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Kim SH, Españo E, Padasas BT, Son JH, Oh J, Webby RJ, Lee YR, Park CS, Kim JK. Influenza Virus-Derived CD8 T Cell Epitopes: Implications for the Development of Universal Influenza Vaccines. Immune Netw 2024; 24:e19. [PMID: 38974213 PMCID: PMC11224667 DOI: 10.4110/in.2024.24.e19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 07/09/2024] Open
Abstract
The influenza virus poses a global health burden. Currently, an annual vaccine is used to reduce influenza virus-associated morbidity and mortality. Most influenza vaccines have been developed to elicit neutralizing Abs against influenza virus. These Abs primarily target immunodominant epitopes derived from hemagglutinin (HA) or neuraminidase (NA) of the influenza virus incorporated in vaccines. However, HA and NA are highly variable proteins that are prone to antigenic changes, which can reduce vaccine efficacy. Therefore, it is essential to develop universal vaccines that target immunodominant epitopes derived from conserved regions of the influenza virus, enabling cross-protection among different virus variants. The internal proteins of the influenza virus serve as ideal targets for universal vaccines. These internal proteins are presented by MHC class I molecules on Ag-presenting cells, such as dendritic cells, and recognized by CD8 T cells, which elicit CD8 T cell responses, reducing the likelihood of disease and influenza viral spread by inducing virus-infected cell apoptosis. In this review, we highlight the importance of CD8 T cell-mediated immunity against influenza viruses and that of viral epitopes for developing CD8 T cell-based influenza vaccines.
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Affiliation(s)
- Sang-Hyun Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
- Department of Pharmaceutics, College of Pharmacy, Chungbuk National University, Cheongju 28644, Korea
| | - Erica Españo
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | | | - Ju-Ho Son
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | - Jihee Oh
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38195, USA
| | - Young-Ran Lee
- Bio-Convergence R&D Division, Korea Institute of Ceramic Engineering and Technology, Cheongju 28160, Korea
| | - Chan-Su Park
- Department of Pharmaceutics, College of Pharmacy, Chungbuk National University, Cheongju 28644, Korea
| | - Jeong-Ki Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
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2
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Lopez CE, Zacharias ZR, Ross KA, Narasimhan B, Waldschmidt TJ, Legge KL. Polyanhydride nanovaccine against H3N2 influenza A virus generates mucosal resident and systemic immunity promoting protection. NPJ Vaccines 2024; 9:96. [PMID: 38822003 PMCID: PMC11143372 DOI: 10.1038/s41541-024-00883-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 05/07/2024] [Indexed: 06/02/2024] Open
Abstract
Influenza A virus (IAV) causes significant morbidity and mortality worldwide due to seasonal epidemics and periodic pandemics. The antigenic drift/shift of IAV continually gives rise to new strains and subtypes, aiding IAV in circumventing previously established immunity. As a result, there has been substantial interest in developing a broadly protective IAV vaccine that induces, durable immunity against multiple IAVs. Previously, a polyanhydride nanoparticle-based vaccine or nanovaccine (IAV-nanovax) encapsulating H1N1 IAV antigens was reported, which induced pulmonary B and T cell immunity and resulted in cross-strain protection against IAV. A key feature of IAV-nanovax is its ability to easily incorporate diverse proteins/payloads, potentially increasing its ability to provide broad protection against IAV and/or other pathogens. Due to human susceptibility to both H1N1 and H3N2 IAV, several H3N2 nanovaccines were formulated herein with multiple IAV antigens to examine the "plug-and-play" nature of the polyanhydride nanovaccine platform and determine their ability to induce humoral and cellular immunity and broad-based protection similar to IAV-nanovax. The H3N2-based IAV nanovaccine formulations induced systemic and mucosal B cell responses which were associated with antigen-specific antibodies. Additionally, systemic and lung-tissue resident CD4 and CD8 T cell responses were enhanced post-vaccination. These immune responses corresponded with protection against both homologous and heterosubtypic IAV infection. Overall, these results demonstrate the plug-and-play nature of the polyanhydride nanovaccine platform and its ability to generate immunity and protection against IAV utilizing diverse antigenic payloads.
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Affiliation(s)
- Christopher E Lopez
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Zeb R Zacharias
- Interdisciplinary Immunology Graduate Program, Department of Pathology, University of Iowa, Iowa City, IA, USA
| | | | - Balaji Narasimhan
- Nanovaccine Institute, Iowa State University, Ames, IA, USA
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Thomas J Waldschmidt
- Interdisciplinary Immunology Graduate Program, Department of Pathology, University of Iowa, Iowa City, IA, USA
- Nanovaccine Institute, Iowa State University, Ames, IA, USA
| | - Kevin L Legge
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
- Interdisciplinary Immunology Graduate Program, Department of Pathology, University of Iowa, Iowa City, IA, USA.
- Nanovaccine Institute, Iowa State University, Ames, IA, USA.
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3
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Sui Y, Meyer TJ, Fennessey CM, Keele BF, Dadkhah K, Ma C, LaBranche CC, Breed MW, Kramer JA, Li J, Howe SE, Ferrari G, Williams LD, Cam M, Kelly MC, Shen X, Tomaras GD, Montefiori D, Greten TF, Miller CJ, Berzofsky JA. Innate protection against intrarectal SIV acquisition by a live SHIV vaccine. JCI Insight 2024; 9:e175800. [PMID: 38912579 PMCID: PMC11383375 DOI: 10.1172/jci.insight.175800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 05/08/2024] [Indexed: 06/25/2024] Open
Abstract
Identifying immune correlates of protection is a major challenge in AIDS vaccine development. Anti-Envelope antibodies have been considered critical for protection against SIV/HIV (SHIV) acquisition. Here, we evaluated the efficacy of an SHIV vaccine against SIVmac251 challenge, where the role of antibody was excluded, as there was no cross-reactivity between SIV and SHIV envelope antibodies. After 8 low-dose intrarectal challenges with SIVmac251, 12 SHIV-vaccinated animals demonstrated efficacy, compared with 6 naive controls, suggesting protection was achieved in the absence of anti-envelope antibodies. Interestingly, CD8+ T cells (and some NK cells) were not essential for preventing viral acquisition, as none of the CD8-depleted macaques were infected by SIVmac251 challenges. Initial investigation of protective innate immunity revealed that protected animals had elevated pathways related to platelet aggregation/activation and reduced pathways related to interferon and responses to virus. Moreover, higher expression of platelet factor 4 on circulating platelet-leukocyte aggregates was associated with reduced viral acquisition. Our data highlighted the importance of innate immunity, identified mechanisms, and may provide opportunities for novel HIV vaccines or therapeutic strategy development.
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Affiliation(s)
| | - Thomas J Meyer
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | | | | | - Kimia Dadkhah
- Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Chi Ma
- Thoracic and GI Malignancies Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Matthew W Breed
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Bethesda, Maryland, USA
| | - Josh A Kramer
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Bethesda, Maryland, USA
| | | | | | | | - LaTonya D Williams
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - David Montefiori
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tim F Greten
- Thoracic and GI Malignancies Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Christopher J Miller
- Center for Comparative Medicine, University of California, Davis, Davis, California, USA
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4
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Nguyen THO, Rowntree LC, Chua BY, Thwaites RS, Kedzierska K. Defining the balance between optimal immunity and immunopathology in influenza virus infection. Nat Rev Immunol 2024:10.1038/s41577-024-01029-1. [PMID: 38698083 DOI: 10.1038/s41577-024-01029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 05/05/2024]
Abstract
Influenza A viruses remain a global threat to human health, with continued pandemic potential. In this Review, we discuss our current understanding of the optimal immune responses that drive recovery from influenza virus infection, highlighting the fine balance between protective immune mechanisms and detrimental immunopathology. We describe the contribution of innate and adaptive immune cells, inflammatory modulators and antibodies to influenza virus-specific immunity, inflammation and immunopathology. We highlight recent human influenza virus challenge studies that advance our understanding of susceptibility to influenza and determinants of symptomatic disease. We also describe studies of influenza virus-specific immunity in high-risk groups following infection and vaccination that inform the design of future vaccines to promote optimal antiviral immunity, particularly in vulnerable populations. Finally, we draw on lessons from the COVID-19 pandemic to refocus our attention to the ever-changing, highly mutable influenza A virus, predicted to cause future global pandemics.
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Affiliation(s)
- Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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5
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Foo IJH, Chua BY, Clemens EB, Chang SY, Jia X, McQuilten HA, Yap AHY, Cabug AF, Ashayeripanah M, McWilliam HEG, Villadangos JA, Evrard M, Mackay LK, Wakim LM, Fazakerley JK, Kedzierska K, Kedzierski L. Prior infection with unrelated neurotropic virus exacerbates influenza disease and impairs lung T cell responses. Nat Commun 2024; 15:2619. [PMID: 38521764 PMCID: PMC10960853 DOI: 10.1038/s41467-024-46822-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 03/25/2024] Open
Abstract
Immunity to infectious diseases is predominantly studied by measuring immune responses towards a single pathogen, although co-infections are common. In-depth mechanisms on how co-infections impact anti-viral immunity are lacking, but are highly relevant to treatment and prevention. We established a mouse model of co-infection with unrelated viruses, influenza A (IAV) and Semliki Forest virus (SFV), causing disease in different organ systems. SFV infection eight days before IAV infection results in prolonged IAV replication, elevated cytokine/chemokine levels and exacerbated lung pathology. This is associated with impaired lung IAV-specific CD8+ T cell responses, stemming from suboptimal CD8+ T cell activation and proliferation in draining lymph nodes, and dendritic cell paralysis. Prior SFV infection leads to increased blood brain barrier permeability and presence of IAV RNA in brain, associated with increased trafficking of IAV-specific CD8+ T cells and establishment of long-term tissue-resident memory. Relative to lung IAV-specific CD8+ T cells, brain memory IAV-specific CD8+ T cells have increased TCR repertoire diversity within immunodominant DbNP366+CD8+ and DbPA224+CD8+ responses, featuring suboptimal TCR clonotypes. Overall, our study demonstrates that infection with an unrelated neurotropic virus perturbs IAV-specific immune responses and exacerbates IAV disease. Our work provides key insights into therapy and vaccine regimens directed against unrelated pathogens.
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Affiliation(s)
- Isabelle Jia-Hui Foo
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Department of Veterinary Biosciences, Faculty of Science, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - So Young Chang
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Ashley Huey Yiing Yap
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Aira F Cabug
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Mitra Ashayeripanah
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hamish E G McWilliam
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Department of Biochemistry and Pharmacology; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - John K Fazakerley
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Department of Veterinary Biosciences, Faculty of Science, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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6
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Fasoulis R, Rigo MM, Antunes DA, Paliouras G, Kavraki LE. Transfer learning improves pMHC kinetic stability and immunogenicity predictions. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2024; 13:100030. [PMID: 38577265 PMCID: PMC10994007 DOI: 10.1016/j.immuno.2023.100030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
The cellular immune response comprises several processes, with the most notable ones being the binding of the peptide to the Major Histocompability Complex (MHC), the peptide-MHC (pMHC) presentation to the surface of the cell, and the recognition of the pMHC by the T-Cell Receptor. Identifying the most potent peptide targets for MHC binding, presentation and T-cell recognition is vital for developing peptide-based vaccines and T-cell-based immunotherapies. Data-driven tools that predict each of these steps have been developed, and the availability of mass spectrometry (MS) datasets has facilitated the development of accurate Machine Learning (ML) methods for class-I pMHC binding prediction. However, the accuracy of ML-based tools for pMHC kinetic stability prediction and peptide immunogenicity prediction is uncertain, as stability and immunogenicity datasets are not abundant. Here, we use transfer learning techniques to improve stability and immunogenicity predictions, by taking advantage of a large number of binding affinity and MS datasets. The resulting models, TLStab and TLImm, exhibit comparable or better performance than state-of-the-art approaches on different stability and immunogenicity test sets respectively. Our approach demonstrates the promise of learning from the task of peptide binding to improve predictions on downstream tasks. The source code of TLStab and TLImm is publicly available at https://github.com/KavrakiLab/TL-MHC.
