1
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Richard G, Ruggiero N, Steinberg GD, Martin WD, De Groot AS. Neoadjuvant personalized cancer vaccines: the final frontier? Expert Rev Vaccines 2024; 23:205-212. [PMID: 38189107 DOI: 10.1080/14760584.2024.2303015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
INTRODUCTION Clinical trials of personalized cancer vaccines have shown that on-demand therapies that are manufactured for each patient, result in activated T cell responses against individual tumor neoantigens. However, their use has been traditionally restricted to adjuvant settings and late-stage cancer therapy. There is growing support for the implementation of PCV earlier in the cancer therapy timeline, for reasons that will be discussed in this review. AREAS COVERED The efficacy of cancer vaccines may be to some extent dependent on treatment(s) given prior to vaccine administration. Tumors can undergo radical immunoediting following treatment with immunotherapies, such as checkpoint inhibitors, which may affect the presence of the very mutations targeted by cancer vaccines. This review will cover the topics of neoantigen cancer vaccines, tumor immunoediting, and therapy timing. EXPERT OPINION Therapy timing remains a critical topic to address in optimizing the efficacy of personalized cancer vaccines. Most personalized cancer vaccines are being evaluated in late-stage cancer patients and after treatment with checkpoint inhibitors, but they may offer a greater benefit to the patient if administered in earlier clinical settings, such as the neoadjuvant setting, where patients are not facing T cell exhaustion and/or a further compromised immune system.
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Affiliation(s)
| | | | - Gary D Steinberg
- EpiVax Therapeutics, Inc., Providence, RI, USA
- RUSH University, Chicago, IL, 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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2
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Makowski EK, Wang T, Zupancic JM, Huang J, Wu L, Schardt JS, De Groot AS, Elkins SL, Martin WD, Tessier PM. Optimization of therapeutic antibodies for reduced self-association and non-specific binding via interpretable machine learning. Nat Biomed Eng 2024; 8:45-56. [PMID: 37666923 PMCID: PMC10842909 DOI: 10.1038/s41551-023-01074-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 06/29/2023] [Indexed: 09/06/2023]
Abstract
Antibody development, delivery, and efficacy are influenced by antibody-antigen affinity interactions, off-target interactions that reduce antibody bioavailability and pharmacokinetics, and repulsive self-interactions that increase the stability of concentrated antibody formulations and reduce their corresponding viscosity. Yet identifying antibody variants with optimal combinations of these three types of interactions is challenging. Here we show that interpretable machine-learning classifiers, leveraging antibody structural features descriptive of their variable regions and trained on experimental data for a panel of 80 clinical-stage monoclonal antibodies, can identify antibodies with optimal combinations of low off-target binding in a common physiological-solution condition and low self-association in a common antibody-formulation condition. For three clinical-stage antibodies with suboptimal combinations of off-target binding and self-association, the classifiers predicted variable-region mutations that optimized non-affinity interactions while maintaining high-affinity antibody-antigen interactions. Interpretable machine-learning models may facilitate the optimization of antibody candidates for therapeutic applications.
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Affiliation(s)
- Emily K Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tiexin Wang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer M Zupancic
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jie Huang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Peter M Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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3
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Haltaufderhyde K, Roberts BJ, Khan S, Terry F, Boyle CM, McAllister M, Martin W, Rosenberg A, De Groot AS. Correction to: Immunoinformatic Risk Assessment of Host Cell Proteins During Process Development for Biologic Therapeutics. AAPS J 2023; 26:6. [PMID: 38114731 DOI: 10.1208/s12248-023-00868-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
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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4
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Ricotti S, Garay AS, Etcheverrigaray M, Amadeo GI, De Groot AS, Martin W, Mufarrege EF. Development of IFNβ-1a versions with reduced immunogenicity and full in vitro biological activity for the treatment of multiple sclerosis. Clin Immunol 2023; 257:109831. [PMID: 37931868 DOI: 10.1016/j.clim.2023.109831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
IFNβ (recombinant interferon Beta) has been widely used for the treatment of Multiple sclerosis for the last four decades. Despite the human origin of the IFNβ sequence, IFNβ is immunogenic, and unwanted immune responses in IFNβ-treated patients may compromise its efficacy and safety in the clinic. In this study, we applied the DeFT (De-immunization of Functional Therapeutics) approach to producing functional, de-immunized versions of IFNβ-1a. Two de-immunized versions of IFNβ-1a were produced in CHO cells and designated as IFNβ-1a(VAR1) and IFNβ-1a(VAR2). First, the secondary and tertiary protein structures were analyzed by circular dichroism spectroscopy. Then, the variants were also tested for functionality. While IFNβ-1a(VAR2) showed similar in vitro antiviral activity to the original protein, IFNβ-1a(VAR1) exhibited 40% more biological potency. Finally, in vivo assays using HLA-DR transgenic mice revealed that the de-immunized variants showed a markedly reduced immunogenicity when compared to the originator.
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Affiliation(s)
- Sonia Ricotti
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Alberto Sergio Garay
- Laboratory of Molecular Modeling, FBCB (School of Biochemistry and Biological Sciences), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Marina Etcheverrigaray
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Gabriel Ignacio Amadeo
- Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina
| | - Anne S De Groot
- EpiVax, Inc., Providence, RI 02903, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | | | - Eduardo Federico Mufarrege
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, Santa Fe S3000ZAA, Argentina.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Eickhoff CS, Meza KA, Terry FE, Colbert CG, Blazevic A, Gutiérrez AH, Stone ET, Brien JD, Pinto AK, El Sahly HM, Mulligan MJ, Rouphael N, Alcaide ML, Tomashek KM, Focht C, Martin WD, Moise L, De Groot AS, Hoft DF. Identification of immunodominant T cell epitopes induced by natural Zika virus infection. Front Immunol 2023; 14:1247876. [PMID: 37705976 PMCID: PMC10497216 DOI: 10.3389/fimmu.2023.1247876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Zika virus (ZIKV) is a flavivirus primarily transmitted by Aedes species mosquitoes, first discovered in Africa in 1947, that disseminated through Southeast Asia and the Pacific Islands in the 2000s. The first ZIKV infections in the Americas were identified in 2014, and infections exploded through populations in Brazil and other countries in 2015/16. ZIKV infection during pregnancy can cause severe brain and eye defects in offspring, and infection in adults has been associated with higher risks of Guillain-Barré syndrome. We initiated a study to describe the natural history of Zika (the disease) and the immune response to infection, for which some results have been reported. In this paper, we identify ZIKV-specific CD4+ and CD8+ T cell epitopes that induce responses during infection. Two screening approaches were utilized: an untargeted approach with overlapping peptide arrays spanning the entire viral genome, and a targeted approach utilizing peptides predicted to bind human MHC molecules. Immunoinformatic tools were used to identify conserved MHC class I supertype binders and promiscuous class II binding peptide clusters predicted to bind 9 common class II alleles. T cell responses were evaluated in overnight IFN-γ ELISPOT assays. We found that MHC supertype binding predictions outperformed the bulk overlapping peptide approach. Diverse CD4+ T cell responses were observed in most ZIKV-infected participants, while responses to CD8+ T cell epitopes were more limited. Most individuals developed a robust T cell response against epitopes restricted to a single MHC class I supertype and only a single or few CD8+ T cell epitopes overall, suggesting a strong immunodominance phenomenon. Noteworthy is that many epitopes were commonly immunodominant across persons expressing the same class I supertype. Nearly all of the identified epitopes are unique to ZIKV and are not present in Dengue viruses. Collectively, we identified 31 immunogenic peptides restricted by the 6 major class I supertypes and 27 promiscuous class II epitopes. These sequences are highly relevant for design of T cell-targeted ZIKV vaccines and monitoring T cell responses to Zika virus infection and vaccination.
