSweep, a structure-based protein design and deimmunization algorithm, has been used to produce a panel of seven beta-lactamase drug candidates having 27-47% reductions in predicted epitope content. Despite bearing eight mutations each, all seven engineered enzymes maintained good stability and activity. At the same time, the variants exhibited dramatically reduced interaction with human class II major histocompatibility complex proteins, key regulators of anti-drug immune responses. When compared to 8-mutation designs generated with a sequence-based deimmunization algorithm, the structure-based designs retained greater thermostability and possessed fewer high affinity epitopes, the dominant drivers of anti-biotherapeutic immune responses. These experimental results validate the first structure-based deimmunization algorithm capable of mapping optimal biotherapeutic design space. By designing optimal mutations that reduce immunogenic potential while imparting favorable intramolecular interactions, broadly distributed epitopes may be simultaneously targeted using high mutational loads.
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Affiliation(s)
- Regina S Salvat
- Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755
| | | | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755.
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755.
- Program in Molecular and Cellular Biology, Dartmouth, Hanover, New Hampshire.
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38
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Lorentz KM, Kontos S, Diaceri G, Henry H, Hubbell JA. Engineered binding to erythrocytes induces immunological tolerance to E. coli asparaginase. SCIENCE ADVANCES 2015; 1:e1500112. [PMID: 26601215 PMCID: PMC4646778 DOI: 10.1126/sciadv.1500112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/14/2015] [Indexed: 05/29/2023]
Abstract
Antigen-specific immune responses to protein drugs can hinder efficacy and compromise safety because of drug neutralization and secondary clinical complications. We report a tolerance induction strategy to prevent antigen-specific humoral immune responses to therapeutic proteins. Our modular, biomolecular approach involves engineering tolerizing variants of proteins such that they bind erythrocytes in vivo upon injection, on the basis of the premise that aged erythrocytes and the payloads they carry are cleared tolerogenically, driving the deletion of antigen-specific T cells. We demonstrate that binding the clinical therapeutic enzyme Escherichia coli l-asparaginase to erythrocytes in situ antigen-specifically abrogates development of antibody titers by >1000-fold and extends the pharmacodynamic effect of the drug 10-fold in mice. Additionally, a single pretreatment dose of erythrocyte-binding asparaginase tolerized mice to multiple subsequent doses of the wild-type enzyme. This strategy for reducing antigen-specific humoral responses may enable more effective and safer treatment with therapeutic proteins and drug candidates that are hampered by immunogenicity.
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Affiliation(s)
- Kristen M. Lorentz
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Anokion SA, CH-1024 Ecublens, Switzerland
| | - Stephan Kontos
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Anokion SA, CH-1024 Ecublens, Switzerland
| | - Giacomo Diaceri
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Hugues Henry
- Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Jeffrey A. Hubbell
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Anokion SA, CH-1024 Ecublens, Switzerland
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
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Therapeutic outcomes, assessments, risk factors and mitigation efforts of immunogenicity of therapeutic protein products. Cell Immunol 2015; 295:118-26. [DOI: 10.1016/j.cellimm.2015.03.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 12/20/2022]
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40
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Salvat RS, Parker AS, Choi Y, Bailey-Kellogg C, Griswold KE. Mapping the Pareto optimal design space for a functionally deimmunized biotherapeutic candidate. PLoS Comput Biol 2015; 11:e1003988. [PMID: 25568954 PMCID: PMC4288714 DOI: 10.1371/journal.pcbi.1003988] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/14/2014] [Indexed: 12/25/2022] Open
Abstract
The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the undominated variants for which no other single design exhibits better performance in both criteria. Here, the Pareto frontier of a therapeutic enzyme has been designed, constructed, and evaluated experimentally. Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions. These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates. Given this capacity to rapidly assess and design for tradeoffs between protein immunogenicity and functionality, these algorithms may prove useful in augmenting, accelerating, and de-risking experimental deimmunization efforts. Protein therapeutics have created a revolution in disease therapy, providing improved outcomes for prevalent illnesses and conditions while at the same time yielding treatments for diseases that were previously intractable. However, this powerful class of drugs is subject to their own unique challenges and risk factors. In particular, the biological origins of therapeutic proteins predispose them towards eliciting a detrimental immune response from the patient's own body. Therefore, fully capitalizing on the medicinal reservoir of natural and engineered proteins will require efficient, effective, and broadly applicable deimmunization technologies. We have developed deimmunization algorithms that simultaneously optimize therapeutic candidates for both low immunogenicity and high-level activity and stability. Here, we combine computational modeling and experimental analysis to show that the process of protein deimmunization manifests inherent tradeoffs between immunogenic potential and biomolecular function. Our experimental results demonstrate that dual objective optimization allows us to assess and design for these tradeoffs, thereby enabling facile construction of deimmunized variants that span a broad range of immunogenicity and functionality performance parameters. Thus, we can rapidly map the design space for deimmunized drug candidates, and we can use this information to guide selection of engineered proteins that are most likely to meet performance benchmarks for a given clinical application.
