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Hamza H, Ghosh M, Löffler MW, Rammensee HG, Planz O. Identification and relative abundance of naturally presented and cross-reactive influenza A virus MHC class I-restricted T cell epitopes. Emerg Microbes Infect 2024; 13:2306959. [PMID: 38240239 PMCID: PMC10854457 DOI: 10.1080/22221751.2024.2306959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
Cytotoxic T lymphocytes are key for controlling viral infection. Unravelling CD8+ T cell-mediated immunity to distinct influenza virus strains and subtypes across prominent HLA types is relevant for combating seasonal infections and emerging new variants. Using an immunopeptidomics approach, naturally presented influenza A virus-derived ligands restricted to HLA-A*24:02, HLA-A*68:01, HLA-B*07:02, and HLA-B*51:01 molecules were identified. Functional characterization revealed multifunctional memory CD8+ T cell responses for nine out of sixteen peptides. Peptide presentation kinetics was optimal around 12 h post infection and presentation of immunodominant epitopes shortly after infection was not always persistent. Assessment of immunogenic epitopes revealed that they are highly conserved across the major zoonotic reservoirs and may contain a single substitution in the vicinity of the anchor residues. These findings demonstrate how the identified epitopes promote T cell pools, possibly cross-protective in individuals and can be potential targets for vaccination.
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Affiliation(s)
- Hazem Hamza
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Virology Laboratory, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Michael Ghosh
- Institute for Immunology, University of Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Institute for Clinical and Experimental Transfusion Medicine, Medical Faculty of Tübingen, Tübingen, Germany
- Centre for Clinical Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence CMFI (EXC2124) "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
| | - Oliver Planz
- Institute for Immunology, University of Tübingen, Tübingen, Germany
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Ahn YM, Maddumage JC, Grant EJ, Chatzileontiadou DS, Perera WG, Baker BM, Szeto C, Gras S. The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific. Curr Res Struct Biol 2024; 7:100148. [PMID: 38742159 PMCID: PMC11089313 DOI: 10.1016/j.crstbi.2024.100148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/11/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024] Open
Abstract
CD8+ T cells are crucial for viral elimination and recovery from viral infection. Nonetheless, the current understanding of the T cell response to SARS-CoV-2 at the antigen level remains limited. The Spike protein is an external structural protein that is prone to mutations, threatening the efficacy of current vaccines. Therefore, we have characterised the immune response towards the immunogenic Spike-derived peptide (S976-984, VLNDILSRL), restricted to the HLA-A*02:01 molecule, which is mutated in both Alpha (S982A) and Omicron BA.1 (L981F) variants of concern. We determined that the mutation in the Alpha variant (S982A) impacted both the stability and conformation of the peptide, bound to HLA-A*02:01, in comparison to the original S976-984. We identified a longer and overlapping immunogenic peptide (S975-984, SVLNDILSRL) that could be presented by HLA-A*02:01, HLA-A*11:01 and HLA-B*13:01 allomorphs. We showed that S975-specific CD8+ T cells were weakly cross-reactive to the mutant peptides despite their similar conformations when presented by HLA-A*11:01. Altogether, our results show that the impact of SARS-CoV-2 mutations on peptide presentation is HLA allomorph-specific, and that post vaccination there are T cells able to react and cross-react towards the variant of concern peptides.