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Affiliation(s)
- Romanos Fasoulis
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
| | - Mauricio Menegatti Rigo
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
| | - Dinler Amaral Antunes
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd, Houston, 77004, TX, United States
| | - Georgios Paliouras
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E and 27 Neapoleos St, Athens, 15341, Greece
| | - Lydia E. Kavraki
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
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7
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Ricker CA, Meli K, Van Allen EM. Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer 2024; 12:e008306. [PMID: 38191244 PMCID: PMC10826578 DOI: 10.1136/jitc-2023-008306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Immuno-oncology holds promise for transforming patient care having achieved durable clinical response rates across a variety of advanced and metastatic cancers. Despite these achievements, only a minority of patients respond to immunotherapy, underscoring the importance of elucidating molecular mechanisms responsible for response and resistance to inform the development and selection of treatments. Breakthroughs in molecular sequencing technologies have led to the generation of an immense amount of genomic and transcriptomic sequencing data that can be mined to uncover complex tumor-immune interactions using computational tools. In this review, we discuss existing and emerging computational methods that contextualize the composition and functional state of the tumor microenvironment, infer the reactivity and clonal dynamics from reconstructed immune cell receptor repertoires, and predict the antigenic landscape for immune cell recognition. We further describe the advantage of multi-omics analyses for capturing multidimensional relationships and artificial intelligence techniques for integrating omics data with histopathological and radiological images to encapsulate patterns of treatment response and tumor-immune biology. Finally, we discuss key challenges impeding their widespread use and clinical application and conclude with future perspectives. We are hopeful that this review will both serve as a guide for prospective researchers seeking to use existing tools for scientific discoveries and inspire the optimization or development of novel tools to enhance precision, ultimately expediting advancements in immunotherapy that improve patient survival and quality of life.
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Affiliation(s)
- Cora A Ricker
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kevin Meli
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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8
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Gibadullin R, Morris RK, Niu J, Sidney J, Sette A, Gellman SH. Thioamide Analogues of MHC I Antigen Peptides. J Am Chem Soc 2023; 145:25559-25569. [PMID: 37968794 PMCID: PMC10782604 DOI: 10.1021/jacs.3c05300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Short, synthetic peptides that are displayed by major histocompatibility complex I (MHC I) can stimulate CD8 T cells in vivo to destroy virus-infected or cancer cells. The development of such peptides as vaccines that provide protective immunity, however, is limited by rapid proteolytic degradation. Introduction of unnatural amino acid residues can suppress MHC I antigen proteolysis, but the modified peptides typically display lower affinity for MHC I and/or diminished ability to activate CD8 T cells relative to native antigen. Here, we report a new strategy for modifying MHC I antigens to enhance resistance to proteolysis while preserving MHC I affinity and T cell activation properties. This approach, replacing backbone amide groups with thioamides, was evaluated in two well-characterized antigens presented by HLA-A2, a common human MHC I. For each antigen, singly modified thioamide analogues retained affinity for HLA-A2 and activated T cells specific for the native antigen, as measured via interferon-γ secretion. In each system, we identified a highly potent triply substituted thioamide antigen ("thio-antigen") that displayed substantial resistance to proteolytic cleavage. Collectively, our results suggest that thio-antigens may represent a general and readily accessible source of potent vaccine candidates that resist degradation.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Present address: Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Rylie K. Morris
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jiani Niu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
- Department of Medicine, University of California, San Diego, California 92093, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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9
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van de Sandt CE, Nguyen THO, Gherardin NA, Crawford JC, Samir J, Minervina AA, Pogorelyy MV, Rizzetto S, Szeto C, Kaur J, Ranson N, Sonda S, Harper A, Redmond SJ, McQuilten HA, Menon T, Sant S, Jia X, Pedrina K, Karapanagiotidis T, Cain N, Nicholson S, Chen Z, Lim R, Clemens EB, Eltahla A, La Gruta NL, Crowe J, Lappas M, Rossjohn J, Godfrey DI, Thomas PG, Gras S, Flanagan KL, Luciani F, Kedzierska K. Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan. Nat Immunol 2023; 24:1890-1907. [PMID: 37749325 PMCID: PMC10602853 DOI: 10.1038/s41590-023-01633-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/24/2023] [Indexed: 09/27/2023]
Abstract
CD8+ T cells provide robust antiviral immunity, but how epitope-specific T cells evolve across the human lifespan is unclear. Here we defined CD8+ T cell immunity directed at the prominent influenza epitope HLA-A*02:01-M158-66 (A2/M158) across four age groups at phenotypic, transcriptomic, clonal and functional levels. We identify a linear differentiation trajectory from newborns to children then adults, followed by divergence and a clonal reset in older adults. Gene profiles in older adults closely resemble those of newborns and children, despite being clonally distinct. Only child-derived and adult-derived A2/M158+CD8+ T cells had the potential to differentiate into highly cytotoxic epitope-specific CD8+ T cells, which was linked to highly functional public T cell receptor (TCR)αβ signatures. Suboptimal TCRαβ signatures in older adults led to less proliferation, polyfunctionality, avidity and recognition of peptide mutants, although displayed no signs of exhaustion. These data suggest that priming T cells at different stages of life might greatly affect CD8+ T cell responses toward viral infections.
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Affiliation(s)
- Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Jerome Samir
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Simone Rizzetto
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Christopher Szeto
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jasveen Kaur
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Nicole Ranson
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Sabrina Sonda
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Alice Harper
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Samuel J Redmond
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tejas Menon
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kate Pedrina
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Theo Karapanagiotidis
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Natalie Cain
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ratana Lim
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Auda Eltahla
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nicole L La Gruta
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, Victoria, Australia
| | - Martha Lappas
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jamie Rossjohn
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Dale I Godfrey
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephanie Gras
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katie L Flanagan
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, Victoria, Australia
- Tasmanian Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, Tasmania, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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10
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Zheng MZ, Tan TK, Villalon-Letelier F, Lau H, Deng YM, Fritzlar S, Valkenburg SA, Gu H, Poon LL, Reading PC, Townsend AR, Wakim LM. Single-cycle influenza virus vaccine generates lung CD8 + Trm that cross-react against viral variants and subvert virus escape mutants. SCIENCE ADVANCES 2023; 9:eadg3469. [PMID: 37683004 PMCID: PMC10491285 DOI: 10.1126/sciadv.adg3469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Influenza virus-specific tissue-resident memory (Trm) CD8+ T cells located along the respiratory tract provide cross-strain protection against a breadth of influenza viruses. We show that immunization with a single-cycle influenza virus vaccine candidate (S-FLU) results in the deposition of influenza virus nucleoprotein (NP)-specific CD8+ Trm along the respiratory tract that were more cross-reactive against viral variants and less likely to drive the development of cytotoxic T lymphocyte (CTL) escape mutants, as compared to the lung memory NP-specific CD8+ T cell pool established following influenza infection. This immune profile was linked to the limited inflammatory response evoked by S-FLU vaccination, which increased TCR repertoire diversity within the memory CD8+ T cell compartment. Cumulatively, this work shows that S-FLU vaccination evokes a clonally diverse, cross-reactive memory CD8+ T cell pool, which protects against severe disease without driving the virus to rapidly evolve and escape, and thus represents an attractive vaccine for use against rapidly mutating influenza viruses.
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Affiliation(s)
- Ming Z. M. Zheng
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Fernando Villalon-Letelier
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Hilda Lau
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Svenja Fritzlar
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Sophie A. Valkenburg
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo L. M. Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Patrick C. Reading
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Alain R. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, UK
- Centre for Translational Immunology, Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, OX3 7FZ Oxford, UK
| | - Linda M. Wakim
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
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11
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Lanfermeijer J, van de Ven K, van Dijken H, Hendriks M, Talavera Ormeño CMP, de Heij F, Roholl P, Borghans JAM, van Baarle D, de Jonge J. Modified influenza M1 58-66 peptide vaccination induces non-relevant T-cells and may enhance pathology after challenge. NPJ Vaccines 2023; 8:116. [PMID: 37573454 PMCID: PMC10423225 DOI: 10.1038/s41541-023-00705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/11/2023] [Indexed: 08/14/2023] Open
Abstract
CD8 + T cells are promising targets for vaccination against influenza A virus (IAV) infection. Their induction via peptide vaccination is not trivial, because peptides are weakly immunogenic. One strategy to overcome this is by vaccination with chemically enhanced altered peptide ligands (CPLs), which have improved MHC-binding and immunogenicity. It remains unknown how peptide-modification affects the resulting immune response. We studied the effect of CPLs derived from the influenza M158-66 epitope (GILGFVFTL) on the T-cell response. In HLA-A2*0201 transgenic mice, CPL-vaccination led to higher T-cell frequencies, but only a small percentage of the induced T cells recognized the GILG-wildtype (WT) peptide. CPL-vaccination resulted in a lower richness of the GILG-WT-specific T-cell repertoire and no improved protection against IAV-infection compared to GILG-WT peptide-vaccination. One CPL even appeared to enhance pathology after IAV-challenge. CPL-vaccination thus induces T cells not targeting the original peptide, which may lead to potential unwanted side effects.
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Affiliation(s)
- Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen van de Ven
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Harry van Dijken
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Hendriks
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Cami M P Talavera Ormeño
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Femke de Heij
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Virology & Immunology Research. Dept Medical Microbiology and Infection prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Jørgen de Jonge
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
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12
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Zhang W, Kedzierski L, Chua BY, Mayo M, Lonzi C, Rigas V, Middleton BF, McQuilten HA, Rowntree LC, Allen LF, Purcell RA, Tan HX, Petersen J, Chaurasia P, Mordant F, Pogorelyy MV, Minervina AA, Crawford JC, Perkins GB, Zhang E, Gras S, Clemens EB, Juno JA, Audsley J, Khoury DS, Holmes NE, Thevarajan I, Subbarao K, Krammer F, Cheng AC, Davenport MP, Grubor-Bauk B, Coates PT, Christensen B, Thomas PG, Wheatley AK, Kent SJ, Rossjohn J, Chung AW, Boffa J, Miller A, Lynar S, Nelson J, Nguyen THO, Davies J, Kedzierska K. Robust and prototypical immune responses toward COVID-19 vaccine in First Nations peoples are impacted by comorbidities. Nat Immunol 2023; 24:966-978. [PMID: 37248417 PMCID: PMC10232372 DOI: 10.1038/s41590-023-01508-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/10/2023] [Indexed: 05/31/2023]
Abstract
High-risk groups, including Indigenous people, are at risk of severe COVID-19. Here we found that Australian First Nations peoples elicit effective immune responses to COVID-19 BNT162b2 vaccination, including neutralizing antibodies, receptor-binding domain (RBD) antibodies, SARS-CoV-2 spike-specific B cells, and CD4+ and CD8+ T cells. In First Nations participants, RBD IgG antibody titers were correlated with body mass index and negatively correlated with age. Reduced RBD antibodies, spike-specific B cells and follicular helper T cells were found in vaccinated participants with chronic conditions (diabetes, renal disease) and were strongly associated with altered glycosylation of IgG and increased interleukin-18 levels in the plasma. These immune perturbations were also found in non-Indigenous people with comorbidities, indicating that they were related to comorbidities rather than ethnicity. However, our study is of a great importance to First Nations peoples who have disproportionate rates of chronic comorbidities and provides evidence of robust immune responses after COVID-19 vaccination in Indigenous people.
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Affiliation(s)
- Wuji Zhang
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, 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
| | - Mark Mayo
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Claire Lonzi
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Vanessa Rigas
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Bianca F Middleton
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Ruth A Purcell
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jan Petersen
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Priyanka Chaurasia
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Francesca Mordant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | - Griffith B Perkins
- Central and Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Eva Zhang
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Macquarie University, Sydney, New South Wales, Australia
| | - Stephanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jennifer Audsley
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - David S Khoury
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Irani Thevarajan
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Services, Royal Melbourne Hospital and Doherty Department, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Allen C Cheng
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School and School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Monash Infectious Diseases, Monash Health and School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Branka Grubor-Bauk
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - P Toby Coates
- Central and Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Britt Christensen
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, Victoria, Australia
- Melbourne Sexual Health Centre, Infectious Diseases Department, Alfred Health, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Amy W Chung
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - John Boffa
- Central Australian Aboriginal Congress, Alice Springs, Northern Territory, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, Queensland, Australia
| | - Sarah Lynar
- Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, Northern Territory, Australia
| | - Jane Nelson
- Menzies School of Health Research, Darwin, Northern Territory, 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.
| | - Jane Davies
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
- Center for Influenza Disease and Emergence Response, Melbourne, Victoria, Australia.
