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Zhang J, Askenase P, Jaenisch R, Crumpacker CS. Approaches to pandemic prevention - the chromatin vaccine. Front Immunol 2023; 14:1324084. [PMID: 38143744 PMCID: PMC10739501 DOI: 10.3389/fimmu.2023.1324084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023] Open
Abstract
Developing effective vaccines against viral infections have significant impacts on development, prosperity and well-being of human populations. Thus, successful vaccines such as smallpox and polio vaccines, have promoted global societal well-being. In contrast, ineffective vaccines may fuel arguments that retard scientific progress. We aim to stimulate a multilevel discussion on how to develop effective vaccines against recent and future pandemics by focusing on acquired immunodeficiency syndrome (AIDS), coronavirus disease (COVID) and other viral infections. We appeal to harnessing recent achievements in this field specifically towards a cure for current pandemics and prevention of the next pandemics. Among these, we propose to apply the HIV DNA in chromatin format - an end product of aborted HIV integration in episomal forms, i.e., the chromatin vaccines (cVacc), to elicit the epigenetic silencing and memory that prevent viral replication and infection.
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Affiliation(s)
- Jielin Zhang
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Philip Askenase
- Allergy & Clinical Immunology, Yale School of Medicine, New Haven, CT, United States
| | - Rudolf Jaenisch
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Clyde S. Crumpacker
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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2
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Poboinev VV, Khrustalev VV, Akunevich AA, Shalygo NV, Stojarov AN, Khrustaleva TA, Kordyukova LV. Peptide Models of the Cytoplasmic Tail of Influenza A/H1N1 Virus Hemagglutinin Expand Understanding its pH-Dependent Modes of Interaction with Matrix Protein M1. Protein J 2023:10.1007/s10930-023-10101-z. [PMID: 36952102 PMCID: PMC10034248 DOI: 10.1007/s10930-023-10101-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 03/24/2023]
Abstract
Influenza A virus hemagglutinin (HA) is a major virus antigen. No cryo-electron microscopy or X-ray data can be obtained for the HA intraviral (cytoplasmic) domain (CT) post-translationally modified with long fatty acid residues bound to three highly conserved cysteines. We recently proposed a model of HA CT of Influenza A/H1N1 virus possessing an antiparallel beta structure based on the experimental secondary structure analysis of four 14-15 amino acid long synthetic peptides, corresponding to the HA CT sequence, with free or acetaminomethylated cysteines. To dispel doubts about possible non-specific "amyloid-like" aggregation of those synthetic peptides in phosphate buffer solution, we have determined the order of oligomers based on blue native gel electrophoresis, membrane filtration, fluorescence spectroscopy and molecular modeling approaches. We have found that unmodified peptides form only low molecular weight oligomers, while modified peptides form both oligomers of low order similar to those found for unmodified peptides and high order conglomerates, which however are not of beta-amyloid-like fold. This study confirms that the beta structure previously detected by circular dichroism spectroscopy analysis is more likely the result of intrinsic propensity of the HA CT amino acid sequence than the consequence of aggregation. The structures of low order oligomers of the synthetic peptides were used for in silico experiments on modeling of HA CT interactions with matrix protein M1 at physiological and acidic pH levels and revealed two different areas of binding. Finally, tripeptides capable of blocking interactions between HA CT and M1 were proposed.
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3
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Svitek N, Saya R, Zhang H, Nene V, Steinaa L. Systematic Determination of TCR–Antigen and Peptide–MHC Binding Kinetics among Field Variants of a Theileria parva Polymorphic CTL Epitope. THE JOURNAL OF IMMUNOLOGY 2022; 208:549-561. [PMID: 35031580 PMCID: PMC8802549 DOI: 10.4049/jimmunol.2100400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/23/2021] [Indexed: 11/24/2022]
Abstract
Positions 1–3 in the Tp9 CTL epitope are required for binding to BoLA-1*023:01. Positions 5–8 in the Tp9 epitope are required for TCR recognition in diverse CTLs. Tp9-specific CTLs from Muguga-immunized animals can cross-react with variants 4 and 7.
