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Tarke A, Zhang Y, Methot N, Narowski TM, Phillips E, Mallal S, Frazier A, Filaci G, Weiskopf D, Dan JM, Premkumar L, Scheuermann RH, Sette A, Grifoni A. Targets and cross-reactivity of human T cell recognition of common cold coronaviruses. Cell Rep Med 2023; 4:101088. [PMID: 37295422 PMCID: PMC10242702 DOI: 10.1016/j.xcrm.2023.101088] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/17/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
The coronavirus (CoV) family includes several viruses infecting humans, highlighting the importance of exploring pan-CoV vaccine strategies to provide broad adaptive immune protection. We analyze T cell reactivity against representative Alpha (NL63) and Beta (OC43) common cold CoVs (CCCs) in pre-pandemic samples. S, N, M, and nsp3 antigens are immunodominant, as shown for severe acute respiratory syndrome 2 (SARS2), while nsp2 and nsp12 are Alpha or Beta specific. We further identify 78 OC43- and 87 NL63-specific epitopes, and, for a subset of those, we assess the T cell capability to cross-recognize sequences from representative viruses belonging to AlphaCoV, sarbecoCoV, and Beta-non-sarbecoCoV groups. We find T cell cross-reactivity within the Alpha and Beta groups, in 89% of the instances associated with sequence conservation >67%. However, despite conservation, limited cross-reactivity is observed for sarbecoCoV, indicating that previous CoV exposure is a contributing factor in determining cross-reactivity. Overall, these results provide critical insights in developing future pan-CoV vaccines.
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Affiliation(s)
- Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Experimental Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, 16132 Genoa, Italy
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Nils Methot
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Tara M Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Gilberto Filaci
- Center of Excellence for Biomedical Research, Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
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Tarke A, Zhang Y, Methot N, Narowski TM, Phillips E, Mallal S, Frazier A, Filaci G, Weiskopf D, Dan JM, Premkumar L, Scheuermann RH, Sette A, Grifoni A. Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522794. [PMID: 36656777 PMCID: PMC9844015 DOI: 10.1101/2023.01.04.522794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Coronavirus (CoV) family includes a variety of viruses able to infect humans. Endemic CoVs that can cause common cold belong to the alphaCoV and betaCoV genera, with the betaCoV genus also containing subgenera with zoonotic and pandemic concern, including sarbecoCoV (SARS-CoV and SARS-CoV-2) and merbecoCoV (MERS-CoV). It is therefore warranted to explore pan-CoV vaccine concepts, to provide adaptive immune protection against new potential CoV outbreaks, particularly in the context of betaCoV sub lineages. To explore the feasibility of eliciting CD4 + T cell responses widely cross-recognizing different CoVs, we utilized samples collected pre-pandemic to systematically analyze T cell reactivity against representative alpha (NL63) and beta (OC43) common cold CoVs (CCC). Similar to previous findings on SARS-CoV-2, the S, N, M, and nsp3 antigens were immunodominant for both viruses while nsp2 and nsp12 were immunodominant for NL63 and OC43, respectively. We next performed a comprehensive T cell epitope screen, identifying 78 OC43 and 87 NL63-specific epitopes. For a selected subset of 18 epitopes, we experimentally assessed the T cell capability to cross-recognize sequences from representative viruses belonging to alphaCoV, sarbecoCoV, and beta-non-sarbecoCoV groups. We found general conservation within the alpha and beta groups, with cross-reactivity experimentally detected in 89% of the instances associated with sequence conservation of >67%. However, despite sequence conservation, limited cross-reactivity was observed in the case of sarbecoCoV (50% of instances), indicating that previous CoV exposure to viruses phylogenetically closer to this subgenera is a contributing factor in determining cross-reactivity. Overall, these results provided critical insights in the development of future pan-CoV vaccines.
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Affiliation(s)
- Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Experimental Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, 16132, Italy
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Nils Methot
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Tara M. Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Gilberto Filaci
- Center of Excellence for Biomedical Research, Department of Internal Medicine, University of Genoa, Genoa 16132, Italy;,Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, Genoa 16132, Italy
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Pathology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA,These authors contributed equally
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA,These authors contributed equally
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,These authors contributed equally,Lead Contact
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Liu X, Zhao T, Wang L, Li M, Sun C, Shu Y. Strategies targeting hemagglutinin cocktail as a potential universal influenza vaccine. Front Microbiol 2022; 13:1014122. [PMID: 36246271 PMCID: PMC9558277 DOI: 10.3389/fmicb.2022.1014122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Vaccination is the most effective means of protecting people from influenza virus infection. The effectiveness of existing vaccines is very limited due to antigenic drift of the influenza virus. Therefore, there is a requirement to develop a universal vaccine that provides broad and long-lasting protection against influenza. CD8+ T-cell response played a vital role in controlling influenza virus infection, reducing viral load, and less clinical syndrome. In this study, we optimized the HA sequences of human seasonal influenza viruses (H1N1, H3N2, Victoria, and Yamagata) by designing multivalent vaccine antigen sets using a mosaic vaccine design strategy and genetic algorithms, and designed an HA mosaic cocktail containing the most potential CTL epitopes of seasonal influenza viruses. We then tested the recombinant mosaic antigen, which has a significant number of potential T-cell epitopes. Results from genetic evolutionary analyses and 3D structural simulations demonstrated its potential to be an effective immunogen. In addition, we have modified an existing neutralizing antibody-based seasonal influenza virus vaccine to include a component that activates cross-protective T cells, which would provide an attractive strategy for improving human protection against seasonal influenza virus drift and mutation and provide an idea for the development of a rationally designed influenza vaccine targeting T lymphocyte immunity.
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Affiliation(s)
- Xuejie Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Tianyi Zhao
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Liangliang Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Minchao Li
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yuelong Shu,
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Sette A, Saphire EO. Inducing broad-based immunity against viruses with pandemic potential. Immunity 2022; 55:738-748. [PMID: 35545026 DOI: 10.1016/j.immuni.2022.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 02/08/2023]
Abstract
The brutal toll of another viral pandemic can be blunted by investing now in research that uncovers mechanisms of broad-based immunity so we may have vaccines and therapeutics at the ready. We do not know exactly what pathogen may trigger the next wave or next pandemic. We do know, however, that the human immune system must respond and must be bolstered with effective vaccines and other therapeutics to preserve lives and livelihoods. These countermeasures must focus on features conserved among families of pathogens in order to be responsive against something yet to emerge. Here, we focus on immunological approaches to mitigate the impact of the next emerging virus pandemic by developing vaccines that elicit both broadly protective antibodies and T cells. Identifying human immune mechanisms of broad protection against virus families with pandemic potential will be our best defense for humanity in the future.
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Affiliation(s)
- Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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Hensen L, Illing PT, Rowntree LC, Davies J, Miller A, Tong SYC, Habel JR, van de Sandt CE, Flanagan K, Purcell AW, Kedzierska K, Clemens EB. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Front Immunol 2022; 13:812393. [PMID: 35603215 PMCID: PMC9121770 DOI: 10.3389/fimmu.2022.812393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells are a pivotal part of the immune response to viruses, playing a key role in disease outcome and providing long-lasting immunity to conserved pathogen epitopes. Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different HLA allotypes across different ethnicities. Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses. We describe an immunopeptidomics approach to sequence HLA-bound peptides presented on virus-infected cells by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using antigen presenting cell lines that stably express the HLA alleles characteristic of Indigenous Australians, this approach has been successfully used to comprehensively identify influenza-specific CD8+ T cell epitopes restricted by HLA allotypes predominant in Indigenous Australians, including HLA-A*24:02 and HLA-A*11:01. This is an essential step in ensuring high vaccine coverage and efficacy in Indigenous populations globally, known to be at high risk from influenza disease and other respiratory infections.