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13
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Gao Y, Bergman I. Anti-tumor memory CD4 and CD8 T-cells quantified by bulk T-cell receptor (TCR) clonal analysis. Front Immunol 2023; 14:1137054. [PMID: 37033929 PMCID: PMC10076582 DOI: 10.3389/fimmu.2023.1137054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Simple, reliable methods to detect anti-tumor memory T-cells are necessary to develop a clinical tumor vaccination program. A mouse model of curative viral onco-immunotherapy found that peritoneal tumor challenge following cure identified an oligoclonal anti-tumor memory CD4 and CD8 T-cell response. Clonotypes differed among the challenged animals but were congruent in blood, spleen and peritoneal cells (PC) of the same animal. Adoptive transfer demonstrated that the high-frequency responding T-cells were tumor specific. Tetramer analysis confirmed that clonotype frequency determined by T-cell receptor (TCR)- chain (TRB) analysis closely approximated cell clone frequency. The mean frequency of resting anti-tumor memory CD4 T-cells in unchallenged spleen was 0.028% and of memory CD8 T-cells was 0.11% which was not high enough to distinguish them from background. Stimulation produced a mean ~10-fold increase in splenic and 100-fold increase in peritoneal anti-tumor memory T-cell clonotypes. This methodology can be developed to use blood and tissue sampling to rapidly quantify the effectiveness of a tumor vaccine or any vaccine generating therapeutic T-cells.
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Affiliation(s)
- Yanhua Gao
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Ira Bergman
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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14
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Barber-Axthelm IM, Wragg KM, Esterbauer R, Amarasena TH, Barber-Axthelm VR, Wheatley AK, Gibbon AM, Kent SJ, Juno JA. Phenotypic and functional characterization of pharmacologically expanded Vγ9Vδ2 T cells in pigtail macaques. iScience 2023; 26:106269. [PMID: 36936791 PMCID: PMC10014287 DOI: 10.1016/j.isci.2023.106269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/22/2022] [Accepted: 02/19/2023] [Indexed: 03/12/2023] Open
Abstract
While gaining interest as treatment for cancer and infectious disease, the clinical efficacy of Vγ9Vδ2 T cell-based immunotherapeutics has to date been limited. An improved understanding of γδ T cell heterogeneity across lymphoid and non-lymphoid tissues, before and after pharmacological expansion, is required. Here, we describe the phenotype and tissue distribution of Vγ9Vδ2 T cells at steady state and following in vivo pharmacological expansion in pigtail macaques. Intravenous phosphoantigen administration with subcutaneous rhIL-2 drove robust expansion of Vγ9Vδ2 T cells in blood and pulmonary mucosa, while expansion was confined to the pulmonary mucosa following intratracheal antigen administration. Peripheral blood Vγ9Vδ2 T cell expansion was polyclonal, and associated with a significant loss of CCR6 expression due to IL-2-mediated receptor downregulation. Overall, we show the tissue distribution and phenotype of in vivo pharmacologically expanded Vγ9Vδ2 T cells can be altered based on the antigen administration route, with implications for tissue trafficking and the clinical efficacy of Vγ9Vδ2 T cell immunotherapeutics.
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Affiliation(s)
- Isaac M. Barber-Axthelm
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kathleen M. Wragg
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Robyn Esterbauer
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thakshila H. Amarasena
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Valerie R.B. Barber-Axthelm
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Anne M. Gibbon
- Monash Animal Research Platform, Monash University, Clayton, VIC 3800, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Jennifer A. Juno
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
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15
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Shah SZ, Jabbar B, Mirza MU, Waqas M, Aziz S, Halim SA, Ali A, Rafique S, Idrees M, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean-Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target. Vaccines (Basel) 2022; 11:61. [PMID: 36679906 PMCID: PMC9867508 DOI: 10.3390/vaccines11010061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Crimean-Congo haemorrhagic fever (CCHF), caused by Crimean-Congo haemorrhagic fever virus (CCHFV), is a disease of worldwide importance (endemic yet not limited to Asia, Middle East, and Africa) and has triggered several outbreaks amounting to a case fatality rate of 10-40% as per the World Health Organization. Genetic diversity and phylogenetic data revealed that the Asia-1 genotype of CCHFV remained dominant in Pakistan, where 688 confirmed cases were reported between the 2012-2022 period. Currently, no approved vaccine is available to tackle the viral infection. Epitope-based vaccine design has gained significant attention in recent years due to its safety, timeliness, and cost efficiency compared to conventional vaccines. In the present study, we employed a robust immunoinformatics-based approach targeting the structural glycoproteins G1 and G2 of CCHFV (Asia-1 genotype) to design a multi-epitope vaccine construct. Five B-cells and six cytotoxic T-lymphocytes (CTL) epitopes were mapped and finalized from G1 and G2 and were fused with suitable linkers (EAAAK, GGGS, AAY, and GPGPG), a PADRE sequence (13 aa), and an adjuvant (50S ribosomal protein L7/L12) to formulate a chimeric vaccine construct. The selected CTL epitopes showed high affinity and stable binding with the binding groove of common human HLA class I molecules (HLA-A*02:01 and HLA-B*44:02) and mouse major histocompatibility complex class I molecules. The chimeric vaccine was predicted to be an antigenic, non-allergenic, and soluble molecule with a suitable physicochemical profile. Molecular docking and molecular dynamics simulation indicated a stable and energetically favourable interaction between the constructed antigen and Toll-like receptors (TLR2, TLR3, and TLR4). Our results demonstrated that innate, adaptive, and humoral immune responses could be elicited upon administration of such a potent muti-epitope vaccine construct. These results could be helpful for an experimental vaccinologist to develop an effective vaccine against the Asia-1 genotype of CCHFV.
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Affiliation(s)
- Syed Zawar Shah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2404, Khartoum 11111, Sudan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
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16
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Muraduzzaman AKM, Illing PT, Mifsud NA, Purcell AW. Understanding the Role of HLA Class I Molecules in the Immune Response to Influenza Infection and Rational Design of a Peptide-Based Vaccine. Viruses 2022; 14:2578. [PMID: 36423187 PMCID: PMC9695287 DOI: 10.3390/v14112578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Influenza A virus is a respiratory pathogen that is responsible for regular epidemics and occasional pandemics that result in substantial damage to life and the economy. The yearly reformulation of trivalent or quadrivalent flu vaccines encompassing surface glycoproteins derived from the current circulating strains of the virus does not provide sufficient cross-protection against mismatched strains. Unlike the current vaccines that elicit a predominant humoral response, vaccines that induce CD8+ T cells have demonstrated a capacity to provide cross-protection against different influenza strains, including novel influenza viruses. Immunopeptidomics, the mass spectrometric identification of human-leukocyte-antigen (HLA)-bound peptides isolated from infected cells, has recently provided key insights into viral peptides that can serve as potential T cell epitopes. The critical elements required for a strong and long-living CD8+ T cell response are related to both HLA restriction and the immunogenicity of the viral peptide. This review examines the importance of HLA and the viral immunopeptidome for the design of a universal influenza T-cell-based vaccine.
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Affiliation(s)
| | | | - Nicole A. Mifsud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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Nguyen AT, Lau HMP, Sloane H, Jayasinghe D, Mifsud NA, Chatzileontiadou DSM, Grant EJ, Szeto C, Gras S. Homologous peptides derived from influenza A, B and C viruses induce variable CD8 + T cell responses with cross-reactive potential. Clin Transl Immunology 2022; 11:e1422. [PMID: 36275878 PMCID: PMC9581725 DOI: 10.1002/cti2.1422] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Objective Influenza A, B and C viruses (IAV, IBV and ICV, respectively) circulate globally, infecting humans and causing widespread morbidity and mortality. Here, we investigate the T cell response towards an immunodominant IAV epitope, NP265‐273, and its IBV and ICV homologues, presented by HLA‐A*03:01 molecule expressed in ~ 4% of the global population (~ 300 million people). Methods We assessed the magnitude (tetramer staining) and quality of the CD8+ T cell response (intracellular cytokine staining) towards NP265‐IAV and described the T cell receptor (TCR) repertoire used to recognise this immunodominant epitope. We next assessed the immunogenicity of NP265‐IAV homologue peptides from IBV and ICV and the ability of CD8+ T cells to cross‐react towards these homologous peptides. Furthermore, we determined the structures of NP265‐IAV and NP323‐IBV peptides in complex with HLA‐A*03:01 by X‐ray crystallography. Results Our study provides a detailed characterisation of the CD8+ T cell response towards NP265‐IAV and its IBV and ICV homologues. The data revealed a diverse repertoire for NP265‐IAV that is associated with superior anti‐viral protection. Evidence of cross‐reactivity between the three different influenza virus strain‐derived epitopes was observed, indicating the discovery of a potential vaccination target that is broad enough to cover all three influenza strains. Conclusion We show that while there is a potential to cross‐protect against distinct influenza virus lineages, the T cell response was stronger against the IAV peptide than IBV or ICV, which is an important consideration when choosing targets for future vaccine design.
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Affiliation(s)
- Andrea T Nguyen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Hiu Ming Peter Lau
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Hannah Sloane
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Dhilshan Jayasinghe
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Nicole A Mifsud
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Demetra SM Chatzileontiadou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Emma J Grant
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Christopher Szeto
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia,Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
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18
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Rowntree LC, Nguyen THO, Kedzierski L, Neeland MR, Petersen J, Crawford JC, Allen LF, Clemens EB, Chua B, McQuilten HA, Minervina AA, Pogorelyy MV, Chaurasia P, Tan HX, Wheatley AK, Jia X, Amanat F, Krammer F, Allen EK, Sonda S, Flanagan KL, Jumarang J, Pannaraj PS, Licciardi PV, Kent SJ, Bond KA, Williamson DA, Rossjohn J, Thomas PG, Tosif S, Crawford NW, van de Sandt CE, Kedzierska K. SARS-CoV-2-specific T cell memory with common TCRαβ motifs is established in unvaccinated children who seroconvert after infection. Immunity 2022; 55:1299-1315.e4. [PMID: 35750048 PMCID: PMC9174177 DOI: 10.1016/j.immuni.2022.06.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 11/05/2022]
Abstract
As the establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell memory in children remains largely unexplored, we recruited convalescent COVID-19 children and adults to define their circulating memory SARS-CoV-2-specific CD4+ and CD8+ T cells prior to vaccination. We analyzed epitope-specific T cells directly ex vivo using seven HLA class I and class II tetramers presenting SARS-CoV-2 epitopes, together with Spike-specific B cells. Unvaccinated children who seroconverted had comparable Spike-specific but lower ORF1a- and N-specific memory T cell responses compared with adults. This agreed with our TCR sequencing data showing reduced clonal expansion in children. A strong stem cell memory phenotype and common T cell receptor motifs were detected within tetramer-specific T cells in seroconverted children. Conversely, children who did not seroconvert had tetramer-specific T cells of predominantly naive phenotypes and diverse TCRαβ repertoires. Our study demonstrates the generation of SARS-CoV-2-specific T cell memory with common TCRαβ motifs in unvaccinated seroconverted children after their first virus encounter.
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Affiliation(s)
- Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Melanie R Neeland
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC 3000, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jan Petersen
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Brendon Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Priyanka Chaurasia
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sabrina Sonda
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS 7248, Australia
| | - Katie L Flanagan
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS 7248, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; School of Health and Biomedical Science, RMIT University, Melbourne, VIC 3000, Australia; Tasmanian Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, TAS 7250, Australia
| | - Jaycee Jumarang
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Departments of Pediatrics and Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Paul V Licciardi
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC 3000, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3000, Australia; Melbourne Sexual Health Centre, Infectious Diseases Department, Alfred Health, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Katherine A Bond
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3000, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shidan Tosif
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC 3000, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia; Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, VIC 3000, Australia
| | - Nigel W Crawford
- Infection and Immunity, Murdoch Children's Research Institute, Melbourne, VIC 3000, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3000, Australia; Department of General Medicine, Royal Children's Hospital Melbourne, Melbourne, VIC 3000, Australia; Royal Children's Hospital Melbourne, Immunisation Service, Melbourne, VIC 3000, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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Zhu MM, Niu BW, Liu LL, Yang H, Qin BY, Peng XH, Chen LX, Liu Y, Wang C, Ren XN, Xu CH, Zhou XH, Li F. Development of a humanized HLA-A30 transgenic mouse model. Animal Model Exp Med 2022; 5:350-361. [PMID: 35791899 PMCID: PMC9434587 DOI: 10.1002/ame2.12225] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background There are remarkable genetic differences between animal major histocompatibility complex (MHC) systems and the human leukocyte antigen (HLA) system. HLA transgenic humanized mouse model systems offer a much better method to study the HLA‐A‐related principal mechanisms for vaccine development and HLA‐A‐restricted responses against infection in human. Methods A recombinant gene encoding the chimeric HLA‐A30 monochain was constructed. This HHD molecule contains the following: α1‐α2 domains of HLA‐A30, α3 and cytoplasmic domains of H‐2Db, linked at its N‐terminus to the C‐terminus of human β2m by a 15‐amino‐acid peptide linker. The recombinant gene encoding the chimeric HLA‐A30 monochain cassette was introduced into bacterial artificial chromosome (BAC) CH502‐67J3 containing the HLA‐A01 gene locus by Red‐mediated homologous recombination. Modified BAC CH502‐67J3 was microinjected into the pronuclei of wild‐type mouse oocytes. This humanized mouse model was further used to assess the immune responses against influenza A virus (H1N1) pdm09 clinically isolated from human patients. Immune cell population, cytokine production, and histopathology in the lung were analyzed. Results We describe a novel human β2m‐HLA‐A30 (α1α2)‐H‐2Db (α3 transmembrane cytoplasmic) (HHD) monochain transgenic mouse strain, which contains the intact HLA‐A01 gene locus including 49 kb 5′‐UTR and 74 kb 3′‐UTR of HLA‐A01*01. Five transgenic lines integrated into the large genomic region of HLA‐A gene locus were obtained, and the robust expression of exogenous transgene was detected in various tissues from A30‐18# and A30‐19# lines encompassing the intact flanking sequences. Flow cytometry revealed that the introduction of a large genomic region in HLA‐A gene locus can influence the immune cell constitution in humanized mice. Pdm09 infection caused a similar immune response among HLA‐A30 Tg humanized mice and wild‐type mice, and induced the rapid increase of cytokines, including IFN‐γ, TNF‐α, and IL‐6, in both HLA‐A30 humanized Tg mice and wild‐type mice. The expression of HLA‐A30 transgene was dramatically promoted in tissues from A30‐9# line at 3 days post‐infection (dpi). Conclusions We established a promising preclinical research animal model of HLA‐A30 Tg humanized mouse, which could accelerate the identification of novel HLA‐A30‐restricted epitopes and vaccine development, and support the study of HLA‐A‐restricted responses against infection in humans.