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Affiliation(s)
- You Min Ahn
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
| | - Janesha C. Maddumage
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
| | - Emma J. Grant
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Demetra S.M. Chatzileontiadou
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - W.W.J. Gihan Perera
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Christopher Szeto
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
- Australian Synchrotron, ANSTO, Clayton, Victoria, Australia
| | - Stephanie Gras
- Infection & Immunity Program, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Agriculture (SABE), La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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4
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Menon T, Illing PT, Chaurasia P, McQuilten HA, Shepherd C, Rowntree LC, Petersen J, Littler DR, Khuu G, Huang Z, Allen LF, Rockman S, Crowe J, Flanagan KL, Wakim LM, Nguyen THO, Mifsud NA, Rossjohn J, Purcell AW, van de Sandt CE, Kedzierska K. CD8 + T-cell responses towards conserved influenza B virus epitopes across anatomical sites and age. Nat Commun 2024; 15:3387. [PMID: 38684663 PMCID: PMC11059233 DOI: 10.1038/s41467-024-47576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Influenza B viruses (IBVs) cause substantive morbidity and mortality, and yet immunity towards IBVs remains understudied. CD8+ T-cells provide broadly cross-reactive immunity and alleviate disease severity by recognizing conserved epitopes. Despite the IBV burden, only 18 IBV-specific T-cell epitopes restricted by 5 HLAs have been identified currently. A broader array of conserved IBV T-cell epitopes is needed to develop effective cross-reactive T-cell based IBV vaccines. Here we identify 9 highly conserved IBV CD8+ T-cell epitopes restricted to HLA-B*07:02, HLA-B*08:01 and HLA-B*35:01. Memory IBV-specific tetramer+CD8+ T-cells are present within blood and tissues. Frequencies of IBV-specific CD8+ T-cells decline with age, but maintain a central memory phenotype. HLA-B*07:02 and HLA-B*08:01-restricted NP30-38 epitope-specific T-cells have distinct T-cell receptor repertoires. We provide structural basis for the IBV HLA-B*07:02-restricted NS1196-206 (11-mer) and HLA-B*07:02-restricted NP30-38 epitope presentation. Our study increases the number of IBV CD8+ T-cell epitopes, and defines IBV-specific CD8+ T-cells at cellular and molecular levels, across tissues and age.
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Affiliation(s)
- Tejas Menon
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T Illing
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Priyanka Chaurasia
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Chloe Shepherd
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jan Petersen
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Grace Khuu
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ziyi Huang
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- CSL Seqirus Ltd, Parkville, VIC, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, VIC, Australia
| | - Katie L Flanagan
- Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
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5
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Ren X, Amarajeewa AWP, Jayasinghe MDT, Garstka MA. Differences in F pocket impact on HLA I genetic associations with autoimmune diabetes. Front Immunol 2024; 15:1342335. [PMID: 38596688 PMCID: PMC11003304 DOI: 10.3389/fimmu.2024.1342335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction Human leukocyte antigen (HLA) I molecules present antigenic peptides to activate CD8+ T cells. Type 1 Diabetes (T1D) is an auto-immune disease caused by aberrant activation of the CD8+ T cells that destroy insulin-producing pancreatic β cells. Some HLA I alleles were shown to increase the risk of T1D (T1D-predisposing alleles), while some reduce this risk (T1D-protective alleles). Methods Here, we compared the T1D-predisposing and T1D-protective allotypes concerning peptide binding, maturation, localization and surface expression and correlated it with their sequences and energetic profiles using experimental and computational methods. Results T1D-predisposing allotypes had more peptide-bound forms and higher plasma membrane levels than T1D-protective allotypes. This was related to the fact that position 116 within the F pocket was more conserved and made more optimal contacts with the neighboring residues in T1D-predisposing allotypes than in protective allotypes. Conclusion Our work uncovers that specific polymorphisms in HLA I molecules potentially influence their susceptibility to T1D.
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Affiliation(s)
- Xu Ren
- Department of Urology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Endocrinology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - A. W. Peshala Amarajeewa
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | | | - Malgorzata A. Garstka
- Department of Urology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Endocrinology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Tumor and Immunology, Precision Medical Institute, Western China Science and Technology Innovation Port, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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7
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Leong SL, Gras S, Grant EJ. Fighting flu: novel CD8 + T-cell targets are required for future influenza vaccines. Clin Transl Immunology 2024; 13:e1491. [PMID: 38362528 PMCID: PMC10867544 DOI: 10.1002/cti2.1491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Seasonal influenza viruses continue to cause severe medical and financial complications annually. Although there are many licenced influenza vaccines, there are billions of cases of influenza infection every year, resulting in the death of over half a million individuals. Furthermore, these figures can rise in the event of a pandemic, as seen throughout history, like the 1918 Spanish influenza pandemic (50 million deaths) and the 1968 Hong Kong influenza pandemic (~4 million deaths). In this review, we have summarised many of the currently licenced influenza vaccines available across the world and current vaccines in clinical trials. We then briefly discuss the important role of CD8+ T cells during influenza infection and why future influenza vaccines should consider targeting CD8+ T cells. Finally, we assess the current landscape of known immunogenic CD8+ T-cell epitopes and highlight the knowledge gaps required to be filled for the design of rational future influenza vaccines that incorporate CD8+ T cells.