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Affiliation(s)
- Regina S. Salvat
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America
| | - Andrew S. Parker
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail: (CBK); (KEG)
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America
- Program in Molecular and Cellular Biology, Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail: (CBK); (KEG)
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41
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Tunstall O, Astermark J. Strategies for reducing inhibitor formation in severe haemophilia. Eur J Haematol 2015; 94 Suppl 77:45-50. [DOI: 10.1111/ejh.12501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2014] [Indexed: 01/28/2023]
Affiliation(s)
| | - Jan Astermark
- Department for Haematology and Vascular Diseases; Malmö Centre for Thrombosis and Haemostasis; Skåne University Hospital; Malmö Sweden
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42
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Engineered antigen-specific human regulatory T cells: immunosuppression of FVIII-specific T- and B-cell responses. Blood 2014; 125:1107-15. [PMID: 25498909 DOI: 10.1182/blood-2014-04-566786] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Expansion of human regulatory T cells (Tregs) for clinical applications offers great promise for the treatment of undesirable immune responses in autoimmunity, transplantation, allergy, and antidrug antibody responses, including inhibitor responses in hemophilia A patients. However, polyclonal Tregs are nonspecific and therefore could potentially cause global immunosuppression. To avoid this undesirable outcome, the generation of antigen-specific Tregs would be advantageous. Herein, we report the production and properties of engineered antigen-specific Tregs, created by transduction of a recombinant T-cell receptor obtained from a hemophilia A subject's T-cell clone, into expanded human FoxP3(+) Tregs. Such engineered factor VIII (FVIII)-specific Tregs efficiently suppressed the proliferation and cytokine production of FVIII-specific T-effector cells. Moreover, studies with an HLA-transgenic, FVIII-deficient mouse model demonstrated that antibody production from FVIII-primed spleen cells in vitro were profoundly inhibited in the presence of these FVIII-specific Tregs, suggesting potential utility to treat anti-FVIII inhibitory antibody formation in hemophilia A patients.
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43
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C3d adjuvant effects are mediated through the activation of C3d-specific autoreactive T cells. Immunol Cell Biol 2014; 93:189-97. [PMID: 25385064 PMCID: PMC4323994 DOI: 10.1038/icb.2014.89] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 09/12/2014] [Accepted: 09/12/2014] [Indexed: 01/08/2023]
Abstract
Complement fragment C3d covalently attached to antigens enhances immune responses, particularly for antigens lacking T cell epitopes. Enhancement has been attributed to receptor cross-linking between complement receptor CR2 (CD21) and polysaccharide antigen to surface IgM on naïve B cells. Paradoxically, C3d has still been shown to increase immune responses in CD21 KO mice, suggesting that an auxiliary activation pathway exists. In prior studies, we demonstrated the CD21-independent C3d adjuvant effect might be due to T cell recognition of C3d T helper epitopes processed and presented by MHC class II on the B cell surface. C3d peptide sequences containing concentrated clusters of putative human C3 T cell epitopes were identified using the epitope-mapping algorithm, EpiMatrix. These peptide sequences were synthesized and shown in vitro to bind multiple HLA-DR alleles with high affinity, and induce IFNγ responses in healthy donor PBMCs. In the present studies, we establish further correlations between HLA binding and HLA-specific lymphocyte reactions with select epitope clusters. Additionally, we show that the T cell phenotype of C3d-specific reactive T cells is CD4+CD45RO+ memory T cells. Finally, mutation of a single T cell epitope residing within the P28 peptide segment of C3d resulted in significantly diminished adjuvant activity in BALB/c mice. Collectively, these studies support the hypothesis that the paradoxical enhancement of immune responses by C3d in the absence of CD21 is due to internalization and processing of C3d into peptides that activate autoreactive CD4+ T helper cells in the context of HLA class II.