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Affiliation(s)
- Christopher S. Eickhoff
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
| | - Krystal A. Meza
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
| | | | - Chase G. Colbert
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
| | - Azra Blazevic
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
| | | | - E. Taylor Stone
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, United States
| | - James D. Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, United States
| | - Amelia K. Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, United States
| | - Hana M. El Sahly
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Mark J. Mulligan
- New York University Grossman School of Medicine, Division of Infectious Diseases and Immunology, New York, NY, United States
| | - Nadine Rouphael
- Emory University School of Medicine, Division of Infectious Diseases, Department of Internal Medicine, Atlanta, GA, United States
| | - Maria L. Alcaide
- University of Miami, Division of Infectious Diseases, Miller School of Medicine, Miami, FL, United States
| | - Kay M. Tomashek
- Division of Microbiology, Immunology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Chris Focht
- The Emmes Company, LLC., Rockville, MD, United States
| | | | | | - Anne S. De Groot
- EpiVax, Inc., Providence, RI, United States
- University of Georgia Center for Vaccines and Immunology, Athens, GA, United States
| | - Daniel F. Hoft
- Department of Internal Medicine, Saint Louis University, Division of Infectious Diseases, Allergy, and Immunology, Saint Louis, MO, United States
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO, United States
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10
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Mufarrege EF, Peña LC, Etcheverrigaray M, De Groot AS, Martin W. Specific sequence mutations in a long-lasting rhIFN-α2b version reduce in vitro and in vivo immunogenicity and increase in vitro protein stability. Heliyon 2023; 9:e14670. [PMID: 37020947 PMCID: PMC10068115 DOI: 10.1016/j.heliyon.2023.e14670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
For decades, recombinant human interferon alpha (rhIFN-α2b) has been used to treat emerging and chronic viral diseases. However, rhIFN-α2b is immunogenic and has a short in vivo half-life. To solve these limitations, two long-lasting hyperglycosylated proteins with reduced immunogenicity were developed and designated as 4N-IFN(VAR1) and 4N-IFN(VAR3). Here, we continue to study the relevant characteristics of these therapeutic candidates. Thus, we demonstrated that both de-immunized IFN versions elicited significantly lower neutralizing antibody responses than the original molecule in HLA-DR1 transgenic mice, confirming our previous in vitro protein immunogenicity data. Also, we found that these biobetters exhibited remarkable stability when exposed to different physical factors that the protein product may encounter during its production process and storage, such as low pH, thermal stress, and repeated freezing/thawing cycles. Taking into consideration our previous and present results, 4N-IFN(VAR1) and 4N-IFN-4N(VAR3) appear to be valuable candidates for the treatment of human viral diseases.
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Affiliation(s)
- Eduardo Federico Mufarrege
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, S3000ZAA, Santa Fe, Argentina
- Corresponding author. Ciudad Universitaria, Paraje “El Pozo” – c.c 242, S3000ZAA, Santa Fe, Argentina.
| | - Lucía Carolina Peña
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, S3000ZAA, Santa Fe, Argentina
| | - Marina Etcheverrigaray
- UNL, CONICET, FBCB (School of Biochemistry and Biological Sciences), CBL (Biotechnological Center of Litoral), Ciudad Universitaria, Ruta Nacional 168, Km 472.4, C.C. 242, S3000ZAA, Santa Fe, Argentina
| | - Anne S. De Groot
- EpiVax, Inc., Providence, RI, 02903, USA
- Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, 02903, USA
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11
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Chen J, Tan S, Avadhanula V, Moise L, Piedra PA, De Groot AS, Bahl J. Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. PLoS Comput Biol 2023; 19:e1010360. [PMID: 36626370 PMCID: PMC9870173 DOI: 10.1371/journal.pcbi.1010360] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/23/2023] [Accepted: 12/07/2022] [Indexed: 01/11/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a major cause of lower respiratory infection. Despite more than 60 years of research, there is no licensed vaccine. While B cell response is a major focus for vaccine design, the T cell epitope profile of RSV is also important for vaccine development. Here, we computationally predicted putative T cell epitopes in the Fusion protein (F) and Glycoprotein (G) of RSV wild circulating strains by predicting Major Histocompatibility Complex (MHC) class I and class II binding affinity. We limited our inferences to conserved epitopes in both F and G proteins that have been experimentally validated. We applied multidimensional scaling (MDS) to construct T cell epitope landscapes to investigate the diversity and evolution of T cell profiles across different RSV strains. We find the RSV strains are clustered into three RSV-A groups and two RSV-B groups on this T epitope landscape. These clusters represent divergent RSV strains with potentially different immunogenic profiles. In addition, our results show a greater proportion of F protein T cell epitope content conservation among recent epidemic strains, whereas the G protein T cell epitope content was decreased. Importantly, our results suggest that RSV-A and RSV-B have different patterns of epitope drift and replacement and that RSV-B vaccines may need more frequent updates. Our study provides a novel framework to study RSV T cell epitope evolution. Understanding the patterns of T cell epitope conservation and change may be valuable for vaccine design and assessment.
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Affiliation(s)
- Jiani Chen
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
| | - Swan Tan
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Leonard Moise
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- EpiVax Inc., Providence, Rhode Island, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anne S. De Groot
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- EpiVax Inc., Providence, Rhode Island, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
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12
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Crippin T, Tounkara K, Squibb E, Beseme S, Barry K, Sangare K, Coulibaly S, Fané P, Bagayoko A, Koita OA, Teguété I, De Groot AS. A story-telling cloth approach to motivating cervical cancer screening in Mali. Front Public Health 2022; 10:1051536. [PMID: 36589936 PMCID: PMC9800037 DOI: 10.3389/fpubh.2022.1051536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Ninety percent of deaths from Cervical cancer (CC) caused by Human Papilloma Virus (HPV) occur in low- and middle-income countries. CC is the 2nd most common cause of cancer in women in West Africa, where 12,000 women develop cervical cancer and more than 6,000 die from the disease, annually. While HPV vaccination and CC screening have dramatically reduced the incidence of CC and mortality from CC in developed countries, prevention of CC in West Africa is often limited to visual inspection of the cervix and surgical intervention. In previous studies of CC in Mali, we demonstrated that knowledge about the link between HPV and CC is limited, and that screening for CC is often delayed until women are symptomatic. For this intervention, a story-telling cloth (West African-style printed pagne) was designed for use as a starting point for educational sessions run by community health workers. Community outreach using the cloth during 6 months of 2015 resulted in a 5-fold higher uptake of cervical cancer screening and increased awareness of the potential to vaccinate adolescents against CC. 3,271 women were motivated to visit one of five participating clinics for CC screening, where a mere 600 women had been screened during the previous year. This study shows that a comprehensive, visual, community-centered education campaign coupled with coordinated support for local clinics improves uptake of CC screening.