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Affiliation(s)
- Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T. Illing
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C. Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jane Davies
- Menzies School of Health Research, Darwin, NT, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, QLD, Australia
| | - Steven Y. C. Tong
- Menzies School of Health Research, Darwin, NT, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer R. Habel
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Katie L. Flanagan
- Department of Infectious Diseases and Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- *Correspondence: Katherine Kedzierska,
| | - E. Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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HLA-A*11:01-restricted CD8+ T cell immunity against influenza A and influenza B viruses in Indigenous and non-Indigenous people. PLoS Pathog 2022; 18:e1010337. [PMID: 35255101 PMCID: PMC8929706 DOI: 10.1371/journal.ppat.1010337] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/17/2022] [Accepted: 02/03/2022] [Indexed: 11/19/2022] Open
Abstract
HLA-A*11:01 is one of the most prevalent human leukocyte antigens (HLAs), especially in East Asian and Oceanian populations. It is also highly expressed in Indigenous people who are at high risk of severe influenza disease. As CD8+ T cells can provide broadly cross-reactive immunity to distinct influenza strains and subtypes, including influenza A, B and C viruses, understanding CD8+ T cell immunity to influenza viruses across prominent HLA types is needed to rationally design a universal influenza vaccine and generate protective immunity especially for high-risk populations. As only a handful of HLA-A*11:01-restricted CD8+ T cell epitopes have been described for influenza A viruses (IAVs) and epitopes for influenza B viruses (IBVs) were still unknown, we embarked on an epitope discovery study to define a CD8+ T cell landscape for HLA-A*11:01-expressing Indigenous and non-Indigenous Australian people. Using mass-spectrometry, we identified IAV- and IBV-derived peptides presented by HLA-A*11:01 during infection. 79 IAV and 57 IBV peptides were subsequently screened for immunogenicity in vitro with peripheral blood mononuclear cells from HLA-A*11:01-expressing Indigenous and non-Indigenous Australian donors. CD8+ T cell immunogenicity screening revealed two immunogenic IAV epitopes (A11/PB2320-331 and A11/PB2323-331) and the first HLA-A*11:01-restricted IBV epitopes (A11/M41-49, A11/NS1186-195 and A11/NP511-520). The immunogenic IAV- and IBV-derived peptides were >90% conserved among their respective influenza viruses. Identification of novel immunogenic HLA-A*11:01-restricted CD8+ T cell epitopes has implications for understanding how CD8+ T cell immunity is generated towards IAVs and IBVs. These findings can inform the development of rationally designed, broadly cross-reactive influenza vaccines to ensure protection from severe influenza disease in HLA-A*11:01-expressing individuals. Influenza A and influenza B viral infections cause significant morbidity and mortality. Established CD8+ T cell immunity directed at conserved viral regions provides protection against influenza viruses, drives rapid recovery, and leads to less severe clinical outcomes. Killer CD8+ T cells recognising viral peptides presented by HLA class I glycoproteins can provide broad immunity across distinct influenza strains and subtypes. Using immunopeptidomics, we identified novel CD8+ T cell targets for influenza A and influenza B viruses in the context of HLA-A*11:01, an HLA-I allomorph highly prevalent in East Asia and Oceania, including Indigenous populations. Our study provides key insights for T cell-directed vaccines and immunotherapies.
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Takagi A, Matsui M. Identification of HLA-A*24:02-Restricted CTL Candidate Epitopes Derived from the Nonstructural Polyprotein 1a of SARS-CoV-2 and Analysis of Their Conservation Using the Mutation Database of SARS-CoV-2 Variants. Microbiol Spectr 2021; 9:e0165921. [PMID: 34937174 PMCID: PMC8694169 DOI: 10.1128/spectrum.01659-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/24/2021] [Indexed: 01/11/2023] Open
Abstract
COVID-19 vaccines are currently being administered worldwide and playing a critical role in controlling the pandemic. They have been designed to elicit neutralizing antibodies against Spike protein of the original SARS-CoV-2, and hence they are less effective against SARS-CoV-2 variants with mutated Spike than the original virus. It is possible that novel variants with abilities of enhanced transmissibility and/or immunoevasion will appear in the near future and perfectly escape from vaccine-elicited immunity. Therefore, the current vaccines may need to be improved to compensate for the viral evolution. For this purpose, it may be beneficial to take advantage of CD8+ cytotoxic T lymphocytes (CTLs). Several lines of evidence suggest the contribution of CTLs on the viral control in COVID-19, and CTLs target a wide range of proteins involving comparatively conserved nonstructural proteins. Here, we identified 22 HLA-A*24:02-restricted CTL candidate epitopes derived from the nonstructural polyprotein 1a (pp1a) of SARS-CoV-2 using computational algorithms, HLA-A*24:02 transgenic mice and the peptide-encapsulated liposomes. We focused on pp1a and HLA-A*24:02 because pp1a is relatively conserved and HLA-A*24:02 is predominant in East Asians such as Japanese. The conservation analysis revealed that the amino acid sequences of 7 out of the 22 epitopes were hardly affected by a number of mutations in the Sequence Read Archive database of SARS-CoV-2 variants. The information of such conserved epitopes might be useful for designing the next-generation COVID-19 vaccine that is universally effective against any SARS-CoV-2 variants by the induction of both anti-Spike neutralizing antibodies and CTLs specific for conserved epitopes. IMPORTANCE COVID-19 vaccines have been designed to elicit neutralizing antibodies against the Spike protein of the original SARS-CoV-2, and hence they are less effective against variants. It is possible that novel variants will appear and escape from vaccine-elicited immunity. Therefore, the current vaccines may need to be improved to compensate for the viral evolution. For this purpose, it may be beneficial to take advantage of CD8+ cytotoxic T lymphocytes (CTLs). Here, we identified 22 HLA-A*24:02-restricted CTL candidate epitopes derived from the nonstructural polyprotein 1a (pp1a) of SARS-CoV-2. We focused on pp1a and HLA-A*24:02 because pp1a is conserved and HLA-A*24:02 is predominant in East Asians. The conservation analysis revealed that the amino acid sequences of 7 out of the 22 epitopes were hardly affected by mutations in the database of SARS-CoV-2 variants. The information might be useful for designing the next-generation COVID-19 vaccine that is universally effective against any variants.
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Affiliation(s)
- Akira Takagi
- School of Medical Technology, Faculty of Health and Medical Care, Saitama Medical University, Yamane, Hidaka-city, Saitama, Japan
| | - Masanori Matsui
- Department of Microbiology, Faculty of Medicine, Saitama Medical University, Morohongo, Moroyama-cho, Iruma-gun, Saitama, Japan
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Broad-Based Influenza-Specific CD8 + T Cell Response without the Typical Immunodominance Hierarchy and Its Potential Implication. Viruses 2021; 13:v13061080. [PMID: 34198851 PMCID: PMC8229067 DOI: 10.3390/v13061080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Syngeneic murine systems have pre-fixed MHC, making them an imperfect model for investigating the impact of MHC polymorphism on immunodominance in influenza A virus (IAV) infections. To date, there are few studies focusing on MHC allelic differences and its impact on immunodominance even though it is well documented that an individual’s HLA plays a significant role in determining immunodominance hierarchy. Here, we describe a broad-based CD8+ T cell response in a healthy individual to IAV infection rather than a typical immunodominance hierarchy. We used a systematic antigen screen approach combined with epitope prediction to study such a broad CD8+ T cell response to IAV infection. We show CD8+ T cell responses to nine IAV proteins and identify their minimal epitope sequences. These epitopes are restricted to HLA-B*44:03, HLA-A*24:02 and HLA-A*33:03 and seven out of the nine epitopes are novel (NP319–330# (known and demonstrated minimal epitope positions are subscripted; otherwise, amino acid positions are shown as normal text (for example NP 319–330 or NP 313–330)), M1124–134, M27–15, NA337–346, PB239–49, HA445–453 and NS1195–203). Additionally, most of these novel epitopes are highly conserved among H1N1 and H3N2 strains that circulated in Australia and other parts of the world.
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9
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CD8 + T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph. Nat Commun 2021; 12:2931. [PMID: 34006841 PMCID: PMC8132304 DOI: 10.1038/s41467-021-23212-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/19/2021] [Indexed: 02/03/2023] Open
Abstract
Indigenous people worldwide are at high risk of developing severe influenza disease. HLA-A*24:02 allele, highly prevalent in Indigenous populations, is associated with influenza-induced mortality, although the basis for this association is unclear. Here, we define CD8+ T-cell immune landscapes against influenza A (IAV) and B (IBV) viruses in HLA-A*24:02-expressing Indigenous and non-Indigenous individuals, human tissues, influenza-infected patients and HLA-A*24:02-transgenic mice. We identify immunodominant protective CD8+ T-cell epitopes, one towards IAV and six towards IBV, with A24/PB2550-558-specific CD8+ T cells being cross-reactive between IAV and IBV. Memory CD8+ T cells towards these specificities are present in blood (CD27+CD45RA- phenotype) and tissues (CD103+CD69+ phenotype) of healthy individuals, and effector CD27-CD45RA-PD-1+CD38+CD8+ T cells in IAV/IBV patients. Our data show influenza-specific CD8+ T-cell responses in Indigenous Australians, and advocate for T-cell-mediated vaccines that target and boost the breadth of IAV/IBV-specific CD8+ T cells to protect high-risk HLA-A*24:02-expressing Indigenous and non-Indigenous populations from severe influenza disease.
