1
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Roberts BJ, Mattei AE, Howard KE, Weaver JL, Liu H, Lelias S, Martin WD, Verthelyi D, Pang E, Edwards KJ, De Groot AS. Assessing the immunogenicity risk of salmon calcitonin peptide impurities using in silico and in vitro methods. Front Pharmacol 2024; 15:1363139. [PMID: 39185315 PMCID: PMC11341359 DOI: 10.3389/fphar.2024.1363139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/10/2024] [Indexed: 08/27/2024] Open
Abstract
Advances in synthetic peptide synthesis have enabled rapid and cost-effective peptide drug manufacturing. For this reason, peptide drugs that were first produced using recombinant DNA (rDNA) technology are now being produced using solid- and liquid-phase peptide synthesis. While peptide synthesis has some advantages over rDNA expression methods, new peptide-related impurities that differ from the active pharmaceutical ingredient (API) may be generated during synthesis. These impurity byproducts of the original peptide sequence feature amino acid insertions, deletions, and side-chain modifications that may alter the immunogenicity risk profile of the drug product. Impurities resulting from synthesis have become the special focus of regulatory review and approval for human use, as outlined in the FDA's Center for Drug Evaluation and Research guidance document, "ANDAs for Certain Highly Purified Synthetic Peptide Drug Products That Refer to Listed Drugs of rDNA Origin," published in 2021. This case study illustrates how in silico and in vitro methods can be applied to assess the immunogenicity risk of impurities that may be present in synthetic generic versions of the salmon calcitonin (SCT) drug product. Sponsors of generic drug abbreviated new drug applications (ANDAs) should consider careful control of these impurities (for example, keeping the concentration of the immunogenic impurities below the cut-off recommended by FDA regulators). Twenty example SCT impurities were analyzed using in silico tools and assessed as having slightly more or less immunogenic risk potential relative to the SCT API peptide. Class II human leukocyte antigen (HLA)-binding assays provided independent confirmation that a 9-mer sequence present in the C-terminus of SCT binds promiscuously to multiple HLA DR alleles, while T-cell assays confirmed the expected T-cell responses to SCT and selected impurities. In silico analysis combined with in vitro assays that directly compare the API to each individual impurity peptide may be a useful approach for assessing the potential immunogenic risk posed by peptide impurities that are present in generic drug products.
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Affiliation(s)
| | | | - Kristina E. Howard
- Division of Applied Regulatory Sciences, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - James L. Weaver
- Division of Applied Regulatory Sciences, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Hao Liu
- Division of Therapeutic Performance I, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | | | | | - Daniela Verthelyi
- Division of Biotechnology Review and Research III, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Eric Pang
- Division of Therapeutic Performance I, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
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2
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Dargaud Y, Leuci A, Ruiz AR, Lacroix-Desmazes S. Efanesoctocog alfa: the renaissance of Factor VIII replacement therapy. Haematologica 2024; 109:2436-2444. [PMID: 38356459 PMCID: PMC11290510 DOI: 10.3324/haematol.2023.284498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
Efanesoctocog alfa (Altuviiio,TM Sanofi-SOBI) is a B domain-deleted single-chain Factor VIII (FVIII) connected to D'D3 domain of von Willebrand Factor (vWF). Its ingenious design allows efanesoctocog alfa to operate independently of endogenous vWF and results in an outstanding 3-4 times longer half-life compared to standard and extended half-life (EHL) FVIII products. The prolonged half-life ensures sustained high levels of factor activity, maintaining normal to near-normal ranges for the majority of the week, facilitating the convenience of once-weekly administration. Efanesoctocog alfa received regulatory approval in 2023 for application in both adults and children with inherited hemophilia A in the United States and Japan. Its sanctioned use encompasses both prophylaxis and 'on demand' treatment for bleeding episodes. The European Medicines Agency (EMA) is currently undertaking a comprehensive review of Altuviiio. TM This comprehensive review focuses on the immunological profile of efanesoctocog alfa, a highly sophisticated new class of EHL FVIII molecule. The integration of the vWF D'D3 domain, XTEN polypeptides, and potential regulatory T-cell epitopes within various segments of efanesoctocog alfa collectively serves as a mitigating factor against the development of a neutralizing T-cell-mediated immune response. We hypothesize that such distinctive attribute may significantly reduce the risk of neutralizing antibodies, particularly in previously untreated patients. The discussion extends beyond regulatory approval to encompass the preclinical and clinical development of efanesoctocog alfa, including considerations for laboratory monitoring. The review also highlights areas that warrant further investigation to deepen our understanding of this groundbreaking therapeutic agent.
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Affiliation(s)
- Yesim Dargaud
- French Reference Center for Haemophilia, Clinical Haemostasis Unit, Hopital Louis Pradel, Lyon, France; UR4609 Research Unit on Haemostasis and Thrombosis, University Claude Bernard Lyon 1, Lyon.
| | - Alexandre Leuci
- UR4609 Research Unit on Haemostasis and Thrombosis, University Claude Bernard Lyon 1, Lyon
| | - Alejandra Reyes Ruiz
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université de Paris, F-75006 Paris
| | - Sebastien Lacroix-Desmazes
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, CNRS, Sorbonne Université, Université de Paris, F-75006 Paris
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3
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Miah SMS, Lelias S, Gutierrez AH, McAllister M, Boyle CM, Moise L, De Groot AS. A SARS-CoV-2 NSP7 homolog of a Treg epitope suppresses CD4+ and CD8+ T cell memory responses. Front Immunol 2023; 14:1290688. [PMID: 38124752 PMCID: PMC10731459 DOI: 10.3389/fimmu.2023.1290688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/03/2023] [Indexed: 12/23/2023] Open
Abstract
Pathogens escape host defenses by T-cell epitope mutation or deletion (immune escape) and by simulating the appearance of human T cell epitopes (immune camouflage). We identified a highly conserved, human-like T cell epitope in non-structural protein 7 (NSP7) of SARS-CoV-2, RNA-dependent RNA polymerase (RdRp) hetero-tetramer complex. Remarkably, this T cell epitope has significant homology to a T regulatory cell epitope (Tregitope) previously identified in the Fc region of human immunoglobulin G (IgG) (Tregitope 289). We hypothesized that the SARS-CoV-2 NSP7 epitope (NSP7-289) may induce suppressive responses by engaging and activating pre-existing regulatory T cells. We therefore compared NSP7-289 and IgG Tregitopes (289 and 289z, a shorter version of 289 that isolates the shared NSP7 epitope) in vitro. Tregitope peptides 289, 289z and NSP7-289 bound to multiple HLA-DRB1 alleles in vitro and suppressed CD4+ and CD8+ T cell memory responses. Identification and in vitro validation of SARS-CoV-2 NSP7-289 provides further evidence of immune camouflage and suggests that pathogens can use human-like epitopes to evade immune response and potentially enhance host tolerance. Further exploration of the role of cross-conserved Tregs in human immune responses to pathogens such as SARS-CoV-2 is warranted.
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Affiliation(s)
| | | | | | | | | | | | - 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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4
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De Groot AS, Khan S, Mattei AE, Lelias S, Martin WD. Does human homology reduce the potential immunogenicity of non-antibody scaffolds? Front Immunol 2023; 14:1215939. [PMID: 38022550 PMCID: PMC10664710 DOI: 10.3389/fimmu.2023.1215939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Biologics developers are moving beyond antibodies for delivery of a wide range of therapeutic interventions. These non-antibody modalities are often based on 'natural' protein scaffolds that are modified to deliver bioactive sequences. Both human-derived and non-human-sourced scaffold proteins have been developed. New types of "non-antibody" scaffolds are still being discovered, as they offer attractive alternatives to monoclonals due to their smaller size, improved stability, and ease of synthesis. They are believed to have low immunogenic potential. However, while several human-sourced protein scaffolds have not been immunogenic in clinical studies, this may not predict their overall performance in other therapeutic applications. A preliminary evaluation of their potential for immunogenicity is warranted. Immunogenicity risk potential has been clearly linked to the presence of T "helper" epitopes in the sequence of biologic therapeutics. In addition, tolerogenic epitopes are present in some human proteins and may decrease their immunogenic potential. While the detailed sequences of many non-antibody scaffold therapeutic candidates remain unpublished, their backbone sequences are available for review and analysis. We assessed 12 example non-antibody scaffold backbone sequences using our epitope-mapping tools (EpiMatrix) for this perspective. Based on EpiMatrix scoring, their HLA DRB1-restricted T cell epitope content appears to be lower than the average protein, and sequences that may act as tolerogenic epitopes are present in selected human-derived scaffolds. Assessing the potential immunogenicity of scaffold proteins regarding self and non-self T cell epitopes may be of use for drug developers and clinicians, as these exciting new non-antibody molecules begin to emerge from the preclinical pipeline into clinical use.
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Affiliation(s)
- Anne S. De Groot
- EpiVax, Providence, RI, United States
- University of Georgia, Center for Vaccines and Immunology, Athens, GA, United States
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5
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Dower WJ, Park AI, Bakker AV, Cwirla SE, Pongtornpipat P, Williams BM, Joshi P, Baxter BA, Needels MC, Barrett RW. A mechanistically novel peptide agonist of the IL-7 receptor that addresses limitations of IL-7 cytokine therapy. PLoS One 2023; 18:e0286834. [PMID: 37874823 PMCID: PMC10597491 DOI: 10.1371/journal.pone.0286834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Interleukin (IL)-7 is broadly active on T-cell populations, and modified versions have been clinically evaluated for a variety of therapeutic applications, including cancer, lymphopenia, and infectious diseases; and found to be relatively well-tolerated and biologically active. Here we describe novel IL-7R agonists that are unrelated in structure to IL-7, bind to the receptor subunits differently from IL-7, but closely emulate IL-7 biology. The small size, low structural complexity, and the natural amino acid composition of the pharmacologically active peptide MDK1472 allows facile incorporation into protein structures, such as the IgG2-Fc fusion MDK-703. This molecule possesses properties potentially better suited to therapeutic applications than native IL-7 or its derivatives. We compared these compounds with IL-7 for immune cell selectivity, induction of IL-7R signaling, receptor-mediated internalization, proliferation, and generation of immune cell phenotypes in human and non-human primate (NHP) peripheral blood cells in vitro; and found them to be similar in biological activity to IL-7. In cynomolgus macaques, MDK-703 exhibits a circulating half-life of 46 hr and produces sustained T-cell expansion characteristic of IL-7 treatment. In the huCD34+-engrafted NSG mouse model of the human immune system, MDK-703 induces an immune cell profile very similar to that generated by IL-7-derived compounds; including the pronounced expansion of memory T-cells, particularly the population of stem-like memory T-cells (Tscm) which may be important for anti-tumor activities reported with IL-7 treatment. Clinical administration of IL-7 and modified variants has been reported to induce anti-drug antibodies (ADAs), including IL-7 neutralizing antibodies. The novel peptide agonist reported here scores very low in predicted immunogenicity, and because the peptide lacks sequence similarity with IL-7, the problematic immunogenic neutralization of endogenous cytokine should not occur. The properties we report here implicate MDK-703 as a candidate for clinical evaluation in oncology, anti-viral and other infectious disease, vaccine enhancement, and treatment of lymphopenia.
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Affiliation(s)
- William J. Dower
- Medikine, Inc., Menlo Park, California, United States of America
| | | | - Alice V. Bakker
- Medikine, Inc., Menlo Park, California, United States of America
| | - Steven E. Cwirla
- Medikine, Inc., Menlo Park, California, United States of America
| | | | - Blake M. Williams
- Medikine, Inc., Menlo Park, California, United States of America
- Department of Biomedical Engineering, and Center for Quantitative Bioinformatics and Quantitative Biology, Colleges of Engineering and Medicine, University of Illinois Chicago, IL, United States of America
| | - Prarthana Joshi
- Medikine, Inc., Menlo Park, California, United States of America
| | - Bryan A. Baxter
- Medikine, Inc., Menlo Park, California, United States of America
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6
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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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7
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Haltaufderhyde K, Roberts BJ, Khan S, Terry F, Boyle CM, McAllister M, Martin W, Rosenberg A, De Groot AS. Immunoinformatic Risk Assessment of Host Cell Proteins During Process Development for Biologic Therapeutics. AAPS J 2023; 25:87. [PMID: 37697150 DOI: 10.1208/s12248-023-00852-z] [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: 06/14/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023] Open
Abstract
The identification and removal of host cell proteins (HCPs) from biologic products is a critical step in drug development. Despite recent improvements to purification processes, biologics such as monoclonal antibodies, enzyme replacement therapies, and vaccines that are manufactured in a range of cell lines and purified using diverse processes may contain HCP impurities, making it necessary for developers to identify and quantify impurities during process development for each drug product. HCPs that contain sequences that are less conserved with human homologs may be more immunogenic than those that are more conserved. We have developed a computational tool, ISPRI-HCP, that estimates the immunogenic potential of HCP sequences by evaluating and quantifying T cell epitope density and relative conservation with similar T cell epitopes in the human proteome. Here we describe several case studies that support the use of this method for classifying candidate HCP impurities according to their immunogenicity risk.