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Affiliation(s)
| | | | - Eliza Squibb
- GAIA Vaccine Foundation, Providence, RI, United States
| | - Sarah Beseme
- GAIA Vaccine Foundation, Providence, RI, United States
| | - Katherine Barry
- The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Kotou Sangare
- Laboratory of Applied Molecular Biology, University of Sciences, Techniques, and Technologies, Bamako, Mali
| | | | - Pinda Fané
- Department of Regional Health, Bamako, Mali
| | | | - Ousmane A. Koita
- Laboratory of Applied Molecular Biology, University of Sciences, Techniques, and Technologies, Bamako, Mali
| | | | - Anne S. De Groot
- GAIA Vaccine Foundation, Providence, RI, United States,*Correspondence: Anne S. De Groot
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13
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Barry K, Suskin JA, Testa J, Leonard M, De Groot AS. Expanding access to COVID-19 testing, vaccination and treatment at a free clinic for uninsured Spanish-speaking adults in Providence, RI. Hum Vaccin Immunother 2022; 18:2144604. [PMID: 36373716 DOI: 10.1080/21645515.2022.2144604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The COVID-19 pandemic disproportionately impacted uninsured and minority populations, contributing to and reinforcing long-lasting health inequities. Clínica Esperanza/Hope Clinic (CEHC), a free clinic serving uninsured individuals, is one 'safety-net' clinic that improved access to COVID-19 testing and vaccinations for an at-risk population during the pandemic. A retrospective review was performed to quantify COVID-19 testing and vaccination rates for clinic participants, which were compared to rates in the general population. 51.7% of patients seeking COVID-related care at CEHC were uninsured, compared to 8% in Providence and 4.8% in Rhode Island. CEHC performed 5,623 COVID-19 tests for 4,498 unique individuals, a total of 15,783 vaccines were administered, and 10 to 20% of COVID-care participants reported food insecurity during the study period. The prevalence of COVID-19 in the uninsured population and the high demand for vaccines highlight the important role that free clinics can play in the pandemic setting.
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Affiliation(s)
- Katherine Barry
- The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Johanna A Suskin
- The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Julia Testa
- Clínica Esperanza/Hope Clinic, Providence, RI, USA
| | | | - Anne S De Groot
- Clínica Esperanza/Hope Clinic, Providence, RI, USA.,EpiVax, Inc, Providence, RI, USA
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14
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Tan S, Moise L, Pearce DS, Kyriakis CS, Gutiérrez AH, Ross TM, Bahl J, De Groot AS. H1N1 G4 swine influenza T cell epitope analysis in swine and human vaccines and circulating strains uncovers potential risk to swine and humans. Influenza Other Respir Viruses 2022; 17:e13058. [PMID: 36285342 PMCID: PMC9835423 DOI: 10.1111/irv.13058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Pandemic influenza viruses may emerge from animal reservoirs and spread among humans in the absence of cross-reactive antibodies in the human population. Immune response to highly conserved T cell epitopes in vaccines may still reduce morbidity and limit the spread of the new virus even when cross-protective antibody responses are lacking. METHODS We used an established epitope content prediction and comparison tool, Epitope Content Comparison (EpiCC), to assess the potential for emergent H1N1 G4 swine influenza A virus (G4) to impact swine and human populations. We identified and computed the total cross-conserved T cell epitope content in HA sequences of human seasonal and experimental influenza vaccines, swine influenza vaccines from Europe and the United States (US) against G4. RESULTS The overall T cell epitope content of US commercial swine vaccines was poorly conserved with G4, with an average T cell epitope coverage of 35.7%. EpiCC scores for the comparison between current human influenza vaccines and circulating human influenza strains were also very low. In contrast, the T cell epitope coverage of a recent European swine influenza vaccine (HL03) was 65.8% against G4. CONCLUSIONS Poor T cell epitope cross-conservation between emergent G4 and swine and human influenza vaccines in the US may enable G4 to spread in swine and spillover to human populations in the absence of protective antibody response. One European influenza vaccine, HL03, may protect against emergent G4. This study illustrates the use of the EpiCC tool for prospective assessment of existing vaccine strains against emergent viruses in swine and human populations.
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Affiliation(s)
- Swan Tan
- Department of Infectious Diseases, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA
| | - Lenny Moise
- Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,EpiVax Inc.ProvidenceRhode IslandUSA
| | - Douglas S. Pearce
- Zoetis Inc., Veterinary Medicine Research and DevelopmentKalamazooMichiganUSA
| | - Constantinos S. Kyriakis
- Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Department of Pathobiology, College of Veterinary MedicineAuburn UniversityAuburnAlabamaUSA
| | | | - Ted M. Ross
- Department of Infectious Diseases, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA
| | - Justin Bahl
- Department of Infectious Diseases, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Institute of BioinformaticsUniversity of GeorgiaAthensGeorgiaUSA,Department of Epidemiology and BiostatisticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Anne S. De Groot
- Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,EpiVax Inc.ProvidenceRhode IslandUSA
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15
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Moise L, Meyers LM, Jang H, Grizotte-Lake M, Boyle CM, McGonnigal B, Ge P, Ross TM, De Groot AS. Novel H7N9 influenza immunogen design enhances mobilization of seasonal influenza T cell memory in H3N2 pre-immune mice. Hum Vaccin Immunother 2022; 18:2082191. [PMID: 35704783 DOI: 10.1080/21645515.2022.2082191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Strategies that improve influenza vaccine immunogenicity are critical for the development of vaccines for pandemic preparedness. Hemagglutinin (HA)-specific CD4+ T cell epitopes support protective B cell responses against seasonal influenza. However, in the case of avian H7N9, which poses a pandemic threat, HA elicits only weak neutralizing antibody responses in infection and vaccination without adjuvant. We hypothesized that an immune-engineered H7N9 HA incorporating a broadly reactive H3N2 HA-specific memory CD4+ T cell epitope that replaces a regulatory T cell-inducing epitope at the corresponding position in H7N9 HA could harness preexisting influenza T cell immunity to increase CD4+ T cells that are needed for protective antibody development. We designed and produced a virus-like particle (VLP) vaccine that carries the epitope augmented H7N9 HA (OPT1) and immunized HLA-DR3 transgenic mice with established H3N2 immunity. OPT1-VLPs stimulated higher stem cell, central, and effector memory CD4+ T cell levels over wild type VLP immunization. In addition, activated, IL-21-producing follicular helper T cell frequencies were enhanced. This novel immunogen design strategy illustrates that site-specific modifications aimed to augment T cell epitope content enhance CD4+ T cell responses among critical subpopulations capable of aiding protective immune responses upon antigen re-encounter and that mobilization of immune memory can be used to overcome the poor immunogenicity of avian influenza viruses.