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Affiliation(s)
- Samuel Liwei Leong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Emma J Grant
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
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8
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Sueangoen N, Grove H, Chuangchot N, Prasopsiri J, Rungrotmongkol T, Sanachai K, Darai N, Thongchot S, Suriyaphol P, Sa-Nguanraksa D, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Stimulating T cell responses against patient-derived breast cancer cells with neoantigen peptide-loaded peripheral blood mononuclear cells. Cancer Immunol Immunother 2024; 73:43. [PMID: 38349410 PMCID: PMC10864427 DOI: 10.1007/s00262-024-03627-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024]
Abstract
Breast cancer stands as a formidable global health challenge for women. While neoantigens exhibit efficacy in activating T cells specific to cancer and instigating anti-tumor immune responses, the accuracy of neoantigen prediction remains suboptimal. In this study, we identified neoantigens from the patient-derived breast cancer cells, PC-B-142CA and PC-B-148CA cells, utilizing whole-genome and RNA sequencing. The pVAC-Seq pipeline was employed, with minor modification incorporating criteria (1) binding affinity of mutant (MT) peptide with HLA (IC50 MT) ≤ 500 nm in 3 of 5 algorithms and (2) IC50 wild type (WT)/MT > 1. Sequencing results unveiled 2513 and 3490 somatic mutations, and 646 and 652 non-synonymous mutations in PC-B-142CA and PC-B-148CA, respectively. We selected the top 3 neoantigens to perform molecular dynamic simulation and synthesized 9-12 amino acid neoantigen peptides, which were then pulsed onto healthy donor peripheral blood mononuclear cells (PBMCs). Results demonstrated that T cells activated by ADGRL1E274K, PARP1E619K, and SEC14L2R43Q peptides identified from PC-B-142CA exhibited significantly increased production of interferon-gamma (IFN-γ), while PARP1E619K and SEC14L2R43Q peptides induced the expression of CD107a on T cells. The % tumor cell lysis was notably enhanced by T cells activated with MT peptides across all three healthy donors. Moreover, ALKBH6V83M and GAAI823T peptides from PC-B-148CA remarkably stimulated IFN-γ- and CD107a-positive T cells, displaying high cell-killing activity against target cancer cells. In summary, our findings underscore the successful identification of neoantigens with anti-tumor T cell functions and highlight the potential of personalized neoantigens as a promising avenue for breast cancer treatment.
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Grants
- R016341038 The Research and Innovation Grant, the National Research Council of Thailand, Ministry of Higher Education, Science, Research and Innovation
- R016341038 The Research and Innovation Grant, the National Research Council of Thailand, Ministry of Higher Education, Science, Research and Innovation
- R016334002 Siriraj Research Grant, Faculty of Medicine Siriraj Hospital, Mahidol University
- R016334002 Siriraj Research Grant, Faculty of Medicine Siriraj Hospital, Mahidol University
- Mahidol University
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Affiliation(s)
- Natthaporn Sueangoen
- Graduate Program in Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Harald Grove
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nisa Chuangchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jaturawitt Prasopsiri
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Nitchakan Darai
- ASEAN Institute for Health Development, Mahidol University, Nakon Pathom, Thailand
| | - Suyanee Thongchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Doonyapat Sa-Nguanraksa
- Division of Head Neck and Breast Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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9
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Hulme KD, Tong ZWM, Rowntree LC, van de Sandt CE, Ronacher K, Grant EJ, Dorey ES, Gallo LA, Gras S, Kedzierska K, Barrett HL, Short KR. Increasing HbA1c is associated with reduced CD8 + T cell functionality in response to influenza virus in a TCR-dependent manner in individuals with diabetes mellitus. Cell Mol Life Sci 2024; 81:35. [PMID: 38214784 PMCID: PMC10786977 DOI: 10.1007/s00018-023-05010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 01/13/2024]
Abstract
Diabetes mellitus is on the rise globally and is a known susceptibility factor for severe influenza virus infections. However, the mechanisms by which diabetes increases the severity of an influenza virus infection are yet to be fully defined. Diabetes mellitus is hallmarked by high glucose concentrations in the blood. We hypothesized that these high glucose concentrations affect the functionality of CD8+ T cells, which play a key role eliminating virus-infected cells and have been shown to decrease influenza disease severity. To study the effect of hyperglycemia on CD8+ T cell function, we stimulated peripheral blood mononuclear cells (PBMCs) from donors with and without diabetes with influenza A virus, anti-CD3/anti-CD28-coated beads, PMA and ionomycin (PMA/I), or an influenza viral peptide pool. After stimulation, cells were assessed for functionality [as defined by expression of IFN-γ, TNF-α, macrophage inflammatory protein (MIP)-1β, and lysosomal-associated membrane protein-1 (CD107a)] using flow cytometry. Our results showed that increasing HbA1c correlated with a reduction in TNF-α production by CD8+ T cells in response to influenza stimulation in a TCR-specific manner. This was not associated with any changes to CD8+ T cell subsets. We conclude that hyperglycemia impairs CD8+ T cell function to influenza virus infection, which may be linked with the increased risk of severe influenza in patients with diabetes.