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44
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Bailey-Kellogg C, Gutiérrez AH, Moise L, Terry F, Martin WD, De Groot AS. CHOPPI: a web tool for the analysis of immunogenicity risk from host cell proteins in CHO-based protein production. Biotechnol Bioeng 2014; 111:2170-82. [PMID: 24888712 PMCID: PMC4282101 DOI: 10.1002/bit.25286] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/14/2014] [Accepted: 05/07/2014] [Indexed: 02/04/2023]
Abstract
Despite high quality standards and continual process improvements in manufacturing, host cell protein (HCP) process impurities remain a substantial risk for biological products. Even at low levels, residual HCPs can induce a detrimental immune response compromising the safety and efficacy of a biologic. Consequently, advanced-stage clinical trials have been cancelled due to the identification of antibodies against HCPs. To enable earlier and rapid assessment of the risks in Chinese Hamster Ovary (CHO)-based protein production of residual CHO protein impurities (CHOPs), we have developed a web tool called CHOPPI, for CHO Protein Predicted Immunogenicity. CHOPPI integrates information regarding the possible presence of CHOPs (expression and secretion) with characterizations of their immunogenicity (T cell epitope count and density, and relative conservation with human counterparts). CHOPPI can generate a report for a specified CHO protein (e.g., identified from proteomics or immunoassays) or characterize an entire specified subset of the CHO genome (e.g., filtered based on confidence in transcription and similarity to human proteins). The ability to analyze potential CHOPs at a genomic scale provides a baseline to evaluate relative risk. We show here that CHOPPI can identify clear differences in immunogenicity risk among previously validated CHOPs, as well as identify additional “risky” CHO proteins that may be expressed during production and induce a detrimental immune response upon delivery. We conclude that CHOPPI is a powerful tool that provides a valuable computational complement to existing experimental approaches for CHOP risk assessment and can focus experimental efforts in the most important directions. Biotechnol. Bioeng. 2014;111: 2170–2182.
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45
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Computationally driven deletion of broadly distributed T cell epitopes in a biotherapeutic candidate. Cell Mol Life Sci 2014; 71:4869-80. [PMID: 24880662 DOI: 10.1007/s00018-014-1652-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/23/2014] [Accepted: 05/16/2014] [Indexed: 12/12/2022]
Abstract
Biotherapeutics are subject to immune surveillance within the body, and anti-biotherapeutic immune responses can compromise drug efficacy and patient safety. Initial development of targeted antidrug immune memory is coordinated by T cell recognition of immunogenic subsequences, termed "T cell epitopes." Biotherapeutics may therefore be deimmunized by mutating key residues within cognate epitopes, but there exist complex trade-offs between immunogenicity, mutational load, and protein structure-function. Here, a protein deimmunization algorithm has been applied to P99 beta-lactamase, a component of antibody-directed enzyme prodrug therapies. The algorithm, integer programming for immunogenic proteins, seamlessly integrates computational prediction of T cell epitopes with both 1- and 2-body sequence potentials that assess protein tolerance to epitope-deleting mutations. Compared to previously deimmunized P99 variants, which bore only one or two mutations, the enzymes designed here contain 4-5 widely distributed substitutions. As a result, they exhibit broad reductions in major histocompatibility complex recognition. Despite their high mutational loads and markedly reduced immunoreactivity, all eight engineered variants possessed wild-type or better catalytic activity. Thus, the protein design algorithm is able to disrupt broadly distributed epitopes while maintaining protein function. As a result, this computational tool may prove useful in expanding the repertoire of next-generation biotherapeutics.
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46
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Salvat R, Moise L, Bailey-Kellogg C, Griswold KE. A high throughput MHC II binding assay for quantitative analysis of peptide epitopes. J Vis Exp 2014. [PMID: 24686319 DOI: 10.3791/51308] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Biochemical assays with recombinant human MHC II molecules can provide rapid, quantitative insights into immunogenic epitope identification, deletion, or design(1,2). Here, a peptide-MHC II binding assay is scaled to 384-well format. The scaled down protocol reduces reagent costs by 75% and is higher throughput than previously described 96-well protocols(1,3-5). Specifically, the experimental design permits robust and reproducible analysis of up to 15 peptides against one MHC II allele per 384-well ELISA plate. Using a single liquid handling robot, this method allows one researcher to analyze approximately ninety test peptides in triplicate over a range of eight concentrations and four MHC II allele types in less than 48 hr. Others working in the fields of protein deimmunization or vaccine design and development may find the protocol to be useful in facilitating their own work. In particular, the step-by-step instructions and the visual format of JoVE should allow other users to quickly and easily establish this methodology in their own labs.