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Affiliation(s)
- Meng-Min Zhu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Bo-Wen Niu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Ling-Ling Liu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Hua Yang
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Bo-Yin Qin
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xiu-Hua Peng
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Li-Xiang Chen
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yang Liu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Chao Wang
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xiao-Nan Ren
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Chun-Hua Xu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xiao-Hui Zhou
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Feng Li
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
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20
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Buckley PR, Lee CH, Pereira Pinho M, Ottakandathil Babu R, Woo J, Antanaviciute A, Simmons A, Ogg G, Koohy H. HLA-dependent variation in SARS-CoV-2 CD8 + T cell cross-reactivity with human coronaviruses. Immunology 2022; 166:78-103. [PMID: 35143694 PMCID: PMC9111820 DOI: 10.1111/imm.13451] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/26/2021] [Accepted: 01/17/2022] [Indexed: 11/29/2022] Open
Abstract
The conditions and extent of cross-protective immunity between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and common-cold human coronaviruses (HCoVs) remain open despite several reports of pre-existing T cell immunity to SARS-CoV-2 in individuals without prior exposure. Using a pool of functionally evaluated SARS-CoV-2 peptides, we report a map of 126 immunogenic peptides with high similarity to 285 MHC-presented peptides from at least one HCoV. Employing this map of SARS-CoV-2-non-homologous and homologous immunogenic peptides, we observe several immunogenic peptides with high similarity to human proteins, some of which have been reported to have elevated expression in severe COVID-19 patients. After combining our map with SARS-CoV-2-specific TCR repertoire data from COVID-19 patients and healthy controls, we show that public repertoires for the majority of convalescent patients are dominated by TCRs cognate to non-homologous SARS-CoV-2 peptides. We find that for a subset of patients, >50% of their public SARS-CoV-2-specific repertoires consist of TCRs cognate to homologous SARS-CoV-2-HCoV peptides. Further analysis suggests that this skewed distribution of TCRs cognate to homologous or non-homologous peptides in COVID-19 patients is likely to be HLA-dependent. Finally, we provide 10 SARS-CoV-2 peptides with known cognate TCRs that are conserved across multiple coronaviruses and are predicted to be recognized by a high proportion of the global population. These findings may have important implications for COVID-19 heterogeneity, vaccine-induced immune responses, and robustness of immunity to SARS-CoV-2 and its variants.
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Affiliation(s)
- Paul R. Buckley
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Mariana Pereira Pinho
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Rosana Ottakandathil Babu
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Jeongmin Woo
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Agne Antanaviciute
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
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21
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Bull MB, Gu H, Ma FNL, Perera LP, Poon LLM, Valkenburg SA. Next-generation T cell-activating vaccination increases influenza virus mutation prevalence. SCIENCE ADVANCES 2022; 8:eabl5209. [PMID: 35385318 PMCID: PMC8986104 DOI: 10.1126/sciadv.abl5209] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
To determine the potential for viral adaptation to T cell responses, we probed the full influenza virus genome by next-generation sequencing directly ex vivo from infected mice, in the context of an experimental T cell-based vaccine, an H5N1-based viral vectored vaccinia vaccine Wyeth/IL-15/5Flu, versus the current standard-of-care, seasonal inactivated influenza vaccine (IIV) and unvaccinated conditions. Wyeth/IL-15/5Flu vaccination was coincident with increased mutation incidence and frequency across the influenza genome; however, mutations were not enriched within T cell epitope regions, but high allele frequency mutations within conserved hemagglutinin stem regions and PB2 mammalian adaptive mutations arose. Depletion of CD4+ and CD8+ T cell subsets led to reduced frequency of mutants in vaccinated mice; therefore, vaccine-mediated T cell responses were important drivers of virus diversification. Our findings suggest that Wyeth/IL-15/5Flu does not generate T cell escape mutants but increases stochastic events for virus adaptation by stringent bottlenecks.
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Affiliation(s)
- Maireid B. Bull
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Fionn N. L. Ma
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Liyanage P. Perera
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1374, USA
| | - Leo L. M. Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sophie A. Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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22
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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: 15] [Impact Index Per Article: 7.5] [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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23
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Chiozzini C, Ridolfi B, Federico M. Extracellular Vesicles and Their Use as Vehicles of Immunogens. Methods Mol Biol 2022; 2504:177-198. [PMID: 35467287 DOI: 10.1007/978-1-0716-2341-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Healthy cells constitutively release lipid bilayered vesicles of different sizes and recognizing different biogenesis, collectively referred to as extracellular vesicles (EVs). EVs can be distinguished in exosomes and microvesicles. Biological and biomedical research on EVs is an emerging field that is rapidly growing. Many EV features including biogenesis, cell uptake, and functions still require unambiguous elucidation. Nevertheless, it has been well established that EVs are involved in communication among cells, tissues, and organs under both healthy and disease conditions by virtue of their ability to deliver macromolecules to target cells. Here, we summarize most recent findings regarding biogenesis, structure, and functions of both exosomes and microvesicles. In addition, the use of EVs as delivery tools to induce CD8+ T cell immunity is addressed compared to current designs exploiting enveloped viral vectors and virus-like particles. Finally, we describe a both safe and original approach conceived for the induction of strong CTL immunity against antigens uploaded in EVs constitutively released by muscle cells.
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Affiliation(s)
- Chiara Chiozzini
- National Center for Global Health, Istituto Superiore di Sanità (ISS), Rome, Italy.
| | - Barbara Ridolfi
- National Center for Global Health, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Maurizio Federico
- National Center for Global Health, Istituto Superiore di Sanità (ISS), Rome, Italy
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24
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Szeto C, Nguyen AT, Lobos CA, Chatzileontiadou DSM, Jayasinghe D, Grant EJ, Riboldi-Tunnicliffe A, Smith C, Gras S. Molecular Basis of a Dominant SARS-CoV-2 Spike-Derived Epitope Presented by HLA-A*02:01 Recognised by a Public TCR. Cells 2021; 10:cells10102646. [PMID: 34685626 PMCID: PMC8534114 DOI: 10.3390/cells10102646] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
The data currently available on how the immune system recognises the SARS-CoV-2 virus is growing rapidly. While there are structures of some SARS-CoV-2 proteins in complex with antibodies, which helps us understand how the immune system is able to recognise this new virus; however, we lack data on how T cells are able to recognise this virus. T cells, especially the cytotoxic CD8+ T cells, are critical for viral recognition and clearance. Here we report the X-ray crystallography structure of a T cell receptor, shared among unrelated individuals (public TCR) in complex with a dominant spike-derived CD8+ T cell epitope (YLQ peptide). We show that YLQ activates a polyfunctional CD8+ T cell response in COVID-19 recovered patients. We detail the molecular basis for the shared TCR gene usage observed in HLA-A*02:01+ individuals, providing an understanding of TCR recognition towards a SARS-CoV-2 epitope. Interestingly, the YLQ peptide conformation did not change upon TCR binding, facilitating the high-affinity interaction observed.
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Affiliation(s)
- Christopher Szeto
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia; (C.S.); (A.T.N.); (C.A.L.); (D.S.M.C.); (D.J.); (E.J.G.)
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Andrea T. Nguyen
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia; (C.S.); (A.T.N.); (C.A.L.); (D.S.M.C.); (D.J.); (E.J.G.)
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Christian A. Lobos
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia; (C.S.); (A.T.N.); (C.A.L.); (D.S.M.C.); (D.J.); (E.J.G.)
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Demetra S. M. Chatzileontiadou
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia; (C.S.); (A.T.N.); (C.A.L.); (D.S.M.C.); (D.J.); (E.J.G.)
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Dhilshan Jayasinghe
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia; (C.S.); (A.T.N.); (C.A.L.); (D.S.M.C.); (D.J.); (E.J.G.)
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Emma J. Grant
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia; (C.S.); (A.T.N.); (C.A.L.); (D.S.M.C.); (D.J.); (E.J.G.)
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | | | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephanie Gras
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia; (C.S.); (A.T.N.); (C.A.L.); (D.S.M.C.); (D.J.); (E.J.G.)
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Correspondence:
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25
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Lu T, Zhang Z, Zhu J, Wang Y, Jiang P, Xiao X, Bernatchez C, Heymach JV, Gibbons DL, Wang J, Xu L, Reuben A, Wang T. Deep learning-based prediction of the T cell receptor-antigen binding specificity. NAT MACH INTELL 2021; 3:864-875. [PMID: 36003885 PMCID: PMC9396750 DOI: 10.1038/s42256-021-00383-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/01/2021] [Indexed: 02/05/2023]
Abstract
Neoantigens play a key role in the recognition of tumor cells by T cells. However, only a small proportion of neoantigens truly elicit T cell responses, and fewer clues exist as to which neoantigens are recognized by which T cell receptors (TCRs). We built a transfer learning-based model, named pMHC-TCR binding prediction network (pMTnet), to predict TCR-binding specificities of neoantigens, and T cell antigens in general, presented by class I major histocompatibility complexes (pMHCs). pMTnet was comprehensively validated by a series of analyses, and showed advance over previous work by a large margin. By applying pMTnet in human tumor genomics data, we discovered that neoantigens were generally more immunogenic than self-antigens, but HERV-E, a special type of self-antigen that is re-activated in kidney cancer, is more immunogenic than neoantigens. We further discovered that patients with more clonally expanded T cells exhibiting better affinity against truncal, rather than subclonal, neoantigens, had more favorable prognosis and treatment response to immunotherapy, in melanoma and lung cancer but not in kidney cancer. Predicting TCR-neoantigen/antigen pairs is one of the most daunting challenges in modern immunology. However, we achieved an accurate prediction of the pairing only using the TCR sequence (CDR3β), antigen sequence, and class I MHC allele, and our work revealed unique insights into the interactions of TCRs and pMHCs in human tumors using pMTnet as a discovery tool.