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Affiliation(s)
| | - Brian J Roberts
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | - Sundos Khan
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | - Frances Terry
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | | | | | - William Martin
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | - Amy Rosenberg
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA
| | - Anne S De Groot
- EpiVax, Inc, 188 Valley St #424, Providence, Rhode Island, USA.
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA.
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8
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Nakamura Y, Moi ML, Shiina T, Shin-I T, Suzuki R. Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases. Viruses 2023; 15:v15051186. [PMID: 37243272 DOI: 10.3390/v15051186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
T-cell recognition of antigen epitopes is a crucial step for the induction of adaptive immune responses, and the identification of such T-cell epitopes is, therefore, important for understanding diverse immune responses and controlling T-cell immunity. A number of bioinformatic tools exist that predict T-cell epitopes; however, many of these methods highly rely on evaluating conventional peptide presentation by major histocompatibility complex (MHC) molecules, but they ignore epitope sequences recognized by T-cell receptor (TCR). Immunogenic determinant idiotopes are present on the variable regions of immunoglobulin molecules expressed on and secreted by B-cells. In idiotope-driven T-cell/B-cell collaboration, B-cells present the idiotopes on MHC molecules for recognition by idiotope-specific T-cells. According to the idiotype network theory formulated by Niels Jerne, such idiotopes found on anti-idiotypic antibodies exhibit molecular mimicry of antigens. Here, by combining these concepts and defining the patterns of TCR-recognized epitope motifs (TREMs), we developed a T-cell epitope prediction method that identifies T-cell epitopes derived from antigen proteins by analyzing B-cell receptor (BCR) sequences. This method allowed us to identify T-cell epitopes that contain the same TREM patterns between BCR and viral antigen sequences in two different infectious diseases caused by dengue virus and SARS-CoV-2 infection. The identified epitopes were among the T-cell epitopes detected in previous studies, and T-cell stimulatory immunogenicity was confirmed. Thus, our data support this method as a powerful tool for the discovery of T-cell epitopes from BCR sequences.
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Affiliation(s)
| | - Meng Ling Moi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | | | - Ryuji Suzuki
- Repertoire Genesis Inc., Osaka 567-0085, Japan
- Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, National Hospital Organization Sagamihara National Hospital, Kanagawa 252-0392, Japan
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9
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Hall-Swan S, Slone J, Rigo MM, Antunes DA, Lizée G, Kavraki LE. PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure. Front Immunol 2023; 14:1108303. [PMID: 37187737 PMCID: PMC10175663 DOI: 10.3389/fimmu.2023.1108303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Introduction Peptide-HLA class I (pHLA) complexes on the surface of tumor cells can be targeted by cytotoxic T-cells to eliminate tumors, and this is one of the bases for T-cell-based immunotherapies. However, there exist cases where therapeutic T-cells directed towards tumor pHLA complexes may also recognize pHLAs from healthy normal cells. The process where the same T-cell clone recognizes more than one pHLA is referred to as T-cell cross-reactivity and this process is driven mainly by features that make pHLAs similar to each other. T-cell cross-reactivity prediction is critical for designing T-cell-based cancer immunotherapies that are both effective and safe. Methods Here we present PepSim, a novel score to predict T-cell cross-reactivity based on the structural and biochemical similarity of pHLAs. Results and discussion We show our method can accurately separate cross-reactive from non-crossreactive pHLAs in a diverse set of datasets including cancer, viral, and self-peptides. PepSim can be generalized to work on any dataset of class I peptide-HLAs and is freely available as a web server at pepsim.kavrakilab.org.
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Affiliation(s)
- Sarah Hall-Swan
- Department of Computer Science, Rice University, Houston, TX, United States
| | - Jared Slone
- Department of Computer Science, Rice University, Houston, TX, United States
| | - Mauricio M. Rigo
- Department of Computer Science, Rice University, Houston, TX, United States
| | - Dinler A. Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Lydia E. Kavraki
- Department of Computer Science, Rice University, Houston, TX, United States
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10
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Wirsching S, Fichter M, Cacicedo ML, Landfester K, Gehring S. Modification of Regulatory T Cell Epitopes Promotes Effector T Cell Responses to Aspartyl/Asparaginyl β-Hydroxylase. Int J Mol Sci 2022; 23:ijms232012444. [PMID: 36293298 PMCID: PMC9604227 DOI: 10.3390/ijms232012444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 12/28/2022] Open
Abstract
Cancer is a leading cause of death worldwide. The search for innovative therapeutic approaches is a principal focus of medical research. Vaccine strategies targeting a number of tumor-associated antigens are currently being evaluated. To date, none have garnered significant success. Purportedly, an immunosuppressive tumor microenvironment and the accumulation of regulatory T cells contribute to a lack of tumor vaccine efficacy. Aspartyl/asparaginyl β-hydroxylase (ASPH), a promising therapeutic target, is overexpressed in a variety of malignant tumors but is expressed negligibly in normal tissues. Computer analysis predicted that ASPH expresses four peptide sequences (epitopes) capable of stimulating regulatory T cell activity. The abolition of these putative regulatory T cell epitopes increased the CD4+ and CD8+ effector T cell responses to monocyte-derived dendritic cells pulsed with a modified, epitope-depleted version of ASPH in an ex vivo human lymphoid tissue-equivalent coculture system while simultaneously decreasing the overall number of FoxP3+ regulatory T cells. These findings suggest that the efficacy of all new vaccine candidates would profit from screening and eliminating potential tolerogenic regulatory T cell epitopes.
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Affiliation(s)
- Sebastian Wirsching
- Children’s Hospital, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Michael Fichter
- Department of Dermatology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Maximiliano L. Cacicedo
- Children’s Hospital, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Stephan Gehring
- Children’s Hospital, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Correspondence: ; Tel.: +49-6131-3560
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11
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Jackson KR, Antunes DA, Talukder AH, Maleki AR, Amagai K, Salmon A, Katailiha AS, Chiu Y, Fasoulis R, Rigo MM, Abella JR, Melendez BD, Li F, Sun Y, Sonnemann HM, Belousov V, Frenkel F, Justesen S, Makaju A, Liu Y, Horn D, Lopez-Ferrer D, Huhmer AF, Hwu P, Roszik J, Hawke D, Kavraki LE, Lizée G. Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PNAS NEXUS 2022; 1:pgac124. [PMID: 36003074 PMCID: PMC9391200 DOI: 10.1093/pnasnexus/pgac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Human leukocyte antigen class I (HLA-I) molecules bind and present peptides at the cell surface to facilitate the induction of appropriate CD8+ T cell-mediated immune responses to pathogen- and self-derived proteins. The HLA-I peptide-binding cleft contains dominant anchor sites in the B and F pockets that interact primarily with amino acids at peptide position 2 and the C-terminus, respectively. Nonpocket peptide-HLA interactions also contribute to peptide binding and stability, but these secondary interactions are thought to be unique to individual HLA allotypes or to specific peptide antigens. Here, we show that two positively charged residues located near the top of peptide-binding cleft facilitate interactions with negatively charged residues at position 4 of presented peptides, which occur at elevated frequencies across most HLA-I allotypes. Loss of these interactions was shown to impair HLA-I/peptide binding and complex stability, as demonstrated by both in vitro and in silico experiments. Furthermore, mutation of these Arginine-65 (R65) and/or Lysine-66 (K66) residues in HLA-A*02:01 and A*24:02 significantly reduced HLA-I cell surface expression while also reducing the diversity of the presented peptide repertoire by up to 5-fold. The impact of the R65 mutation demonstrates that nonpocket HLA-I/peptide interactions can constitute anchor motifs that exert an unexpectedly broad influence on HLA-I-mediated antigen presentation. These findings provide fundamental insights into peptide antigen binding that could broadly inform epitope discovery in the context of viral vaccine development and cancer immunotherapy.
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Affiliation(s)
- Kyle R Jackson
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Amjad H Talukder
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ariana R Maleki
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kano Amagai
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Avery Salmon
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Arjun S Katailiha
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Romanos Fasoulis
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Jayvee R Abella
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Brenda D Melendez
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Fenge Li
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yimo Sun
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Heather M Sonnemann
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | | - Yang Liu
- ThermoFisher Scientific, San Jose, CA, USA
| | - David Horn
- ThermoFisher Scientific, San Jose, CA, USA
| | | | | | - Patrick Hwu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David Hawke
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Gregory Lizée
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
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12
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Laurén I, Havervall S, Ng H, Lord M, Pettke A, Greilert‐Norin N, Gabrielsson L, Chourlia A, Amoêdo‐Leite C, Josyula VS, Eltahir M, Kerzeli I, Falk AJ, Hober J, Christ W, Wiberg A, Hedhammar M, Tegel H, Burman J, Xu F, Pin E, Månberg A, Klingström J, Christoffersson G, Hober S, Nilsson P, Philipson M, Dönnes P, Lindsay R, Thålin C, Mangsbo S. Long-term SARS-CoV-2-specific and cross-reactive cellular immune responses correlate with humoral responses, disease severity, and symptomatology. Immun Inflamm Dis 2022; 10:e595. [PMID: 35349756 PMCID: PMC8962644 DOI: 10.1002/iid3.595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cellular immune memory responses post coronavirus disease 2019 (COVID-19) have been difficult to assess due to the risks of contaminating the immune response readout with memory responses stemming from previous exposure to endemic coronaviruses. The work herein presents a large-scale long-term follow-up study investigating the correlation between symptomology and cellular immune responses four to five months post seroconversion based on a unique severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific peptide pool that contains no overlapping peptides with endemic human coronaviruses. METHODS Peptide stimulated memory T cell responses were assessed with dual interferon-gamma (IFNγ) and interleukin (IL)-2 Fluorospot. Serological analyses were performed using a multiplex antigen bead array. RESULTS Our work demonstrates that long-term SARS-CoV-2-specific memory T cell responses feature dual IFNγ and IL-2 responses, whereas cross-reactive memory T cell responses primarily generate IFNγ in response to SARS-CoV-2 peptide stimulation. T cell responses correlated to long-term humoral immune responses. Disease severity as well as specific COVID-19 symptoms correlated with the magnitude of the SARS-CoV-2-specific memory T cell response four to five months post seroconversion. CONCLUSION Using a large cohort and a SARS-CoV-2-specific peptide pool we were able to substantiate that initial disease severity and symptoms correlate with the magnitude of the SARS-CoV-2-specific memory T cell responses.
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Affiliation(s)
- Ida Laurén
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Sebastian Havervall
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Henry Ng
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Martin Lord
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | | | - Nina Greilert‐Norin
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Lena Gabrielsson
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Aikaterini Chourlia
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Catarina Amoêdo‐Leite
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Vijay S. Josyula
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Mohamed Eltahir
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
- Department of Immunology, Genetics, and PathologyUppsala UniversityUppsalaSweden
| | - Iliana Kerzeli
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - August J. Falk
- Division of Affinity Proteomics, Department of Protein ScienceKTH Royal Institute of Technology, Science for Life LaboratoryStockholmSweden
| | - Jonathan Hober
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Wanda Christ
- Department of Medicine HuddingeKarolinska Institute, Centre for Infectious MedicineStockholmSweden
| | - Anna Wiberg
- Department of Immunology, Genetics, and PathologyUppsala UniversityUppsalaSweden
| | - My Hedhammar
- Division of Protein Technology, Department of Protein ScienceKTH Royal Institute of TechnologyStockholmSweden
| | - Hanna Tegel
- Division of Protein Technology, Department of Protein ScienceKTH Royal Institute of TechnologyStockholmSweden
| | - Joachim Burman
- Department of NeuroscienceUppsala UniversityUppsalaSweden
| | - Feifei Xu
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Elisa Pin
- Division of Affinity Proteomics, Department of Protein ScienceKTH Royal Institute of Technology, Science for Life LaboratoryStockholmSweden
| | - Anna Månberg
- Division of Affinity Proteomics, Department of Protein ScienceKTH Royal Institute of Technology, Science for Life LaboratoryStockholmSweden
| | - Jonas Klingström
- Department of Medicine HuddingeKarolinska Institute, Centre for Infectious MedicineStockholmSweden
| | - Gustaf Christoffersson
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Sophia Hober
- Division of Protein Technology, Department of Protein ScienceKTH Royal Institute of TechnologyStockholmSweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein ScienceKTH Royal Institute of Technology, Science for Life LaboratoryStockholmSweden
| | - Mia Philipson
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | | | - Robin Lindsay
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Charlotte Thålin
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Sara Mangsbo
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
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13
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Jawa V, Maamary J, Swanson M, Zhang S, Montgomery D. Implementing a Clinical Immunogenicity Strategy using Preclinical Risk Assessment Outputs. J Pharm Sci 2022; 111:960-969. [PMID: 35122828 DOI: 10.1016/j.xphs.2022.01.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 12/27/2022]
Abstract
Immunogenicity to biologics is often observed following dosing in human subjects during clinical trials. Both product and host specific factors may be implicated in contributing to a potential immune response. However, even if such risk factors are identified and eliminated as part of the rational quality by design approaches, the outcome in clinic can be uncertain and challenging to predict. Several tools have been employed to identify these risk factors and consequent mitigation approaches implemented prior to dosing in humans. However, the complexity of the immune system with an interplay of network of immune cells involved in driving a long- term immune response as well as patient characteristics, can make it challenging to predict the outcome in clinic. This perspective will provide an insight into recent advances in the risk assessment approaches that are utilized during preclinical stage of development of a biologic. The outputs from such tools can help to rank order and select the most optimal candidate with the least likelihood of an immune response and can further drive the development of a clinical bioanalytical and immunogenicity monitoring strategy. Such a strategy can be proactively shared with the regulators along with the proposal to streamline clinical immunogenicity and personalizing the outcome based on pharmacogenomics and other patient-related factors. This paper provides a roadmap on performing risk assessments through a systematic identification of risks and their mitigations wherever possible. Recommendations on incorporating the key components of such risk assessments as part of the new regulatory submissions are also provided. Shorter abstract Immunogenicity to biologics is common during clinical trials. Both product and host specific factors have been implicated. Several risk assessment tools can be used to identify and mitigate the risk factors responsible for immunogenicity. An insight into recent advances in the risk assessment approaches will be presented. The outputs can define a risk score and guide the clinical bioanalytical and immunogenicity monitoring strategy. A roadmap on performing risk assessments through a systematic identification of risks and their mitigations wherever possible is provided. Best practices for a risk assessment strategy and recommendations on the content for IND and the Integrated summary of Immunogenicity are also provided.