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Nainu F, Abidin RS, Bahar MA, Frediansyah A, Emran TB, Rabaan AA, Dhama K, Harapan H. SARS-CoV-2 reinfection and implications for vaccine development. Hum Vaccin Immunother 2020; 16:3061-3073. [PMID: 33393854 PMCID: PMC8641611 DOI: 10.1080/21645515.2020.1830683] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/07/2020] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic continues to constitute a public health emergency of international concern. Multiple vaccine candidates for COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have entered clinical trials. However, some evidence suggests that patients who have recovered from COVID-19 can be reinfected. For example, in China, two discharged COVID-19 patients who had recovered and fulfilled the discharge criteria for COVID-19 were retested positive to a reverse transcription polymerase chain reaction (RT-PCR) assay for the virus. This finding is critical and could hamper COVID-19 vaccine development. This review offers literature-based evidence of reinfection with SARS-CoV-2, provides explanation for the possibility of SARS-CoV-2 reinfection both from the agent and host points of view, and discusses its implication for COVID-19 vaccine development.
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Affiliation(s)
- Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, 90245, Tamalanrea, Makassar, Indonesia
| | - Rufika Shari Abidin
- Faculty of Medicine, Hasanuddin University, 90245, Tamalanrea, Makassar, Indonesia
| | - Muh. Akbar Bahar
- Faculty of Pharmacy, Hasanuddin University, 90245, Tamalanrea, Makassar, Indonesia
| | - Andri Frediansyah
- Research Division for Natural Product Technology (BPTBA), Indonesian Institute of Sciences (LIPI), 55861, Wonosari, Indonesia
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, 72076, Tübingen, Germany
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, 4381, Chittagong, Bangladesh
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, 243122, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, 23111, Banda Aceh, Indonesia
- Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, 23111, Banda Aceh, Indonesia
- Department of Microbiology, School of Medicine, Universitas Syiah Kuala, 23111, Banda Aceh, Indonesia
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11
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Koutsakos M, Illing PT, Nguyen THO, Mifsud NA, Crawford JC, Rizzetto S, Eltahla AA, Clemens EB, Sant S, Chua BY, Wong CY, Allen EK, Teng D, Dash P, Boyd DF, Grzelak L, Zeng W, Hurt AC, Barr I, Rockman S, Jackson DC, Kotsimbos TC, Cheng AC, Richards M, Westall GP, Loudovaris T, Mannering SI, Elliott M, Tangye SG, Wakim LM, Rossjohn J, Vijaykrishna D, Luciani F, Thomas PG, Gras S, Purcell AW, Kedzierska K. Human CD8 + T cell cross-reactivity across influenza A, B and C viruses. Nat Immunol 2019; 20:613-625. [PMID: 30778243 DOI: 10.1038/s41590-019-0320-6] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Influenza A, B and C viruses (IAV, IBV and ICV, respectively) circulate globally and infect humans, with IAV and IBV causing the most severe disease. CD8+ T cells confer cross-protection against IAV strains, however the responses of CD8+ T cells to IBV and ICV are understudied. We investigated the breadth of CD8+ T cell cross-recognition and provide evidence of CD8+ T cell cross-reactivity across IAV, IBV and ICV. We identified immunodominant CD8+ T cell epitopes from IBVs that were protective in mice and found memory CD8+ T cells directed against universal and influenza-virus-type-specific epitopes in the blood and lungs of healthy humans. Lung-derived CD8+ T cells displayed tissue-resident memory phenotypes. Notably, CD38+Ki67+CD8+ effector T cells directed against novel epitopes were readily detected in IAV- or IBV-infected pediatric and adult subjects. Our study introduces a new paradigm whereby CD8+ T cells confer unprecedented cross-reactivity across all influenza viruses, a key finding for the design of universal vaccines.
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Affiliation(s)
- Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Patricia T Illing
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Simone Rizzetto
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Auda A Eltahla
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Chinn Yi Wong
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - E Kaitlynn Allen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Don Teng
- Infection and Immunity Program & Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David F Boyd
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ludivine Grzelak
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Biology Department, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, Cachan, France
| | - Weiguang Zeng
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Aeron C Hurt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ian Barr
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Applied Biomedical Sciences, Federation University, Churchill, Victoria, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Seqirus, Parkville, Victoria, Australia
| | - David C Jackson
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tom C Kotsimbos
- Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Central Clinical School, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Michael Richards
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Glen P Westall
- Lung Transplant Unit, Alfred Hospital, Melbourne, Victoria, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | | | - Michael Elliott
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Chris O'Brien Lifehouse Cancer Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Dhanasekaran Vijaykrishna
- Infection and Immunity Program & Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephanie Gras
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
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12
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Vaccination potential of B and T epitope-enriched NP and M2 against Influenza A viruses from different clades and hosts. PLoS One 2018; 13:e0191574. [PMID: 29377916 PMCID: PMC5788337 DOI: 10.1371/journal.pone.0191574] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 01/08/2018] [Indexed: 12/30/2022] Open
Abstract
To avoid outbreaks of influenza virus epidemics and pandemics among human populations, modern medicine requires the development of new universal vaccines that are able to provide protection from a wide range of influenza A virus strains. In the course of development of a universal vaccine, it is necessary to consider that immunity must be generated even against viruses from different hosts because new human epidemic virus strains have their origins in viruses of birds and other animals. We have enriched conserved viral proteins–nucleoprotein (NP) and matrix protein 2 (M2)—by B and T-cell epitopes not only human origin but also swine and avian origin. For this purpose, we analyzed M2 and NP sequences with respect to changes in the sequences of known T and B-cell epitopes and chose conserved and evolutionarily significant epitopes. Eventually, we found consensus sequences of M2 and NP that have the maximum quantity of epitopes that are 100% coincident with them. Consensus epitope-enriched amino acid sequences of M2 and NP proteins were included in a recombinant adenoviral vector. Immunization with Ad5-tet-M2NP induced strong CD8 and CD4 T cells responses, specific to each of the encoded antigens, i.e. M2 and NP. Eight months after immunization with Ad5-tet-M2NP, high numbers of M2- and NP-responding “effector memory” CD44posCD62neg T cells were found in the mouse spleens, which revealed a long-term T cell immune memory conferred by the immunization. In all, the challenge experiments showed an extraordinarily wide-ranging efficacy of protection by the Ad5-tet-M2NP vaccine, covering 5 different heterosubtypes of influenza A virus (2 human, 2 avian and 1 swine).
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Korenkov D, Nguyen THO, Isakova-Sivak I, Smolonogina T, Brown LE, Kedzierska K, Rudenko L. Live Attenuated Influenza Vaccines engineered to express the nucleoprotein of a recent isolate stimulate human influenza CD8 + T cells more relevant to current infections. Hum Vaccin Immunother 2018; 14:941-946. [PMID: 29252117 DOI: 10.1080/21645515.2017.1417713] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Live attenuated influenza vaccines (LAIV) induce CD8+ T lymphocyte responses that play an important role in killing virus-infected cells. Despite the relative conservation of internal influenza A proteins, the epitopes recognized by T cells can undergo drift under immune pressure. The internal proteins of Russian LAIVs are derived from the master donor virus A/Leningrad/134/17/57 (Len/17) isolated 60 years ago and as such, some CD8+ T cell epitopes may vary between the vaccine and circulating wild-type strains. To partially overcome this issue, the nucleoprotein (NP) gene of wild-type virus can be incorporated into LAIV reassortant virus, along with the HA and NA genes. The present study compares the human CD8+ T cell memory responses to H3N2 LAIVs with the Len/17 or the wild-type NP using an in vitro model.