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Affiliation(s)
- Tianshi Lu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Ze Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - James Zhu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Peixin Jiang
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Xue Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - John V. Heymach
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Don L. Gibbons
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Alexandre Reuben
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
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26
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Abdella S, Tessema M, Tasew G, Defar A, Deressa A, Regasa F, Teka F, Tigabu E, Nigussie D, Belachew T, Molla M, Deribew A, Abebe W, Yigzaw T, Nigatu T, Mitike G, Haile T, Taame H, Ahmed M, Nigatu F, Tolesa T, Wolka E, Amogne W, Laillou A, Amare M, Fufa Y, Argaw A, Waganew W, Azazh A, Worku A, Redae B, Sultan M, Walelegn M, Tefera M, Yifru S, Argaw R, Brehau N, Teklu S, Demoz G, Seman Y, Salasibew M, Ejeta E, Whiting SJ, Wolday D, Tollera G, Abate E, Duguma D. Prognostic factors and outcomes of COVID-19 cases in Ethiopia: multi-center cohort study protocol. BMC Infect Dis 2021; 21:956. [PMID: 34530744 PMCID: PMC8443913 DOI: 10.1186/s12879-021-06652-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 09/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) and became pandemic after emerging in Wuhan, China, in December 2019. Several studies have been conducted to understand the key features of COVID-19 and its public health impact. However, the prognostic factors of COVID-19 are not well studied in the African setting. In this study, we aim to determine the epidemiological and clinical features of COVID-19 cases, immunological and virological courses, interaction with nutritional status, and response to treatment for COVID-19 patients in Ethiopia. METHODS A multi-center cohort study design will be performed. Patients with confirmed COVID-19 infection admitted to selected treatment centers will be enrolled irrespective of their symptoms and followed-up for 12 months. Baseline epidemiological, clinical, laboratory and imaging data will be collected from treatment records, interviews, physical measurements, and biological samples. Follow-up data collection involves treatment and prognostic outcomes to be measured using different biomarkers and clinical parameters. Data collection will be done electronically using the Open Data Kit (ODK) software package and then exported to STATA/SPSS for analysis. Both descriptive and multivariable analyses will be performed to assess the independent determinants of the treatment outcome and prognosis to generate relevant information for informed prevention and case management. The primary outcomes of this study are death/survival and viral shedding. Secondary outcomes include epidemiological characteristics, clinical features, genetic frequency shifts (genotypic variations), and nutritional status. DISCUSSION This is the first large prospective cohort study of patients in hospitals with COVID-19 in Ethiopia. The results will enable us to better understand the epidemiology of SARS-CoV-2 in Africa. This study will also provide useful information for effective public health measures and future pandemic preparedness and in response to outbreaks. It will also support policymakers in managing the epidemic based on scientific evidence. TRIAL REGISTRATION The Protocol prospectively registered in ClinicalTrials.gov (NCT04584424) on 30 October, 2020.
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Affiliation(s)
- Saro Abdella
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Geremew Tasew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Atkure Defar
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Asefa Deressa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Feyisa Regasa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Frehiwot Teka
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Eyasu Tigabu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | | | | | | | | | - Tsinuel Nigatu
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Getnet Mitike
- International Institute for Primary Health Care, Addis Ababa, Ethiopia
| | | | | | - Muhammed Ahmed
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Frehiwot Nigatu
- International Institute for Primary Health Care, Addis Ababa, Ethiopia
| | - Tola Tolesa
- Saint Paul's Hospital, Addis Ababa, Ethiopia
| | - Eskinder Wolka
- International Institute for Primary Health Care, Addis Ababa, Ethiopia
| | | | | | - Misker Amare
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Yaregal Fufa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | | | | | | | | | | | | | - Sisay Yifru
- Ethiopian Ministry of Health, Addis Ababa, Ethiopia
| | - Rahel Argaw
- Ethiopian Ministry of Health, Addis Ababa, Ethiopia
| | - Natinael Brehau
- COVID-19 Isolation and Treatment Center, Eka Kotebe General Hospital, Addis Ababa, Ethiopia
| | - Sisay Teklu
- Ethiopian Ministry of Health, Addis Ababa, Ethiopia
| | - Getachew Demoz
- COVID-19 Isolation and Treatment Center, Eka Kotebe General Hospital, Addis Ababa, Ethiopia
| | - Yakob Seman
- Ethiopian Ministry of Health, Addis Ababa, Ethiopia
| | | | - Eshetu Ejeta
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Susan J Whiting
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | | | | | - Ebba Abate
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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27
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Rostaminia S, Aghaei SS, Farahmand B, Nazari R, Ghaemi A. Computational Design and Analysis of a Multi-epitope Against Influenza A virus. Int J Pept Res Ther 2021; 27:2625-2638. [PMID: 34539293 PMCID: PMC8435298 DOI: 10.1007/s10989-021-10278-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 12/28/2022]
Abstract
Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed. So, designing an effective vaccine against Influenza A virus is a critical issue in the field of medical biotechnology. For this reason, to combat this disease, we have designed a novel multi-epitope vaccine candidate based on the several conserved and potential linear B-cell and T-cell binding epitopes by using the in silico approach. This vaccine consists of an ER signal conserved sequence, the PADRE conserved epitope and two conserved epitopes of Influenza matrix protein 2. T-cell binding epitopes from Matrix protein 2 were predicted by in silico tools of epitope prediction. The selected epitopes were joined by flexible linkers and physicochemical properties, toxicity, and allergenecity were investigated. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. The final multi-epitope construct was modeled, confirmed by different programs and the molecular interactions with immune receptors were considered. The molecular docking assay indicated the interactions with immune-stimulatory toll-like receptor 3 (TLR3) and major histocompatibility complex class I (MHCI). The HADDOCK and H DOCK servers were used to make docking analysis, respectively. The docking analysis indicated a strong and stable binding interaction between the vaccine construct with major histocompatibility complex (MHC) class I and toll-like receptor 3. Overall, the findings suggest that the current vaccine may be a promising vaccine to prevent Influenza infection.
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Affiliation(s)
- Samaneh Rostaminia
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | | | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, 69, P.O.Box: 1316943551, Tehran, Iran
| | - Raziye Nazari
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, 69, P.O.Box: 1316943551, Tehran, Iran
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28
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Virus-Induced CD8 + T-Cell Immunity and Its Exploitation to Contain the SARS-CoV-2 Pandemic. Vaccines (Basel) 2021; 9:vaccines9080922. [PMID: 34452047 PMCID: PMC8402519 DOI: 10.3390/vaccines9080922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/17/2021] [Indexed: 01/08/2023] Open
Abstract
The current battle against Severe Acute Respiratory Syndrome (SARS)-Coronavirus-2 benefits from the worldwide distribution of different vaccine formulations. All anti-SARS-CoV-2 vaccines in use are conceived to induce anti-Spike neutralizing antibodies. However, this strategy still has unresolved issues, the most relevant of which are: (i) the resistance to neutralizing antibodies of emerging SARS-CoV-2 variants and (ii) the waning of neutralizing antibodies. On the other hand, both pre-clinical evidence and clinical evidence support the idea that the immunity sustained by antigen-specific CD8+ T lymphocytes can complement and also surrogate the antiviral humoral immunity. As a distinctive feature, anti-SARS-CoV-2 CD8+ T-driven immunity maintains its efficacy even in the presence of viral protein mutations. In addition, on the basis of data obtained in survivors of the SARS-CoV epidemic, this immunity is expected to last for several years. In this review, both the mechanisms and role of CD8+ T-cell immunity in viral infections, particularly those induced by SARS-CoV and SARS-CoV-2, are analyzed. Moreover, a CD8+ T-cell-based vaccine platform relying on in vivo engineered extracellular vesicles is described. When applied to SARS-CoV-2, this strategy was proven to induce a strong immunogenicity, holding great promise for its translation into the clinic.
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29
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Chaurasia P, Nguyen THO, Rowntree LC, Juno JA, Wheatley AK, Kent SJ, Kedzierska K, Rossjohn J, Petersen J. Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein. J Biol Chem 2021; 297:101065. [PMID: 34384783 PMCID: PMC8352664 DOI: 10.1016/j.jbc.2021.101065] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 01/02/2023] Open
Abstract
CD8+ T cells play an important role in vaccination and immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although numerous SARS-CoV-2 CD8+ T cell epitopes have been identified, the molecular basis underpinning T cell receptor (TCR) recognition of SARS-CoV-2-specific T cells remains unknown. The T cell response directed toward SARS-CoV-2 spike protein–derived S269–277 peptide presented by the human leukocyte antigen (HLA)-A∗02:01 allomorph (hereafter the HLA-A2S269–277 epitope) is, to date, the most immunodominant SARS-CoV-2 epitope found in individuals bearing this allele. As HLA-A2S269–277-specific CD8+ T cells utilize biased TRAV12 gene usage within the TCR α-chain, we sought to understand the molecular basis underpinning this TRAV12 dominance. We expressed four TRAV12+ TCRs which bound the HLA-A2S269–277 complex with low micromolar affinity and determined the crystal structure of the HLA-A2S269–277 binary complex, and subsequently a ternary structure of the TRAV12+ TCR complexed to HLA-A2S269–277. We found that the TCR made extensive contacts along the entire length of the S269–277 peptide, suggesting that the TRAV12+ TCRs would be sensitive to sequence variation within this epitope. To examine this, we investigated cross-reactivity toward analogous peptides from existing SARS-CoV-2 variants and closely related coronaviruses. We show via surface plasmon resonance and tetramer studies that the TRAV12+ T cell repertoire cross-reacts poorly with these analogous epitopes. Overall, we defined the structural basis underpinning biased TCR recognition of CD8+ T cells directed at an immunodominant epitope and provide a framework for understanding TCR cross-reactivity toward viral variants within the S269–277 peptide.
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Affiliation(s)
- Priyanka Chaurasia
- Infection and Immunity Program and 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, Melbourne, Victoria, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| | - Jamie Rossjohn
- Infection and Immunity Program and 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, United Kingdom.
| | - Jan Petersen
- Infection and Immunity Program and 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.
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30
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Yang Z, Hua L, Yang M, Liu SQ, Shen J, Li W, Long Q, Bai H, Yang X, Ren Z, Zheng X, Sun W, Ye C, Li D, Zheng P, He J, Chen Y, Huang W, Peng X, Ma Y. RBD-Modified Bacterial Vesicles Elicited Potential Protective Immunity against SARS-CoV-2. NANO LETTERS 2021; 21:5920-5930. [PMID: 34279108 PMCID: PMC8315139 DOI: 10.1021/acs.nanolett.1c00680] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/02/2021] [Indexed: 05/13/2023]
Abstract
The disease caused by SARS-CoV-2 infection threatens human health. In this study, we used high-pressure homogenization technology not only to efficiently drive the bacterial membrane to produce artificial vesicles but also to force the fusion protein ClyA-receptor binding domain (RBD) to pass through gaps in the bacterial membrane to increase the contact between ClyA-RBD and the membrane. Therefore, the load of ClyA-RBD on the membrane is substantially increased. Using this technology, we constructed a "ring-like" bacterial biomimetic vesicle (BBV) loaded with polymerized RBD (RBD-BBV). RBD-BBVs injected subcutaneously can accumulate in lymph nodes, promote antigen uptake and processing, and elicit SARS-CoV-2-specific humoral and cellular immune responses in mice. In conclusion, we evaluated the potential of this novel bacterial vesicle as a vaccine delivery system and provided a new idea for the development of SARS-CoV-2 vaccines.
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Affiliation(s)
- Zhongqian Yang
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Liangqun Hua
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
- Yunnan
University, Kunming, China
| | - Mengli Yang
- National
Kunming High-level Biosafety Primate Research Center, Institute of
Medical Biology, Chinese Academy of Medical
Sciences and Peking Union Medical College, Kunming, China
| | - Shu-Qun Liu
- Yunnan
University, Kunming, China
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, China
| | - Jianxin Shen
- Yunnan
University, Kunming, China
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan & School of Life Sciences, Yunnan
University, Kunming, China
| | - Weiran Li
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Qiong Long
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Hongmei Bai
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Xu Yang
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Zhaoling Ren
- The
Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming
Medical University, Kunming, China
| | - Xiao Zheng
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
- Yunnan
University, Kunming, China
| | - Wenjia Sun
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Chao Ye
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Duo Li
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
- Department
of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, China
| | - Peng Zheng
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Jinrong He
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
- Kunming
Medical University, Kunming, China
| | - Yongjun Chen
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Weiwei Huang
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
| | - Xiaozhong Peng
- National
Kunming High-level Biosafety Primate Research Center, Institute of
Medical Biology, Chinese Academy of Medical
Sciences and Peking Union Medical College, Kunming, China
- State
Key Laboratory of Medical Molecular Biology, Department of Molecular
Biology and Biochemistry, Institute of Basic Medical Sciences, Medical
Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking
Union Medical College, Beijing, China
| | - Yanbing Ma
- Laboratory
of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union
Medical College, Kunming, China
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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: 24] [Impact Index Per Article: 8.0] [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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CD4 + T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features. Cell Rep 2021; 32:107885. [PMID: 32668259 PMCID: PMC7370177 DOI: 10.1016/j.celrep.2020.107885] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 01/20/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
T cell recognition of peptides presented by human leukocyte antigens (HLAs) is mediated by the highly variable T cell receptor (TCR). Despite this built-in TCR variability, individuals can mount immune responses against viral epitopes by using identical or highly related TCRs expressed on CD8+ T cells. Characterization of these TCRs has extended our understanding of the molecular mechanisms that govern the recognition of peptide-HLA. However, few examples exist for CD4+ T cells. Here, we investigate CD4+ T cell responses to the internal proteins of the influenza A virus that correlate with protective immunity. We identify five internal epitopes that are commonly recognized by CD4+ T cells in five HLA-DR1+ subjects and show conservation across viral strains and zoonotic reservoirs. TCR repertoire analysis demonstrates several shared gene usage biases underpinned by complementary biochemical features evident in a structural comparison. These epitopes are attractive targets for vaccination and other T cell therapies.