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Affiliation(s)
- Leonard Moise
- EpiVax, Inc., Providence, RI, USA.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | | | - Hyesun Jang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | | | | | | | - Pan Ge
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.,Department of Infectious Diseases, University of Georgia, Athens, GA, 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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16
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Sluder AE, Raju Paul S, Moise L, Dold C, Richard G, Silva-Reyes L, Baeten LA, Scholzen A, Reeves PM, Pollard AJ, Garritsen A, Bowen RA, De Groot AS, Rollier C, Poznansky MC. Evaluation of a Human T Cell-Targeted Multi-Epitope Vaccine for Q Fever in Animal Models of Coxiella burnetii Immunity. Front Immunol 2022; 13:901372. [PMID: 35651616 PMCID: PMC9149306 DOI: 10.3389/fimmu.2022.901372] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
T cell-mediated immunity plays a central role in the control and clearance of intracellular Coxiella burnetii infection, which can cause Q fever. Therefore, we aimed to develop a novel T cell-targeted vaccine that induces pathogen-specific cell-mediated immunity to protect against Q fever in humans while avoiding the reactogenicity of the current inactivated whole cell vaccine. Human HLA class II T cell epitopes from C. burnetii were previously identified and selected by immunoinformatic predictions of HLA binding, conservation in multiple C. burnetii isolates, and low potential for cross-reactivity with the human proteome or microbiome. Epitopes were selected for vaccine inclusion based on long-lived human T cell recall responses to corresponding peptides in individuals that had been naturally exposed to the bacterium during a 2007-2010 Q fever outbreak in the Netherlands. Multiple viral vector-based candidate vaccines were generated that express concatemers of selected epitope sequences arranged to minimize potential junctional neo-epitopes. The vaccine candidates caused no antigen-specific reactogenicity in a sensitized guinea pig model. A subset of the vaccine epitope peptides elicited antigenic recall responses in splenocytes from C57BL/6 mice previously infected with C. burnetii. However, immunogenicity of the vaccine candidates in C57BL/6 mice was dominated by a single epitope and this was insufficient to confer protection against an infection challenge, highlighting the limitations of assessing human-targeted vaccine candidates in murine models. The viral vector-based vaccine candidates induced antigen-specific T cell responses to a broader array of epitopes in cynomolgus macaques, establishing a foundation for future vaccine efficacy studies in this large animal model of C. burnetii infection.
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Affiliation(s)
- Ann E Sluder
- 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
| | | | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, The National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | | | - Laura Silva-Reyes
- Oxford Vaccine Group, Department of Paediatrics, The National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - 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
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, The National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | | | - Richard A Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | | | - Christine Rollier
- Oxford Vaccine Group, Department of Paediatrics, The National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, United States
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17
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Suskin JA, Barry K, Satish E, Leonard M, De Groot AS. Meeting Gynecologic Needs and Assuring Adherence to Screening Guidelines at a Student-Run Free Clinic for Uninsured, Low-Income Women. R I Med J (2013) 2022; 105:51-55. [PMID: 35617043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Uninsured, low-income, Spanish-speaking patients face barriers to obtaining gynecologic care in the United States. Clínica Esperanza/Hope Clinic, a free clinic in Rhode Island, hosts a biweekly Women's Clinic (WC) established and run by local medical students. METHODS A retrospective chart review identified gyne- cologic services provided, needs met and adherence to screening guidelines at WC between June 2017 and May 2021. RESULTS During 80 clinics, 278 patients were seen. 362 encounters occurred, with 288 missed appointments. Women primarily attended WC for routine care (159, 43.9%) or abnormal uterine bleeding (41, 11.3%). Common services provided include gynecologic exams (302, 27.0%), Pap smears (221, 19.7%), and STI screening (166, 14.8%). Pap smear and mammography guidelines were adhered to during 92.3% and 94.1% of visits, respectively. CONCLUSIONS Accessible gynecologic care is a significant unmet need for uninsured, Spanish-speaking patients. These findings demonstrate the importance of gynecologic care at free clinics and warrant their expansion.
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Affiliation(s)
- Johanna A Suskin
- The Warren Alpert Medical School of Brown University, Providence, RI
| | - Katherine Barry
- The Warren Alpert Medical School of Brown University, Providence, RI
| | - Ella Satish
- The Warren Alpert Medical School of Brown University, Providence, RI
| | | | - Anne S De Groot
- Clínica Esperanza/Hope Clinic, Providence, RI; EpiVax, Inc., Providence, RI
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18
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Mattei AE, Gutierrez AH, Martin WD, Terry FE, Roberts BJ, Rosenberg AS, De Groot AS. In silico Immunogenicity Assessment for Sequences Containing Unnatural Amino Acids: A Method Using Existing in silico Algorithm Infrastructure and a Vision for Future Enhancements. Front Drug Discov (Lausanne) 2022; 2:952326. [PMID: 36945694 PMCID: PMC10026553 DOI: 10.3389/fddsv.2022.952326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The in silico prediction of T cell epitopes within any peptide or biologic drug candidate serves as an important first step for assessing immunogenicity. T cell epitopes bind human leukocyte antigen (HLA) by a well-characterized interaction of amino acid side chains and pockets in the HLA molecule binding groove. Immunoinformatics tools, such as the EpiMatrix algorithm, have been developed to screen natural amino acid sequences for peptides that will bind HLA. In addition to commonly occurring in synthetic peptide impurities, unnatural amino acids (UAA) are also often incorporated into novel peptide therapeutics to improve properties of the drug product. To date, the HLA binding properties of peptides containing UAA are not accurately estimated by most algorithms. Both scenarios warrant the need for enhanced predictive tools. The authors developed an in silico method for modeling the impact of a given UAA on a peptide's likelihood of binding to HLA and, by extension, its immunogenic potential. In silico assessment of immunogenic potential allows for risk-based selection of best candidate peptides in further confirmatory in vitro, ex vivo and in vivo assays, thereby reducing the overall cost of immunogenicity evaluation. Examples demonstrating in silico immunogenicity prediction for product impurities that are commonly found in formulations of the generic peptides teriparatide and semaglutide are provided. Next, this article discusses how HLA binding studies can be used to estimate the binding potentials of commonly encountered UAA and "correct" in silico estimates of binding based on their naturally occurring counterparts. As demonstrated here, these in vitro binding studies are usually performed with known ligands which have been modified to contain UAA in HLA anchor positions. An example using D-amino acids in relative binding position 1 (P1) of the PADRE peptide is presented. As more HLA binding data become available, new predictive models allowing for the direct estimation of HLA binding for peptides containing UAA can be established.
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19
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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: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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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: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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McCarthy M, Barry K, Estrada C, Veliz B, Rosales D, Leonard M, De Groot AS. Recruitment, Training, and Roles of the Bilingual, Bicultural Navegantes: Developing a Specialized Workforce of Community Health Workers to Serve a Low-Income, Spanish-Speaking Population in Rhode Island. Front Public Health 2021; 9:666566. [PMID: 34150707 PMCID: PMC8213204 DOI: 10.3389/fpubh.2021.666566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Clínica Esperanza/Hope Clinic (CEHC) employs Navegantes, who are specially-trained bilingual Community Health Workers (CHW), as key team members who improve the ability of the clinic to provide care for and improve the health status of a large population of uninsured Spanish-speaking patients in Providence, Rhode Island. Given the growing demand for CHWs at the clinic and in the broader healthcare sector in the state, CEHC developed the Advanced Navegante Training Program (ANTP). The ANTP prepares community members to become certified CHWs who are equipped to provide patient navigation and lifestyle coaching as well as professional medical interpretation services. The ANTP is developed and taught by CEHC Navegantes who themselves are bilingual and bicultural peers of trainees as well as the population that CEHC serves. Upon graduation, ANTP trainees have been able to attain higher-paying and fulfilling careers in a range of healthcare and other community settings. The ANTP offers a low-cost, community-based model for training CHWs who are uniquely prepared to promote health and well-being among medically underserved patients.
