1
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Edmans MD, Connelley TK, Morgan S, Pediongco TJ, Jayaraman S, Juno JA, Meehan BS, Dewar PM, Maze EA, Roos EO, Paudyal B, Mak JY, Liu L, Fairlie DP, Wang H, Corbett AJ, McCluskey J, Benedictus L, Tchilian E, Klenerman P, Eckle SB. MAIT cell-MR1 reactivity is highly conserved across multiple divergent species. J Biol Chem 2024:107338. [PMID: 38705391 DOI: 10.1016/j.jbc.2024.107338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 04/03/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are a subset of unconventional T cells that recognize small molecule metabolites presented by MHC-I related protein 1 (MR1), via an αβ T cell receptor (TCR). MAIT TCRs feature an essentially invariant TCR α-chain, which is highly conserved between mammals. Similarly, MR1 is the most highly conserved MHC-I like molecule. This extreme conservation, including the mode of interaction between the MAIT TCR and MR1, has been shown to allow for species-mismatched reactivities unique in T cell biology thereby allowing the use of selected species-mismatched MR1-antigen (MR1-Ag) tetramers in comparative immunology studies. However, the pattern of cross-reactivity of species-mismatched MR1-Ag tetramers in identifying MAIT cells in diverse species has not been formally assessed. We developed novel cattle and pig MR1-Ag tetramers and utilized these alongside previously developed human, mouse and pig-tailed macaque MR1-Ag tetramers to characterize cross-species tetramer reactivities. MR1-Ag tetramers from each species identified T cell populations in distantly related species with specificity that was comparable to species-matched MR1-Ag tetramers. However, there were subtle differences in staining characteristics with practical implications for the accurate identification of MAIT cells. Pig MR1 is sufficiently conserved across species that pig MR1-Ag tetramers identified MAIT cells from the other species. However, MAIT cells in pigs were at the limits of phenotypic detection. In the absence of sheep MR1-Ag tetramers, a MAIT cell population in sheep blood was identified phenotypically, utilizing species-mismatched MR1-Ag tetramers. Collectively, our results validate the use and limitations of species-mismatched MR1-Ag tetramers in comparative immunology studies.
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Affiliation(s)
- Matthew D Edmans
- Department of Enhanced Host Responses, The Pirbright Institute, Pirbright, United Kingdom; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.
| | - Timothy K Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, Roslin, United Kingdom
| | - Sophie Morgan
- Department of Enhanced Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | - Troi J Pediongco
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Siddharth Jayaraman
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, Roslin, United Kingdom
| | - Jennifer A Juno
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Bronwyn S Meehan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Phoebe M Dewar
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Emmanuel A Maze
- Department of Enhanced Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | - Eduard O Roos
- Department of Enhanced Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | - Basu Paudyal
- Department of Enhanced Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | - Jeffrey Yw Mak
- Centre for Chemistry and Drug Discovery, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ligong Liu
- Centre for Chemistry and Drug Discovery, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - David P Fairlie
- Centre for Chemistry and Drug Discovery, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Huimeng Wang
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Lindert Benedictus
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, Roslin, United Kingdom; Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Elma Tchilian
- Department of Enhanced Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Sidonia Bg Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
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2
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Provine NM, Al-Diwani A, Agarwal D, Dooley K, Heslington A, Murchison AG, Garner LC, Sheerin F, Klenerman P, Irani SR. Fine needle aspiration of human lymph nodes reveals cell populations and soluble interactors pivotal to immunological priming. Eur J Immunol 2024; 54:e2350872. [PMID: 38388988 DOI: 10.1002/eji.202350872] [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: 11/01/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Lymph node (LN) fine needle aspiration (LN FNA) represents a powerful technique for minimally invasive sampling of human LNs in vivo and has been used effectively to directly study aspects of the human germinal center response. However, systematic deep phenotyping of the cellular populations and cell-free proteins recovered by LN FNA has not been performed. Thus, we studied human cervical LN FNAs as a proof-of-concept and used single-cell RNA-sequencing and proteomic analysis to benchmark this compartment, define the purity of LN FNA material, and facilitate future studies in this immunologically pivotal environment. Our data provide evidence that LN FNAs contain bone-fide LN-resident innate immune populations, with minimal contamination of blood material. Examination of these populations reveals unique biology not predictable from equivalent blood-derived populations. LN FNA supernatants represent a specific source of lymph- and lymph node-derived proteins, and can, aided by transcriptomics, identify likely receptor-ligand interactions. This represents the first description of the types and abundance of immune cell populations and cell-free proteins that can be efficiently studied by LN FNA. These findings are of broad utility for understanding LN physiology in health and disease, including infectious or autoimmune perturbations, and in the case of cervical nodes, neuroscience.