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Affiliation(s)
| | - Leonard Moise
- Institute for Immunology and Informatics, University of Rhode Island
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47
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van Haren SD, Wroblewska A, Herczenik E, Kaijen PH, Ruminska A, ten Brinke A, Meijer AB, Voorberg J. Limited promiscuity of HLA-DRB1 presented peptides derived of blood coagulation factor VIII. PLoS One 2013; 8:e80239. [PMID: 24244658 PMCID: PMC3828219 DOI: 10.1371/journal.pone.0080239] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 10/01/2013] [Indexed: 11/19/2022] Open
Abstract
The formation of inhibitory antibodies directed against coagulation factor VIII (FVIII) is a severe complication in the treatment of hemophilia A patients. The induction of anti-FVIII antibodies is a CD4+ T cell-dependent process. Activation of FVIII-specific CD4+ T cells is dependent on the presentation of FVIII-derived peptides on MHC class II by antigen-presenting cells. Previously, we have shown that FVIII-pulsed human monocyte-derived dendritic cells can present peptides from several FVIII domains. In this study we show that FVIII peptides are presented on immature as well as mature dendritic cells. In immature dendritic cells half of the FVIII-loaded MHC class II molecules are retained within the cell, whereas in LPS-matured dendritic cells the majority of MHC class II/peptide complexes is present on the plasma membrane. Time-course studies revealed that presentation of FVIII-derived peptides was optimal between 12 and 24 hours after maturation but persisted for at least 96 hours. We also show that macrophages are able to internalize FVIII as efficiently as dendritic cells, however FVIII was presented on MHC class II with a lower efficiency and with different epitopes compared to dendritic cells. In total, 48 FVIII core-peptides were identified using a DCs derived of 8 different donors. Five HLA-promiscuous FVIII peptide regions were found – these were presented by at least 4 out of 8 donors. The remaining 42 peptide core regions in FVIII were presented by DCs derived from a single (30 peptides) or two to three donors (12 peptides). Overall, our findings show that a broad repertoire of FVIII peptides can be presented on HLA-DR.
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Affiliation(s)
- Simon D. van Haren
- Department of Plasma Proteins, Sanquin-AMC Landsteiner and Van Creveld Laboratory, Amsterdam, The Netherlands
| | - Aleksandra Wroblewska
- Department of Plasma Proteins, Sanquin-AMC Landsteiner and Van Creveld Laboratory, Amsterdam, The Netherlands
| | - Eszter Herczenik
- Department of Plasma Proteins, Sanquin-AMC Landsteiner and Van Creveld Laboratory, Amsterdam, The Netherlands
| | - Paul H. Kaijen
- Department of Plasma Proteins, Sanquin-AMC Landsteiner and Van Creveld Laboratory, Amsterdam, The Netherlands
| | - Aleksandra Ruminska
- Department of Plasma Proteins, Sanquin-AMC Landsteiner and Van Creveld Laboratory, Amsterdam, The Netherlands
| | - Anja ten Brinke
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands
| | - Alexander B. Meijer
- Department of Plasma Proteins, Sanquin-AMC Landsteiner and Van Creveld Laboratory, Amsterdam, The Netherlands
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jan Voorberg
- Department of Plasma Proteins, Sanquin-AMC Landsteiner and Van Creveld Laboratory, Amsterdam, The Netherlands
- * E-mail:
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48
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De Groot AS, Terry F, Cousens L, Martin W. Beyond humanization and de-immunization: tolerization as a method for reducing the immunogenicity of biologics. Expert Rev Clin Pharmacol 2013; 6:651-62. [PMID: 24164613 PMCID: PMC4086238 DOI: 10.1586/17512433.2013.835698] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Immune responses to some monoclonal antibodies (mAbs) and biologic proteins interfere with their efficacy due to the development of anti-drug antibodies (ADA). In the case of mAbs, most ADA target 'foreign' sequences present in the complementarity determining regions (CDRs). Humanization of the mAb sequence is one approach that has been used to render biologics less foreign to the human immune system. However, fully human mAbs can also drive immunogenicity. De-immunization (removing epitopes) has been used to reduce biologic protein immunogenicity. Here, we discuss a third approach to reducing the immunogenicity of biologics: introduction of Treg epitopes that stimulate Treg function and induce tolerance to the biologic protein. Supplementing humanization (replacing xeno-sequences with human) and de-immunization (reducing T effector epitopes) with tolerization (introducing Treg epitopes) where feasible, as a means of improving biologics 'quality by design', may lead to the development of ever more clinically effective, but less immunogenic, biologics.