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Affiliation(s)
- Meghan McCarthy
- Clínica Esperanza/Hope Clinic, Providence, RI, United States.,The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Katherine Barry
- Clínica Esperanza/Hope Clinic, Providence, RI, United States.,The Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Cindy Estrada
- Clínica Esperanza/Hope Clinic, Providence, RI, United States
| | - Brenda Veliz
- Clínica Esperanza/Hope Clinic, Providence, RI, United States
| | - Damaris Rosales
- Clínica Esperanza/Hope Clinic, Providence, RI, United States
| | - Morgan Leonard
- Clínica Esperanza/Hope Clinic, Providence, RI, United States
| | - Anne S De Groot
- Clínica Esperanza/Hope Clinic, Providence, RI, United States.,EpiVax, Inc., Providence, RI, United States.,University of Georgia, Athens, GA, United States
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Barry K, McCarthy M, Melikian G, Almeida-Monroe V, Leonard M, De Groot AS. Responding to COVID-19 in an Uninsured Hispanic/Latino Community: Testing, Education and Telehealth at a Free Clinic in Providence. R I Med J (2013) 2020; 103:41-46. [PMID: 33126788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The COVID-19 pandemic has exacerbated the effects of existing health disparities throughout the United States. While Hispanic/Latino individuals account for only 16% of the Rhode Island (RI) population, Rhode Island Department of Health (RIDOH) data show that 45% of COVID-19 cases and 36% of individuals who have been hospitalized identify as Hispanic/Latino. Clínica Esperanza/Hope Clinic (CEHC) mobilized a comprehensive effort to offer telehealth visits, health education and accessible, walk-up COVID-19 testing for low-income, uninsured and Spanish-speaking individuals living in Rhode Island. With support from CEHC volunteers, the City of Providence, the State of Rhode Island, and local foundations, CEHC has administered 1,649 individual COVID-19 tests as of October 2020. The overall COVID-19 test positivity rate at CEHC was 23%, peaking in April at 48%. Additionally, CEHC has distributed more than 1,600 meal boxes to patients experiencing food insecurity, provided emergency financial resources, while rapidly scaling up healthcare services for the increasing numbers of uninsured individuals in RI.
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Affiliation(s)
- Katherine Barry
- Project Manager, Clínica Esperanza/Hope Clinic, Providence, RI
| | - Meghan McCarthy
- Project Manager, Clínica Esperanza/Hope Clinic, Providence, RI
| | | | | | | | - Anne S De Groot
- Volunteer Medical Director, Clínica Esperanza/Hope Clinic, Providence, RI; CEO/CSO, EpiVax, Inc., Providence, RI; Professor (Research), University of Georgia, Athens, GA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Moise L, Ross TM, Hoft DF, Martin WD, De Groot AS. Exploit T cell Immunity for Rapid, Safe and Effective COVID-19 Vaccines. Expert Rev Vaccines 2020; 19:781-784. [PMID: 32962468 DOI: 10.1080/14760584.2020.1825946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Leonard Moise
- EpiVax, Inc ., Providence, RI, USA.,Institute for Immunology and Informatics, University of Rhode Island , Providence, RI, USA.,Center for Vaccines and Immunology, University of Georgia , Athens, GA, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia , Athens, GA, USA
| | - Daniel F Hoft
- Departments of Molecular Microbiology & Immunology and Internal Medicine, Division of Infectious Diseases, Allergy & Immunology, Saint Louis University , St. Louis, MO, 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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32
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Jang H, Meyers LM, Boyle C, De Groot AS, Moise L, Ross TM. Immune-engineered H7N9 influenza hemagglutinin improves protection against viral influenza virus challenge. Hum Vaccin Immunother 2020; 16:2042-2050. [PMID: 32783766 PMCID: PMC7553694 DOI: 10.1080/21645515.2020.1793711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The influenza hemagglutinin (HA) isolated from avian H7N9 influenza virus strains elicit weak immune responses. This low immunogenicity may be due to a regulatory T cell (Treg)-stimulating epitopes in HA from the H7N9 isolate A/Anhui/1/2013 (Anh/13). In this report, this Treg stimulating sequence was removed from the wild-type (WT) H7 HA amino acid sequence and replaced with a conserved CD4 + T cell stimulating sequences from human seasonal H3N2 strains and designed OPT1 H7 HA. The effectiveness of this optimized H7 HA protein was determined using a humanized mouse (HLA-DR3) expressing the human leukocyte antigen (HLA) DR3 allele. HLA-DR3 mice were pre-immunized by infecting with H3N2 influenza virus, A/Hong Kong/4108/2014 and then vaccinated intramuscularly with either the WT H7 HA from Anh/13 or the OPT1 H7 HA antigen without adjuvant. The OPT1 H7 HA vaccination group elicited higher H7 HA-specific IgG titers that resulted in a lower mortality, weight loss, and lung viral titer following lethal challenge with the H7N9 Anh/13 influenza virus compared to WT-vaccinated mice. Overall, T-cell epitope-engineered vaccines can improve the immunogenicity of H7 HA antigens resulting in enhanced survival and lower morbidity against H7N9 influenza virus challenge.
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Affiliation(s)
- Hyesun Jang
- Department of Infectious Diseases, University of Georgia , Athens, GA, USA.,Center for Vaccines and Immunology, University of Georgia , Athens, GA, USA
| | | | | | - Anne S De Groot
- Center for Vaccines and Immunology, University of Georgia , Athens, GA, USA.,EpiVax , Providence, RI, USA
| | - Lenny Moise
- EpiVax , Providence, RI, USA.,Institute of Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island , Providence, RI, USA
| | - Ted M Ross
- Department of Infectious Diseases, University of Georgia , Athens, GA, USA.,Center for Vaccines and Immunology, University of Georgia , Athens, GA, 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: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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35
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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36
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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37
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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38
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Kumar NR, DuVernois G, Almeida-Monroe V, Siegert N, De Groot AS. Evaluating the Impact of a Student-Run Women's Clinic on Access to Gynecologic Care for Uninsured Women in Rhode Island. R I Med J (2013) 2019; 102:52-56. [PMID: 31795536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clinica Esperanza/Hope Clinic (CEHC) is a free clinic providing primary care to a predominantly Spanish-speaking, uninsured patient population in Rhode Island with limited access to gynecologic care. In 2015, medical students at the Alpert Medical School of Brown University started the Women's Clinic of Clinica Esperanza (WCCE), a "clinic within the clinic," recruiting physician preceptors and obtaining funding to support WCCE operations. For complex issues, clinic services were supplemented by a subspecialty referral system at a local hospital. Interim results over a two-year period ending in May 2017 are reported here. Medical students organized 48 women's clinics and provided 83 Pap smears, 138 breast exams, 42 mammogram referrals, 35 STI tests, and 19 vaginitis screens, among other activities. As the example of WCCE shows, student-run clinics can utilize medical students' relationships with providers and unique funding sources to expand access to specialty care for uninsured patients.