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Affiliation(s)
- Vibha Jawa
- Nonclinical Disposition and Bioanalysis, Bristol-Myers Squibb, Princeton, NJ 08648, USA.
| | - Jad Maamary
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), Merck & Co., Inc., Kenilworth, NJ 07033 USA
| | - Michael Swanson
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), Merck & Co., Inc., Kenilworth, NJ 07033 USA
| | - Shuli Zhang
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), Merck & Co., Inc., Kenilworth, NJ 07033 USA
| | - Diana Montgomery
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM), Merck & Co., Inc., Kenilworth, NJ 07033 USA
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14
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Richard G, Princiotta MF, Bridon D, Martin WD, Steinberg GD, De Groot AS. Neoantigen-based personalized cancer vaccines: the emergence of precision cancer immunotherapy. Expert Rev Vaccines 2021; 21:173-184. [PMID: 34882038 DOI: 10.1080/14760584.2022.2012456] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The field of cancer therapy has undergone a major transformation in less than a decade due to the introduction of checkpoint inhibitors, the advent of next generation sequencing and the discovery of neoantigens. The key observation that the breadth of each patient's immune response to the unique mutations or neoantigens present in their tumor is directly related to their survival has led oncologists to focus on driving immune responses to neoantigens through vaccination. Oncology has entered the era of precision immunotherapy, and cancer vaccine development is undergoing a paradigm shift. AREAS COVERED Neoantigens are short peptide sequences found in tumors, but not noncancerous tissues, the vast majority of which are unique to each patient. In addition to providing a description of the distinguishing features of neoantigen discovery platforms, this review will address cross-cutting personalized cancer vaccine design themes and developmental stumbling blocks. EXPERT OPINION Immunoinformatic pipelines that can rapidly scan cancer genomes and identify 'the best' neoantigens are in high demand. Despite the need for such tools, immunoinformatic methods for identifying neoepitopes in cancer genomes are diverse and have not been well-validated. Validation of 'personalized vaccine design pipelines' will bring about a revolution in neoantigen-based vaccine design and delivery.
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Affiliation(s)
| | | | | | | | - Gary D Steinberg
- EpiVax Therapeutics, Inc., Providence, RI, USA.,Perlmutter Cancer Center, Department of Urology at NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI, USA.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
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15
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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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16
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Kotraiah V, Phares TW, Terry FE, Hindocha P, Silk SE, Nielsen CM, Moise L, Tucker KD, Ashfield R, Martin WD, De Groot AS, Draper SJ, Gutierrez GM, Noe AR. Identification and Immune Assessment of T Cell Epitopes in Five Plasmodium falciparum Blood Stage Antigens to Facilitate Vaccine Candidate Selection and Optimization. Front Immunol 2021; 12:690348. [PMID: 34305923 PMCID: PMC8294059 DOI: 10.3389/fimmu.2021.690348] [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: 04/02/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
The hurdles to effective blood stage malaria vaccine design include immune evasion tactics used by the parasite such as redundant invasion pathways and antigen variation among circulating parasite strains. While blood stage malaria vaccine development primarily focuses on eliciting optimal humoral responses capable of blocking erythrocyte invasion, clinically-tested Plasmodium falciparum (Pf) vaccines have not elicited sterile protection, in part due to the dramatically high levels of antibody needed. Recent development efforts with non-redundant, conserved blood stage antigens suggest both high antibody titer and rapid antibody binding kinetics are important efficacy factors. Based on the central role of helper CD4 T cells in development of strong, protective immune responses, we systematically analyzed the class II epitope content in five leading Pf blood stage antigens (RH5, CyRPA, RIPR, AMA1 and EBA175) using in silico, in vitro, and ex vivo methodologies. We employed in silico T cell epitope analysis to enable identification of 67 HLA-restricted class II epitope clusters predicted to bind a panel of nine HLA-DRB1 alleles. We assessed a subset of these for HLA-DRB1 allele binding in vitro, to verify the in silico predictions. All clusters assessed (40 clusters represented by 46 peptides) bound at least two HLA-DR alleles in vitro. The overall epitope prediction to in vitro HLA-DRB1 allele binding accuracy was 71%. Utilizing the set of RH5 class II epitope clusters (10 clusters represented by 12 peptides), we assessed stimulation of T cells collected from HLA-matched RH5 vaccinees using an IFN-γ T cell recall assay. All clusters demonstrated positive recall responses, with the highest responses – by percentage of responders and response magnitude – associated with clusters located in the N-terminal region of RH5. Finally, a statistically significant correlation between in silico epitope predictions and ex vivo IFN-γ recall response was found when accounting for HLA-DR matches between the epitope predictions and donor HLA phenotypes. This is the first comprehensive analysis of class II epitope content in RH5, CyRPA, RIPR, AMA1 and EBA175 accompanied by in vitro HLA binding validation for all five proteins and ex vivo T cell response confirmation for RH5.
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Affiliation(s)
| | | | | | | | - Sarah E Silk
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | | | | | - Rebecca Ashfield
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - Anne S De Groot
- EpiVax Inc., Providence, RI, United States.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Simon J Draper
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - Amy R Noe
- Leidos Life Sciences, Leidos Inc., Frederick, MD, United States
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17
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De Groot AS, Desai AK, Lelias S, Miah SMS, Terry FE, Khan S, Li C, Yi JS, Ardito M, Martin WD, Kishnani PS. Immune Tolerance-Adjusted Personalized Immunogenicity Prediction for Pompe Disease. Front Immunol 2021; 12:636731. [PMID: 34220802 PMCID: PMC8242953 DOI: 10.3389/fimmu.2021.636731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/20/2021] [Indexed: 11/13/2022] Open
Abstract
Infantile-onset Pompe disease (IOPD) is a glycogen storage disease caused by a deficiency of acid alpha-glucosidase (GAA). Treatment with recombinant human GAA (rhGAA, alglucosidase alfa) enzyme replacement therapy (ERT) significantly improves clinical outcomes; however, many IOPD children treated with rhGAA develop anti-drug antibodies (ADA) that render the therapy ineffective. Antibodies to rhGAA are driven by T cell responses to sequences in rhGAA that differ from the individuals' native GAA (nGAA). The goal of this study was to develop a tool for personalized immunogenicity risk assessment (PIMA) that quantifies T cell epitopes that differ between nGAA and rhGAA using information about an individual's native GAA gene and their HLA DR haplotype, and to use this information to predict the risk of developing ADA. Four versions of PIMA have been developed. They use EpiMatrix, a computational tool for T cell epitope identification, combined with an HLA-restricted epitope-specific scoring feature (iTEM), to assess ADA risk. One version of PIMA also integrates JanusMatrix, a Treg epitope prediction tool to identify putative immunomodulatory (regulatory) T cell epitopes in self-proteins. Using the JanusMatrix-adjusted version of PIMA in a logistic regression model with data from 48 cross-reactive immunological material (CRIM)-positive IOPD subjects, those with scores greater than 10 were 4-fold more likely to develop ADA (p<0.03) than those that had scores less than 10. We also confirmed the hypothesis that some GAA epitopes are immunomodulatory. Twenty-one epitopes were tested, of which four were determined to have an immunomodulatory effect on T effector response in vitro. The implementation of PIMA V3J on a secure-access website would allow clinicians to input the individual HLA DR haplotype of their IOPD patient and the GAA pathogenic variants associated with each GAA allele to calculate the patient's relative risk of developing ADA, enhancing clinical decision-making prior to initiating treatment with ERT. A better understanding of immunogenicity risk will allow the implementation of targeted immunomodulatory approaches in ERT-naïve settings, especially in CRIM-positive patients, which may in turn improve the overall clinical outcomes by minimizing the development of ADA. The PIMA approach may also be useful for other types of enzyme or factor replacement therapies.
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Affiliation(s)
- Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Ankit K Desai
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | | | | | | | | | - Cindy Li
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - John S Yi
- Department of Surgery, Duke University Medical Center, Durham, NC, United States
| | | | | | - Priya S Kishnani
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
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18
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Noe AR, Terry FE, Schanen BC, Sassano E, Hindocha P, Phares TW, Moise L, Christen JM, Tucker KD, Kotraiah V, Drake DR, Martin WD, De Groot AS, Gutierrez GM. Bridging Computational Vaccinology and Vaccine Development Through Systematic Identification, Characterization, and Downselection of Conserved and Variable Circumsporozoite Protein CD4 T Cell Epitopes From Diverse Plasmodium falciparum Strains. Front Immunol 2021; 12:689920. [PMID: 34168657 PMCID: PMC8217813 DOI: 10.3389/fimmu.2021.689920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
An effective malaria vaccine must prevent disease in a range of populations living in regions with vastly different transmission rates and protect against genetically-diverse Plasmodium falciparum (Pf) strains. The protective efficacy afforded by the currently licensed malaria vaccine, Mosquirix™, promotes strong humoral responses to Pf circumsporozoite protein (CSP) 3D7 but protection is limited in duration and by strain variation. Helper CD4 T cells are central to development of protective immune responses, playing roles in B cell activation and maturation processes, cytokine production, and stimulation of effector T cells. Therefore, we took advantage of recent in silico modeling advances to predict and analyze human leukocyte antigen (HLA)-restricted class II epitopes from PfCSP – across the entire PfCSP 3D7 sequence as well as in 539 PfCSP sequence variants – with the goal of improving PfCSP-based malaria vaccines. Specifically, we developed a systematic workflow to identify peptide sequences capable of binding HLA-DR in a context relevant to achieving broad human population coverage utilizing cognate T cell help and with limited T regulatory cell activation triggers. Through this workflow, we identified seven predicted class II epitope clusters in the N- and C-terminal regions of PfCSP 3D7 and an additional eight clusters through comparative analysis of 539 PfCSP sequence variants. A subset of these predicted class II epitope clusters was synthesized as peptides and assessed for HLA-DR binding in vitro. Further, we characterized the functional capacity of these peptides to prime and activate human peripheral blood mononuclear cells (PBMCs), by monitoring cytokine response profiles using MIMIC® technology (Modular IMmune In vitro Construct). Utilizing this decision framework, we found sufficient differential cellular activation and cytokine profiles among HLA-DR-matched PBMC donors to downselect class II epitope clusters for inclusion in a vaccine targeting PfCSP. Importantly, the downselected clusters are not highly conserved across PfCSP variants but rather, they overlap a hypervariable region (TH2R) in the C-terminus of the protein. We recommend assessing these class II epitope clusters within the context of a PfCSP vaccine, employing a test system capable of measuring immunogenicity across a broad set of HLA-DR alleles.