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Affiliation(s)
- Katina D Hulme
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Zhen Wei Marcus Tong
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Katharina Ronacher
- Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD, Australia
| | - Emma J Grant
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Emily S Dorey
- Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
| | - Linda A Gallo
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Moreton Bay, QLD, Australia
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Helen L Barrett
- Mater Research Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
- Obstetric Medicine, The Royal Hospital for Women, Randwick, NSW, Australia
- School of Medicine, UNSW, Randwick, NSW, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD, Australia.
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10
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Mao Y, Xiao X, Zhang J, Mou X, Zhao W. Designing a multi-epitope vaccine against Peptostreptococcus anaerobius based on an immunoinformatics approach. Synth Syst Biotechnol 2023; 8:757-770. [PMID: 38099061 PMCID: PMC10720267 DOI: 10.1016/j.synbio.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/15/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023] Open
Abstract
Peptostreptococcus anaerobius is an anaerobic bacterium, which has been found selectively en-riched in the fecal and mucosal microbiota of colorectal cancer (CRC) patients. Emerging evidence suggest P. anaerobius may contribute to the development of CRC in human. In this study, we designed a multi-epitope chimeric vaccine against P. anaerobius PCWBR2, a recently identified adhesin that interacts directly with colon cell lines by binding α2/β1 integrin frequently overexpressed in human CRC tumors and cell lines. Immunoinformatics tools predicted six cytotoxic T lymphocyte epitopes, five helper T lymphocyte epitopes, and six linear B lymphocyte epitopes. The predicted epitopes were joined with AAY or GPGPG linkers and a previously reported TLR4 agonist was added to the vaccine construct's N terminal as an adjuvant using EAAAK linkers and the order of epitopes was optimized. Further in silico analysis revealed that the vaccine construct possesses satisfactory antigenicity, allergenicity, solubility, physicochemical properties, adjuvant-TLR4 molecular docking, and immune profile characteristics. Our study provided a promising design for vaccines against P. anaerobius.
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Affiliation(s)
- Yudan Mao
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Xianzun Xiao
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Jie Zhang
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Xiangyu Mou
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Wenjing Zhao
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [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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12
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Purcell RA, Theisen RM, Arnold KB, Chung AW, Selva KJ. Polyfunctional antibodies: a path towards precision vaccines for vulnerable populations. Front Immunol 2023; 14:1183727. [PMID: 37600816 PMCID: PMC10433199 DOI: 10.3389/fimmu.2023.1183727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/30/2023] [Indexed: 08/22/2023] Open
Abstract
Vaccine efficacy determined within the controlled environment of a clinical trial is usually substantially greater than real-world vaccine effectiveness. Typically, this results from reduced protection of immunologically vulnerable populations, such as children, elderly individuals and people with chronic comorbidities. Consequently, these high-risk groups are frequently recommended tailored immunisation schedules to boost responses. In addition, diverse groups of healthy adults may also be variably protected by the same vaccine regimen. Current population-based vaccination strategies that consider basic clinical parameters offer a glimpse into what may be achievable if more nuanced aspects of the immune response are considered in vaccine design. To date, vaccine development has been largely empirical. However, next-generation approaches require more rational strategies. We foresee a generation of precision vaccines that consider the mechanistic basis of vaccine response variations associated with both immunogenetic and baseline health differences. Recent efforts have highlighted the importance of balanced and diverse extra-neutralising antibody functions for vaccine-induced protection. However, in immunologically vulnerable populations, significant modulation of polyfunctional antibody responses that mediate both neutralisation and effector functions has been observed. Here, we review the current understanding of key genetic and inflammatory modulators of antibody polyfunctionality that affect vaccination outcomes and consider how this knowledge may be harnessed to tailor vaccine design for improved public health.