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Affiliation(s)
- Natasha R Kumar
- Department of Obstetrics and Gynecology, Northwestern University, Chicago IL
| | - Gabriele DuVernois
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - Nicole Siegert
- Department of Family Medicine, Warren Alpert Medical School of Brown University, Providence, RI
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39
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De Groot AS, Skowron G, White JR, Boyle C, Richard G, Serreze D, Martin WD. Therapeutic administration of Tregitope-Human Albumin Fusion with Insulin Peptides to promote Antigen-Specific Adaptive Tolerance Induction. Sci Rep 2019; 9:16103. [PMID: 31695065 PMCID: PMC6834854 DOI: 10.1038/s41598-019-52331-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 10/16/2019] [Indexed: 01/12/2023] Open
Abstract
Type 1 Diabetes (T1D) is an autoimmune disease that is associated with effector T cell (Teff) destruction of insulin-producing pancreatic beta-islet cells. Among the therapies being evaluated for T1D is the restoration of regulatory T cell (Treg) activity, specifically directed toward down-modulation of beta-islet antigen-specific T effector cells. This is also known as antigen-specific adaptive tolerance induction for T1D (T1D ASATI). Tregitopes (T regulatory cell epitopes) are natural T cell epitopes derived from immunoglobulin G (IgG) that were identified in 2008 and have been evaluated in several autoimmune disease models. In the T1D ASATI studies presented here, Tregitope peptides were administered to non-obese diabetic (NOD) mice at the onset of diabetes within two clinically-relevant delivery systems (liposomes and in human serum albumin [HSA]-fusion products) in combination with preproinsulin (PPI) target antigen peptides. The combination of Tregitope-albumin fusions and PPI peptides reduced the incidence of severe diabetes and reversed mild diabetes, over 49 days of treatment and observation. Combining HSA-Tregitope fusions with PPI peptides is a promising ASATI approach for therapy of T1D.
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Affiliation(s)
- Anne S. De Groot
- grid.421087.8EpiVax, Inc., 188 Valley St., Providence, RI 02909 USA
| | - Gail Skowron
- grid.421087.8EpiVax, Inc., 188 Valley St., Providence, RI 02909 USA
| | | | - Christine Boyle
- grid.421087.8EpiVax, Inc., 188 Valley St., Providence, RI 02909 USA
| | - Guilhem Richard
- grid.421087.8EpiVax, Inc., 188 Valley St., Providence, RI 02909 USA
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40
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Salerno-Gonçalves R, Tettelin H, Luo D, Guo Q, Ardito MT, Martin WD, De Groot AS, Sztein MB. Differential functional patterns of memory CD4 + and CD8 + T-cells from volunteers immunized with Ty21a typhoid vaccine observed using a recombinant Escherichia coli system expressing S. Typhi proteins. Vaccine 2019; 38:258-270. [PMID: 31629569 DOI: 10.1016/j.vaccine.2019.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 02/01/2023]
Abstract
It is widely accepted that CD4+ and CD8+ T-cells play a significant role in protection against Salmonella enterica serovar Typhi (S. Typhi), the causative agent of the typhoid fever. However, the antigen specificity of these T-cells remains largely unknown. Previously, we demonstrated the feasibility of using a recombinant Escherichia coli (E. coli) expression system to uncover the antigen specificity of CD4+ and CD8+ T cells. Here, we expanded these studies to include the evaluation of 12 additional S. Typhi proteins: 4 outer membrane proteins (OmpH, OmpL, OmpR, OmpX), 3 Vi-polysaccharide biosynthesis proteins (TviA, TviB, TviE), 3 cold shock proteins (CspA, CspB, CspC), and 2 conserved hypothetical proteins (Chp 1 and Chp2), all selected based on the bioinformatic analyses of the content of putative T-cell epitopes. CD4+ and CD8+ T cells from 15 adult volunteers, obtained before and 42 days after immunization with oral live attenuated Ty21a vaccine, were assessed for their functionality (i.e., production of cytokines and cytotoxic expression markers in response to stimulation with selected antigens) as measured by flow cytometry. Although volunteers differed on their T-cell antigen specificity, we observed T-cell immune responses against all S. Typhi proteins evaluated. These responses included 9 proteins, OmpH, OmpR, TviA, TviE, CspA, CspB, CspC, Chp 1 and Chp 2, which have not been previously reported to elicit T-cell responses. Interestingly, we also observed that, regardless of the protein, the functional patterns of the memory T-cells were different between CD4+ and CD8+ T cells. In sum, these studies demonstrated the feasibility of using bioinformatic analysis and the E. coli expressing system described here to uncover novel immunogenic T-cell proteins that could serve as potential targets for the production of protein-based vaccines.
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Affiliation(s)
- Rosângela Salerno-Gonçalves
- Center for Vaccine Development and Global Health (CVD), Department of Pediatrics, University of Maryland School of Medicine, 685 West Baltimore Street, HSF1, Baltimore, MD 21201, USA.
| | - Hervé Tettelin
- Department of Microbiology and Immunology and Institute for Genome Sciences (IGS), University of Maryland School of Medicine, 670 West Baltimore Street, HSF3, Baltimore, MD 21201, USA
| | - David Luo
- Center for Vaccine Development and Global Health (CVD), Department of Pediatrics, University of Maryland School of Medicine, 685 West Baltimore Street, HSF1, Baltimore, MD 21201, USA
| | - Qin Guo
- Department of Microbiology and Immunology and Institute for Genome Sciences (IGS), University of Maryland School of Medicine, 670 West Baltimore Street, HSF3, Baltimore, MD 21201, USA
| | - Matthew T Ardito
- Institute for Immunology and Informatics (iCubed), Department of Cell and Molecular Biology, University of Rhode Island, 80 Washington Street, Providence, RI, USA; EpiVax, Inc., 188 Valley Street Suite 424, Providence, RI, USA
| | - William D Martin
- Institute for Immunology and Informatics (iCubed), Department of Cell and Molecular Biology, University of Rhode Island, 80 Washington Street, Providence, RI, USA; EpiVax, Inc., 188 Valley Street Suite 424, Providence, RI, USA
| | - Anne S De Groot
- Institute for Immunology and Informatics (iCubed), Department of Cell and Molecular Biology, University of Rhode Island, 80 Washington Street, Providence, RI, USA; EpiVax, Inc., 188 Valley Street Suite 424, Providence, RI, USA
| | - Marcelo B Sztein
- Center for Vaccine Development and Global Health (CVD), Department of Pediatrics, University of Maryland School of Medicine, 685 West Baltimore Street, HSF1, Baltimore, MD 21201, USA
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Wada Y, Nithichanon A, Nobusawa E, Moise L, Martin WD, Yamamoto N, Terahara K, Hagiwara H, Odagiri T, Tashiro M, Lertmemongkolchai G, Takeyama H, De Groot AS, Ato M, Takahashi Y. Publisher Correction: A humanized mouse model identifies key amino acids for low immunogenicity of H7N9 vaccines. Sci Rep 2019; 9:14730. [PMID: 31594990 PMCID: PMC6783480 DOI: 10.1038/s41598-019-50828-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Yamato Wada
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, 162-8480, Japan
| | - Arnone Nithichanon
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.,Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, 40002, Khon Kaen, Thailand
| | - Eri Nobusawa