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Affiliation(s)
- Amy R Noe
- Leidos Life Sciences, Leidos Inc., Frederick, MD, United States
| | | | - Brian C Schanen
- Sanofi Pasteur, VaxDesign Campus, Orlando, FL, United States
| | - Emily Sassano
- Sanofi Pasteur, VaxDesign Campus, Orlando, FL, United States
| | | | | | | | | | | | | | - Donald R Drake
- Sanofi Pasteur, VaxDesign Campus, Orlando, FL, United States
| | | | - Anne S De Groot
- EpiVax Inc., Providence, RI, United States.,University of Georgia Center for Vaccines and Immunology, Athens, GA, United States
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19
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Meyers LM, Gutiérrez AH, Boyle CM, Terry F, McGonnigal BG, Salazar A, Princiotta MF, Martin WD, De Groot AS, Moise L. Highly conserved, non-human-like, and cross-reactive SARS-CoV-2 T cell epitopes for COVID-19 vaccine design and validation. NPJ Vaccines 2021; 6:71. [PMID: 33986292 PMCID: PMC8119491 DOI: 10.1038/s41541-021-00331-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/01/2021] [Indexed: 12/24/2022] Open
Abstract
Natural and vaccine-induced SARS-CoV-2 immunity in humans has been described but correlates of protection are not yet defined. T cells support the SARS-CoV-2 antibody response, clear virus-infected cells, and may be required to block transmission. In this study, we identified peptide epitopes associated with SARS-CoV-2 T-cell immunity. Using immunoinformatic methods, T-cell epitopes from spike, membrane, and envelope were selected for maximal HLA-binding potential, coverage of HLA diversity, coverage of circulating virus, and minimal potential cross-reactivity with self. Direct restimulation of PBMCs collected from SARS-CoV-2 convalescents confirmed 66% of predicted epitopes, whereas only 9% were confirmed in naive individuals. However, following a brief period of epitope-specific T-cell expansion, both cohorts demonstrated robust T-cell responses to 97% of epitopes. HLA-DR3 transgenic mouse immunization with peptides co-formulated with poly-ICLC generated a potent Th1-skewed, epitope-specific memory response, alleviating safety concerns of enhanced respiratory disease associated with Th2 induction. Taken together, these epitopes may be used to improve our understanding of natural and vaccine-induced immunity, and to facilitate the development of T-cell-targeted vaccines that harness pre-existing SARS-CoV-2 immunity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Anne S De Groot
- EpiVax, Inc., Providence, RI, USA.
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.
| | - Leonard Moise
- EpiVax, Inc., Providence, RI, USA.
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.
- Institute for Immunology and Immunoinformatics, University of Rhode Island, Providence, RI, USA.
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20
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Multi-step screening of neoantigens' HLA- and TCR-interfaces improves prediction of survival. Sci Rep 2021; 11:9983. [PMID: 33976291 PMCID: PMC8113358 DOI: 10.1038/s41598-021-89016-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Improvement of risk stratification through prognostic biomarkers may enhance the personalization of cancer patient monitoring and treatment. We used Ancer, an immunoinformatic CD8, CD4, and regulatory T cell neoepitope screening system, to perform an advanced neoantigen analysis of genomic data derived from the urothelial cancer cohort of The Cancer Genome Atlas. Ancer demonstrated improved prognostic stratification and five-year survival prediction compared to standard analyses using tumor mutational burden or neoepitope identification using NetMHCpan and NetMHCIIpan. The superiority of Ancer, shown in both univariate and multivariate survival analyses, is attributed to the removal of neoepitopes that do not contribute to tumor immunogenicity based on their homology with self-epitopes. This analysis suggests that the presence of a higher number of unique, non-self CD8- and CD4-neoepitopes contributes to cancer survival, and that prospectively defining these neoepitopes using Ancer is a novel prognostic or predictive biomarker.
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21
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Tucker KD, Schanen BC, Phares TW, Sassano E, Terry FE, Hindocha P, Moise L, Kotraiah V, Martin WD, De Groot AS, Drake DR, Gutierrez GM, Noe AR. Identification, Selection and Immune Assessment of Liver Stage CD8 T Cell Epitopes From Plasmodium falciparum. Front Immunol 2021; 12:684116. [PMID: 34025684 PMCID: PMC8138313 DOI: 10.3389/fimmu.2021.684116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Immunization with radiation-attenuated sporozoites (RAS) has been shown to protect against malaria infection, primarily through CD8 T cell responses, but protection is limited based on parasite strain. Therefore, while CD8 T cells are an ideal effector population target for liver stage malaria vaccine development strategies, such strategies must incorporate conserved epitopes that cover a large range of class I human leukocyte antigen (HLA) supertypes to elicit cross-strain immunity across the target population. This approach requires identifying and characterizing a wide range of CD8 T cell epitopes for incorporation into a vaccine such that coverage across a large range of class I HLA alleles is attained. Accordingly, we devised an experimental framework to identify CD8 T cell epitopes from novel and minimally characterized antigens found at the pre-erythrocytic stage of parasite development. Through in silico analysis we selected conserved P. falciparum proteins, using P. vivax orthologues to establish stringent conservation parameters, predicted to have a high number of T cell epitopes across a set of six class I HLA alleles representative of major supertypes. Using the decision framework, five proteins were selected based on the density and number of predicted epitopes. Selected epitopes were synthesized as peptides and evaluated for binding to the class I HLA alleles in vitro to verify in silico binding predictions, and subsequently for stimulation of human T cells using the Modular IMmune In-vitro Construct (MIMIC®) technology to verify immunogenicity. By combining the in silico tools with the ex vivo high throughput MIMIC platform, we identified 15 novel CD8 T cell epitopes capable of stimulating an immune response in alleles across the class I HLA panel. We recommend these epitopes should be evaluated in appropriate in vivo humanized immune system models to determine their protective efficacy for potential inclusion in future vaccines.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Anne S. De Groot
- EpiVax Inc., Providence, RI, United States
- University of Georgia Center for Vaccines and Immunology, Athens, GA, United States
| | | | | | - Amy R. Noe
- Leidos Life Sciences, Leidos Inc., Frederick, MD, United States
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22
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Tan S, Gutiérrez AH, Gauger PC, Opriessnig T, Bahl J, Moise L, De Groot AS. Quantifying the Persistence of Vaccine-Related T Cell Epitopes in Circulating Swine Influenza A Strains from 2013-2017. Vaccines (Basel) 2021; 9:vaccines9050468. [PMID: 34066605 PMCID: PMC8148565 DOI: 10.3390/vaccines9050468] [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] [Received: 03/12/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 12/02/2022] Open
Abstract
When swine flu vaccines and circulating influenza A virus (IAV) strains are poorly matched, vaccine-induced antibodies may not protect from infection. Highly conserved T cell epitopes may, however, have a disease-mitigating effect. The degree of T cell epitope conservation among circulating strains and vaccine strains can vary, which may also explain differences in vaccine efficacy. Here, we evaluate a previously developed conserved T cell epitope-based vaccine and determine the persistence of T cell epitope conservation over time. We used a pair-wise homology score to define the conservation between the vaccine’s swine leukocyte antigen (SLA) class I and II-restricted epitopes and T cell epitopes found in 1272 swine IAV strains sequenced between 2013 and 2017. Twenty-four of the 48 total T cell epitopes included in the epitope-based vaccine were highly conserved and found in >1000 circulating swine IAV strains over the 5-year period. In contrast, commercial swine IAV vaccines developed in 2013 exhibited a declining conservation with the circulating IAV strains over the same 5-year period. Conserved T cell epitope vaccines may be a useful adjunct for commercial swine flu vaccines and to improve protection against influenza when antibodies are not cross-reactive.
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Affiliation(s)
- Swan Tan
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (S.T.); (J.B.)
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; or
| | | | - Phillip Charles Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (P.C.G.); or (T.O.)
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (P.C.G.); or (T.O.)
- Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Justin Bahl
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (S.T.); (J.B.)
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; or
| | - Leonard Moise
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; or
- EpiVax Inc., Providence, RI 02909, USA;
| | - Anne Searls De Groot
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; or
- EpiVax Inc., Providence, RI 02909, USA;
- Correspondence: or or ; Tel.: +1-401-952-4227
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23
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Dembele M, Tao S, Massoud AH, Miah SMS, Lelias S, De Groot AS, Mazer BD. Tregitopes Improve Asthma by Promoting Highly Suppressive and Antigen-Specific Tregs. Front Immunol 2021; 12:634509. [PMID: 33953711 PMCID: PMC8089381 DOI: 10.3389/fimmu.2021.634509] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/26/2021] [Indexed: 01/09/2023] Open
Abstract
Tregitopes (T regulatory epitopes) are IgG-derived peptides with high affinity to major histocompatibility complex class II (MHCII), that are known to promote tolerance by activating T regulatory cell (Treg) activity. Here we characterized the effect of IgG Tregitopes in a well-established murine model of allergic asthma, demonstrating in vivo antigen-specific tolerance via adoptive transfer of Tregitope-and-allergen-activated Tregs. Asthma is a heterogeneous chronic inflammatory condition affecting the airways and impacting over 300 million individuals worldwide. Treatment is suppressive, and no current therapy addresses immune regulation in severely affected asthmatics. Although high dose intra-venous immunoglobulin (IVIg) is not commonly used in the asthma clinic setting, it has been shown to improve severe asthma in children and in adults. In our laboratory, we previously demonstrated that IVIg abrogates airway hyperresponsiveness (AHR) in a murine model of asthma and induces suppressive antigen-specific T-regulatory cells. We hypothesized that IgG-derived Tregitopes would modulate allergic airway disease by inducing highly suppressive antigen-specific Tregs capable of diminishing T effector cell responses and establishing antigen-specific tolerance. Using ovalbumin (OVA-) and ragweed-driven murine models of allergic airway disease, we characterized the immunoregulatory properties of Tregitopes and performed Treg adoptive transfer to OVA- and ragweed-allergic mice to test for allergen specificity. Treatment with Tregitopes attenuated allergen-induced airway hyperresponsiveness and lung inflammation. We demonstrated that Tregitopes induce highly suppressive allergen-specific Tregs. The tolerogenic action of IgG Tregitopes in our model is very similar to that of IVIg, so we foresee that IgG Tregitopes could potentially replace steroid-based treatment and can offer a synthetic alternative to IVIg in a range of inflammatory and allergic conditions.
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MESH Headings
- Adoptive Transfer
- Animals
- Animals, Genetically Modified
- Anti-Asthmatic Agents/pharmacology
- Antigens, Plant
- Asthma/drug therapy
- Asthma/immunology
- Asthma/metabolism
- Asthma/physiopathology
- Bronchoconstriction/drug effects
- Cells, Cultured
- Cytokines/metabolism
- Disease Models, Animal
- Epitopes, T-Lymphocyte/drug effects
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Humans
- Immunoglobulin Fab Fragments/pharmacology
- Immunoglobulin Fc Fragments/pharmacology
- Inflammation Mediators/metabolism
- Lung/drug effects
- Lung/immunology
- Lung/metabolism
- Lung/physiopathology
- Lymphocyte Activation/drug effects
- Mice, Inbred C57BL
- Ovalbumin
- Plant Extracts
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- T-Lymphocytes, Regulatory/transplantation
- Mice
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Affiliation(s)
- Marieme Dembele
- The Research Institute of the McGill University Health Centre, Division of Pediatric Allergy Immunology and Dermatology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, QC, Canada
| | - Shao Tao
- The Research Institute of the McGill University Health Centre, Division of Pediatric Allergy Immunology and Dermatology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, QC, Canada
| | - Amir H. Massoud
- The Research Institute of the McGill University Health Centre, Division of Pediatric Allergy Immunology and Dermatology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, QC, Canada
| | | | | | - Anne S. De Groot
- EpiVax, Inc., Providence, RI, United States
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Bruce D. Mazer
- The Research Institute of the McGill University Health Centre, Division of Pediatric Allergy Immunology and Dermatology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, QC, Canada
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24
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Cavalluzzo B, Ragone C, Mauriello A, Petrizzo A, Manolio C, Caporale A, Vitagliano L, Ruvo M, Buonaguro L, Tagliamonte M. Identification and characterization of heteroclitic peptides in TCR-binding positions with improved HLA-binding efficacy. J Transl Med 2021; 19:89. [PMID: 33637105 PMCID: PMC7913412 DOI: 10.1186/s12967-021-02757-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 01/03/2023] Open
Abstract
The antigenicity as well as the immunogenicity of tumor associated antigens (TAAs) may need to be potentiated in order to break the immunological tolerance. To this aim, heteroclitic peptides were designed introducing specific substitutions in the residue at position 4 (p4) binding to TCR. The effect of such modifications also on the affinity to the major histocompatibility class I (MHC-I) molecule was assessed. The Trp2 antigen, specific for the mouse melanoma B16F10 cells, as well as the HPV-E7 antigen, specific for the TC1 tumor cell lines, were used as models. Affinity of such heteroclitic peptides to HLA was predicted by bioinformatics tools and the most promising ones were validated by structural conformational and HLA binding analyses. Overall, we demonstrated that TAAs modified at the TCR-binding p4 residue are predicted to have higher affinity to MHC-I molecules. Experimental evaluation confirms the stronger binding, suggesting that this strategy may be very effective for designing new vaccines with improved antigenic efficacy.