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Affiliation(s)
- Ruth A. Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Robert M. Theisen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Kelly B. Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Amy W. Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Kevin J. Selva
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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13
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Pecher AC, Hensen L, Klein R, Schairer R, Lutz K, Atar D, Seitz C, Stanger A, Schneider J, Braun C, Schmidt M, Horger M, Bornemann A, Faul C, Bethge W, Henes J, Lengerke C. CD19-Targeting CAR T Cells for Myositis and Interstitial Lung Disease Associated With Antisynthetase Syndrome. JAMA 2023; 329:2154-2162. [PMID: 37367976 PMCID: PMC10300719 DOI: 10.1001/jama.2023.8753] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/04/2023] [Indexed: 06/28/2023]
Abstract
Importance Autoimmune disorders can affect various organs and if refractory, can be life threatening. Recently, CD19-targeting-chimeric antigen receptor (CAR) T cells were efficacious as an immune suppressive agent in 6 patients with refractory systemic lupus erythematosus and in 1 patient with antisynthetase syndrome. Objective To test the safety and efficacy of CD19-targeting CAR T cells in a patient with severe antisynthetase syndrome, a complex autoimmune disorder with evidence for B- and T-cell involvement. Design, Setting, and Participants This case report describes a patient with antisynthetase syndrome with progressive myositis and interstitial lung disease refractory to available therapies (including rituximab and azathioprine), who was treated with CD19-targeting CAR T cells in June 2022 at University Hospital Tübingen in Tübingen, Germany, with the last follow-up in February 2023. Mycophenolate mofetil was added to the treatment to cotarget CD8+ T cells, hypothesized to contribute to disease activity. Exposure Prior to treatment with CD19-targeting CAR T cells, the patient received conditioning therapy with fludarabine (25 mg/m2 [5 days before until 3 days before]) and cyclophosphamide (1000 mg/m2 [3 days before]) followed by infusion of CAR T cells (1.23×106/kg [manufactured by transduction of autologous T cells with a CD19 lentiviral vector and amplification in the CliniMACS Prodigy system]) and mycophenolate mofetil (2 g/d) 35 days after CD19-targeting CAR T-cell infusion. Main Outcomes and Measures The patient's response to therapy was followed by magnetic resonance imaging of the thigh muscle, Physician Global Assessment, functional muscle and pulmonary tests, and peripheral blood quantification of anti-Jo-1 antibody levels, lymphocyte subsets, immunoglobulins, and serological muscle enzymes. Results Rapid clinical improvement was observed after CD19-targeting CAR T-cell infusion. Eight months after treatment, the patient's scores on the Physician Global Assessment and muscle and pulmonary function tests improved, and there were no detectable signs of myositis on magnetic resonance imaging. Serological muscle enzymes (alanine aminotransferase, aspartate aminotransferase, creatinine kinase, and lactate dehydrogenase), CD8+ T-cell subsets, and inflammatory cytokine secretion in the peripheral blood mononuclear cells (interferon gamma, interleukin 1 [IL-1], IL-6, and IL-13) were all normalized. Further, there was a reduction in anti-Jo-1 antibody levels and a partial recovery of IgA (to 67% of normal value), IgG (to 87%), and IgM (to 58%). Conclusions and Relevance CD19-targeting CAR T cells directed against B cells and plasmablasts deeply reset B-cell immunity. Together with mycophenolate mofetil, CD19-targeting CAR T cells may break pathologic B-cell, as well as T-cell responses, inducing remission in refractory antisynthetase syndrome.