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Affiliation(s)
- D Korenkov
- a Department of Virology , Institute of Experimental Medicine , Saint Petersburg , Russia.,b Department of Microbiology & Immunology , University of Melbourne, at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - T H O Nguyen
- b Department of Microbiology & Immunology , University of Melbourne, at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - I Isakova-Sivak
- a Department of Virology , Institute of Experimental Medicine , Saint Petersburg , Russia
| | - T Smolonogina
- a Department of Virology , Institute of Experimental Medicine , Saint Petersburg , Russia
| | - L E Brown
- b Department of Microbiology & Immunology , University of Melbourne, at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - K Kedzierska
- b Department of Microbiology & Immunology , University of Melbourne, at The Peter Doherty Institute for Infection & Immunity , Melbourne , VIC , Australia
| | - L Rudenko
- a Department of Virology , Institute of Experimental Medicine , Saint Petersburg , Russia
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14
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Bloom JD. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct 2017; 12:1. [PMID: 28095902 PMCID: PMC5240389 DOI: 10.1186/s13062-016-0172-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022] Open
Abstract
Background Sites of positive selection are identified by comparing observed evolutionary patterns to those expected under a null model for evolution in the absence of such selection. For protein-coding genes, the most common null model is that nonsynonymous and synonymous mutations fix at equal rates; this unrealistic model has limited power to detect many interesting forms of selection. Results I describe a new approach that uses a null model based on experimental measurements of a gene’s site-specific amino-acid preferences generated by deep mutational scanning in the lab. This null model makes it possible to identify both diversifying selection for repeated amino-acid change and differential selection for mutations to amino acids that are unexpected given the measurements made in the lab. I show that this approach identifies sites of adaptive substitutions in four genes (lactamase, Gal4, influenza nucleoprotein, and influenza hemagglutinin) far better than a comparable method that simply compares the rates of nonsynonymous and synonymous substitutions. Conclusions As rapid increases in biological data enable increasingly nuanced descriptions of the constraints on individual protein sites, approaches like the one here can improve our ability to identify many interesting forms of selection in natural sequences. Reviewers This article was reviewed by Sebastian Maurer-Stroh, Olivier Tenaillon, and Tal Pupko. All three reviewers are members of the Biology Direct editorial board. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0172-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, 98109, WA, USA.
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15
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Di Mario G, Sciaraffia E, Facchini M, Gubinelli F, Soprana E, Panigada M, Bernasconi V, Garulli B, Siccardi A, Donatelli I, Castrucci MR. Protective immunity against influenza in HLA-A2 transgenic mice by modified vaccinia virus Ankara vectored vaccines containing internal influenza proteins. Pathog Glob Health 2017; 111:76-82. [PMID: 28079473 PMCID: PMC5375616 DOI: 10.1080/20477724.2016.1275465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The emergence of novel strains of influenza A viruses with hemagglutinins (HAs) that are antigenically distinct from those circulating in humans, and thus have pandemic potential, pose concerns and call for the development of more broadly protective influenza vaccines. In the present study, modified vaccinia virus Ankara (MVA) encoding internal influenza antigens were evaluated for their immunogenicity and ability to protect HLA-A2.1 transgenic (AAD) mice from infection with influenza viruses. METHODS MVAs expressing NP (MVA-NP), M1 (MVA-M1) or polymerase PB1 (MVA-PB1) of A/California/4/09 (CA/09) virus were generated and used to immunize AAD mice. Antibodies and CD8+T cell responses were assessed by ELISA and ELISPOT, respectively, and challenge experiments were performed by infecting vaccinated mice with CA/09 virus. RESULTS CD8+T cells specific to immunodominant and subdominant epitopes on the internal influenza proteins were elicited by MVA-based vectors in AAD mice, whereas influenza-specific antibodies were detected only in MVA-NP-immunized mice. Both M1- and NP-based MVA vaccines, regardless of whether they were applied individually or in combination, conferred protection against lethal influenza virus challenge. CONCLUSION Our data further emphasize the promising potential of MVA vector expressing internal antigens toward the development of a universal influenza vaccine.
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Affiliation(s)
- Giuseppina Di Mario
- a Department of Infectious Diseases , Istituto Superiore di Sanità , Rome , Italy
| | - Ester Sciaraffia
- a Department of Infectious Diseases , Istituto Superiore di Sanità , Rome , Italy
| | - Marzia Facchini
- a Department of Infectious Diseases , Istituto Superiore di Sanità , Rome , Italy
| | - Francesco Gubinelli
- b Molecular Immunology Unit , San Raffaele Research Institute , Milan , Italy
| | - Elisa Soprana
- b Molecular Immunology Unit , San Raffaele Research Institute , Milan , Italy
| | - Maddalena Panigada
- b Molecular Immunology Unit , San Raffaele Research Institute , Milan , Italy
| | | | - Bruno Garulli
- c Department of Biology and Biotechnology "Charles Darwin" , Sapienza University of Rome , Rome , Italy
| | - Antonio Siccardi
- b Molecular Immunology Unit , San Raffaele Research Institute , Milan , Italy
| | - Isabella Donatelli
- a Department of Infectious Diseases , Istituto Superiore di Sanità , Rome , Italy
| | - Maria R Castrucci
- a Department of Infectious Diseases , Istituto Superiore di Sanità , Rome , Italy
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16
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Sheikh QM, Gatherer D, Reche PA, Flower DR. Towards the knowledge-based design of universal influenza epitope ensemble vaccines. Bioinformatics 2016; 32:3233-3239. [PMID: 27402904 PMCID: PMC5079473 DOI: 10.1093/bioinformatics/btw399] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/14/2016] [Accepted: 06/18/2016] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes. RESULTS To exemplify our approach we designed two epitope ensemble vaccines comprising highly conserved and experimentally verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96 and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97 and 88% coverage of observed subtypes. AVAILABILITY AND IMPLEMENTATION http://imed.med.ucm.es/Tools/episopt.html CONTACT: d.r.flower@aston.ac.uk.
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Affiliation(s)
- Qamar M Sheikh
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster LA1 4YW, UK
| | - Pedro A Reche
- Facultad de Medicina, Departamento de Microbiologia I, Universidad Complutense de Madrid, Madrid, Spain
| | - Darren R Flower
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
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17
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Moise L, Gutierrez A, Kibria F, Martin R, Tassone R, Liu R, Terry F, Martin B, De Groot AS. iVAX: An integrated toolkit for the selection and optimization of antigens and the design of epitope-driven vaccines. Hum Vaccin Immunother 2016; 11:2312-21. [PMID: 26155959 PMCID: PMC4635942 DOI: 10.1080/21645515.2015.1061159] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Computational vaccine design, also known as computational vaccinology, encompasses epitope mapping, antigen selection and immunogen design using computational tools. The iVAX toolkit is an integrated set of tools that has been in development since 1998 by De Groot and Martin. It comprises a suite of immunoinformatics algorithms for triaging candidate antigens, selecting immunogenic and conserved T cell epitopes, eliminating regulatory T cell epitopes, and optimizing antigens for immunogenicity and protection against disease. iVAX has been applied to vaccine development programs for emerging infectious diseases, cancer antigens and biodefense targets. Several iVAX vaccine design projects have had success in pre-clinical studies in animal models and are progressing toward clinical studies. The toolkit now incorporates a range of immunoinformatics tools for infectious disease and cancer immunotherapy vaccine design. This article will provide a guide to the iVAX approach to computational vaccinology.
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Affiliation(s)
- Leonard Moise
- a Institute for Immunology and Informatics; University of Rhode Island ; Providence , RI USA
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18
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Grant EJ, Quiñones-Parra SM, Clemens EB, Kedzierska K. Human influenza viruses and CD8(+) T cell responses. Curr Opin Virol 2016; 16:132-142. [PMID: 26974887 DOI: 10.1016/j.coviro.2016.01.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 12/19/2022]
Abstract
Influenza A viruses (IAVs) cause significant morbidity and mortality worldwide, despite new strain-specific vaccines being available annually. As IAV-specific CD8(+) T cells promote viral control in the absence of neutralizing antibodies, and can mediate cross-reactive immunity toward distinct IAVs to drive rapid recovery from both mild and severe influenza disease, there is great interest in developing a universal T cell vaccine. However, despite detailed studies in mouse models of influenza virus infection, there is still a paucity of data on human epitope-specific CD8(+) T cell responses to IAVs. This review focuses on our current understanding of human CD8(+) T cell immunity against distinct IAVs and discusses the possibility of achieving a CD8(+) T cell mediated-vaccine that protects against multiple, distinct IAV strains across diverse human populations. We also review the importance of CD8(+) T cell immunity in individuals highly susceptible to severe influenza infection, including those hospitalised with influenza, the elderly and Indigenous populations.