CTLs are known to contribute to immunity toward Theileria parva, the causative agent of East Coast fever. The Tp967–75 CTL epitope from the Muguga strain of T. parva is polymorphic in other parasite strains. Identifying the amino acids important for MHC class I binding, as well as TCR recognition of epitopes, can allow the strategic selection of Ags to induce cellular immunity toward T. parva. In this study, we characterized the amino acids important for MHC class I binding and TCR recognition in the Tp967–75 epitope using alanine scanning and a series of variant peptide sequences to probe these interactions. In a peptide–MHC class I binding assay, we found that the amino acids at positions 1, 2, and 3 were critical for binding to its restricting MHC class I molecule BoLA-1*023:01. With IFN-γ ELISPOT and peptide–MHC class I Tet staining assays on two parasite-specific bovine CTL lines, we showed that amino acids at positions 5–8 in the epitope were required for TCR recognition. Only two of eight naturally occurring polymorphic Tp9 epitopes were recognized by both CTLs. Finally, using a TCR avidity assay, we found that a higher TCR avidity was associated with a stronger functional response toward one of two variants recognized by the CTL. These data add to the growing knowledge on the cross-reactivity of epitope-specific CTLs and specificities that may be required in the selection of Ags in the design of a wide-spectrum vaccine for East Coast fever.
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Affiliation(s)
- Nicholas Svitek
- International Livestock Research Institute, Animal and Human Health Program, Nairobi, Kenya; and
| | - Rosemary Saya
- International Livestock Research Institute, Animal and Human Health Program, Nairobi, Kenya; and
| | - Houshuang Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Minhang District, Shanghai, China
| | - Vishvanath Nene
- International Livestock Research Institute, Animal and Human Health Program, Nairobi, Kenya; and
| | - Lucilla Steinaa
- International Livestock Research Institute, Animal and Human Health Program, Nairobi, Kenya; and
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Abstract
The immune response elicited by vaccines against microorganisms makes it the most successful medical interventions against infectious diseases. Conventional vaccines have limitations in inducing immunity against many types of pathogenic microorganism. The genetic diversity of microorganisms, coupled with the high degree of sequence variability in antigenic proteins, presents a challenge to developing broadly effective conventional vaccines. Atomic-resolution structure determination is crucial for understanding antigenic protein function. Cryo-electron microscopy, nuclear magnetic resonance spectroscopy coupled with bioinformatics provide three-dimensional structure of the antigenic proteins and provide a wealth of information about the organization of individual atoms and their chemical makeup. The atomic detail information of proteins offers enormous potential to rationally engineer proteins to enhance their properties and act as effective immunogens to induce immunity. The observation that whole protein antigens are not necessarily essential for inducing immunity has led to the emergence "structural vaccinology." Structure-based vaccines are designed on the rationale that protective epitopes should be sufficient to induce immune responses and provide protection against pathogens. In 2013 we published a review on structure-based vaccines (Thomas and Luxon. Expert Rev Vaccines 12 1301-11, 2013). This review states the progress in development of structure-based vaccines since the first review.
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Affiliation(s)
- Sunil Thomas
- Lankenau Institute for Medical Research, Wynnewood, PA, USA.