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Affiliation(s)
- Beatrice Cavalluzzo
- Innovative Immunological Models Lab, Istituto Nazionale Tumori "Fond. G. Pascale", Via Mariano Semmola, 1, 80131, Naples, Italy
| | - Concetta Ragone
- Innovative Immunological Models Lab, Istituto Nazionale Tumori "Fond. G. Pascale", Via Mariano Semmola, 1, 80131, Naples, Italy
| | - Angela Mauriello
- Innovative Immunological Models Lab, Istituto Nazionale Tumori "Fond. G. Pascale", Via Mariano Semmola, 1, 80131, Naples, Italy
| | - Annacarmen Petrizzo
- Innovative Immunological Models Lab, Istituto Nazionale Tumori "Fond. G. Pascale", Via Mariano Semmola, 1, 80131, Naples, Italy
| | - Carmen Manolio
- Innovative Immunological Models Lab, Istituto Nazionale Tumori "Fond. G. Pascale", Via Mariano Semmola, 1, 80131, Naples, Italy
| | - Andrea Caporale
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy.,Istituto Di Cristallografia-CNR, c/o area Science Park S.S. 14 Km 163.5 Basovizza, 34149, Trieste, Italy
| | | | - Menotti Ruvo
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Luigi Buonaguro
- Innovative Immunological Models Lab, Istituto Nazionale Tumori "Fond. G. Pascale", Via Mariano Semmola, 1, 80131, Naples, Italy
| | - Maria Tagliamonte
- Innovative Immunological Models Lab, Istituto Nazionale Tumori "Fond. G. Pascale", Via Mariano Semmola, 1, 80131, Naples, Italy.
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25
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Li X, An Y, Liao J, Xiao L, Swanson M, Martinez-Fonts K, Pavon JA, Sherer EC, Jawa V, Wang F, Gao X, Letarte S, Richardson DD. Identification and characterization of a residual host cell protein hexosaminidase B associated with N-glycan degradation during the stability study of a therapeutic recombinant monoclonal antibody product. Biotechnol Prog 2021; 37:e3128. [PMID: 33476097 PMCID: PMC8365702 DOI: 10.1002/btpr.3128] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/22/2020] [Accepted: 01/12/2021] [Indexed: 12/30/2022]
Abstract
Host cell proteins (HCPs) are process‐related impurities derived from host organisms, which need to be controlled to ensure adequate product quality and safety. In this study, product quality attributes were tracked for several monoclonal antibodies (mAbs) under the intended storage and accelerated stability conditions. One product quality attribute not expected to be stability indicating is the N‐glycan heterogeneity profile. However, significant N‐glycan degradation was observed for one mAb under accelerated and stressed stability conditions. The root cause for this instability was attributed to hexosaminidase B (HEXB), an enzyme known to remove terminal N‐acetylglucosamine (GlcNAc). HEXB was identified by liquid chromatography–mass spectrometry (LC–MS)‐based proteomics approach to be enriched in the impacted stability batches from mAb‐1. Subsequently, enzymatic and targeted multiple reaction monitoring (MRM) MS assays were developed to support process and product characterization. A potential interaction between HEXB and mAb‐1 was initially observed from the analysis of process intermediates by proteomics among several mAbs and later supported by computational modeling. An improved bioprocess was developed to significantly reduce HEXB levels in the final drug substance. A risk assessment was conducted by evaluating the in silico immunogenicity risk and the impact on product quality. To the best of our knowledge, HEXB is the first residual HCP reported to have impact on the glycan profile of a formulated drug product. The combination of different analytical tools, mass spectrometry, and computational modeling provides a general strategy on how to study residual HCP for biotherapeutics development.
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Affiliation(s)
- Xuanwen Li
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Yan An
- Biologics Analytical Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Jing Liao
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Li Xiao
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Michael Swanson
- Predictive and Clinical Immunogenicity, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Kirby Martinez-Fonts
- Biologics Analytical Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Jorge Alexander Pavon
- Biologics Analytical Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Edward C Sherer
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Vibha Jawa
- Predictive and Clinical Immunogenicity, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Fengqiang Wang
- Biologics Analytical Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Xinliu Gao
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Simon Letarte
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Douglas D Richardson
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, New Jersey, USA
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26
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De Groot AS, Rosenberg AS, Miah SMS, Skowron G, Roberts BJ, Lélias S, Terry FE, Martin WD. Identification of a potent regulatory T cell epitope in factor V that modulates CD4+ and CD8+ memory T cell responses. Clin Immunol 2021; 224:108661. [PMID: 33412295 DOI: 10.1016/j.clim.2020.108661] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023]
Abstract
Identification of T cell epitopes that are recognized by Tregs may elucidate the relative contributions of thymic Tregs and induced Tregs to control of autoimmune diseases and allergy. One such T regulatory cell epitope or 'Tregitope', derived from blood Factor V, is described here. Tregs responding to Tregitope FV621 are potent suppressors of CD4+ T effector responses to Tetanus Toxoid in an in vitro bystander suppression assay, strongly inhibit proliferation of effector CD8+ T cells, down-modulate CD86 and HLA DR on antigen-presenting cells, and enhance expression of granzyme B in Tregs. Tregitope FV621 also suppresses anti-OVA immune responses in vivo. The immunomodulatory effect of Tregitope FV621 is enhanced when conjugated to albumin, suggesting that the short half-life of Tregitope peptides can be prolonged. The in silico tools used to prospectively identify the FV Tregitope described here, when combined with in vitro /in vivo validating assays, may facilitate future Tregitope discoveries.
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Affiliation(s)
- Anne S De Groot
- EpiVax, Inc., Providence, RI, USA; Center for Vaccines and Immunology, University of Georgia, USA.
| | - Amy S Rosenberg
- Center for Drug Evaluation and Research, FDA, White Oak, MD, USA
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27
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Ong E, Huang X, Pearce R, Zhang Y, He Y. Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering. Comput Struct Biotechnol J 2020; 19:518-529. [PMID: 33398234 PMCID: PMC7773544 DOI: 10.1016/j.csbj.2020.12.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 01/12/2023] Open
Abstract
The development of effective and safe vaccines is the ultimate way to efficiently stop the ongoing COVID-19 pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Built on the fact that SARS-CoV-2 utilizes the association of its Spike (S) protein with the human angiotensin-converting enzyme 2 (ACE2) receptor to invade host cells, we computationally redesigned the S protein sequence to improve its immunogenicity and antigenicity. Toward this purpose, we extended an evolutionary protein design algorithm, EvoDesign, to create thousands of stable S protein variants that perturb the core protein sequence but keep the surface conformation and B cell epitopes. The T cell epitope content and similarity scores of the perturbed sequences were calculated and evaluated. Out of 22,914 designs with favorable stability energy, 301 candidates contained at least two pre-existing immunity-related epitopes and had promising immunogenic potential. The benchmark tests showed that, although the epitope restraints were not included in the scoring function of EvoDesign, the top S protein design successfully recovered 31 out of the 32 major histocompatibility complex (MHC)-II T cell promiscuous epitopes in the native S protein, where two epitopes were present in all seven human coronaviruses. Moreover, the newly designed S protein introduced nine new MHC-II T cell promiscuous epitopes that do not exist in the wildtype SARS-CoV-2. These results demonstrated a new and effective avenue to enhance a target protein's immunogenicity using rational protein design, which could be applied for new vaccine design against COVID-19 and other pathogens.
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Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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28
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Self-Replicating RNAs Drive Protective Anti-tumor T Cell Responses to Neoantigen Vaccine Targets in a Combinatorial Approach. Mol Ther 2020; 29:1186-1198. [PMID: 33278563 DOI: 10.1016/j.ymthe.2020.11.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Accepted: 11/25/2020] [Indexed: 12/15/2022] Open
Abstract
Historically poor clinical results of tumor vaccines have been attributed to weakly immunogenic antigen targets, limited specificity, and vaccine platforms that fail to induce high-quality polyfunctional T cells, central to mediating cellular immunity. We show here that the combination of antigen selection, construct design, and a robust vaccine platform based on the Synthetically Modified Alpha Replicon RNA Technology (SMARRT), a self-replicating RNA, leads to control of tumor growth in mice. Therapeutic immunization with SMARRT replicon-based vaccines expressing tumor-specific neoantigens or tumor-associated antigen were able to generate polyfunctional CD4+ and CD8+ T cell responses in mice. Additionally, checkpoint inhibitors, or co-administration of cytokine also expressed from the SMARRT platform, synergized to enhance responses further. Lastly, SMARRT-based immunization of non-human primates was able to elicit high-quality T cell responses, demonstrating translatability and clinical feasibility of synthetic replicon technology for therapeutic oncology vaccines.
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29
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Buonaguro L, Tagliamonte M. Selecting Target Antigens for Cancer Vaccine Development. Vaccines (Basel) 2020; 8:vaccines8040615. [PMID: 33080888 PMCID: PMC7711972 DOI: 10.3390/vaccines8040615] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022] Open
Abstract
One of the principal goals of cancer immunotherapy is the development of efficient therapeutic cancer vaccines that are able to elicit an effector as well as memory T cell response specific to tumor antigens. In recent years, the attention has been focused on the personalization of cancer vaccines. However, the efficacy of therapeutic cancer vaccines is still disappointing despite the large number of vaccine strategies targeting different tumors that have been evaluated in recent years. While the preclinical data have frequently shown encouraging results, clinical trials have not provided satisfactory data to date. The main reason for such failures is the complexity of identifying specific target tumor antigens that should be unique or overexpressed only by the tumor cells compared to normal cells. Most of the tumor antigens included in cancer vaccines are non-mutated overexpressed self-antigens, eliciting mainly T cells with low-affinity T cell receptors (TCR) unable to mediate an effective anti-tumor response. In this review, the target tumor antigens employed in recent years in the development of therapeutic cancer vaccine strategies are described, along with potential new classes of tumor antigens such as the human endogenous retroviral elements (HERVs), unconventional antigens, and/or heteroclitic peptides.
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30
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Moise L, Gutiérrez AH, Khan S, Tan S, Ardito M, Martin WD, De Groot AS. New Immunoinformatics Tools for Swine: Designing Epitope-Driven Vaccines, Predicting Vaccine Efficacy, and Making Vaccines on Demand. Front Immunol 2020; 11:563362. [PMID: 33123135 PMCID: PMC7571332 DOI: 10.3389/fimmu.2020.563362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022] Open
Abstract
Novel computational tools for swine vaccine development can expand the range of immunization approaches available to prevent economically devastating swine diseases and spillover events between pigs and humans. PigMatrix and EpiCC are two new tools for swine T cell epitope identification and vaccine efficacy analysis that have been integrated into an existing computational vaccine design platform named iVAX. The iVAX platform is already in use for the development of human vaccines, thus integration of these tools into iVAX improves and expands the utility of the platform overall by making previously validated immunoinformatics tools, developed for humans, available for use in the design and analysis of swine vaccines. PigMatrix predicts T cell epitopes for a broad array of class I and class II swine leukocyte antigen (SLA) using matrices that enable the scoring of sequences for likelihood of binding to SLA. PigMatrix facilitates the prospective selection of T cell epitopes from the sequences of swine pathogens for vaccines and permits the comparison of those predicted epitopes with "self" (the swine proteome) and with sequences from other strains. Use of PigMatrix with additional tools in the iVAX toolkit also enables the computational design of vaccines in silico, for testing in vivo. EpiCC uses PigMatrix to analyze existing or proposed vaccines for their potential to protect, based on a comparison between T cell epitopes in the vaccine and circulating strains of the same pathogen. Performing an analysis of T cell epitope relatedness analysis using EpiCC may facilitate vaccine selection when a novel strain emerges in a herd and also permits analysis of evolutionary drift as a means of immune escape. This review of novel computational immunology tools for swine describes the application of PigMatrix and EpiCC in case studies, such as the design of cross-conserved T cell epitopes for swine influenza vaccine or for African Swine Fever. We also describe the application of EpiCC for determination of the best vaccine strains to use against circulating viral variants of swine influenza, swine rotavirus, and porcine circovirus type 2. The availability of these computational tools accelerates infectious disease research for swine and enable swine vaccine developers to strategically advance their vaccines to market.
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Affiliation(s)
- Lenny Moise
- EpiVax, Inc., Providence, RI, United States.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | | | | | - Swan Tan
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, 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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31
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Zhu J, Kim J, Xiao X, Wang Y, Luo D, Jiang S, Chen R, Xu L, Zhang H, Moise L, Gutierrez AH, De Groot AS, Xiao G, Schoggins JW, Zhan X, Wang T, Xie Y. The immune vulnerability landscape of the 2019 Novel Coronavirus, SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.02.08.939553. [PMID: 32908981 PMCID: PMC7480032 DOI: 10.1101/2020.02.08.939553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The outbreak of the 2019 Novel Coronavirus (SARS-CoV-2) rapidly spread from Wuhan, China to more than 150 countries, areas, or territories, causing staggering numbers of infections and deaths. In this study, bioinformatics analyses were performed on 5,568 complete genomes of SARS-CoV-2 virus to predict the T cell and B cell immunogenic epitopes of all viral proteins, which formed a systematic immune vulnerability landscape of SARS-CoV-2. The immune vulnerability and genetic variation profiles of SARS-CoV were compared with those of SARS-CoV and MERS-CoV. In addition, a web portal was developed to broadly share the data and results as a resource for the research community. Using this resource, we showed that genetic variations in SARS-CoV-2 are associated with loss of B cell immunogenicity, an increase in CD4+ T cell immunogenicity, and a minimum loss in CD8+ T cell immunogenicity, indicating the existence of a curious correlation between SARS-CoV-2 genetic evolutions and the immunity pressure from the host. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic/vaccine development and mechanistic research.