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Affiliation(s)
- Nicholas M Provine
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam Al-Diwani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- University Department of Psychiatry, University of Oxford, Oxford, UK
| | - Devika Agarwal
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kyla Dooley
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amelia Heslington
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew G Murchison
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fintan Sheerin
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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3
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Drury RE, Camara S, Chelysheva I, Bibi S, Sanders K, Felle S, Emary K, Phillips D, Voysey M, Ferreira DM, Klenerman P, Gilbert SC, Lambe T, Pollard AJ, O'Connor D. Multi-omics analysis reveals COVID-19 vaccine induced attenuation of inflammatory responses during breakthrough disease. Nat Commun 2024; 15:3402. [PMID: 38649734 PMCID: PMC11035709 DOI: 10.1038/s41467-024-47463-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
The immune mechanisms mediating COVID-19 vaccine attenuation of COVID-19 remain undescribed. We conducted comprehensive analyses detailing immune responses to SARS-CoV-2 virus in blood post-vaccination with ChAdOx1 nCoV-19 or a placebo. Samples from randomised placebo-controlled trials (NCT04324606 and NCT04400838) were taken at baseline, onset of COVID-19-like symptoms, and 7 days later, confirming COVID-19 using nucleic amplification test (NAAT test) via real-time PCR (RT-PCR). Serum cytokines were measured with multiplexed immunoassays. The transcriptome was analysed with long, short and small RNA sequencing. We found attenuation of RNA inflammatory signatures in ChAdOx1 nCoV-19 compared with placebo vaccinees and reduced levels of serum proteins associated with COVID-19 severity. KREMEN1, a putative alternative SARS-CoV-2 receptor, was downregulated in placebo compared with ChAdOx1 nCoV-19 vaccinees. Vaccination ameliorates reductions in cell counts across leukocyte populations and platelets noted at COVID-19 onset, without inducing potentially deleterious Th2-skewed immune responses. Multi-omics integration links a global reduction in miRNA expression at COVID-19 onset to increased pro-inflammatory responses at the mRNA level. This study reveals insights into the role of COVID-19 vaccines in mitigating disease severity by abrogating pro-inflammatory responses associated with severe COVID-19, affirming vaccine-mediated benefit in breakthrough infection, and highlighting the importance of clinically relevant endpoints in vaccine evaluation.