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Affiliation(s)
- Ann-Christin Pecher
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Luca Hensen
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Rebekka Schairer
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Katrin Lutz
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Daniel Atar
- Department of Pediatric Hematology and Oncology, Children’s Hospital, University Hospital Tübingen, Tübingen, Germany
| | - Christian Seitz
- Department of Pediatric Hematology and Oncology, Children’s Hospital, University Hospital Tübingen, Tübingen, Germany
| | - Anna Stanger
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Janine Schneider
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Christiane Braun
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Marina Schmidt
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Marius Horger
- Department for Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen, Germany
| | - Antje Bornemann
- Department of Pathology and Neuropathology and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Christoph Faul
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Wolfgang Bethge
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Joerg Henes
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Claudia Lengerke
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, Tübingen, Germany
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14
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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: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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15
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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. [PMID: 36423187 DOI: 10.3390/v14112578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [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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16
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Liu X, Zhao T, Wang L, Li M, Sun C, Shu Y. Strategies targeting hemagglutinin cocktail as a potential universal influenza vaccine. Front Microbiol 2022; 13:1014122. [PMID: 36246271 PMCID: PMC9558277 DOI: 10.3389/fmicb.2022.1014122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Vaccination is the most effective means of protecting people from influenza virus infection. The effectiveness of existing vaccines is very limited due to antigenic drift of the influenza virus. Therefore, there is a requirement to develop a universal vaccine that provides broad and long-lasting protection against influenza. CD8+ T-cell response played a vital role in controlling influenza virus infection, reducing viral load, and less clinical syndrome. In this study, we optimized the HA sequences of human seasonal influenza viruses (H1N1, H3N2, Victoria, and Yamagata) by designing multivalent vaccine antigen sets using a mosaic vaccine design strategy and genetic algorithms, and designed an HA mosaic cocktail containing the most potential CTL epitopes of seasonal influenza viruses. We then tested the recombinant mosaic antigen, which has a significant number of potential T-cell epitopes. Results from genetic evolutionary analyses and 3D structural simulations demonstrated its potential to be an effective immunogen. In addition, we have modified an existing neutralizing antibody-based seasonal influenza virus vaccine to include a component that activates cross-protective T cells, which would provide an attractive strategy for improving human protection against seasonal influenza virus drift and mutation and provide an idea for the development of a rationally designed influenza vaccine targeting T lymphocyte immunity.
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Affiliation(s)
- Xuejie Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Tianyi Zhao
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Liangliang Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Minchao Li
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yuelong Shu,
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17
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Grant EJ, Gras S. Protocol for generation of human peptide-specific primary CD8+ T cell lines. STAR Protoc 2022; 3:101590. [PMID: 35942343 PMCID: PMC9356162 DOI: 10.1016/j.xpro.2022.101590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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18
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Yao K, Li J, Wang H, Lu R, Yang X, Luo M, Wang N, Wang Z, Liu C, Jing T, Chen S, Cortés E, Maier SA, Zhang S, Li T, Yu Y, Liu Y, Kang X, Liang H. Mechanistic Insights into OC-COH Coupling in CO 2 Electroreduction on Fragmented Copper. J Am Chem Soc 2022; 144:14005-14011. [PMID: 35904545 DOI: 10.1021/jacs.2c01044] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The carbon-carbon (C-C) bond formation is essential for the electroconversion of CO2 into high-energy-density C2+ products, and the precise coupling pathways remain controversial. Although recent computational investigations have proposed that the OC-COH coupling pathway is more favorable in specific reaction conditions than the well-known CO dimerization pathway, the experimental evidence is still lacking, partly due to the separated catalyst design and mechanistic/spectroscopic exploration. Here, we employ density functional theory calculations to show that on low-coordinated copper sites, the *CO bindings are strengthened, and the adsorbed *CO coupling with their hydrogenation species, *COH, receives precedence over CO dimerization. Experimentally, we construct a fragmented Cu catalyst with abundant low-coordinated sites, exhibiting a 77.8% Faradaic efficiency for C2+ products at 300 mA cm-2. With a suite of in situ spectroscopic studies, we capture an *OCCOH intermediate on the fragmented Cu surfaces, providing direct evidence to support the OC-COH coupling pathway. The mechanistic insights of this research elucidate how to design materials in favor of OC-COH coupling toward efficient C2+ production from CO2 reduction.