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Affiliation(s)
- James Zhu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Xue Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Danni Luo
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Shuang Jiang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Ran Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - He Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Lenny Moise
- EpiVax, Inc. RI, USA, 02909
- Center for Vaccines and Immunology, University of Georgia, GA, USA, 30605
| | | | - Anne S. De Groot
- EpiVax, Inc. RI, USA, 02909
- Center for Vaccines and Immunology, University of Georgia, GA, USA, 30605
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - John W. Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
- EpiVax, Inc. RI, USA, 02909
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Ong E, Huang X, Pearce R, Zhang Y, He Y. Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.14.251496. [PMID: 32817949 PMCID: PMC7430581 DOI: 10.1101/2020.08.14.251496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The current COVID-19 pandemic caused by SARS-CoV-2 has resulted in millions of confirmed cases and thousands of deaths globally. Extensive efforts and progress have been made to develop effective and safe vaccines against COVID-19. A primary target of these vaccines is the SARS-CoV-2 spike (S) protein, and many studies utilized structural vaccinology techniques to either stabilize the protein or fix the receptor-binding domain at certain states. In this study, we extended an evolutionary protein design algorithm, EvoDesign, to create thousands of stable S protein variants without perturbing the surface conformation and B cell epitopes of the S protein. We then evaluated the mutated S protein candidates based on predicted MHC-II T cell promiscuous epitopes as well as the epitopes' similarity to human peptides. The presented strategy aims to improve the S protein's immunogenicity and antigenicity by inducing stronger CD4 T cell response while maintaining the protein's native structure and function. The top EvoDesign S protein candidate (Design-10705) recovered 31 out of 32 MHC-II T cell promiscuous epitopes in the native S protein, in which two epitopes were present in all seven human coronaviruses. This newly designed S protein also introduced nine new MHC-II T cell promiscuous epitopes and showed high structural similarity to its native conformation. The proposed structural vaccinology method provides an avenue to rationally design the antigen's structure with increased immunogenicity, which could be applied to the rational design of new COVID-19 vaccine candidates.
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Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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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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De Groot AS, Moise L, Terry F, Gutierrez AH, Hindocha P, Richard G, Hoft DF, Ross TM, Noe AR, Takahashi Y, Kotraiah V, Silk SE, Nielsen CM, Minassian AM, Ashfield R, Ardito M, Draper SJ, Martin WD. Better Epitope Discovery, Precision Immune Engineering, and Accelerated Vaccine Design Using Immunoinformatics Tools. Front Immunol 2020; 11:442. [PMID: 32318055 PMCID: PMC7154102 DOI: 10.3389/fimmu.2020.00442] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/26/2020] [Indexed: 12/19/2022] Open
Abstract
Computational vaccinology includes epitope mapping, antigen selection, and immunogen design using computational tools. Tools that facilitate the in silico prediction of immune response to biothreats, emerging infectious diseases, and cancers can accelerate the design of novel and next generation vaccines and their delivery to the clinic. Over the past 20 years, vaccinologists, bioinformatics experts, and advanced programmers based in Providence, Rhode Island, USA have advanced the development of an integrated toolkit for vaccine design called iVAX, that is secure and user-accessible by internet. This integrated set of immunoinformatic tools comprises algorithms for scoring and triaging candidate antigens, selecting immunogenic and conserved T cell epitopes, re-engineering or eliminating regulatory T cell epitopes, and re-designing antigens to induce immunogenicity and protection against disease for humans and livestock. Commercial and academic applications of iVAX have included identifying immunogenic T cell epitopes in the development of a T-cell based human multi-epitope Q fever vaccine, designing novel influenza vaccines, identifying cross-conserved T cell epitopes for a malaria vaccine, and analyzing immune responses in clinical vaccine studies. Animal vaccine applications to date have included viral infections of pigs such as swine influenza A, PCV2, and African Swine Fever. “Rapid-Fire” applications for biodefense have included a demonstration project for Lassa Fever and Q fever. As recent infectious disease outbreaks underscore the significance of vaccine-driven preparedness, the integrated set of tools available on the iVAX toolkit stand ready to help vaccine developers deliver genome-derived, epitope-driven vaccines.
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Affiliation(s)
- Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Institute for Immunology and Informatics, Providence, RI, United States
| | - Leonard Moise
- EpiVax, Inc., Providence, RI, United States.,Institute for Immunology and Informatics, Providence, RI, United States
| | | | - Andres H Gutierrez
- EpiVax, Inc., Providence, RI, United States.,Institute for Immunology and Informatics, Providence, RI, United States
| | | | | | - Daniel Fredric Hoft
- Departments of Molecular Microbiology & Immunology and Internal Medicine, Division of Infectious Diseases, Allergy & Immunology, Saint Louis University, St. Louis, MO, United States
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Amy R Noe
- Leidos Life Sciences, Frederick, MD, United States
| | | | | | - Sarah E Silk
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | - Simon J Draper
- Jenner Institute, University of Oxford, Oxford, United Kingdom
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Bandrick M, Gutiérrez AH, Desai P, Rincon G, Martin WD, Terry FE, De Groot AS, Foss DL. T cell epitope content comparison (EpiCC) analysis demonstrates a bivalent PCV2 vaccine has greater T cell epitope overlap with field strains than monovalent PCV2 vaccines. Vet Immunol Immunopathol 2020; 223:110034. [PMID: 32278900 DOI: 10.1016/j.vetimm.2020.110034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/17/2020] [Accepted: 03/03/2020] [Indexed: 01/14/2023]
Abstract
Porcine circovirus type 2 (PCV2) has one of the highest evolutionary rates among DNA viruses. Traditionally, PCV2 vaccines have been based on the 2a genotype as this was the first genotype discovered. Today, eight genotypes of PCV2 viruses have been identified, and, taken together with the rapid evolutionary rate, propensity to recombine, and high rate of vaccination, further variation in PCV2 is expected. For these reasons, there is a growing genetic gap between available vaccines and field strains. When selecting vaccines, it is important to consider vaccines that contain T cell epitopes that are well-matched to the circulating strains. To quantify the relatedness between PCV2 vaccines and field strains, we predicted and compared their T cell epitope content and calculated Epitope Content Comparison (EpiCC) scores using established in silico tools. T cell epitopes predicted to bind common class I and class II swine leukocyte antigen (SLA) alleles were identified from two major structural proteins, the capsid (encoded by ORF2) and the replicase (encoded by ORF1). The T cell epitope content of three commercial PCV2a-based vaccines (a baculovirus expressed PCV2a ORF2 [VacAlt], a PCV1-PCV2a chimeric virus vaccine [VacA] and a combination cPCV2a-cPCV2b chimeric virus vaccine [VacAB]) and an experimental PCV2b ORF2-based chimeric virus vaccine [VacB] (Table 1), were compared to that of 161 PCV2 field strains (representing genotypes a-f). The T cell epitope content and conservation between vaccine and field strains varied. While all vaccine strains provided broad coverage of the field strains including heterologous genotypes, none of the vaccines covered all the putative T cell epitopes identified in the field strains. PCV2a-based vaccine strains generally scored higher in terms of conserved epitope content against PCV2a field isolates but were not identical. The PCV2b-based vaccine strain had higher scores against PCV2b and PCV2d field strains. The combination PCV2a-PCV2b vaccine (VacAB) had, on average, the highest EpiCC score. PCV2 continues to evolve and EpiCC analysis provides a new tool to assess the possible impact of virus genetic divergence on T cell epitope coverage of vaccine strains. Given that multiple genotypes are currently found and may co-exist on farms, this analysis suggests that a combination of PCV2a and PCV2b vaccine strains may be required to provide optimal coverage of current and future field isolates.
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Affiliation(s)
| | | | | | | | | | | | - 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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Kruiswijk C, Richard G, Salverda MLM, Hindocha P, Martin WD, De Groot AS, Van Riet E. In silico identification and modification of T cell epitopes in pertussis antigens associated with tolerance. Hum Vaccin Immunother 2020; 16:277-285. [PMID: 31951773 PMCID: PMC7062413 DOI: 10.1080/21645515.2019.1703453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The resurgence of whooping cough since the introduction of acellular (protein) vaccines has led to a renewed interest in the development of improved pertussis vaccines; Outer Membrane Vesicles (OMVs) carrying pertussis antigens have emerged as viable candidates. An in silico immunogenicity screen was carried out on 49 well-known Bordetella pertussis proteins in order to better understand their potential role toward the efficacy of pertussis OMVs for vaccine design; seven proteins were identified as being good candidates for including in optimized cellular and acellular pertussis vaccines. We then screened these antigens for putative tolerance-inducing sequences, as proteins with reduced tolerogenicity have improved vaccine potency in preclinical models. We used specialized homology tools (JanusMatrix) to identify peptides in the proteins that were cross-reactive with human sequences. Four of the 19 identified cross-reactive peptides were detolerized in silico using a separate tool, OptiMatrix, which disrupted the potential of these peptides to bind to human HLA and murine MHC. Four selected cross-reactive peptides and their detolerized variants were synthesized and their binding to a set of eight common HLA class II alleles was assessed in vitro. Reduced binding affinity to HLA class II was observed for the detolerized variants compared to the wild-type peptides, highlighting the potential of this approach for designing more efficacious pertussis vaccines.
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Affiliation(s)
- Corine Kruiswijk
- Department of Experimental Immunology & Clinical Research, Intravacc, Bilthoven, Netherlands
| | | | - Merijn L M Salverda
- Department of Experimental Immunology & Clinical Research, Intravacc, Bilthoven, Netherlands
| | | | | | | | - Elly Van Riet
- Department of Experimental Immunology & Clinical Research, Intravacc, Bilthoven, Netherlands
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Coxiella burnetii Epitope-Specific T-Cell Responses in Patients with Chronic Q Fever. Infect Immun 2019; 87:IAI.00213-19. [PMID: 31331958 DOI: 10.1128/iai.00213-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
Infection with Coxiella burnetii, the causative agent of Q fever, can result in life-threatening persistent infection. Reactogenicity hinders worldwide implementation of the only licensed human Q fever vaccine. We previously demonstrated long-lived immunoreactivity in individuals with past symptomatic and asymptomatic Coxiella infection (convalescents) to promiscuous HLA class II C. burnetii epitopes, providing the basis for a novel T-cell targeted subunit vaccine. In this study, we investigated in a cohort of 22 individuals treated for persistent infection (chronic Q fever) whether they recognize the same set of epitopes or distinct epitopes that could be candidates for a therapeutic vaccine or aid in the diagnosis of persistent infection. In cultured enzyme-linked immunosorbent spot (ELISpot) assays, individuals with chronic Q fever showed strong class II epitope-specific responses that were largely overlapping with the peptide repertoire identified previously for convalescents. Five additional peptides were recognized more frequently by chronic subjects, but there was no combination of epitopes uniquely recognized by or nonreactive in subjects with chronic Q fever. Consistent with more recent/prolonged exposure, we found, however, stronger ex vivo responses by direct ELISpot to both whole-cell C. burnetii and individual peptides in chronic patients than in convalescents. In conclusion, we have validated and expanded a previously published set of candidate epitopes for a novel T-cell targeted subunit Q fever vaccine in treated patients with chronic Q fever and demonstrated that they successfully mounted a T-cell response comparable to that of convalescents. Finally, we demonstrated that individuals treated for chronic Q fever mount a broader ex vivo response to class II epitopes than convalescents, which could be explored for diagnostic purposes.
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Eickhoff CS, Terry FE, Peng L, Meza KA, Sakala IG, Van Aartsen D, Moise L, Martin WD, Schriewer J, Buller RM, De Groot AS, Hoft DF. Highly conserved influenza T cell epitopes induce broadly protective immunity. Vaccine 2019; 37:5371-5381. [PMID: 31331771 DOI: 10.1016/j.vaccine.2019.07.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 12/30/2022]
Abstract
Influenza world-wide causes significant morbidity and mortality annually, and more severe pandemics when novel strains evolve to which humans are immunologically naïve. Because of the high viral mutation rate, new vaccines must be generated based on the prevalence of circulating strains every year. New approaches to induce more broadly protective immunity are urgently needed. Previous research has demonstrated that influenza-specific T cells can provide broadly heterotypic protective immunity in both mice and humans, supporting the rationale for developing a T cell-targeted universal influenza vaccine. We used state-of-the art immunoinformatic tools to identify putative pan-HLA-DR and HLA-A2 supertype-restricted T cell epitopes highly conserved among > 50 widely diverse influenza A strains (representing hemagglutinin types 1, 2, 3, 5, 7 and 9). We found influenza peptides that are highly conserved across influenza subtypes that were also predicted to be class I epitopes restricted by HLA-A2. These peptides were found to be immunoreactive in HLA-A2 positive but not HLA-A2 negative individuals. Class II-restricted T cell epitopes that were highly conserved across influenza subtypes were identified. Human CD4+ T cells were reactive with these conserved CD4 epitopes, and epitope expanded T cells were responsive to both H1N1 and H3N2 viruses. Dendritic cell vaccines pulsed with conserved epitopes and DNA vaccines encoding these epitopes were developed and tested in HLA transgenic mice. These vaccines were highly immunogenic, and more importantly, vaccine-induced immunity was protective against both H1N1 and H3N2 influenza challenges. These results demonstrate proof-of-principle that conserved T cell epitopes expressed by widely diverse influenza strains can induce broadly protective, heterotypic influenza immunity, providing strong support for further development of universally relevant multi-epitope T cell-targeting influenza vaccines.