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Affiliation(s)
- Emma J Grant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sergio M Quiñones-Parra
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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Xiang K, Ying G, Yan Z, Shanshan Y, Lei Z, Hongjun L, Maosheng S. Progress on adenovirus-vectored universal influenza vaccines. Hum Vaccin Immunother 2016; 11:1209-22. [PMID: 25876176 DOI: 10.1080/21645515.2015.1016674] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Influenza virus (IFV) infection causes serious health problems and heavy financial burdens each year worldwide. The classical inactivated influenza virus vaccine (IIVV) and live attenuated influenza vaccine (LAIV) must be updated regularly to match the new strains that evolve due to antigenic drift and antigenic shift. However, with the discovery of broadly neutralizing antibodies that recognize conserved antigens, and the CD8(+) T cell responses targeting viral internal proteins nucleoprotein (NP), matrix protein 1 (M1) and polymerase basic 1 (PB1), it is possible to develop a universal influenza vaccine based on the conserved hemagglutinin (HA) stem, NP, and matrix proteins. Recombinant adenovirus (rAd) is an ideal influenza vaccine vector because it has an ideal stability and safety profile, induces balanced humoral and cell-mediated immune responses due to activation of innate immunity, provides 'self-adjuvanting' activity, can mimic natural IFV infection, and confers seamless protection against mucosal pathogens. Moreover, this vector can be developed as a low-cost, rapid-response vaccine that can be quickly manufactured. Therefore, an adenovirus vector encoding conserved influenza antigens holds promise in the development of a universal influenza vaccine. This review will summarize the progress in adenovirus-vectored universal flu vaccines and discuss future novel approaches.
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Key Words
- ADCC, antibody-dependent cell-mediated cytotoxicity
- APC, antigen-presenting cell
- Ad: adenovirus
- CAR, Coxsackie-Adenovirus Receptor
- CTLs, cytotoxic T lymphocytes
- DC, lung dendritic cells
- DVD, drug–vaccine duo
- FcγRs, Fc receptors for IgG
- HA, hemagglutinin
- HDAd, helper-dependent adenoviral
- HEK293, human embryonic kidney 293 cell
- HI, hemagglutination inhibition
- HLA, human leukocyte antigen
- IF-γ, interferon-γ
- IFV, Influenza virus
- IIVV, inactivated influenza virus vaccine
- IL-2, interleukin-2
- ITRs, inverted terminal repeats
- LAIV, live attenuated influenza vaccine
- M1, matrix protein 1
- M2, matrix protein 2
- MHC-I, major histocompatibility complex class I
- NA, neuraminidase
- NP, nucleoprotein
- RCA, replication competent adenovirus
- VAERD, vaccine-associated enhanced respiratory disease
- adenovirus vector
- broadly neutralizing antibodies
- cellular immunity
- flu, influenza
- hemagglutinin
- humoral immunity
- influenza
- mAbs, monoclonal antibodies
- mucosal immunity
- rAd, recombinant adenovirus
- universal vaccine
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Affiliation(s)
- Kui Xiang
- a Department of Molecular Biology; Institute of Medical Biology; Chinese Academy of Medical Sciences; Peking Union Medical College ; Kunming , Yunnan , PR China
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Abstract
The development of vaccines that could provide broad protection against antigenically variant influenza viruses has long been the ultimate prize in influenza research. Recent developments have pushed us closer to this goal, and such vaccines may now be within reach. This brief review outlines the current approaches to broadly protective vaccines, and the probable hurdles and roadblocks to achieving this goal.
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Affiliation(s)
- John Jay Treanor
- Department of Medicine, University of Rochester School of Medicine and Dentistry, Box 689, 601 Elmwood Avenue, Rochester, NY 14642, United States.
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21
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Prospects for broadly protective influenza vaccines. Vaccine 2015; 33 Suppl 4:D39-45. [DOI: 10.1016/j.vaccine.2015.08.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/02/2015] [Accepted: 08/03/2015] [Indexed: 12/14/2022]
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Abidin RS, Lua LHL, Middelberg APJ, Sainsbury F. Insert engineering and solubility screening improves recovery of virus-like particle subunits displaying hydrophobic epitopes. Protein Sci 2015; 24:1820-8. [PMID: 26401641 DOI: 10.1002/pro.2775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/20/2015] [Indexed: 11/09/2022]
Abstract
The Polyomavirus coat protein, VP1 has been developed as an epitope presentation system able to provoke humoral immunity against a variety of pathogens, such as Influenza and Group A Streptococcus. The ability of the system to carry cytotoxic T cell epitopes on a surface-exposed loop and the impact on protein solubility has not been examined. Four variations of three selected epitopes were cloned into surface-exposed loops of VP1, and expressed in Escherichia coli. VP1 pentamers, also known as capsomeres, were purified via a glutathione-S-transferase tag. Size exclusion chromatography indicated severe aggregation of the recombinant VP1 during enzymatic tag removal resulting from the introduction the hydrophobic epitopes. Inserts were modified to possess double aspartic acid residues at each end of the hydrophobic epitopes and a high-throughput buffer condition screen was implemented with protein aggregation monitored during tag removal by spectrophotometry and dynamic light scattering. These analyses showed that the insertion of charged residues at the extremities of epitopes could improve solubility of capsomeres and revealed multiple windows of opportunity for further condition optimization. A combination of epitope design, pH optimization, and the additive l-arginine permitted the recovery of soluble VP1 pentamers presenting hydrophobic epitopes and their subsequent assembly into virus-like particles.
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Affiliation(s)
- R S Abidin
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
| | - L H L Lua
- Protein Expression Facility, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - A P J Middelberg
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
| | - F Sainsbury
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology Centre for Biomolecular Engineering, St Lucia, Queensland, 4072, Australia
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Rosendahl Huber SK, Camps MGM, Jacobi RHJ, Mouthaan J, van Dijken H, van Beek J, Ossendorp F, de Jonge J. Synthetic Long Peptide Influenza Vaccine Containing Conserved T and B Cell Epitopes Reduces Viral Load in Lungs of Mice and Ferrets. PLoS One 2015; 10:e0127969. [PMID: 26046664 PMCID: PMC4457525 DOI: 10.1371/journal.pone.0127969] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/22/2015] [Indexed: 12/22/2022] Open
Abstract
Currently licensed influenza vaccines mainly induce antibodies against highly variable epitopes. Due to antigenic drift, protection is subtype or strain-specific and regular vaccine updates are required. In case of antigenic shifts, which have caused several pandemics in the past, completely new vaccines need to be developed. We set out to develop a vaccine that provides protection against a broad range of influenza viruses. Therefore, highly conserved parts of the influenza A virus (IAV) were selected of which we constructed antibody and T cell inducing peptide-based vaccines. The B epitope vaccine consists of the highly conserved HA2 fusion peptide and M2e peptide coupled to a CD4 helper epitope. The T epitope vaccine comprises 25 overlapping synthetic long peptides of 26-34 amino acids, thereby avoiding restriction for a certain MHC haplotype. These peptides are derived from nucleoprotein (NP), polymerase basic protein 1 (PB1) and matrix protein 1 (M1). C57BL/6 mice, BALB/c mice, and ferrets were vaccinated with the B epitopes, 25 SLP or a combination of both. Vaccine-specific antibodies were detected in sera of mice and ferrets and vaccine-specific cellular responses were measured in mice. Following challenge, both mice and ferrets showed a reduction of virus titers in the lungs in response to vaccination. Summarizing, a peptide-based vaccine directed against conserved parts of influenza virus containing B and T cell epitopes shows promising results for further development. Such a vaccine may reduce disease burden and virus transmission during pandemic outbreaks.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Viral/immunology
- Databases, Factual
- Dogs
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/immunology
- Female
- Ferrets
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza A Virus, H5N1 Subtype/metabolism
- Influenza Vaccines/immunology
- Lung/virology
- Madin Darby Canine Kidney Cells
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Molecular Sequence Data
- Vaccines, Subunit/chemical synthesis
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
- Viral Load
- Viral Matrix Proteins/chemistry
- Viral Matrix Proteins/immunology
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Affiliation(s)
- S. K. Rosendahl Huber
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - M. G. M. Camps
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - R. H. J. Jacobi
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - J. Mouthaan
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - H. van Dijken
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - J. van Beek
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - F. Ossendorp
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - J. de Jonge
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- * E-mail:
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24
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Adaptive evolution of a novel avian-origin influenza A/H7N9 virus. Genomics 2014; 104:545-53. [PMID: 25449177 DOI: 10.1016/j.ygeno.2014.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 10/25/2014] [Accepted: 10/29/2014] [Indexed: 11/21/2022]
Abstract
In China, the recent outbreak of novel influenza A/H7N9 virus has been assumed to be severe, and it may possibly turn brutal in the near future. In order to develop highly protective vaccines and drugs for the A/H7N9 virus, it is critical to find out the selection pressure of each amino acid site. In the present study, six different statistical methods consisting of four independent codon-based maximum likelihood (CML) methods, one hierarchical Bayesian (HB) method and one branch-site (BS) method, were employed to determine if each amino acid site of A/H7N9 virus is under natural selection pressure. Functions for both positively and negatively selected sites were inferred by annotating these sites with experimentally verified amino acid sites. Comprehensively, the single amino acid site 627 of PB2 protein was inferred as positively selected and it function was identified as a T-cell epitope (TCE). Among the 26 negatively selected amino acid sites of PB2, PB1, PA, HA, NP, NA, M1 and NS2 proteins, only 16 amino acid sites were identified to be involved in TCEs. In addition, 7 amino acid sites including, 608 and 609 of PA, 480 of NP, and 24, 25, 109 and 205 of M1, were identified to be involved in both B-cell epitopes (BCEs) and TCEs. Conversely, the function of positions 62 of PA, and, 43 and 113 of HA was unknown. In conclusion, the seven amino acid sites engaged in both BCEs and TCEs were identified as highly suitable targets, as these sites will be predicted to play a principal role in inducing strong humoral and cellular immune responses against A/H7N9 virus.