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Gibadullin R, Randall CJ, Sidney J, Sette A, Gellman SH. Backbone Modifications of HLA-A2-Restricted Antigens Induce Diverse Binding and T Cell Activation Outcomes. J Am Chem Soc 2021; 143:6470-6481. [PMID: 33881854 DOI: 10.1021/jacs.1c00016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
CD8+ T cells express T cell receptors (TCRs) that recognize short peptide antigens in the context of major histocompatibility class I (MHC I) molecules. This recognition process produces an array of cytokine-mediated signals that help to govern immunological responses. Design of biostable MHC I peptide vaccines containing unnatural subunits is desirable, and synthetic antigens in which a native α-amino acid residue is replaced by a homologous β-amino acid residue (native side chain but extended backbone) might be useful in this regard. We have evaluated the impact of α-to-β backbone modification at a single site on T cell-mediated recognition of six clinically important viral and tumor-associated antigens bound to an MHC I. Effects of this modification on MHC I affinity and T cell activation were measured. Many of these modifications diminish or prevent T cell response. However, a number of α/β-peptide antigens were found to mimic the activity of natural antigens or to enhance maximal T cell response, as measured by interferon-γ release. Results from this broad exploratory study advance our understanding of immunological responses to antigens bearing unnatural modifications and suggest that α/β-peptides could be a source of potent and proteolytically stable variants of native antigens.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Caleb J Randall
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States.,Department of Medicine, University of California, San Diego, California 92093, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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Nguyen THO, Rowntree LC, Petersen J, Chua BY, Hensen L, Kedzierski L, van de Sandt CE, Chaurasia P, Tan HX, Habel JR, Zhang W, Allen LF, Earnest L, Mak KY, Juno JA, Wragg K, Mordant FL, Amanat F, Krammer F, Mifsud NA, Doolan DL, Flanagan KL, Sonda S, Kaur J, Wakim LM, Westall GP, James F, Mouhtouris E, Gordon CL, Holmes NE, Smibert OC, Trubiano JA, Cheng AC, Harcourt P, Clifton P, Crawford JC, Thomas PG, Wheatley AK, Kent SJ, Rossjohn J, Torresi J, Kedzierska K. CD8 + T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope display high naive precursor frequency and TCR promiscuity. Immunity 2021; 54:1066-1082.e5. [PMID: 33951417 PMCID: PMC8049468 DOI: 10.1016/j.immuni.2021.04.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/23/2021] [Accepted: 04/12/2021] [Indexed: 12/16/2022]
Abstract
To better understand primary and recall T cell responses during coronavirus disease 2019 (COVID-19), it is important to examine unmanipulated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells. By using peptide-human leukocyte antigen (HLA) tetramers for direct ex vivo analysis, we characterized CD8+ T cells specific for SARS-CoV-2 epitopes in COVID-19 patients and unexposed individuals. Unlike CD8+ T cells directed toward subdominant epitopes (B7/N257, A2/S269, and A24/S1,208) CD8+ T cells specific for the immunodominant B7/N105 epitope were detected at high frequencies in pre-pandemic samples and at increased frequencies during acute COVID-19 and convalescence. SARS-CoV-2-specific CD8+ T cells in pre-pandemic samples from children, adults, and elderly individuals predominantly displayed a naive phenotype, indicating a lack of previous cross-reactive exposures. T cell receptor (TCR) analyses revealed diverse TCRαβ repertoires and promiscuous αβ-TCR pairing within B7/N105+CD8+ T cells. Our study demonstrates high naive precursor frequency and TCRαβ diversity within immunodominant B7/N105-specific CD8+ T cells and provides insight into SARS-CoV-2-specific T cell origins and subsequent responses.
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Affiliation(s)
- Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jan Petersen
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 060-0808, Japan
| | - Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam 1066CX, the Netherlands
| | - Priyanka Chaurasia
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jennifer R Habel
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Wuji Zhang
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Linda Earnest
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kai Yan Mak
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Kathleen Wragg
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Francesca L Mordant
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD 4870, Australia
| | - Katie L Flanagan
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS 7248, Australia; Department of Immunology and Pathology, Monash University, Commercial Road, Melbourne, VIC 3004, Australia; School of Health and Biomedical Science, RMIT University, Melbourne, VIC 3000, Australia; Tasmanian Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, TAS 7250, Australia
| | - Sabrina Sonda
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS 7248, Australia
| | - Jasveen Kaur
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS 7248, Australia; Tasmanian Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, TAS 7250, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Glen P Westall
- Lung Transplant Unit, Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Fiona James
- Department of Infectious Diseases, Austin Hospital, Heidelberg, VIC 3084, Australia
| | - Effie Mouhtouris
- Department of Infectious Diseases, Austin Hospital, Heidelberg, VIC 3084, Australia
| | - Claire L Gordon
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Hospital, Heidelberg, VIC 3084, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases, Austin Hospital, Heidelberg, VIC 3084, Australia; Department of Medicine and Radiology, The University of Melbourne, Parkville, VIC 3000, Australia; Data Analytics Research and Evaluation (DARE) Centre, Austin Health and The University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Olivia C Smibert
- Department of Infectious Diseases, Austin Hospital, Heidelberg, VIC 3084, Australia; Department of Infectious Diseases, Peter McCallum Cancer Centre, Melbourne, VIC 3000, Australia; The National Centre for Infections in Cancer, Peter McCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Jason A Trubiano
- Department of Infectious Diseases, Peter McCallum Cancer Centre, Melbourne, VIC 3000, Australia; The National Centre for Infections in Cancer, Peter McCallum Cancer Centre, Melbourne, VIC 3000, Australia; Centre for Antibiotic Allergy and Research, Department of Infectious Diseases Austin Health, Heidelberg, VIC 3084, Australia; Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Allen C Cheng
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, VIC 3004, Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | | | | | - Jeremy Chase Crawford
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3000, Australia; Melbourne Sexual Health Centre, Infectious Diseases Department, Alfred Health, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Joseph Torresi
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 060-0808, Japan.
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Ferrantelli F, Chiozzini C, Manfredi F, Giovannelli A, Leone P, Federico M. Simultaneous CD8 + T-Cell Immune Response against SARS-Cov-2 S, M, and N Induced by Endogenously Engineered Extracellular Vesicles in Both Spleen and Lungs. Vaccines (Basel) 2021; 9:240. [PMID: 33801926 PMCID: PMC7999804 DOI: 10.3390/vaccines9030240] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/29/2022] Open
Abstract
Most advanced vaccines against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 are designed to induce antibodies against spike (S) protein. Differently, we developed an original strategy to induce CD8+ T cytotoxic lymphocyte (CTL) immunity based on in vivo engineering of extracellular vesicles (EVs). This is a new vaccination approach based on intramuscular injection of DNA expression vectors coding for a biologically inactive HIV-1 Nef protein (Nefmut) with an unusually high efficiency of incorporation into EVs, even when foreign polypeptides are fused to its C-terminus. Nanovesicles containing Nefmut-fused antigens released by muscle cells can freely circulate into the body and are internalized by antigen-presenting cells. Therefore, EV-associated antigens can be cross-presented to prime antigen-specific CD8+ T-cells. To apply this technology to a strategy of anti-SARS-CoV-2 vaccine, we designed DNA vectors expressing the products of fusion between Nefmut and different viral antigens, namely N- and C-terminal moieties of S (referred to as S1 and S2), M, and N. We provided evidence that all fusion products are efficiently uploaded in EVs. When the respective DNA vectors were injected in mice, a strong antigen-specific CD8+ T cell immunity became detectable in spleens and, most important, in lung airways. Co-injection of DNA vectors expressing the diverse SARS-CoV-2 antigens resulted in additive immune responses in both spleen and lungs. Hence, DNA vectors expressing Nefmut-based fusion proteins can be proposed for new anti-SARS-CoV-2 vaccine strategies.
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Affiliation(s)
- Flavia Ferrantelli
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
| | - Chiara Chiozzini
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
| | - Francesco Manfredi
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
| | - Andrea Giovannelli
- National Center for Animal Experimentation and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Patrizia Leone
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
| | - Maurizio Federico
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (F.F.); (C.C.); (F.M.); (P.L.)
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Zhu Y, Huang C, Su M, Ge Z, Gao L, Shi Y, Wang X, Chen J. Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:495. [PMID: 33850892 PMCID: PMC8039679 DOI: 10.21037/atm-21-835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background The present study aimed to explore residues’ properties interacting with HLA-A*02-restricted peptides on T-cell receptors (TCRs) and their effects on bond types of interaction and binding free energy. Methods We searched the crystal structures of HLA-A*02-restricted peptide-TCR complexes from the Protein Data Bank (PDB) database and subsequently collected relevant parameters. We then employed Schrodinger to analyze the bond types of interaction and Gromacs 2019 to evaluate the TCR-antigen peptide complex’s molecular dynamics simulation. Finally, we compared the changes of bond types of interaction and binding free energy before and after residue substitution to ensure consistency of the conditions before and after residue substitution. Results The main sites on the antigen peptides that formed the intermolecular interaction [hydrogen bond (HB) and pi stack] with TCRs were P4, P8, P2, and P6. The hydrophobicity of the amino acids inside or outside the disulfide bond of TCRs may be related to the intermolecular interaction and binding free energy between TCRs and peptides. Residues located outside the disulfide bond of TCR α or β chains and forming pi stack force played favorable roles in the complex intermolecular interaction and binding free energy. The residues of the TCR α or β chains that interacted with peptides were replaced by alanine (Ala) or glycine (Gly), and their intermolecular binding free energy of the complex had been improved. However, it had nothing to do with the formation of HB. Conclusions The findings of this study suggest that the hydrophobic nature of the amino acids inside or outside the disulfide bonds on the TCR may be associated with the intermolecular interaction and binding between the TCR and polypeptide. The residues located outside the TCR α or β single-chain disulfide bond and forming the pi-stack force showed a beneficial effect on the intermolecular interaction and binding of the complex. In addition, the part of the residues on the TCR α or β single chain that produced bond types of interaction with the polypeptide after being replaced by Ala or Gly, the intermolecular binding free energy of the complex was increased, regardless of whether HB was formed.
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Affiliation(s)
- Ying Zhu
- Department of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Changxin Huang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Meng Su
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Zuanmin Ge
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Lanlan Gao
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Yanfei Shi
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Xuechun Wang
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Jianfeng Chen
- Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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Kedzierska K, Koutsakos M. The ABC of Major Histocompatibility Complexes and T Cell Receptors in Health and Disease. Viral Immunol 2021; 33:160-178. [PMID: 32286182 PMCID: PMC7185345 DOI: 10.1089/vim.2019.0184] [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] [Indexed: 12/31/2022] Open
Abstract
A seminal discovery of major histocompatibility complex (MHC) restriction in T cell recognition by Peter Doherty and Rolf Zinkernagel has led to 45 years of exciting research on the mechanisms governing peptide MHC (pMHC) recognition by T cell receptors (TCRs) and their importance in health and disease. T cells provide a significant level of protection against viral, bacterial, and parasitic infections, as well as tumors, hence, the generation of protective T cell responses is a primary goal for cell-mediated vaccines and immunotherapies. Understanding the mechanisms underlying generation of optimal high-avidity effector T cell responses, memory development, maintenance, and recall is of major importance for the rational design of preventative and therapeutic vaccines/immunotherapies. In this review, we summarize the lessons learned over the last four decades and outline our current understanding of the basis and consequences of pMHC/TCR interactions on T cell development and function, and TCR diversity and composition, driving better clinical outcomes and prevention of viral escape. We also discuss the current models of T cell memory formation and determinants of immunodominant T cell responses in animal models and humans. As TCR composition and diversity can affect both the protective capacity of T cells and protection against viral escape, defining the spectrum of TCR selection has implications for improving the functional efficacy of effector T cell responsiveness and memory formation.