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Affiliation(s)
- Christopher S Eickhoff
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Frances E Terry
- EpiVax, Inc., 188 Valley Street, Suite 424, Providence, RI 02909, United States
| | - Linda Peng
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Krystal A Meza
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Isaac G Sakala
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Daniel Van Aartsen
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Leonard Moise
- EpiVax, Inc., 188 Valley Street, Suite 424, Providence, RI 02909, United States; University of Rhode Island, Institute for Immunology and Informatics, Department of Cell and Molecular Biology, 80 Washington Street, Providence, RI 02903, United States
| | - William D Martin
- EpiVax, Inc., 188 Valley Street, Suite 424, Providence, RI 02909, United States
| | - Jill Schriewer
- Saint Louis University, Department of Molecular Microbiology & Immunology, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - R Mark Buller
- Saint Louis University, Department of Molecular Microbiology & Immunology, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States
| | - Anne S De Groot
- EpiVax, Inc., 188 Valley Street, Suite 424, Providence, RI 02909, United States; University of Rhode Island, Institute for Immunology and Informatics, Department of Cell and Molecular Biology, 80 Washington Street, Providence, RI 02903, United States
| | - Daniel F Hoft
- Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States; Saint Louis University, Department of Molecular Microbiology & Immunology, 1100 S. Grand Blvd., Edward A. Doisy Research Center - 8th Floor, Saint Louis, MO 63104, United States.
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Hewitt JS, Karuppannan AK, Tan S, Gauger P, Halbur PG, Gerber PF, De Groot AS, Moise L, Opriessnig T. A prime-boost concept using a T-cell epitope-driven DNA vaccine followed by a whole virus vaccine effectively protected pigs in the pandemic H1N1 pig challenge model. Vaccine 2019; 37:4302-4309. [PMID: 31248687 DOI: 10.1016/j.vaccine.2019.06.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 01/08/2023]
Abstract
Influenza A virus (IAV) vaccines in pigs generally provide homosubtypic protection but fail to prevent heterologous infections. In this pilot study, the efficacy of an intradermal pDNA vaccine composed of conserved SLA class I and class II T cell epitopes (EPITOPE) against a homosubtypic challenge was compared to an intramuscular commercial inactivated whole virus vaccine (INACT) and a heterologous prime boost approach using both vaccines. Thirty-nine IAV-free, 3-week-old pigs were randomly assigned to one of five groups including NEG-CONTROL (unvaccinated, sham-challenged), INACT-INACT-IAV (vaccinated with FluSure XP® at 4 and 7 weeks, pH1N1 challenged), EPITOPE-INACT-IAV (vaccinated with PigMatrix EDV at 4 and FluSure XP® at 7 weeks, pH1N1 challenged), EPITOPE-EPITOPE-IAV (vaccinated with PigMatrix EDV at 4 and 7 weeks, pH1N1 challenged), and a POS-CONTROL group (unvaccinated, pH1N1 challenged). The challenge was done at 9 weeks of age and pigs were necropsied at day post challenge (dpc) 5. At the time of challenge, all INACT-INACT-IAV pigs, and by dpc 5 all EPITOPE-INACT-IAV pigs were IAV seropositive. IFNγ secreting cells, recognizing vaccine epitope-specific peptides and pH1N1 challenge virus were highest in the EPITOPE-INACT-IAV pigs at challenge. Macroscopic lung lesion scores were reduced in all EPITOPE-INACT-IAV pigs while INACT-INACT-IAV pigs exhibited a bimodal distribution of low and high scores akin to naïve challenged animals. No IAV antigen in lung tissues was detected at necropsy in the EPITOPE-INACT-IAV group, which was similar to naïve unchallenged pigs and different from all other challenged groups. Results suggest that the heterologous prime boost approach using an epitope-driven DNA vaccine followed by an inactivated vaccine was effective against a homosubtypic challenge, and further exploration of this vaccine approach as a practical control measure against heterosubtypic IAV infections is warranted.
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Affiliation(s)
- Joshua S Hewitt
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Anbu K Karuppannan
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Swan Tan
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Phillip Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Patrick G Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Priscilla F Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Anne S De Groot
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA; EpiVax Inc., Providence, RI, USA
| | - Leonard Moise
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA; EpiVax Inc., Providence, RI, USA
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA; The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
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Prediction and Validation of Immunogenic Domains of Pneumococcal Proteins Recognized by Human CD4 + T Cells. Infect Immun 2019; 87:IAI.00098-19. [PMID: 30910792 PMCID: PMC6529658 DOI: 10.1128/iai.00098-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/28/2019] [Indexed: 12/24/2022] Open
Abstract
CD4+ T-cell mechanisms are implied in protection against pneumococcal colonization; however, their target antigens and function are not well defined. In contrast to high-throughput protein arrays for serology, basic antigen tools for CD4+ T-cell studies are lacking. CD4+ T-cell mechanisms are implied in protection against pneumococcal colonization; however, their target antigens and function are not well defined. In contrast to high-throughput protein arrays for serology, basic antigen tools for CD4+ T-cell studies are lacking. Here, we evaluate the potential of a bioinformatics tool for in silico prediction of immunogenicity as a method to reveal domains of pneumococcal proteins targeted by human CD4+ T cells. For 100 pneumococcal proteins, CD4+ T-cell immunogenicity was predicted based on HLA-DRB1 binding motifs. For 20 potentially CD4+ T-cell immunogenic proteins, epitope regions were verified by testing synthetic peptides in T-cell assays using peripheral blood mononuclear cells from healthy adults. Peptide pools of 19 out of 20 proteins evoked T-cell responses. The most frequent responses (detectable in ≥20% of donors tested) were found to SP_0117 (PspA), SP_0468 (putative sortase), SP_0546 (BlpZ), SP_1650 (PsaA), SP_1923 (Ply), SP_2048 (conserved hypothetical protein), SP_2216 (PscB), and SPR_0907 (PhtD). Responding donors had diverging recognition patterns and profiles of signature cytokines (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], interleukin-13 [IL-13], and/or IL-17A) against single-epitope regions. Natural HLA-DR-restricted presentation and recognition of a predicted SP_1923-derived epitope were validated through the isolation of a CD4+ T-cell clone producing IFN-γ, TNF-α, and IL-17A in response to the synthetic peptide, whole protein, and heat-inactivated pneumococcus. This proof of principle for a bioinformatics tool to identify pneumococcal protein epitopes targeted by human CD4+ T cells provides a peptide-based strategy to study cell-mediated immune mechanisms for the pneumococcal proteome, advancing the development of immunomonitoring assays and targeted vaccine approaches.
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Dingman R, Balu-Iyer SV. Immunogenicity of Protein Pharmaceuticals. J Pharm Sci 2019; 108:1637-1654. [PMID: 30599169 PMCID: PMC6720129 DOI: 10.1016/j.xphs.2018.12.014] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023]
Abstract
Protein therapeutics have drastically changed the landscape of treatment for many diseases by providing a regimen that is highly specific and lacks many off-target toxicities. The clinical utility of many therapeutic proteins has been undermined by the potential development of unwanted immune responses against the protein, limiting their efficacy and negatively impacting its safety profile. This review attempts to provide an overview of immunogenicity of therapeutic proteins, including immune mechanisms and factors influencing immunogenicity, impact of immunogenicity, preclinical screening methods, and strategies to mitigate immunogenicity.
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Affiliation(s)
- Robert Dingman
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, New York 14214
| | - Sathy V Balu-Iyer
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, New York 14214.
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42
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Khan S, Parrillo M, Gutierrez AH, Terry FE, Moise L, Martin WD, De Groot AS. Immune escape and immune camouflage may reduce the efficacy of RTS,S vaccine in Malawi. Hum Vaccin Immunother 2019; 16:214-227. [PMID: 30614773 PMCID: PMC7062414 DOI: 10.1080/21645515.2018.1560772] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The RTS,S/AS01 malaria vaccine will undergo a pilot vaccination study in sub-Saharan Africa beginning in 2019. RTS,S/AS01 Phase III trials reported an efficacy of 28.3% (children 5–17 months) and 18.3% (infants 6–12 weeks), with substantial variability across study sites. We postulated that the relatively low efficacy of the RTS,S vaccine and variability across sites may be due to lack of T-cell epitopes in the vaccine antigen, and due to the HLA distribution of the vaccinated population, and/or due to ‘immune camouflage’, an immune escape mechanism. To examine these hypotheses, we used immunoinformatics tools to compare T helper epitopes contained in RTS,S vaccine antigens with Plasmodium falciparum circumsporozoite protein (CSP) variants isolated from infected individuals in Malawi. The prevalence of epitopes restricted by specific HLA-DRB1 alleles was inversely associated with prevalence of the HLA-DRB1 allele in the Malawi study population, suggesting immune escape. In addition, T-cell epitopes in the CSP of strains circulating in Malawi were more often restricted by low-frequency HLA-DRB1 alleles in the population. Furthermore, T-cell epitopes that were highly conserved across CSP variants in Malawi possessed TCR-facing residues that were highly conserved in the human proteome, potentially reducing T-cell help through tolerance. The CSP component of the RTS,S vaccine also exhibited a low degree of T-cell epitope relatedness to circulating variants. These results suggest that RTS,S vaccine efficacy may be impacted by low T-cell epitope content, reduced presentation of T-cell epitopes by prevalent HLA-DRB1, high potential for human-cross-reactivity, and limited conservation with the CSP of circulating malaria strains.
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Affiliation(s)
- Sundos Khan
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Matthew Parrillo
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | | | | | - Leonard Moise
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA.,EpiVax, Inc., Providence, RI, USA
| | | | - Anne S De Groot
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA.,EpiVax, Inc., Providence, RI, USA
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43
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De Groot AS, Kazi ZB, Martin RF, Terry FE, Desai AK, Martin WD, Kishnani PS. HLA- and genotype-based risk assessment model to identify infantile onset pompe disease patients at high-risk of developing significant anti-drug antibodies (ADA). Clin Immunol 2019; 200:66-70. [PMID: 30711607 PMCID: PMC6554735 DOI: 10.1016/j.clim.2019.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/26/2018] [Accepted: 01/31/2019] [Indexed: 11/23/2022]
Abstract
In Pompe disease, anti-drug antibodies (ADA) to acid alpha-glucosidase (GAA) enzyme replacement therapy contribute to early mortality. Assessing individual risk for ADA development is notoriously difficult in (CRIM-positive) patients expressing endogenous GAA. The individualized T cell epitope measure (iTEM) scoring method predicts patient-specific risk of developing ADA against therapeutic recombinant human GAA (rhGAA) using individualized HLA-binding predictions and GAA genotype. CRIM-negative patients were six times more likely to develop high ADA titers than CRIM-positive patients in this retrospective study, whereas patients with high GAA-iTEM scores were 50 times more likely to develop high ADA titers than patients with low GAA-iTEM scores. This approach identifies high-risk IOPD patients requiring immune tolerance induction therapy to prevent significant ADA response to rhGAA leading to a poor clinical outcome and can assess ADA risk in patients receiving replacement therapy for other enzyme or blood factor deficiency disorders.
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Affiliation(s)
| | - Z B Kazi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | | | - A K Desai
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - P S Kishnani
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
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44
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Scholzen A, Richard G, Moise L, Baeten LA, Reeves PM, Martin WD, Brauns TA, Boyle CM, Raju Paul S, Bucala R, Bowen RA, Garritsen A, De Groot AS, Sluder AE, Poznansky MC. Promiscuous Coxiella burnetii CD4 Epitope Clusters Associated With Human Recall Responses Are Candidates for a Novel T-Cell Targeted Multi-Epitope Q Fever Vaccine. Front Immunol 2019; 10:207. [PMID: 30828331 PMCID: PMC6384241 DOI: 10.3389/fimmu.2019.00207] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/23/2019] [Indexed: 12/13/2022] Open
Abstract
Coxiella burnetii, the causative agent of Q fever, is a Gram-negative intracellular bacterium transmitted via aerosol. Regulatory approval of the Australian whole-cell vaccine Q-VAX® in the US and Europe is hindered by reactogenicity in previously exposed individuals. The aim of this study was to identify and rationally select C. burnetii epitopes for design of a safe, effective, and less reactogenic T-cell targeted human Q fever vaccine. Immunoinformatic methods were used to predict 65 HLA class I epitopes and 50 promiscuous HLA class II C. burnetii epitope clusters, which are conserved across strains of C. burnetii. HLA binding assays confirmed 89% of class I and 75% of class II predictions, and 11 HLA class II epitopes elicited IFNγ responses following heterologous DNA/DNA/peptide/peptide prime-boost immunizations of HLA-DR3 transgenic mice. Human immune responses to the predicted epitopes were characterized in individuals naturally exposed to C. burnetii during the 2007–2010 Dutch Q fever outbreak. Subjects were divided into three groups: controls with no immunological evidence of previous infection and individuals with responses to heat-killed C. burnetii in a whole blood IFNγ release assay (IGRA) who remained asymptomatic or who experienced clinical Q fever during the outbreak. Recall responses to C. burnetii epitopes were assessed by cultured IFNγ ELISpot. While HLA class I epitope responses were sparse in this cohort, we identified 21 HLA class II epitopes that recalled T-cell IFNγ responses in 10–28% of IGRA+ subjects. IGRA+ individuals with past asymptomatic and symptomatic C. burnetii infection showed a comparable response pattern and cumulative peptide response which correlated with IGRA responses. None of the peptides elicited reactogenicity in a C. burnetii exposure-primed guinea pig model. These data demonstrate that a substantial proportion of immunoinformatically identified HLA class II epitopes show long-lived immunoreactivity in naturally infected individuals, making them desirable candidates for a novel human multi-epitope Q fever vaccine.