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25
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Soema PC, Rosendahl Huber SK, Willems GJ, Jiskoot W, Kersten GFA, Amorij JP. Influenza T-cell epitope-loaded virosomes adjuvanted with CpG as a potential influenza vaccine. Pharm Res 2014; 32:1505-15. [PMID: 25344321 PMCID: PMC4356889 DOI: 10.1007/s11095-014-1556-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/20/2014] [Indexed: 11/30/2022]
Abstract
Purpose Influenza CD8+ T-cell epitopes are conserved amongst influenza strains and can be recognized by influenza-specific cytotoxic T-cells (CTLs), which can rapidly clear infected cells. An influenza peptide vaccine that elicits these CTLs would therefore be an alternative to current influenza vaccines, which are not cross-reactive. However, peptide antigens are poorly immunogenic due to lack of delivery to antigen presenting cells, and therefore need additional formulation with a suitable delivery system. In this study, the potential of virosomes as a delivery system for an influenza T-cell peptide was investigated. Methods The conserved human HLA-A2.1 influenza T-cell epitope M158–66 was formulated with virosomes. The immunogenicity and protective effect of the peptide-loaded virosomes was assessed in HLA-A2 transgenic mice. Delivery properties of the virosomes were studied in mice and in in vitro dendritic cell cultures. Results Immunization of HLA-A2.1 transgenic C57BL/6 mice with peptide-loaded virosomes in the presence of the adjuvant CpG-ODN 1826 increased the number of peptide-specific CTLs. Vaccination with adjuvanted peptide-loaded virosomes reduced weight loss in mice after heterologous influenza infection. Association with fusion-active virosomes was found to be crucial for antigen uptake by dendritic cells, and subsequent induction of CTLs in mice. Conclusions These results show that influenza virosomes loaded with conserved influenza epitopes could be the basis of a novel cross-protective influenza vaccine. Electronic supplementary material The online version of this article (doi:10.1007/s11095-014-1556-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter C Soema
- Intravacc (Institute for Translational Vaccinology), Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands,
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The immunodominant influenza A virus M158-66 cytotoxic T lymphocyte epitope exhibits degenerate class I major histocompatibility complex restriction in humans. J Virol 2014; 88:10613-23. [PMID: 24990997 DOI: 10.1128/jvi.00855-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Cytotoxic T lymphocytes recognizing conserved peptide epitopes are crucial for protection against influenza A virus (IAV) infection. The CD8 T cell response against the M158-66 (GILGFVFTL) matrix protein epitope is immunodominant when restricted by HLA-A*02, a major histocompatibility complex (MHC) molecule expressed by approximately half of the human population. Here we report that the GILGFVFTL peptide is restricted by multiple HLA-C*08 alleles as well. We observed that M158-66 was able to elicit cytotoxic T lymphocyte (CTL) responses in both HLA-A*02- and HLA-C*08-positive individuals and that GILGFVFTL-specific CTLs in individuals expressing both restriction elements were distinct and not cross-reactive. The crystal structure of GILGFVFTL-HLA-C*08:01 was solved at 1.84 Å, and comparison with the known GILGFVFTL-HLA-A*02:01 structure revealed that the antigen bound both complexes in near-identical conformations, accommodated by binding pockets shaped from shared as well as unique residues. This discovery of degenerate peptide presentation by both HLA-A and HLA-C allelic variants eliciting unique CTL responses to IAV infection contributes fundamental knowledge with important implications for vaccine development strategies. IMPORTANCE The presentation of influenza A virus peptides to elicit immunity is thought to be narrowly restricted, with a single peptide presented by a specific HLA molecule. In this study, we show that the same influenza A virus peptide can be more broadly presented by both HLA-A and HLA-C molecules. This discovery may help to explain the differences in immunity to influenza A virus between individuals and populations and may also aid in the design of vaccines.
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27
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Epistatically interacting substitutions are enriched during adaptive protein evolution. PLoS Genet 2014; 10:e1004328. [PMID: 24811236 PMCID: PMC4014419 DOI: 10.1371/journal.pgen.1004328] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/10/2014] [Indexed: 01/12/2023] Open
Abstract
Most experimental studies of epistasis in evolution have focused on adaptive changes—but adaptation accounts for only a portion of total evolutionary change. Are the patterns of epistasis during adaptation representative of evolution more broadly? We address this question by examining a pair of protein homologs, of which only one is subject to a well-defined pressure for adaptive change. Specifically, we compare the nucleoproteins from human and swine influenza. Human influenza is under continual selection to evade recognition by acquired immune memory, while swine influenza experiences less such selection due to the fact that pigs are less likely to be infected with influenza repeatedly in a lifetime. Mutations in some types of immune epitopes are therefore much more strongly adaptive to human than swine influenza—here we focus on epitopes targeted by human cytotoxic T lymphocytes. The nucleoproteins of human and swine influenza possess nearly identical numbers of such epitopes. However, mutations in these epitopes are fixed significantly more frequently in human than in swine influenza, presumably because these epitope mutations are adaptive only to human influenza. Experimentally, we find that epistatically constrained mutations are fixed only in the adaptively evolving human influenza lineage, where they occur at sites that are enriched in epitopes. Overall, our results demonstrate that epistatically interacting substitutions are enriched during adaptation, suggesting that the prevalence of epistasis is dependent on the underlying evolutionary forces at play. Mutations can fix during evolution for two reasons: they can be beneficial and fix for adaptive reasons, or they can be neutral or deleterious and fix solely by chance. Most studies focus on adaptation, where the evolving population is increasing in fitness due to a new selection pressure. Such studies have found an important evolutionary role for epistasis, the phenomenon where the effect of one mutation depends on another mutation. But adaptation only accounts for a fraction of overall evolutionary change. Here we investigate whether epistasis is as common during non-adaptive as adaptive evolution. We do this by comparing the same protein from human and swine influenza. Human influenza is constantly adapting to escape from the immunity that people acquire from previous influenza infections. But swine influenza is under less pressure to escape from acquired immunity since pigs have shorter lifetimes and are less likely to be infected with influenza multiple times. We find that epistasis is less common during the evolution of the swine influenza protein than its human influenza counterpart. Overall, our results suggest that mutations that interact via epistasis are more likely to fix during adaptive evolution.
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Nucleoprotein of influenza A virus is a major target of immunodominant CD8+ T-cell responses. Immunol Cell Biol 2014; 91:184-94. [PMID: 23399741 DOI: 10.1038/icb.2012.78] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Influenza A virus causes annual epidemics and sporadic pandemics, resulting in significant morbidity and mortality worldwide. Vaccines are currently available; however, they induce a non-strain-cross protective humoral immune response directed against the rapidly mutating surface glycoproteins, and thus need to be updated annually. As T cells are directed against more conserved internal influenza proteins, a T-cell-based vaccine has the potential to induce long-lasting and cross-strain protective CD8(+) T-cell immunity, and in that way minimize the severity of influenza infection. However, to rationally design such vaccines, we need to identify immunogenic T-cell regions within the most antigenic viral proteins. In this study, we have used a systematic approach to identify immunodominant peptides in HLA-A2-negative donors. A broad range of CD8(+) T-cell responses were observed and 6/7 donors had an immunodominant response against the relatively conserved internal nucleoprotein (NP). Dissecting the minimal epitope regions within the immunogenic NP led to the identification of six novel immunodominant epitopes, which include a 12-mer and an 8-mer peptides. The majority of immunodominant epitopes was clustered within the carboxyl terminal 2/3 of the NP protein and were highly conserved. We also subjected NP to three common computer algorithms for epitope prediction and found that most of the novel epitopes would not have been predicted. Our study emphasizes the importance of using a systematic approach to identify immunodominant CD8(+) T-cell responses and suggests that the epitope-rich regions within NP present a promising target for the T-cell-mediated multi-strain influenza vaccine.