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Affiliation(s)
- Kaili Yao
- School of Materials Science and Engineering and Key Laboratory of Efficient Utilization of Low and Medium Grade Energy, Tianjin University, Tianjin 300350, People's Republic of China.,School of Chemical Engineering, Kunming University of Science and Technology, Kunmin 650500, People's Republic of China
| | - Jun Li
- Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Haibin Wang
- School of Materials Science and Engineering and Key Laboratory of Efficient Utilization of Low and Medium Grade Energy, Tianjin University, Tianjin 300350, People's Republic of China
| | - Ruihu Lu
- School of Chemical Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Xiaotao Yang
- School of Mechanical Engineering, Tianjin University, Tianjin 300350, People's Republic of China
| | - Mingchuan Luo
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ning Wang
- Department of Electrical and Computer Engineering, University of Toronto, 35 St George Street, Toronto, Ontario M5S 1A4, Canada
| | - Ziyun Wang
- School of Chemical Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Changxu Liu
- Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.,Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig Maximilians University of Munich, 80539 Munich, Germany
| | - Tan Jing
- College of Chemistry and Material Science, Longyan University, Longyan 364012, People's Republic of China
| | - Songhua Chen
- College of Chemistry and Material Science, Longyan University, Longyan 364012, People's Republic of China
| | - Emiliano Cortés
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig Maximilians University of Munich, 80539 Munich, Germany
| | - Stefan A Maier
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig Maximilians University of Munich, 80539 Munich, Germany.,Department of Physics, Imperial College London, London SW7 2AZ, United Kingdom.,School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - Sheng Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Tieliang Li
- School of Science, Tianjin University, Tianjin 300350, People's Republic of China
| | - Yifu Yu
- School of Science, Tianjin University, Tianjin 300350, People's Republic of China
| | - Yongchang Liu
- State Key Lab of Hydraulic Engineering Simulation and Safety, School of Materials Science and Engineering, Tianjin University, Tianjin 300354, People's Republic of China
| | - Xinchen Kang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Hongyan Liang
- School of Materials Science and Engineering and Key Laboratory of Efficient Utilization of Low and Medium Grade Energy, Tianjin University, Tianjin 300350, People's Republic of China
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19
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Alves DE, Mamelund SE, Dimka J, Simonsen L, Mølbak M, Ørskov S, Sattenspiel L, Tripp L, Noymer A, Chowell-Puente G, Dahal S, Van Doren TP, Wissler A, Heffernan C, Renfree Short K, Battles H, Baker MG. Indigenous peoples and pandemics. Scand J Public Health 2022; 50:662-667. [PMID: 35546099 PMCID: PMC9361406 DOI: 10.1177/14034948221087095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Daniele E Alves
- Centre for Research on Pandemics & Society, Oslo Metropolitan University, Norway
| | - Svenn-Erik Mamelund
- Centre for Research on Pandemics & Society, Oslo Metropolitan University, Norway
| | - Jessica Dimka
- Centre for Research on Pandemics & Society, Oslo Metropolitan University, Norway
| | | | | | | | | | - Lianne Tripp
- Department of Anthropology, University of Northern British Columbia, Canada
| | - Andrew Noymer
- Program in Public Health, University of California, Irvine, USA
| | | | - Sushma Dahal
- Department of Population Health Sciences, Georgia State University, USA
| | | | - Amanda Wissler
- School of Human Evolution and Social Change, Arizona State University, USA
| | - Courtney Heffernan
- Tuberculosis Program Evaluation and Research Unit, University of Alberta, Canada
| | - Kirsty Renfree Short
- School of Chemistry and Molecular Biosciences, University of Queensland, Australia
| | - Heather Battles
- Department of Anthropology, University of Auckland, New Zealand
| | - Michael G Baker
- Health Environment Infection Research Unit, University of Otago, New Zealand
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20
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Hensen L, Illing PT, Rowntree LC, Davies J, Miller A, Tong SYC, Habel JR, van de Sandt CE, Flanagan K, Purcell AW, Kedzierska K, Clemens EB. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Front Immunol 2022; 13:812393. [PMID: 35603215 PMCID: PMC9121770 DOI: 10.3389/fimmu.2022.812393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells are a pivotal part of the immune response to viruses, playing a key role in disease outcome and providing long-lasting immunity to conserved pathogen epitopes. Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different HLA allotypes across different ethnicities. Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses. We describe an immunopeptidomics approach to sequence HLA-bound peptides presented on virus-infected cells by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using antigen presenting cell lines that stably express the HLA alleles characteristic of Indigenous Australians, this approach has been successfully used to comprehensively identify influenza-specific CD8+ T cell epitopes restricted by HLA allotypes predominant in Indigenous Australians, including HLA-A*24:02 and HLA-A*11:01. This is an essential step in ensuring high vaccine coverage and efficacy in Indigenous populations globally, known to be at high risk from influenza disease and other respiratory infections.