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan
| | - Leonard Moise
- Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA.,EpiVax Inc, Providence, RI, USA
| | | | - Norio Yamamoto
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan.,Department of Infection Control Science, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan
| | - Kazutaka Terahara
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan
| | - Masato Tashiro
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan
| | - Ganjana Lertmemongkolchai
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, 40002, Khon Kaen, Thailand
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, 162-8480, Japan
| | - Anne S De Groot
- Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA.,EpiVax Inc, Providence, RI, USA
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
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42
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Hoffmann PR, Hoffmann FW, Premeaux TA, Fujita T, Soprana E, Panigada M, Chew GM, Richard G, Hindocha P, Menor M, Khadka VS, Deng Y, Moise L, Ndhlovu LC, Siccardi A, Weinberg AD, De Groot AS, Bertino P. Multi-antigen Vaccination With Simultaneous Engagement of the OX40 Receptor Delays Malignant Mesothelioma Growth and Increases Survival in Animal Models. Front Oncol 2019; 9:720. [PMID: 31428586 PMCID: PMC6688537 DOI: 10.3389/fonc.2019.00720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/19/2019] [Indexed: 01/09/2023] Open
Abstract
Malignant Mesothelioma (MM) is a rare and highly aggressive cancer that develops from mesothelial cells lining the pleura and other internal cavities, and is often associated with asbestos exposure. To date, no effective treatments have been made available for this pathology. Herein, we propose a novel immunotherapeutic approach based on a unique vaccine targeting a series of antigens that we found expressed in different MM tumors, but largely undetectable in normal tissues. This vaccine, that we term p-Tvax, is comprised of a series of immunogenic peptides presented by both MHC-I and -II to generate robust immune responses. The peptides were designed using in silico algorithms that discriminate between highly immunogenic T cell epitopes and other harmful epitopes, such as suppressive regulatory T cell epitopes and autoimmune epitopes. Vaccination of mice with p-Tvax led to antigen-specific immune responses that involved both CD8+ and CD4+ T cells, which exhibited cytolytic activity against MM cells in vitro. In mice carrying MM tumors, p-Tvax increased tumor infiltration of CD4+ T cells. Moreover, combining p-Tvax with an OX40 agonist led to decreased tumor growth and increased survival. Mice treated with this combination immunotherapy displayed higher numbers of tumor-infiltrating CD8+ and CD4+ T cells and reduced T regulatory cells in tumors. Collectively, these data suggest that the combination of p-Tvax with an OX40 agonist could be an effective strategy for MM treatment.
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Affiliation(s)
- Peter R Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Fukun W Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Thomas A Premeaux
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Tsuyoshi Fujita
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Elisa Soprana
- Department of Molecular Immunology, San Raffaele University and Research Institute, Milan, Italy
| | - Maddalena Panigada
- Department of Molecular Immunology, San Raffaele University and Research Institute, Milan, Italy
| | - Glen M Chew
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | | | | | - Mark Menor
- Bioinformatics Core, Department of Complementary and Integrative Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Vedbar S Khadka
- Bioinformatics Core, Department of Complementary and Integrative Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Youping Deng
- Bioinformatics Core, Department of Complementary and Integrative Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Lenny 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
| | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Antonio Siccardi
- Department of Molecular Immunology, San Raffaele University and Research Institute, Milan, Italy
| | - Andrew D Weinberg
- Robert W. Franz Cancer Research Center, Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, OR, 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
| | - Pietro Bertino
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Richard G, Biron B, Boyle C, Ardito M, Moise L, Martin W, Berdugo G, Groot ASD. Abstract 943: Filtering out self-like neoantigens improves immune response to cancer vaccines. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Clinical studies have highlighted the potential of precision cancer immunotherapy to effectively control the tumor of patients across cancer indications. However, recent studies showcase the difficulty of establishing robust CD8 and CD4 T cell responses. We hypothesize that poor cancer vaccine performance may be due in part to the inadvertent inclusion of suppressive T cell neo-epitopes in neoantigen vaccines that may be recognized by regulatory T cells (Tregs).
To test this hypothesis, we used the Ancer™ system to identify and select neo-epitopes from the CT26 syngeneic mouse model. Ancer™ leverages EpiMatrix® and JanusMatrix™, state-of-the-art predictive algorithms that have been extensively validated in prospective vaccine studies for infectious diseases (Moise et al., Hum. Vaccines Immunother 2015; Wada et al., Sci. Rep. 2017). Distinctive features of Ancer™ over other in silico pipelines are its ability to accurately predict CD4 T cell epitopes and to identify tolerated or Treg epitopes.
In a first experiment, optimally selected CT26 neoantigen vaccine candidates were identified with Ancer™ and ranked according to tumor expression level and predicted Class I- and Class II-restricted immunogenicity. Self-like, putative Treg epitopes were removed in this process. Naïve Balb/c mice were immunized subcutaneously with a peptide pool comprised of the 20 highest ranking neoantigens delivered with PolyICLC (Oncovir). Immunization with Ancer™-derived neoantigens induced strong IFNg ELISpot responses compared to controls (p < 0.001). Flow cytometry confirmed the vaccine stimulated multifunctional CD4+ and CD8+ T cells.
In a follow-on experiment, ten self-like neoantigens, from the same CT26 genome, were selected with Ancer™. These neoantigens may be recognized by Tregs due to their high degree of similarity with self, based on JanusMatrix™. Co-administration of the CT26 self-like neoantigens with our optimally designed neoantigen vaccine in naïve Balb/c mice diminished IFNg ELISpot responses by 5-fold compared to vaccination without the self-like neoantigens (p = 0.003).
While it has been well known that Tregs are present in tumors, these results suggest the possibility that tumor-derived neo-epitopes may be recruiting Tregs to the tumor. More importantly, the inadvertent inclusion of Treg driving neoantigens in vaccine formulations may hinder efforts to induce strong T cell-mediated tumor control. In silico screening of neoantigen sequences using specialized tools offers the possibility of enriching and designing new vaccines with higher quality candidates. Efforts are ongoing to determine the effect of Ancer™-derived self-like neoantigens on CD4+ and CD8+ T cells and how the inclusion of self-like neoantigens in vaccines affects their efficacy.