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29
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Dukhovlinov I, Al-Shekhadat R, Fedorova E, Stepanova L, Potapchuk M, Repko I, Rusova O, Orlov A, Tsybalova L, Kiselev O. Study of immunogenicity of recombinant proteins based on hemagglutinin and neuraminidase conservative epitopes of influenza A virus. Med Sci Monit Basic Res 2013; 19:221-7. [PMID: 23969554 PMCID: PMC3762522 DOI: 10.12659/msmbr.884002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background Recombinant hemagglutinin (rHA) and neurominidase (rNA) developed in our investigation are amino acid sequence consensus variants of H1N1 2009 subtype influenza virus strain, also including immunogenic epitopes typical for other influenza virus subtypes (H3N1 and H5N1). Substitutions were made: typical for Russian virus isolates (in HA – S220T, NA – D248N) and in active centers of molecules – R118L, R293L, R368L; C92S, C417S to increase recombinant proteins stability in E. coli. The aim of the present work was to study immunogenicity of the obtained rHA and rNA. Material/Methods Fragments aa 83–469 of NA and aa 61–287 of HA were chosen because they include the main B-cell epitopes and are the minimal structures for correct folding of target proteins. The designed nucleotide sequences were synthesized and purified and the expression of rNA and rNA were analyzed. For immunization and virus challenge we used influenza viruses A/California/04/2009 (H1N1), A/PR/8/34 (H1N1), A/Perth/16/2009 (H3N2), A/Chicken/Kurgan/05/2005 R.G. (H5N1), and B/Florida/04/2006. Specific IgG levels were determined by ELISA in 96-well ELISA plates. Significant differences of survival in mouse groups were analyzed by Mantel-Cox (log-rank) and Gehan-Breslow-Wilcoxon tests. Results The obtained results demonstrate the high immunogenicity and ability of indicated proteins mixture to provide similar cross-protection against influenza viruses of the H1N1 subtype. Conclusions The data obtained suggest efficient pluripotent vaccine creation based on HA and NA conservative regions.
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Terajima M, Babon JAB, Co MDT, Ennis FA. Cross-reactive human B cell and T cell epitopes between influenza A and B viruses. Virol J 2013; 10:244. [PMID: 23886073 PMCID: PMC3726517 DOI: 10.1186/1743-422x-10-244] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/24/2013] [Indexed: 01/26/2023] Open
Abstract
Influenza A and B viruses form different genera, which were originally distinguished by antigenic differences in their nucleoproteins and matrix 1 proteins. Cross-protection between these two genera has not been observed in animal experiments, which is consistent with the low homology in viral proteins common to both viruses except for one of three polymerase proteins, polymerase basic 1 (PB1). Recently, however, antibody and CD4+ T cell epitopes conserved between the two genera were identified in humans. A protective antibody epitope was located in the stalk region of the surface glycoprotein, hemagglutinin, and a CD4+ T cell epitope was located in the fusion peptide of the hemagglutinin. The fusion peptide was also found to contain antibody epitopes in humans and animals. A short stretch of well-conserved peptide was also identified in the other surface glycoprotein, neuraminidase, and antibodies binding to this peptide were generated by peptide immunization in rabbits. Although PB1, the only protein which has relatively high overall sequence homology between influenza A and B viruses, is not considered an immunodominant protein in the T cell responses to influenza A virus infection, amino acid sequence comparisons show that a considerable number of previously identified T cell epitopes in the PB1 of influenza A viruses are conserved in the PB1 of influenza B viruses. These data indicate that B and T cell cross-reactivity exists between influenza A and B viruses, which may have modulatory effects on the disease process and recovery. Although the antibody titers and the specific T cell frequencies induced by natural infection or standard vaccination may not be high enough to provide cross protection in humans, it might be possible to develop immunization strategies to induce these cross-reactive responses more efficiently.
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Affiliation(s)
- Masanori Terajima
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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Liu J, Wu B, Zhang S, Tan S, Sun Y, Chen Z, Qin Y, Sun M, Shi G, Wu Y, Sun M, Liu N, Ning K, Ma Y, Gao B, Yan J, Zhu F, Wang H, Gao GF. Conserved epitopes dominate cross-CD8+ T-cell responses against influenza A H1N1 virus among Asian populations. Eur J Immunol 2013; 43:2055-69. [PMID: 23681926 DOI: 10.1002/eji.201343417] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/05/2013] [Accepted: 05/13/2013] [Indexed: 12/12/2022]
Abstract
Novel strains of influenza A viruses (IAVs) have emerged with high infectivity and/or pathogenicity in recent years, causing worldwide concern. T cells are correlated with protection in humans through cross-reactive immunity against heterosubtypes of IAV. However, the different hierarchical roles of IAV-derived epitopes with distinct levels of polymorphism in the cross-reactive T-cell responses against IAV remain elusive. In this study, immunodominant epitopes scattered throughout the entire proteome of 2009 pandemic influenza A H1N1 virus and seasonal IAVs were synthesized and divided into different pools depending on their conservation. The overall profile of the IAV-specific CD8(+) T-cell immunity was detected by utilizing these peptide pools and also individual peptides. A dominant role of the conserved peptide-specific T-cell immunity was illuminated within the anti-IAV responses, while the CD8(+) T-cell responses against the variable epitopes were lower than the conserved peptides. As previously demonstrated within a Caucasian population, we determined that GL9-specific T cells, which also utilize Vβ 17 TCR (BV19), play a pivotal role in IAV-specific T-cell immunity within an HLA-A2(+) Asian population. Our study objectively reveals the different predominant roles of T-cell epitopes among IAV-specific cross-reactive cellular immunity. This may guide the development of vaccines with cross-T-cell immunogenicity against heterosubtypes of IAV.
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Affiliation(s)
- Jun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Poland GA, Kennedy RB, McKinney BA, Ovsyannikova IG, Lambert ND, Jacobson RM, Oberg AL. Vaccinomics, adversomics, and the immune response network theory: individualized vaccinology in the 21st century. Semin Immunol 2013; 25:89-103. [PMID: 23755893 DOI: 10.1016/j.smim.2013.04.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 03/23/2013] [Accepted: 04/18/2013] [Indexed: 02/08/2023]
Abstract
Vaccines, like drugs and medical procedures, are increasingly amenable to individualization or personalization, often based on novel data resulting from high throughput "omics" technologies. As a result of these technologies, 21st century vaccinology will increasingly see the abandonment of a "one size fits all" approach to vaccine dosing and delivery, as well as the abandonment of the empiric "isolate-inactivate-inject" paradigm for vaccine development. In this review, we discuss the immune response network theory and its application to the new field of vaccinomics and adversomics, and illustrate how vaccinomics can lead to new vaccine candidates, new understandings of how vaccines stimulate immune responses, new biomarkers for vaccine response, and facilitate the understanding of what genetic and other factors might be responsible for rare side effects due to vaccines. Perhaps most exciting will be the ability, at a systems biology level, to integrate increasingly complex high throughput data into descriptive and predictive equations for immune responses to vaccines. Herein, we discuss the above with a view toward the future of vaccinology.