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Affiliation(s)
- Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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Kerstetter LJ, Buckley S, Bliss CM, Coughlan L. Adenoviral Vectors as Vaccines for Emerging Avian Influenza Viruses. Front Immunol 2021; 11:607333. [PMID: 33633727 PMCID: PMC7901974 DOI: 10.3389/fimmu.2020.607333] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
It is evident that the emergence of infectious diseases, which have the potential for spillover from animal reservoirs, pose an ongoing threat to global health. Zoonotic transmission events have increased in frequency in recent decades due to changes in human behavior, including increased international travel, the wildlife trade, deforestation, and the intensification of farming practices to meet demand for meat consumption. Influenza A viruses (IAV) possess a number of features which make them a pandemic threat and a major concern for human health. Their segmented genome and error-prone process of replication can lead to the emergence of novel reassortant viruses, for which the human population are immunologically naïve. In addition, the ability for IAVs to infect aquatic birds and domestic animals, as well as humans, increases the likelihood for reassortment and the subsequent emergence of novel viruses. Sporadic spillover events in the past few decades have resulted in human infections with highly pathogenic avian influenza (HPAI) viruses, with high mortality. The application of conventional vaccine platforms used for the prevention of seasonal influenza viruses, such as inactivated influenza vaccines (IIVs) or live-attenuated influenza vaccines (LAIVs), in the development of vaccines for HPAI viruses is fraught with challenges. These issues are associated with manufacturing under enhanced biosafety containment, and difficulties in propagating HPAI viruses in embryonated eggs, due to their propensity for lethality in eggs. Overcoming manufacturing hurdles through the use of safer backbones, such as low pathogenicity avian influenza viruses (LPAI), can also be a challenge if incompatible with master strain viruses. Non-replicating adenoviral (Ad) vectors offer a number of advantages for the development of vaccines against HPAI viruses. Their genome is stable and permits the insertion of HPAI virus antigens (Ag), which are expressed in vivo following vaccination. Therefore, their manufacture does not require enhanced biosafety facilities or procedures and is egg-independent. Importantly, Ad vaccines have an exemplary safety and immunogenicity profile in numerous human clinical trials, and can be thermostabilized for stockpiling and pandemic preparedness. This review will discuss the status of Ad-based vaccines designed to protect against avian influenza viruses with pandemic potential.
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Affiliation(s)
- Lucas J. Kerstetter
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Stephen Buckley
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Carly M. Bliss
- Division of Cancer & Genetics, Division of Infection & Immunity, School of Medicine, Cardiff University, Wales, United Kingdom
| | - Lynda Coughlan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
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Szeto C, Chatzileontiadou DS, Nguyen AT, Sloane H, Lobos CA, Jayasinghe D, Halim H, Smith C, Riboldi-Tunnicliffe A, Grant EJ, Gras S. The presentation of SARS-CoV-2 peptides by the common HLA-A ∗02:01 molecule. iScience 2021; 24:102096. [PMID: 33521593 PMCID: PMC7825995 DOI: 10.1016/j.isci.2021.102096] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/17/2020] [Accepted: 01/15/2021] [Indexed: 12/27/2022] Open
Abstract
CD8+ T cells are crucial for anti-viral immunity; however, understanding T cell responses requires the identification of epitopes presented by human leukocyte antigens (HLA). To date, few SARS-CoV-2-specific CD8+ T cell epitopes have been described. Internal viral proteins are typically more conserved than surface proteins and are often the target of CD8+ T cells. Therefore, we have characterized eight peptides derived from the internal SARS-CoV-2 nucleocapsid protein predicted to bind HLA-A∗02:01, the most common HLA molecule in the global population. We determined not all peptides could form a complex with HLA-A∗02:01, and the six crystal structures determined revealed that some peptides adopted a mobile conformation. We therefore provide a molecular understanding of SARS-CoV-2 CD8+ T cell epitopes. Furthermore, we show that there is limited pre-existing CD8+ T cell response toward these epitopes in unexposed individuals. Together, these data show that SARS-CoV-2 nucleocapsid might not contain potent epitopes restricted to HLA-A∗02:01. HLA-A∗02:01 individuals have limited pre-existing immunity to SARS-CoV-2 nucleocapsid High-resolution crystal structures of HLA-A∗02:01 presenting SARS-CoV-2 peptides Structural analysis of pHLA shows stability influences peptide immunogenicity
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Affiliation(s)
- Christopher Szeto
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Demetra S.M. Chatzileontiadou
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Andrea T. Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Hannah Sloane
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Christian A. Lobos
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Dhilshan Jayasinghe
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Hanim Halim
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Corey Smith
- QIMR Centre for Immunotherapy and Vaccine Development and Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Emma J. Grant
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Corresponding author
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
- Corresponding author
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TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers. Int J Mol Sci 2020; 22:ijms22010068. [PMID: 33374673 PMCID: PMC7793522 DOI: 10.3390/ijms22010068] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
T cells are a critical part of the adaptive immune system that are able to distinguish between healthy and unhealthy cells. Upon recognition of protein fragments (peptides), activated T cells will contribute to the immune response and help clear infection. The major histocompatibility complex (MHC) molecules, or human leukocyte antigens (HLA) in humans, bind these peptides to present them to T cells that recognise them with their surface T cell receptors (TCR). This recognition event is the first step that leads to T cell activation, and in turn can dictate disease outcomes. The visualisation of TCR interaction with pMHC using structural biology has been crucial in understanding this key event, unravelling the parameters that drive this interaction and their impact on the immune response. The last five years has been the most productive within the field, wherein half of current unique TCR-pMHC-I structures to date were determined within this time. Here, we review the new insights learned from these recent TCR-pMHC-I structures and their impact on T cell activation.
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Exploring the Potential of T-Cells for a Universal Influenza Vaccine. Vaccines (Basel) 2020; 8:vaccines8040598. [PMID: 33050614 PMCID: PMC7711579 DOI: 10.3390/vaccines8040598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 09/30/2020] [Indexed: 01/18/2023] Open
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Attaf M, Roider J, Malik A, Rius Rafael C, Dolton G, Prendergast AJ, Leslie A, Ndung'u T, Kløverpris HN, Sewell AK, Goulder PJ. Cytomegalovirus-Mediated T Cell Receptor Repertoire Perturbation Is Present in Early Life. Front Immunol 2020; 11:1587. [PMID: 33101265 PMCID: PMC7554308 DOI: 10.3389/fimmu.2020.01587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022] Open
Abstract
Human cytomegalovirus (CMV) is a highly prevalent herpesvirus, particularly in sub-Saharan Africa, where it is endemic from infancy. The T cell response against CMV is important in keeping the virus in check, with CD8 T cells playing a major role in the control of CMV viraemia. Human leukocyte antigen (HLA) B*44:03-positive individuals raise a robust response against the NEGVKAAW (NW8) epitope, derived from the immediate-early-2 (IE-2) protein. We previously showed that the T cell receptor (TCR) repertoire raised against the NW8-HLA-B*44:03 complex was oligoclonal and characterised by superdominant clones, which were shared amongst unrelated individuals (i.e., "public"). Here, we address the question of how stable the CMV-specific TCR repertoire is over the course of infection, and whether substantial differences are evident in TCR repertoires in children, compared with adults. We present a longitudinal study of four HIV/CMV co-infected mother-child pairs, who in each case express HLA-B*44:03 and make responses to the NW8 epitope, and analyse their TCR repertoire over a period spanning more than 10 years. Using high-throughput sequencing, the paediatric CMV-specific repertoire was found to be highly diverse. In addition, paediatric repertoires were remarkably similar to adults, with public TCR responses being shared amongst children and adults alike. The CMV-specific repertoire in both adults and children displayed strong fluctuations in TCR clonality and repertoire architecture over time. Previously characterised superdominant clonotypes were readily identifiable in the children at high frequency, suggesting that the distortion of the CMV-specific repertoire is incurred as a direct result of CMV infection rather than a product of age-related "memory inflation." Early distortion of the TCR repertoire was particularly apparent in the case of the TCR-β chain, where oligoclonality was low in children and positively correlated with age, a feature we did not observe for TCR-α. This discrepancy between TCR-α and -β chain repertoire may reflect differential contribution to NW8 recognition. Altogether, the results of the present study provide insight into the formation of the TCR repertoire in early life and pave the way to better understanding of CD8 T cell responses to CMV at the molecular level.
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MESH Headings
- Adolescent
- Adult
- Age Factors
- Antigens, Viral/immunology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Child
- Child, Preschool
- Coinfection
- Cytomegalovirus/immunology
- Cytomegalovirus Infections/immunology
- Cytomegalovirus Infections/metabolism
- Cytomegalovirus Infections/virology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Female
- HIV Infections/immunology
- HIV Infections/virology
- HLA Antigens/immunology
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Peptides/chemistry
- Peptides/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Cell Antigen Receptor Specificity
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Viral Load
- Young Adult
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Affiliation(s)
- Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Julia Roider
- Human Immunodeficiency Virus Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- German Centre for Infection Research, Munich, Germany
- Department of Infectious Diseases, Ludwig-Maximilians-University, Munich, Germany
| | - Amna Malik
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Cristina Rius Rafael
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Andrew J. Prendergast
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Alasdair Leslie
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Infection and Immunity, University College London, London, United Kingdom
| | - Thumbi Ndung'u
- Human Immunodeficiency Virus Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Infection and Immunity, University College London, London, United Kingdom
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, United States
- Virology and Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Henrik N. Kløverpris
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Infection and Immunity, University College London, London, United Kingdom
| | - Andrew K. Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Philip J. Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, United States
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Habel JR, Nguyen THO, van de Sandt CE, Juno JA, Chaurasia P, Wragg K, Koutsakos M, Hensen L, Jia X, Chua B, Zhang W, Tan HX, Flanagan KL, Doolan DL, Torresi J, Chen W, Wakim LM, Cheng AC, Doherty PC, Petersen J, Rossjohn J, Wheatley AK, Kent SJ, Rowntree LC, Kedzierska K. Suboptimal SARS-CoV-2-specific CD8 + T cell response associated with the prominent HLA-A*02:01 phenotype. Proc Natl Acad Sci U S A 2020; 117:24384-24391. [PMID: 32913053 PMCID: PMC7533701 DOI: 10.1073/pnas.2015486117] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
An improved understanding of human T cell-mediated immunity in COVID-19 is important for optimizing therapeutic and vaccine strategies. Experience with influenza shows that infection primes CD8+ T cell memory to peptides presented by common HLA types like HLA-A2, which enhances recovery and diminishes clinical severity upon reinfection. Stimulating peripheral blood mononuclear cells from COVID-19 convalescent patients with overlapping peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the clonal expansion of SARS-CoV-2-specific CD8+ and CD4+ T cells in vitro, with CD4+ T cells being robust. We identified two HLA-A*02:01-restricted SARS-CoV-2-specfic CD8+ T cell epitopes, A2/S269-277 and A2/Orf1ab3183-3191 Using peptide-HLA tetramer enrichment, direct ex vivo assessment of A2/S269+CD8+ and A2/Orf1ab3183+CD8+ populations indicated that A2/S269+CD8+ T cells were detected at comparable frequencies (∼1.3 × 10-5) in acute and convalescent HLA-A*02:01+ patients. These frequencies were higher than those found in uninfected HLA-A*02:01+ donors (∼2.5 × 10-6), but low when compared to frequencies for influenza-specific (A2/M158) and Epstein-Barr virus (EBV)-specific (A2/BMLF1280) (∼1.38 × 10-4) populations. Phenotyping A2/S269+CD8+ T cells from COVID-19 convalescents ex vivo showed that A2/S269+CD8+ T cells were predominantly negative for CD38, HLA-DR, PD-1, and CD71 activation markers, although the majority of total CD8+ T cells expressed granzymes and/or perforin. Furthermore, the bias toward naïve, stem cell memory and central memory A2/S269+CD8+ T cells rather than effector memory populations suggests that SARS-CoV-2 infection may be compromising CD8+ T cell activation. Priming with appropriate vaccines may thus be beneficial for optimizing CD8+ T cell immunity in COVID-19.