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Affiliation(s)
- Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T. Illing
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C. Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jane Davies
- Menzies School of Health Research, Darwin, NT, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, QLD, Australia
| | - Steven Y. C. Tong
- Menzies School of Health Research, Darwin, NT, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer R. Habel
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Katie L. Flanagan
- Department of Infectious Diseases and Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- *Correspondence: Katherine Kedzierska,
| | - E. Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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21
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Habel JR, Nguyen AT, Rowntree LC, Szeto C, Mifsud NA, Clemens EB, Loh L, Chen W, Rockman S, Nelson J, Davies J, Miller A, Tong SYC, Rossjohn J, Gras S, Purcell AW, Hensen L, Kedzierska K, Illing PT. 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 DOI: 10.1371/journal.ppat.1010337] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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22
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Nguyen AT, Szeto C, Gras S. The pockets guide to HLA class I molecules. Biochem Soc Trans 2021; 49:2319-31. [PMID: 34581761 DOI: 10.1042/BST20210410] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 01/11/2023]
Abstract
Human leukocyte antigens (HLA) are cell-surface proteins that present peptides to T cells. These peptides are bound within the peptide binding cleft of HLA, and together as a complex, are recognised by T cells using their specialised T cell receptors. Within the cleft, the peptide residue side chains bind into distinct pockets. These pockets ultimately determine the specificity of peptide binding. As HLAs are the most polymorphic molecules in humans, amino acid variants in each binding pocket influences the peptide repertoire that can be presented on the cell surface. Here, we review each of the 6 HLA binding pockets of HLA class I (HLA-I) molecules. The binding specificity of pockets B and F are strong determinants of peptide binding and have been used to classify HLA into supertypes, a useful tool to predict peptide binding to a given HLA. Over the years, peptide binding prediction has also become more reliable by using binding affinity and mass spectrometry data. Crystal structures of peptide-bound HLA molecules provide a means to interrogate the interactions between binding pockets and peptide residue side chains. We find that most of the bound peptides from these structures conform to binding motifs determined from prediction software and examine outliers to learn how these HLAs are stabilised from a structural perspective.
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23
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Rowntree LC, Petersen J, Juno JA, Chaurasia P, Wragg K, Koutsakos M, Hensen L, Wheatley AK, Kent SJ, Rossjohn J, Kedzierska K, Nguyen TH. SARS-CoV-2-specific CD8 + T-cell responses and TCR signatures in the context of a prominent HLA-A*24:02 allomorph. Immunol Cell Biol 2021; 99:990-1000. [PMID: 34086357 PMCID: PMC8242669 DOI: 10.1111/imcb.12482] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022]
Abstract
In‐depth understanding of human T‐cell‐mediated immunity in coronavirus disease 2019 (COVID‐19) is needed if we are to optimize vaccine strategies and immunotherapies. Identification of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) T‐cell epitopes and generation of peptide–human leukocyte antigen (peptide–HLA) tetramers facilitate direct ex vivo analyses of SARS‐CoV‐2‐specific T cells and their T‐cell receptor (TCR) repertoires. We utilized a combination of peptide prediction and in vitro peptide stimulation to validate novel SARS‐CoV‐2 epitopes restricted by HLA‐A*24:02, one of the most prominent HLA class I alleles, especially in Indigenous and Asian populations. Of the peptides screened, three spike‐derived peptides generated CD8+IFNγ+ responses above background, S1208–1216 (QYIKWPWYI), S448–456 (NYNYLYRLF) and S193–201 (VFKNIDGYF), with S1208 generating immunodominant CD8+IFNγ+ responses. Using peptide–HLA‐I tetramers, we performed direct ex vivo tetramer enrichment for HLA‐A*24:02‐restricted CD8+ T cells in COVID‐19 patients and prepandemic controls. The precursor frequencies for HLA‐A*24:02‐restricted epitopes were within the range previously observed for other SARS‐CoV‐2 epitopes for both COVID‐19 patients and prepandemic individuals. Naïve A24/SARS‐CoV‐2‐specific CD8+ T cells increased nearly 7.5‐fold above the average precursor frequency during COVID‐19, gaining effector and memory phenotypes. Ex vivo single‐cell analyses of TCRαβ repertoires found that the A24/S448+CD8+ T‐cell TCRαβ repertoire was driven by a common TCRβ chain motif, whereas the A24/S1208+CD8+ TCRαβ repertoire was diverse across COVID‐19 patients. Our study provides an in depth characterization and important insights into SARS‐CoV‐2‐specific CD8+ T‐cell responses associated with a prominent HLA‐A*24:02 allomorph. This contributes to our knowledge on adaptive immune responses during primary COVID‐19 and could be exploited in vaccine or immunotherapeutic approaches.
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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
| | - 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
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Priyanka Chaurasia
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kathleen Wragg
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Luca Hensen
- 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
| | - 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
| | - 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, UK
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thi Ho Nguyen
- 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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