| | - Ann Abraham
- Lankenau Institute for Medical Research, Wynnewood, PA, USA
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Designing a multi-epitope vaccine to provoke the robust immune response against influenza A H7N9. Sci Rep 2021; 11:24485. [PMID: 34966175 PMCID: PMC8716528 DOI: 10.1038/s41598-021-03932-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
A new strain of Influenza A Virus (IAV), so-called "H7N9 Avian Influenza", is the first strain of this virus in which a human is infected by transmitting the N9 of influenza virus. Although continuous human-to-human transmission has not been reported, the occurrence of various H7N9-associated epidemics and the lack of production of strong antibodies against H7N9 in humans warn of the potential for H7N9 to become a new pandemic. Therefore, the need for effective vaccination against H7N9 as a life-threatening viral pathogen has become a major concern. The current study reports the design of a multi-epitope vaccine against Hemagglutinin (HA) and Neuraminidase (NA) proteins of H7N9 Influenza A virus by prediction of Cytotoxic T lymphocyte (CTL), Helper T lymphocyte (HTL), IFN-γ and B-cell epitopes. Human β-defensin-3 (HβD-3) and pan HLA DR-binding epitope (PADRE) sequence were considered as adjuvant. EAAAK, AAY, GPGPG, HEYGAEALERAG, KK and RVRR linkers were used as a connector for epitopes. The final construct contained 777 amino acids that are expected to be a recombinant protein of about ~ 86.38 kDa with antigenic and non-allergenic properties after expression. Modeled protein analysis based on the tertiary structure validation, docking studies, and molecular dynamics simulations results like Root-mean-square deviation (RMSD), Gyration, Root-mean-square fluctuation (RMSF) and Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) showed that this protein has a stable construct and capable of being in interaction with Toll-like receptor 7 (TLR7), TLR8 and m826 antibody. Analysis of the obtained data the demonstrates that suggested vaccine has the potential to induce the immune response by stimulating T and Bcells, and may be utilizable for prevention purposes against Avian Influenza A (H7N9).
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Mugunthan SP, Harish MC. Multi-epitope-Based Vaccine Designed by Targeting Cytoadherence Proteins of Mycoplasma gallisepticum. ACS OMEGA 2021; 6:13742-13755. [PMID: 34095666 PMCID: PMC8173551 DOI: 10.1021/acsomega.1c01032] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/04/2021] [Indexed: 05/18/2023]
Abstract
Mycoplasma gallisepticum causes chronic respiratory disease in chickens leading to large economic losses in the poultry industry, and the impacts remain to be a great challenge for a longer period. Among the other approaches, a vaccine targeting the adhesion proteins of M. gallisepticum would be a promising candidate in controlling the infection. Thus, the present study is aimed to design a multi-epitope vaccine candidate using cytoadhesion proteins of M. gallisepticum through an advanced immunoinformatics approach. As a result, the multi-epitope vaccine was constructed, which comprised potential T-cell and B-cell binding epitopes with appropriate adjuvants. The designed multi-epitope vaccine represented high antigenicity with viable physiochemical properties. The prospective three-dimensional structure of the epitope was predicted, refined, and validated. The molecular docking analysis of multi-epitope vaccine candidates with the chicken Toll-like receptor-5 predicted effective binding. Furthermore, codon optimization and in silico cloning ensured high expression. Thus, the present finding indicates that the engineered multi-epitope vaccine is structurally stable and can induce a strong immune response. Furthermore, the multi-epitope vaccine is suggested to be a suitable vaccine candidate for the M. gallisepticum infection due to its effective binding capacity and precise specificity.
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Affiliation(s)
- Susithra Priyadarshni Mugunthan
- Plant Genetic Engineering and Molecular Farming Lab, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore 632115, Tamil Nadu, India
| | - Mani Chandra Harish
- Plant Genetic Engineering and Molecular Farming Lab, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore 632115, Tamil Nadu, India
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Liang C, Bencurova E, Psota E, Neurgaonkar P, Prelog M, Scheller C, Dandekar T. Population-Predicted MHC Class II Epitope Presentation of SARS-CoV-2 Structural Proteins Correlates to the Case Fatality Rates of COVID-19 in Different Countries. Int J Mol Sci 2021; 22:2630. [PMID: 33807854 PMCID: PMC7961590 DOI: 10.3390/ijms22052630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 12/22/2022] Open
Abstract
We observed substantial differences in predicted Major Histocompatibility Complex II (MHCII) epitope presentation of SARS-CoV-2 proteins for different populations but only minor differences in predicted MHCI epitope presentation. A comparison of this predicted epitope MHC-coverage revealed for the early phase of infection spread (till day 15 after reaching 128 observed infection cases) highly significant negative correlations with the case fatality rate. Specifically, this was observed in different populations for MHC class II presentation of the viral spike protein (p-value: 0.0733 for linear regression), the envelope protein (p-value: 0.023), and the membrane protein (p-value: 0.00053), indicating that the high case fatality rates of COVID-19 observed in some countries seem to be related with poor MHC class II presentation and hence weak adaptive immune response against these viral envelope proteins. Our results highlight the general importance of the SARS-CoV-2 structural proteins in immunological control in early infection spread looking at a global census in various countries and taking case fatality rate into account. Other factors such as health system and control measures become more important after the early spread. Our study should encourage further studies on MHCII alleles as potential risk factors in COVID-19 including assessment of local populations and specific allele distributions.