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Affiliation(s)
- Jennifer R Habel
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, 1066 CX Amsterdam, Netherlands
| | - Jennifer A Juno
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Priyanka Chaurasia
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kathleen Wragg
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Luca Hensen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Brendon Chua
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Wuji Zhang
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Katie L Flanagan
- Department of Infectious Diseases, Launceston General Hospital, Launceston, TAS 7250, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS 7248, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC 3800, Australia
- School of Health and Biomedical Science, Royal Melbourne Institute of Technology University, Melbourne, VIC 3000, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD 4814, Australia
| | - Joseph Torresi
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Bundoora 3084 VIC, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, VIC 3004, Australia
| | - Peter C Doherty
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jan Petersen
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton 3800, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton 3800, VIC, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Adam K Wheatley
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Ausralian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Ausralian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
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Rowntree LC, Nguyen THO, Farenc C, Halim H, Hensen L, Rossjohn J, Kotsimbos TC, Purcell AW, Kedzierska K, Gras S, Mifsud NA. A Shared TCR Bias toward an Immunogenic EBV Epitope Dominates in HLA-B*07:02–Expressing Individuals. THE JOURNAL OF IMMUNOLOGY 2020; 205:1524-1534. [DOI: 10.4049/jimmunol.2000249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/19/2020] [Indexed: 11/19/2022]
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Sant S, Quiñones-Parra SM, Koutsakos M, Grant EJ, Loudovaris T, Mannering SI, Crowe J, van de Sandt CE, Rimmelzwaan GF, Rossjohn J, Gras S, Loh L, Nguyen THO, Kedzierska K. HLA-B*27:05 alters immunodominance hierarchy of universal influenza-specific CD8+ T cells. PLoS Pathog 2020; 16:e1008714. [PMID: 32750095 PMCID: PMC7428290 DOI: 10.1371/journal.ppat.1008714] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/14/2020] [Accepted: 06/18/2020] [Indexed: 12/15/2022] Open
Abstract
Seasonal influenza virus infections cause 290,000–650,000 deaths annually and severe morbidity in 3–5 million people. CD8+ T-cell responses towards virus-derived peptide/human leukocyte antigen (HLA) complexes provide the broadest cross-reactive immunity against human influenza viruses. Several universally-conserved CD8+ T-cell specificities that elicit prominent responses against human influenza A viruses (IAVs) have been identified. These include HLA-A*02:01-M158-66 (A2/M158), HLA-A*03:01-NP265-273, HLA-B*08:01-NP225-233, HLA-B*18:01-NP219-226, HLA-B*27:05-NP383-391 and HLA-B*57:01-NP199-207. The immunodominance hierarchies across these universal CD8+ T-cell epitopes were however unknown. Here, we probed immunodominance status of influenza-specific universal CD8+ T-cells in HLA-I heterozygote individuals expressing two or more universal HLAs for IAV. We found that while CD8+ T-cell responses directed towards A2/M158 were generally immunodominant, A2/M158+CD8+ T-cells were markedly diminished (subdominant) in HLA-A*02:01/B*27:05-expressing donors following ex vivo and in vitro analyses. A2/M158+CD8+ T-cells in non-HLA-B*27:05 individuals were immunodominant, contained optimal public TRBV19/TRAV27 TCRαβ clonotypes and displayed highly polyfunctional and proliferative capacity, while A2/M158+CD8+ T cells in HLA-B*27:05-expressing donors were subdominant, with largely distinct TCRαβ clonotypes and consequently markedly reduced avidity, proliferative and polyfunctional efficacy. Our data illustrate altered immunodominance patterns and immunodomination within human influenza-specific CD8+ T-cells. Accordingly, our work highlights the importance of understanding immunodominance hierarchies within individual donors across a spectrum of prominent virus-specific CD8+ T-cell specificities prior to designing T cell-directed vaccines and immunotherapies, for influenza and other infectious diseases. Annual influenza infections cause significant morbidity and morbidity globally. Established T-cell immunity directed at conserved viral regions provides some protection against influenza viruses and promotes rapid recovery, leading to better clinical outcomes. Killer CD8+ T-cells recognising viral peptides in a context of HLA-I glycoproteins, provide the broadest ever reported immunity across distinct influenza strains and subtypes. We asked whether the expression of certain HLA-I alleles affects CD8+ T cells responses. Our study clearly illustrates altered immunodominance hierarchies and immunodomination within broadly-cross-reactive influenza-specific CD8+ T-cells in individuals expressing two or more universal HLA-I alleles, key for T cell-directed vaccines and immunotherapies.
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Affiliation(s)
- Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Sergio M. Quiñones-Parra
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Emma J. Grant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Stuart I. Mannering
- Immunology and Diabetes Unit, St Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, Victoria, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Guus F. Rimmelzwaan
- National Influenza Center and Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - 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, United Kingdom
| | - 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
| | - Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, 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
- * E-mail: (THON); (KK)
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail: (THON); (KK)
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Editorial of Harnessing the Power of T Cells: The Promising Hope for a Universal Influenza Vaccine. Vaccines (Basel) 2020; 8:vaccines8030376. [PMID: 32664485 PMCID: PMC7565606 DOI: 10.3390/vaccines8030376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022] Open
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Souter MNT, Loh L, Li S, Meehan BS, Gherardin NA, Godfrey DI, Rossjohn J, Fairlie DP, Kedzierska K, Pellicci DG, Chen Z, Kjer-Nielsen L, Corbett AJ, McCluskey J, Eckle SBG. Characterization of Human Mucosal-associated Invariant T (MAIT) Cells. ACTA ACUST UNITED AC 2020; 127:e90. [PMID: 31763790 DOI: 10.1002/cpim.90] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are a subset of unconventional T cells restricted by the major histocompatibility complex (MHC) class I-like molecule MHC-related protein 1 (MR1). MAIT cells are found throughout the body, especially in human blood and liver. Unlike conventional T cells, which are stimulated by peptide antigens presented by MHC molecules, MAIT cells recognize metabolite antigens derived from an intermediate in the microbial biosynthesis of riboflavin. MAIT cells mediate protective immunity to infections by riboflavin-producing microbes via the production of cytokines and cytotoxicity. The discovery of stimulating MAIT cell antigens allowed for the development of an analytical tool, the MR1 tetramer, that binds specifically to the MAIT T cell receptor (TCR) and is becoming the gold standard for identification of MAIT cells by flow cytometry. This article describes protocols to characterize the phenotype of human MAIT cells in blood and tissues by flow cytometry using fluorescently labeled human MR1 tetramers alongside antibodies specific for MAIT cell markers. © 2019 by John Wiley & Sons, Inc. The main protocols include: Basic Protocol 1: Determining the frequency and steady-state surface phenotype of human MAIT cells Basic Protocol 2: Determining the activation phenotype of human MAIT cells in blood Basic Protocol 3: Characterizing MAIT cell TCRs using TCR-positive reporter cell lines Alternate protocols are provided for determining the absolute number, transcription factor phenotype, and TCR usage of human MAIT cells; and determining activation phenotype by staining for intracellular markers, measuring secreted cytokines, and measuring fluorescent dye dilution due to proliferation. Additional methods are provided for determining the capacity of MAIT cells to produce cytokine independently of antigen using plate-bound or bead-immobilized CD3/CD28 stimulation; and determining the MR1-Ag dependence of MAIT cell activation using MR1-blocking antibody or competitive inhibition. For TCR-positive reporter cell lines, methods are also provided for evaluating the MAIT TCR-mediated MR1-Ag response, determining the capacity of the reporter lines to produce cytokine independently of antigen, determining the MR1-Ag dependence of the reporter lines, and evaluating the MR1-Ag response of the reporter lines using IL-2 secretion. Support Protocols describe the preparation of PBMCs from human blood, the preparation of single-cell suspensions from tissue, the isolation of MAIT cells by FACS and MACS, cloning MAIT TCRα and β chain genes and MR1 genes for transduction, generating stably and transiently transfected cells lines, generating a stable MR1 knockout antigen-presenting cell line, and generating monocyte-derived dendritic cells.
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Affiliation(s)
- Michael N T Souter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Liyen Loh
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Bronwyn S Meehan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Wales, United Kingdom
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Parkville, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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48
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Yaqinuddin A. Cross-immunity between respiratory coronaviruses may limit COVID-19 fatalities. Med Hypotheses 2020; 144:110049. [PMID: 32758887 PMCID: PMC7326438 DOI: 10.1016/j.mehy.2020.110049] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 06/25/2020] [Indexed: 01/09/2023]
Abstract
Of the seven coronaviruses associated with disease in humans, SARS-CoV, MERS-CoV and SARS-CoV-2 cause considerable mortality but also share significant sequence homology, and potentially antigenic epitopes capable of inducing an immune response. The degree of similarity is such that perhaps prior exposure to one virus could confer partial immunity to another. Indeed, data suggests a considerable amount of cross-reactivity and recognition by the hosts immune response between different coronavirus infections. While the ongoing COVID-19 outbreak rapidly overwhelmed medical facilities of particularly Europe and North America, accounting for 78% of global deaths, only 8% of deaths have occurred in Asia where the outbreak originated. Interestingly, Asia and the Middle East have previously experienced multiple rounds of coronavirus infections, perhaps suggesting buildup of acquired immunity to the causative SARS-CoV-2 that underlies COVID-19. This article hypothesizes that a causative factor underlying such low morbidity in these regions is perhaps (at least in part) due to acquired immunity from multiple rounds of coronavirus infections and discusses the mechanisms and recent evidence to support such assertions. Further investigations of such phenomenon would allow us to examine strategies to confer protective immunity, perhaps aiding vaccine development.
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49
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Luo X, Cui H, Cai L, Zhu W, Yang WC, Patrick M, Zhu S, Huang J, Yao X, Yao Y, He Y, Ji Y. Selection of a Clinical Lead TCR Targeting Alpha-Fetoprotein-Positive Liver Cancer Based on a Balance of Risk and Benefit. Front Immunol 2020; 11:623. [PMID: 32425926 PMCID: PMC7203609 DOI: 10.3389/fimmu.2020.00623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer with a poor prognosis and limited therapeutic options. Alpha-fetoprotein (AFP), an established clinical biomarker of HCC, has been employed as an attractive target for T cell-based immunotherapy against this disease given its high expression in the tumor and restricted expression in normal tissues. We have identified a number of T cell receptors (TCRs) recognizing the HLA-A*02:01 restricted AFP158-166 peptide FMNKFIYEI, providing a TCR candidate pool for identifying TCRs with optimal clinical benefit. To select the ideal AFP TCR for clinical use, we evaluated the efficacy and safety profile of 7 TCRs by testing their potency toward AFP-expressing HCC cells and their specificity based upon reactivity to normal and transformed cells covering a wide variety of primary cell types and HLA serotypes. Furthermore, we assessed their cross-reactivity to potential protein candidates in the human genome by an extensive alanine scan (X-scan). We first selected three TCR candidates based on the in vitro anti-tumor activity. Next we eliminated two potential cross-reactive TCRs based on their reactivity against normal and transformed cells covering a variety of primary cell types and HLA serotypes, respectively. We then excluded the potential cross-reactivity of the selected TCR with a protein candidate identified by X-scan. At present we have selected an AFP TCR with the optimal affinity, function, and safety profile, bearing properties that are expected to allow AFP TCR redirected T cells to specifically differentiate between AFP levels on tumor and normal tissues. An early phase clinical trial using T cells transduced with this TCR to treat HCC patients (NCT03971747) has been initiated.
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Affiliation(s)
- Xiaobing Luo
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
| | - Huijuan Cui
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
| | - Lun Cai
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States
| | - Wei Zhu
- CodexSage LLC., Germantown, MD, United States
| | - Wei-Chih Yang
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
| | - Michael Patrick
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
| | - Shigui Zhu
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
| | - Jiaqi Huang
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
| | - Xin Yao
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
| | - Yihong Yao
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
| | - Yukai He
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Yun Ji
- Cellular Biomedicine Group Inc., Gaithersburg, MD, United States
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50
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Li X, Zhang L, Liu Y, Ma L, Zhang N, Xia C. Structures of the MHC-I molecule BF2*1501 disclose the preferred presentation of an H5N1 virus-derived epitope. J Biol Chem 2020; 295:5292-5306. [PMID: 32152225 PMCID: PMC7170506 DOI: 10.1074/jbc.ra120.012713] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/06/2020] [Indexed: 01/05/2023] Open
Abstract
Lethal infections by strains of the highly-pathogenic avian influenza virus (HPAIV) H5N1 pose serious threats to both the poultry industry and public health worldwide. A lack of confirmed HPAIV epitopes recognized by cytotoxic T lymphocytes (CTLs) has hindered the utilization of CD8+ T-cell-mediated immunity and has precluded the development of effectively diversified epitope-based vaccination approaches. In particular, an HPAIV H5N1 CTL-recognized epitope based on the peptide MHC-I-β2m (pMHC-I) complex has not yet been designed. Here, screening a collection of selected peptides of several HPAIV strains against a specific pathogen-free pMHC-I (pBF2*1501), we identified a highly-conserved HPAIV H5N1 CTL epitope, named HPAIV-PA123-130 We determined the structure of the BF2*1501-PA123-130 complex at 2.1 Å resolution to elucidate the molecular mechanisms of a preferential presentation of the highly-conserved PA123-130 epitope in the chicken B15 lineage. Conformational characteristics of the PA123-130 epitope with a protruding Tyr-7 residue indicated that this epitope has great potential to be recognized by specific TCRs. Moreover, significantly increased numbers of CD8+ T cells specific for the HPAIV-PA123-130 epitope in peptide-immunized chickens indicated that a repertoire of CD8+ T cells can specifically respond to this epitope. We anticipate that the identification and structural characterization of the PA123-130 epitope reported here could enable further studies of CTL immunity against HPAIV H5N1. Such studies may aid in the development of vaccine development strategies using well-conserved internal viral antigens in chickens.
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Affiliation(s)
- Xiaoying Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, People's Republic of China
| | - Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Yanjie Liu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apiculture, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing 100094, People's Republic of China.
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