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Affiliation(s)
| | | | - Leonard Moise
- EpiVax, Inc., Providence, RI, United States.,Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | - Laurie A Baeten
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Patrick M Reeves
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
| | | | - Timothy A Brauns
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
| | | | - Susan Raju Paul
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
| | - Richard Bucala
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Richard A Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | | | - Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, United States
| | - Ann E Sluder
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
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45
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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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46
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Hrdinová J, Verbij FC, Kaijen PHP, Hartholt RB, van Alphen F, Lardy N, Ten Brinke A, Vanhoorelbeke K, Hindocha PJ, De Groot AS, Meijer AB, Voorberg J, Peyron I. Mass spectrometry-assisted identification of ADAMTS13-derived peptides presented on HLA-DR and HLA-DQ. Haematologica 2018; 103:1083-1092. [PMID: 29567779 PMCID: PMC6058777 DOI: 10.3324/haematol.2017.179119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/14/2018] [Indexed: 12/21/2022] Open
Abstract
Formation of microthrombi is a hallmark of acquired thrombotic thrombocytopenic purpura. These microthrombi originate from insufficient processing of ultra large von Willebrand factor multimers by ADAMTS13 due to the development of anti-ADAMTS13 autoantibodies. Several studies have identified the major histocompatibility complex class II alleles HLA-DRB1*11, HLA-DQB1*03 and HLA-DQB1*02:02 as risk factors for acquired thrombotic thrombocytopenic purpura development. Previous research in our department indicated that ADAMTS13 CUB2 domain-derived peptides FINVAPHAR and LIRDTHSLR are presented on HLA-DRB1*11 and HLA-DRB1*03, respectively. Here, we describe the repertoire of ADAMTS13 peptides presented on HLA-DQ. In parallel, the repertoire of ADAMTS13-derived peptides presented on HLA-DR was monitored. Using HLA-DR- and HLA-DQ-specific antibodies, we purified HLA/peptide complexes from ADAMTS13-pulsed monocyte-derived dendritic cells. Using this approach, we identified ADAMTS13-derived peptides presented on HLA-DR for all 9 samples analyzed; ADAMTS13-derived peptides presented on HLA-DQ were identified in 4 out of 9 samples. We were able to confirm the presentation of the CUB2 domain-derived peptides FINVAPHAR and LIRDTHSLR on HLA-DR. In total, 12 different core-peptide sequences were identified on HLA-DR and 8 on HLA-DQ. For HLA-DR11, several potential new core-peptides were found; 4 novel core-peptides were exclusively identified on HLA-DQ. Furthermore, an in silico analysis was performed using the EpiMatrix and JanusMatrix tools to evaluate the eluted peptides, in the context of HLA-DR, for putative effector or regulatory T-cell responses at the population level. The results from this study provide a basis for the identification of immuno-dominant epitopes on ADAMTS13 involved in the onset of acquired thrombotic thrombocytopenic purpura.
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Affiliation(s)
- Johana Hrdinová
- Department of Plasma Proteins, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Fabian C Verbij
- Department of Plasma Proteins, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Paul H P Kaijen
- Department of Plasma Proteins, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Robin B Hartholt
- Department of Plasma Proteins, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Floris van Alphen
- Department of Research Facilities, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Neubury Lardy
- Department of Immunogenetics, Sanquin, Amsterdam, the Netherlands
| | - Anja Ten Brinke
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Belgium
| | | | - Anne S De Groot
- EpiVax Inc., Providence, RI, USA.,Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA
| | - Alexander B Meijer
- Department of Plasma Proteins, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands.,Department of Research Facilities, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands.,Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, the Netherlands
| | - Jan Voorberg
- Department of Plasma Proteins, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands .,Department of Experimental Vascular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - Ivan Peyron
- Department of Plasma Proteins, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, the Netherlands
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47
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Immunodominance in T cell responses elicited against different domains of detoxified pneumolysin PlyD1. PLoS One 2018; 13:e0193650. [PMID: 29509778 PMCID: PMC5839544 DOI: 10.1371/journal.pone.0193650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/15/2018] [Indexed: 12/05/2022] Open
Abstract
Detoxified pneumolysin, PlyD1, is a protein vaccine candidate that induces protection against infections with Streptococcus pneumoniae in mouse models. Despite extensive knowledge on antibody responses against PlyD1, limited information is available about PlyD1 induced T cell recognition. Here we interrogated epitope breadth and functional characteristics of the T cell response to PlyD1 in two mouse strains. BALB/c (H-2d) and C57BL/6 (H-2b) mice were vaccinated with Al(OH)3-adjuvanted or non-adjuvanted PlyD1, or placebo, on day 0, 21 and 42 and were sacrificed at day 56 for collection of sera and spleens. Vaccination with adjuvanted and non-adjuvanted PlyD1 induced anti-pneumolysin IgG antibodies with neutralizing capacity in both mouse strains. Adjuvantation of PlyD1 enhanced the serological responses in both strains. In vitro restimulation of splenocytes with PlyD1 and 18-mer synthetic peptides derived from pneumolysin revealed specific proliferative and cytokine responses. For both mouse strains, one immunodominant and three subdominant natural epitopes were identified. Overlap between H-2d and H-2b restricted T cell epitopes was limited, yet similarities were found between epitopes processed in mice and predicted to be immunogenic in humans. H-2d restricted T cell epitopes were localized in pneumolysin domains 2 and 3, whereas H-2b epitopes were scattered over the protein. Cytokine responses show mostly a Th2 profile, with low levels of Th1 cytokines, in both mouse strains. In conclusion, PlyD1 evokes T cell responses in mice directed against multiple epitope regions, that is dependent on Major Histocompatibility Complex (MHC) background. These results are important to understand human PlyD1 T cell immunogenicity, to guide cell mediated immunity studies in the context of vaccine development.
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48
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Antunes DA, Rigo MM, Freitas MV, Mendes MFA, Sinigaglia M, Lizée G, Kavraki LE, Selin LK, Cornberg M, Vieira GF. Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy. Front Immunol 2017; 8:1210. [PMID: 29046675 PMCID: PMC5632759 DOI: 10.3389/fimmu.2017.01210] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
Immunotherapy has become one of the most promising avenues for cancer treatment, making use of the patient’s own immune system to eliminate cancer cells. Clinical trials with T-cell-based immunotherapies have shown dramatic tumor regressions, being effective in multiple cancer types and for many different patients. Unfortunately, this progress was tempered by reports of serious (even fatal) side effects. Such therapies rely on the use of cytotoxic T-cell lymphocytes, an essential part of the adaptive immune system. Cytotoxic T-cells are regularly involved in surveillance and are capable of both eliminating diseased cells and generating protective immunological memory. The specificity of a given T-cell is determined through the structural interaction between the T-cell receptor (TCR) and a peptide-loaded major histocompatibility complex (MHC); i.e., an intracellular peptide–ligand displayed at the cell surface by an MHC molecule. However, a given TCR can recognize different peptide–MHC (pMHC) complexes, which can sometimes trigger an unwanted response that is referred to as T-cell cross-reactivity. This has become a major safety issue in TCR-based immunotherapies, following reports of melanoma-specific T-cells causing cytotoxic damage to healthy tissues (e.g., heart and nervous system). T-cell cross-reactivity has been extensively studied in the context of viral immunology and tissue transplantation. Growing evidence suggests that it is largely driven by structural similarities of seemingly unrelated pMHC complexes. Here, we review recent reports about the existence of pMHC “hot-spots” for cross-reactivity and propose the existence of a TCR interaction profile (i.e., a refinement of a more general TCR footprint in which some amino acid residues are more important than others in triggering T-cell cross-reactivity). We also make use of available structural data and pMHC models to interpret previously reported cross-reactivity patterns among virus-derived peptides. Our study provides further evidence that structural analyses of pMHC complexes can be used to assess the intrinsic likelihood of cross-reactivity among peptide-targets. Furthermore, we hypothesize that some apparent inconsistencies in reported cross-reactivities, such as a preferential directionality, might also be driven by particular structural features of the targeted pMHC complex. Finally, we explain why TCR-based immunotherapy provides a special context in which meaningful T-cell cross-reactivity predictions can be made.
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Affiliation(s)
- Dinler A Antunes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Maurício M Rigo
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratório de Imunologia Celular e Molecular, Instituto de Pesquisas Biomédicas (IPB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Martiela V Freitas
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marcus F A Mendes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marialva Sinigaglia
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gregory Lizée
- Lizée Lab, Department of Melanoma Medical Oncology - Research, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - Lydia E Kavraki
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Liisa K Selin
- Selin Lab, Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Markus Cornberg
- Cornberg Lab, Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,German Center for Infection Research (DZIF), Partner-Site Hannover-Braunschweig, Hannover, Germany
| | - Gustavo F Vieira
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Porto Alegre, Brazil
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49
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Gokemeijer J, Jawa V, Mitra-Kaushik S. How Close Are We to Profiling Immunogenicity Risk Using In Silico Algorithms and In Vitro Methods?: an Industry Perspective. AAPS JOURNAL 2017; 19:1587-1592. [PMID: 28971356 DOI: 10.1208/s12248-017-0143-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/30/2017] [Indexed: 12/22/2022]
Abstract
In silico HLA-binding algorithms and in vitro T cell-based assays as predictive tools for human immunogenicity risk have made inroads in the biotherapeutic drug discovery and development process. Currently, these tools are being used only for candidate selection or characterization and not for making a go/no-go decision for further development. A clear limitation for a broader implementation is the lack of correlation between the predicted T cell epitope content/immune reactivity potential of a biotherapeutic and the subsequent ADA-related clinical immunogenicity outcome. The current state of technologies and their pros and cons were discussed as a part of the 2016 AAPS National Biotechnology Conference in a themed session. A review of the advances in the area and the session talks along with the ensuing discussions are summarized in this commentary.
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Affiliation(s)
- Jochem Gokemeijer
- Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb, Waltham, Massachusetts, USA
| | - Vibha Jawa
- Biologics and Vaccine Formulations, Merck Sharp & Dohme Corp, 2000 Galloping Hill Road, K-15 H406, Kenilworth, New Jersey, 07033, USA
| | - Shibani Mitra-Kaushik
- Biomarker and Clinical Bioanalysis, Sanofi, 1 The Mountain Road, Framingham, Massachusetts, 01701, USA.
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50
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Reeves PM, Paul SR, Sluder AE, Brauns TA, Poznansky MC. Q-vaxcelerate: A distributed development approach for a new Coxiella burnetii vaccine. Hum Vaccin Immunother 2017; 13:2977-2981. [PMID: 28933682 PMCID: PMC5718828 DOI: 10.1080/21645515.2017.1371377] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Development of vaccines that are both safe and effective remains a costly and time-consuming challenge. To accelerate the pace of development and improve the efficacy and safety of candidate vaccines for both existing and emerging infectious agents, we have used a distributed development approach. This features the managed integration of individual expert groups having the requisite vaccine platforms, pre-clinical models, assays, skills and knowledge pertinent to a specific pathogen into a single, end-to-end development team capable of producing a new vaccine tailored to that particular agent. Distributed development focuses on integrating existing effort across multiple institutions rather than developing new capabilities or consolidating resources within an individual organization. Previously we have used the distributed development strategy to generate vaccine candidates for emerging viral diseases. Coxiella burnetii is a highly infectious and resilient bacterium and the causative agent of Q fever. Treatment for Q fever can require months of antibiotics. The current vaccine for Q-fever is only approved in Australia and requires prescreening due to the potential for severe reactogenicity in previously exposed individuals. Here we discuss Q-VaxCelerate, a distributed development consortium for the development of a new vaccine to prevent Q fever.
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Affiliation(s)
- Patrick M Reeves
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
| | - Susan Raju Paul
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
| | - Ann E Sluder
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
| | - Timothy A Brauns
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
| | - Mark C Poznansky
- a Vaccine and Immunotherapy Center, Division of Infectious Diseases, Department of Medicine , Massachusetts General Hospital , Boston , MA , USA
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