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Affiliation(s)
- Anne S De Groot
- Institute for Immunology and Informatics,University of Rhode Island, 80 Washington Street, Providence, RI 02903,USA
- EpiVax, Inc.,146 Clifford Street, Providence, RI 02903,USA
| | - Frances Terry
- EpiVax, Inc.,146 Clifford Street, Providence, RI 02903,USA
| | - Leslie Cousens
- EpiVax, Inc.,146 Clifford Street, Providence, RI 02903,USA
| | - William Martin
- EpiVax, Inc.,146 Clifford Street, Providence, RI 02903,USA
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49
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Jawa V, Cousens LP, Awwad M, Wakshull E, Kropshofer H, De Groot AS. T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation. Clin Immunol 2013; 149:534-55. [PMID: 24263283 DOI: 10.1016/j.clim.2013.09.006] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/13/2013] [Accepted: 09/14/2013] [Indexed: 02/07/2023]
Abstract
Protein therapeutics hold a prominent and rapidly expanding place among medicinal products. Purified blood products, recombinant cytokines, growth factors, enzyme replacement factors, monoclonal antibodies, fusion proteins, and chimeric fusion proteins are all examples of therapeutic proteins that have been developed in the past few decades and approved for use in the treatment of human disease. Despite early belief that the fully human nature of these proteins would represent a significant advantage, adverse effects associated with immune responses to some biologic therapies have become a topic of some concern. As a result, drug developers are devising strategies to assess immune responses to protein therapeutics during both the preclinical and the clinical phases of development. While there are many factors that contribute to protein immunogenicity, T cell- (thymus-) dependent (Td) responses appear to play a critical role in the development of antibody responses to biologic therapeutics. A range of methodologies to predict and measure Td immune responses to protein drugs has been developed. This review will focus on the Td contribution to immunogenicity, summarizing current approaches for the prediction and measurement of T cell-dependent immune responses to protein biologics, discussing the advantages and limitations of these technologies, and suggesting a practical approach for assessing and mitigating Td immunogenicity.
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50
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Inaba H, Moise L, Martin W, De Groot AS, Desrosiers J, Tassone R, Buchman G, Akamizu T, De Groot LJ. Epitope recognition in HLA-DR3 transgenic mice immunized to TSH-R protein or peptides. Endocrinology 2013; 154:2234-43. [PMID: 23592747 PMCID: PMC5393327 DOI: 10.1210/en.2013-1033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Development of Graves' disease is related to HLA-DR3. The extracellular domain (ECD) of human TSH receptor (hTSH-R) is a crucial antigen in Graves' disease. hTSH-R peptide 37 (amino acids 78-94) is an important immunogenic peptide in DR3 transgenic mice immunized to hTSH-R. This study examined the epitope recognition in DR3 transgenic mice immunized to hTSH-R protein and evaluated the ability of a mutant hTSH-R peptide to attenuate the immunogenicity of hTSH-R peptide 37. DR3 transgenic mice were immunized to recombinant hTSH-R-ECD protein or peptides. A mutant hTSH-R 37 peptide (ISRIYVSIDATLSQLES: 37 m), in which DR3 binding motif position 5 was mutated V>A, and position 8 Q>S, was synthesized. 37 m should bind to HLA-DR3 but not bind T cell receptors. DR3 transgenic mice were immunized to hTSH-R 37 and 37 m. Mice immunized to hTSH-R-ECD protein developed strong anti-hTSH-R antibody, and antisera reacted strongly with hTSH-R peptides 1-5 (20-94), 21 (258-277), 41 (283-297), 36 (376-389), and 31 (399-418). Strikingly, antisera raised to hTSH-R peptide 37 bound to hTSH-R peptides 1-7 (20-112), 10 (132-50), 33 (137-150), 41, 23 (286-305), 24 (301-320), 36, and 31 as well as to hTSH-R-ECD protein. Both antibody titers to hTSH-R 37 and reaction of splenocytes to hTSH-R 37 were significantly reduced in mice immunized to hTSH-R 37 plus 37 m, compared with mice immunized to hTSH-R 37 alone. The ability of immunization to a single peptide to induce antibodies that bind hTSH-R-ECD protein, and multiple unrelated peptides, is a unique observation. Immunogenic reaction to hTSH-R peptide 37 was partially suppressed by 37 m, and this may contribute to immunotherapy of autoimmune thyroid disease.
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Affiliation(s)
- Hidefumi Inaba
- Department of Cellular and Molecular Biology, University of Rhode Island, Kingston, Rhode Island 02881, USA.
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