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Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2013; 2:e00631. [PMID: 23682315 PMCID: PMC3654441 DOI: 10.7554/elife.00631] [Citation(s) in RCA: 245] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/09/2013] [Indexed: 11/28/2022] Open
Abstract
John Maynard Smith compared protein evolution to the game where one word is converted into another a single letter at a time, with the constraint that all intermediates are words: WORD→WORE→GORE→GONE→GENE. In this analogy, epistasis constrains evolution, with some mutations tolerated only after the occurrence of others. To test whether epistasis similarly constrains actual protein evolution, we created all intermediates along a 39-mutation evolutionary trajectory of influenza nucleoprotein, and also introduced each mutation individually into the parent. Several mutations were deleterious to the parent despite becoming fixed during evolution without negative impact. These mutations were destabilizing, and were preceded or accompanied by stabilizing mutations that alleviated their adverse effects. The constrained mutations occurred at sites enriched in T-cell epitopes, suggesting they promote viral immune escape. Our results paint a coherent portrait of epistasis during nucleoprotein evolution, with stabilizing mutations permitting otherwise inaccessible destabilizing mutations which are sometimes of adaptive value. DOI:http://dx.doi.org/10.7554/eLife.00631.001 During evolution, the effect of one mutation on a protein can depend on whether another mutation is also present. This phenomenon is similar to the game in which one word is converted to another word, one letter at a time, subject to the rule that all the intermediate steps are also valid words: for example, the word WORD can be converted to the word GENE as follows: WORD→WORE→GORE→GONE→GENE. In this example, the D must be changed to an E before the W is changed to a G, because GORD is not a valid word. Similarly, during the evolution of a virus, a mutation that helps the virus evade the human immune system might only be tolerated if the virus has acquired another mutation beforehand. This type of mutational interaction would constrain the evolution of the virus, since its capacity to take advantage of the second mutation depends on the first mutation having already occurred. Gong et al. examined whether such interactions have indeed constrained evolution of the influenza virus. Between 1968 and 2007, the nucleoprotein—which acts as a scaffold for the replication of genetic material—in the human H3N2 influenza virus underwent a series of 39 mutations. To test whether all of these mutations could have been tolerated by the 1968 virus, Gong et al. introduced each one individually into the 1968 nucleoprotein. They found that several mutations greatly reduced the fitness of the 1968 virus when introduced on their own, which strongly suggests that these ‘constrained mutations’ became part of the virus’s genetic makeup as a result of interactions with ‘enabling’ mutations. The constrained mutations decreased the stability of the nucleoprotein at high temperatures, while the enabling mutations counteracted this effect. It may, therefore, be possible to identify enabling mutations based on their effects on thermal stability. Intriguingly, the constrained mutations helped the virus overcome one form of human immunity to influenza, suggesting that interactions between mutations might limit the rate at which viruses evolve to evade the immune system. Overall, these results show that interactions among mutations constrain the evolution of the influenza nucleoprotein in a fashion that can be largely understood in terms of protein stability. If the same is true for other proteins and viruses, this work could lead to a deeper understanding of the constraints that govern evolution at the molecular level. DOI:http://dx.doi.org/10.7554/eLife.00631.002
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Affiliation(s)
- Lizhi Ian Gong
- Division of Basic Sciences , Fred Hutchinson Cancer Research Center , Seattle , United States
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Cross-allele cytotoxic T lymphocyte responses against 2009 pandemic H1N1 influenza A virus among HLA-A24 and HLA-A3 supertype-positive individuals. J Virol 2012; 86:13281-94. [PMID: 23015716 DOI: 10.1128/jvi.01841-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Lack of a universal vaccine against all serotypes of influenza A viruses and recent progress on T cell-related vaccines against influenza A virus illuminate the important role of human leukocyte antigen (HLA)-restricted cytotoxic T lymphocytes (CTLs) in anti-influenza virus immunity. However, the diverse HLA alleles among humans complicate virus-specific cellular immunity research, and elucidation of cross-HLA allele T cell responses to influenza virus specificity requires further detailed work. An ideal CTL epitope-based vaccine would cover a broad spectrum of epitope antigens presented by most, if not all, of the HLAs. Here, we evaluated the 2009 pandemic influenza A (H1N1) virus-specific T cell responses among the HLA-A24(+) population using a rationally designed peptide pool during the 2009 pandemic. Unexpectedly, cross-HLA allele T cell responses against the influenza A virus peptides were detected among both HLA-A11(+) and HLA-A24(+) donors. Furthermore, we found cross-responses in the entire HLA-A3 supertype population (including HLA-A11, -A31, -A33, and -A30). The cross-allele antigenic peptides within the peptide pool were identified and characterized, and the crystal structures of the major histocompatibility complex (MHC)-peptide complexes were determined. The subsequent HLA-A24-defined cross-allele peptides recognized by the HLA-A11(+) population were shown to mildly bind to the HLA-A*1101 molecule. Together with the structural models, these results partially explain the cross-allele responses. Our findings elucidate the promiscuity of the cross-allele T cell responses against influenza A viruses and are beneficial for the development of a T cell epitope-based vaccine applied in a broader population.
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Sommerfelt MA. T-cell-mediated and humoral approaches to universal influenza vaccines. Expert Rev Vaccines 2012; 10:1359-61. [PMID: 21988298 DOI: 10.1586/erv.11.127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Valentino MD, Abdul-Alim CS, Maben ZJ, Skrombolas D, Hensley LL, Kawula TH, Dziejman M, Lord EM, Frelinger JA, Frelinger JG. A broadly applicable approach to T cell epitope identification: application to improving tumor associated epitopes and identifying epitopes in complex pathogens. J Immunol Methods 2011; 373:111-26. [PMID: 21872603 DOI: 10.1016/j.jim.2011.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 08/10/2011] [Accepted: 08/11/2011] [Indexed: 12/22/2022]
Abstract
Epitopes are a hallmark of the antigen specific immune response. The identification and characterization of epitopes is essential for modern immunologic studies, from investigating cellular responses against tumors to understanding host/pathogen interactions especially in the case of bacteria with intracellular residence. Here, we have utilized a novel approach to identify T cell epitopes exploiting the exquisite ability of particulate antigens, in the form of beads, to deliver exogenous antigen to both MHC class I and class II pathways for presentation to T cell hybridomas. In the current study, we coupled this functional assay with two distinct protein expression libraries to develop a methodology for the characterization of T cell epitopes. One set of expression libraries containing single amino acid substitutions in a defined epitope sequence was interrogated to identify epitopes with enhanced T cell stimulation for a MHC class I epitope. The second expression library is comprised of the majority of open reading frames from the intracellular pathogen and potential biowarfare agent, Francisella tularensis. By automating aspects of this technology, we have been able to functionally screen and identify novel T cell epitopes within F. tularensis. We have also expanded upon these studies to generate a novel expression vector that enables immunization of recombinant protein into mice, which has been utilized to facilitate T cell epitope discovery for proteins that are critically linked to Francisella pathogenicity. This methodology should be applicable to a variety of systems and other pathogens.
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Affiliation(s)
- Michael D Valentino
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.
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Mester G, Hoffmann V, Stevanović S. Insights into MHC class I antigen processing gained from large-scale analysis of class I ligands. Cell Mol Life Sci 2011; 68:1521-32. [PMID: 21387142 PMCID: PMC11114492 DOI: 10.1007/s00018-011-0659-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 01/06/2023]
Abstract
Short peptides derived from intracellular proteins and presented on MHC class I molecules on the cell surface serve as a showcase for the immune system to detect pathogenic or malignant alterations inside the cell, and the sequencing and analysis of the presented peptide pool has received considerable attention over the last two decades. In this review, we give a comprehensive presentation of the methods employed for the large-scale qualitative and quantitative analysis of the MHC class I ligandome. Furthermore, we focus on insights gained into the underlying processing pathway, especially involving the roles of the proteasome, the TAP complex, and the peptide specificities and motifs of MHC molecules. The identification of post-translational modifications in MHC ligands and their implications for processing are also considered. Finally, we review the correlations of the ligandome to the proteome and the transcriptome.
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Affiliation(s)
- Gabor Mester
- Institute for Cell Biology, Department of Immunology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Vanessa Hoffmann
- Institute for Cell Biology, Department of Immunology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, Eberhard Karls University Tübingen, Tübingen, Germany
- Abteilung für Immunologie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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Abstract
Antigenic changes in influenza virus occur gradually, owing to mutations (antigenic drift), and abruptly, owing to reassortment among subtypes (antigenic shift). Availability of strain-matched vaccines often lags behind these changes, resulting in a shortfall in public health. In animal models, cross-protection by vaccines based on conserved antigens does not completely prevent infection, but greatly reduces morbidity, mortality, virus replication and, thus, viral shedding and spread. Such immunity is especially effective and long-lasting with mucosal administration. Cross-protective immunity in humans is controversial, but is suggested by some epidemiological findings. 'Universal' vaccines protective against all influenza A viruses might substantially reduce severity of infection and limit spread of disease during outbreaks. These vaccines could be used 'off the shelf' early in an outbreak or pandemic, before strain-matched vaccines are available.
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Affiliation(s)
- Suzanne L Epstein
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, MD 20852, USA.
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