Citation Format: Guilhem Richard, Bethany Biron, Christine Boyle, Matthew Ardito, Leonard Moise, William Martin, Gad Berdugo, Anne S. De Groot. Filtering out self-like neoantigens improves immune response to cancer vaccines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 943.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Barry K, McCarthy M, Buckley J, Jacques S, Johnson H, Almeida-Monroe V, De Groot AS. Four Years of CHEER: Cost and QALY Savings of a Free Nurse-run Walk-in Clinic Serving an Uninsured, Predominantly Spanish-speaking Immigrant Population in Providence. J Health Care Poor Underserved 2019; 30:806-819. [PMID: 31130552 DOI: 10.1353/hpu.2019.0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Non-emergent visits to emergency departments by uninsured patients impose unnecessary costs on both patients and safety-net institutions. We evaluated the health and economic impacts of providing free, walk-in care to low-income, uninsured adults-most of them Hispanic-at a free clinic between January 2013 and December 2016. Providing access to health care services for uninsured patients at Clínica Esperanza/Hope Clinic reduced emergency department expenditures in Rhode Island by approximately $448,876 (range: $410,377-$487,375) annually and may have also reduced future healthcare costs for this population by more than $48 million ($12,034,469 annually) over the four-year evaluation period. For every $1 in funding for walk-in clinic operation, delivering free care provided a return on investment of $71.18 (range: $70.95-71.40) in healthcare value. Providing access to non-emergent walk-in care at the more than 12,000 free healthcare clinics nationwide may save billions in ED costs while improving the health of uninsured individuals.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Richard G, Sweis RF, Moise L, Ardito M, Martin WA, Berdugo G, Steinberg GD, Groot ASD. Abstract B089: Application of precision cancer immunotherapy design tools to bladder cancer: Non-self-like neoepitopes as a prognostic biomarker. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-b089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Precision cancer immunotherapy targeting mutations expressed by cancer cells has proven to effectively control the tumor of patients in multiple clinical trials (Sahin et al., Nature 2017; Ott et al., Nature 2017). However, the selection of immunogenic T-cell neo-epitopes remains challenging and many epitopes selected using traditional methodologies fail to induce effector T-cell responses. Poor performance may partially be due to inclusion of mutated epitopes cross-conserved with self-epitopes recognized by regulatory (Treg), anergic, or deleted T-cells. Vaccination with self-epitopes can lead to weak effector responses, active immune suppression, and toxicity due to immune-mediated adverse effects. In addition, most cancer vaccine studies focus on the selection of CD8 T-cell neo-epitopes due to an apparent lack of robust and accurate CD4 T-cell epitope prediction tools. We have developed Ancer, an integrated and streamlined neo-epitope selection pipeline, that accelerates the selection of both CD4 and CD8 T-cell neo-epitopes from next-generation sequencing (NGS) data. Ancer leverages EpiMatrix and JanusMatrix, predictive algorithms that have been extensively validated in prospective vaccine studies for infectious diseases (Moise et al., Hum Vaccines Immunother 2015; Wada et al., Sci Rep 2017). Distinctive features of Ancer are its ability to accurately predict Class II HLA ligands, or CD4 epitopes, with EpiMatrix, and to identify tolerated or Treg epitopes with JanusMatrix. In addition, screening candidate sequences with JanusMatrix enables to the removal of neo-epitopes that may trigger off-target events, which have in some cases abruptly halted the development of promising cancer therapies. Ancer was applied to NGS data derived from the BLCA bladder cancer cohort from The Cancer Genome Atlas (TCGA) database. On average, 55 out of 204 missense mutations in bladder cancer patients’ tumors met Ancer’s quality control standards, in an initial analysis carried out for a representative set of 11 patients. This subset of high-quality missense variants was then screened using Ancer settings defined by the unique HLA of each patient, to derive the best vaccine candidate sequences encompassing these mutations. A median number of 24 (interquartile range: 15-64) candidate sequences were generated for each patient under study. The time required to select sequences for all of the patients in this study was less than two days. This initial analysis of eleven BLCA bladder cancer cohort patients demonstrates the capacity of Ancer to define a sufficient number of candidate sequences for vaccinating bladder cancer patients in a precision immunotherapy setting. We also assessed Ancer’s ability to predict patient outcomes on a larger subset of 58 individuals. While the disease-free status of BLCA patients could not be explained by their tumor mutational burden (AUC = 0.55, p-value = 0.1328), nor by their load of missense mutations (AUC = 0.54, p-value = 0.1740), the number of neoepitopes highly different from self, as defined by Ancer, significantly segregated disease-free patients from patients who recurred or progressed (AUC = 0.68, p-value = 0.0214). These results suggest that defining the number of true neoepitopes using Ancer may represent a novel biomarker for more robust antitumor immune response and higher likelihood of disease-free survival.Our analysis of the BLCA cohort from the TCGA database showcases the value of Ancer in clinical settings. Ancer can be used to identify high-value candidate sequences for inclusion in personalized therapies while removing potentially tolerated or tolerogenic self-epitopes from consideration. Our next step will be to investigate whether Ancer-defined neoepitope load will serve as a biomarker for prognosis and response to therapy in the full BLCA cohort.
Citation Format: Guilhem Richard, Randy F. Sweis, Leonard Moise, Matthew Ardito, William A. Martin, Gad Berdugo, Gary D. Steinberg, Anne S. De Groot. Application of precision cancer immunotherapy design tools to bladder cancer: Non-self-like neoepitopes as a prognostic biomarker [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B089.
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Affiliation(s)
- Guilhem Richard
- EpiVax, Inc., Providence, RI; University of Chicago, Chicago, IL; University of Rhode Island, Providence, RI
| | - Randy F. Sweis
- EpiVax, Inc., Providence, RI; University of Chicago, Chicago, IL; University of Rhode Island, Providence, RI
| | - Leonard Moise
- EpiVax, Inc., Providence, RI; University of Chicago, Chicago, IL; University of Rhode Island, Providence, RI
| | - Matthew Ardito
- EpiVax, Inc., Providence, RI; University of Chicago, Chicago, IL; University of Rhode Island, Providence, RI
| | - William A. Martin
- EpiVax, Inc., Providence, RI; University of Chicago, Chicago, IL; University of Rhode Island, Providence, RI
| | - Gad Berdugo
- EpiVax, Inc., Providence, RI; University of Chicago, Chicago, IL; University of Rhode Island, Providence, RI
| | - Gary D. Steinberg
- EpiVax, Inc., Providence, RI; University of Chicago, Chicago, IL; University of Rhode Island, Providence, RI
| | - Anne S. De Groot
- EpiVax, Inc., Providence, RI; University of Chicago, Chicago, IL; University of Rhode Island, Providence, RI
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50
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Hindocha P, Nair NJ, Pigoga JL, Barry K, McCarthy M, Almeida-Monroe V, De Groot AS. Bridging the [Health Equity] Gap at a Free Clinic for Uninsured Residents of Rhode Island. R I Med J (2013) 2018; 101:27-31. [PMID: 30384516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Poor management of chronic diseases, such as hypertension and diabetes, particularly among the uninsured, places medical and financial burdens on the healthcare system. Clínica Esperanza/Hope Clinic initiated a chronic disease management program for uninsured residents of Rhode Island (RI) called Bridging the [Health Equity] Gap (BTG), which offers continuity of care, quarterly goal-setting appointments, and healthy lifestyle interventions. Outcomes for 549 participants from the initial evaluation period are presented here. Over the first 12 months of enrollment, mean hemoglobin A1c decreased from 10.2% to 8.3% (p<0.001), and mean blood glucose of individuals with diabetes decreased by 51 mg/dL (p<0.01). BTG participants used the local emergency department (ED) 60% less than Medicaid-insured RI residents and had 61% fewer "potentially preventable" ED visits. The positive impact of BTG on chronic disease outcomes and ED usage by uninsured patients suggests that programs like BTG may reduce overall healthcare costs in the state.
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Affiliation(s)
- Pooja Hindocha
- Clínica Esperanza/Hope Clinic, Providence RI; EpiVax, Inc., Providence, RI
| | | | - Jennifer L Pigoga
- Clínica Esperanza/Hope Clinic, Providence, RI; Urban Institute, Washington DC
| | | | | | | | - Anne S De Groot
- Clínica Esperanza/Hope Clinic, Providence, RI; EpiVax, Inc., Providence, RI, University of Rhode Island, Kingston, RI
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