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Affiliation(s)
- Chunguang Liang
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (E.B.); (P.N.)
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (E.B.); (P.N.)
| | - Eric Psota
- Department of Pediatrics, Rheumatology and Special Immunology, University Hospital Würzburg, Pediatric Rheumatology/Special Immunology, Josef-Schneider-Str. 2, 97080 Würzburg, Germany; (E.P.); (M.P.)
| | - Priya Neurgaonkar
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (E.B.); (P.N.)
| | - Martina Prelog
- Department of Pediatrics, Rheumatology and Special Immunology, University Hospital Würzburg, Pediatric Rheumatology/Special Immunology, Josef-Schneider-Str. 2, 97080 Würzburg, Germany; (E.P.); (M.P.)
| | - Carsten Scheller
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (E.B.); (P.N.)
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Topham DJ, DeDiego ML, Nogales A, Sangster MY, Sant A. Immunity to Influenza Infection in Humans. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038729. [PMID: 31871226 PMCID: PMC7919402 DOI: 10.1101/cshperspect.a038729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review discusses the human immune responses to influenza infection with some insights from studies using animal models, such as experimental infection of mice. Recent technological advances in the study of human immune responses have greatly added to our knowledge of the infection and immune responses, and therefore much of the focus is on recent studies that have moved the field forward. We consider the complexity of the adaptive response generated by many sequential encounters through infection and vaccination.
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Affiliation(s)
- David J. Topham
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Marta L. DeDiego
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Madrid, Spain
| | - Aitor Nogales
- Instituto Nacional de Investigación y Tecnologia Agraria y Ailmentaria, 28040 Madrid, Spain
| | - Mark Y. Sangster
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Andrea Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
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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] [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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Kruiswijk C, Richard G, Salverda MLM, Hindocha P, Martin WD, De Groot AS, Van Riet E. In silico identification and modification of T cell epitopes in pertussis antigens associated with tolerance. Hum Vaccin Immunother 2020; 16:277-285. [PMID: 31951773 PMCID: PMC7062413 DOI: 10.1080/21645515.2019.1703453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The resurgence of whooping cough since the introduction of acellular (protein) vaccines has led to a renewed interest in the development of improved pertussis vaccines; Outer Membrane Vesicles (OMVs) carrying pertussis antigens have emerged as viable candidates. An in silico immunogenicity screen was carried out on 49 well-known Bordetella pertussis proteins in order to better understand their potential role toward the efficacy of pertussis OMVs for vaccine design; seven proteins were identified as being good candidates for including in optimized cellular and acellular pertussis vaccines. We then screened these antigens for putative tolerance-inducing sequences, as proteins with reduced tolerogenicity have improved vaccine potency in preclinical models. We used specialized homology tools (JanusMatrix) to identify peptides in the proteins that were cross-reactive with human sequences. Four of the 19 identified cross-reactive peptides were detolerized in silico using a separate tool, OptiMatrix, which disrupted the potential of these peptides to bind to human HLA and murine MHC. Four selected cross-reactive peptides and their detolerized variants were synthesized and their binding to a set of eight common HLA class II alleles was assessed in vitro. Reduced binding affinity to HLA class II was observed for the detolerized variants compared to the wild-type peptides, highlighting the potential of this approach for designing more efficacious pertussis vaccines.
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Affiliation(s)
- Corine Kruiswijk
- Department of Experimental Immunology & Clinical Research, Intravacc, Bilthoven, Netherlands
| | | | - Merijn L M Salverda
- Department of Experimental Immunology & Clinical Research, Intravacc, Bilthoven, Netherlands
| | | | | | | | - Elly Van Riet
- Department of Experimental Immunology & Clinical Research, Intravacc, Bilthoven, Netherlands
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