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Affiliation(s)
- Ruth E Drury
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susana Camara
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Katherine Sanders
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Salle Felle
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Katherine Emary
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel Phillips
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniela M Ferreira
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah C Gilbert
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
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4
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Ali M, Longet S, Neale I, Rongkard P, Chowdhury FUH, Hill J, Brown A, Laidlaw S, Tipton T, Hoque A, Hassan N, Hackstein CP, Adele S, Akther HD, Abraham P, Paul S, Rahman MM, Alam MM, Parvin S, Hoque Mollah F, Hoque MM, Moore SC, Biswas SK, Turtle L, de Silva TI, Ogbe A, Frater J, Barnes E, Tomic A, Carroll MW, Klenerman P, Kronsteiner B, Chowdhury FR, Dunachie SJ. Obesity Differs from Diabetes Mellitus in Antibody and T Cell Responses Post COVID-19 Recovery. Clin Exp Immunol 2024:uxae030. [PMID: 38642547 DOI: 10.1093/cei/uxae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 04/22/2024] Open
Abstract
Obesity and type 2 diabetes (DM) are risk factors for severe COVID-19 outcomes, which disproportionately affect South Asian populations. This study aims to investigate the humoral and cellular immune responses to SARS-CoV-2 in adult COVID-19 survivors with obesity and DM in Bangladesh. In this cross-sectional study, SARS-CoV-2-specific antibody and T cell responses were investigated in 63 healthy and 75 PCR-confirmed COVID-19 recovered individuals in Bangladesh, during the pre-vaccination first wave of the COVID-19 pandemic in 2020. In COVID-19 survivors, SARS-CoV-2 infection induced robust antibody and T cell responses, which correlated with disease severity. After adjusting for age, sex, DM status, disease severity, and time since onset of symptoms, obesity was associated with decreased neutralising antibody titers, and increased SARS-CoV-2 spike-specific IFN-γ response along with increased proliferation and IL-2 production by CD8+ T cells. In contrast, DM was not associated with SARS-CoV-2-specific antibody and T cell responses after adjustment for obesity and other confounders. Obesity is associated with lower neutralising antibody levels and higher T cell responses to SARS-CoV-2 post COVID-19 recovery, while antibody or T cell responses remain unaltered in DM.
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Affiliation(s)
- Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Directorate General of Health Services, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Isabel Neale
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Patpong Rongkard
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Jennifer Hill
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Stephen Laidlaw
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tom Tipton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ashraful Hoque
- Department of Transfusion Medicine, Sheikh Hasina National Burn & Plastics Surgery Institute, Dhaka, Bangladesh
| | - Nazia Hassan
- Department of Internal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Carl-Philipp Hackstein
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Hossain Delowar Akther
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Priyanka Abraham
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Shrebash Paul
- Department of Internal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md Matiur Rahman
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md Masum Alam
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shamima Parvin
- Department of Biochemistry and Molecular Biology, Mugda Medical College, Dhaka, Bangladesh
| | - Forhadul Hoque Mollah
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md Mozammel Hoque
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shona C Moore
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, UK
| | - Subrata K Biswas
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Lance Turtle
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Adriana Tomic
- National Emerging Infectious Diseases Laboratories, Boston University, USA
- Department of Microbiology, Boston University School of Medicine, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Fazle Rabbi Chowdhury
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Internal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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5
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Liu C, Das R, Dijokaite-Guraliuc A, Zhou D, Mentzer AJ, Supasa P, Selvaraj M, Duyvesteyn HME, Ritter TG, Temperton N, Klenerman P, Dunachie SJ, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection. Nat Commun 2024; 15:3284. [PMID: 38627386 PMCID: PMC11021415 DOI: 10.1038/s41467-024-47393-3] [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: 11/30/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 is driven in part by a need to evade the antibody response in the face of high levels of immunity. Here, we isolate spike (S) binding monoclonal antibodies (mAbs) from vaccinees who suffered vaccine break-through infections with Omicron sub lineages BA.4 or BA.5. Twenty eight potent antibodies are isolated and characterised functionally, and in some cases structurally. Since the emergence of BA.4/5, SARS-CoV-2 has continued to accrue mutations in the S protein, to understand this we characterize neutralization of a large panel of variants and demonstrate a steady attrition of neutralization by the panel of BA.4/5 mAbs culminating in total loss of function with recent XBB.1.5.70 variants containing the so-called 'FLip' mutations at positions 455 and 456. Interestingly, activity of some mAbs is regained on the recently reported variant BA.2.86.
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Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Raksha Das
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Alexander J Mentzer
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Piyada Supasa
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
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6
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Cleaver J, Jeffery K, Klenerman P, Lim M, Handunnetthi L, Irani SR, Handel A. The immunobiology of herpes simplex virus encephalitis and post-viral autoimmunity. Brain 2024; 147:1130-1148. [PMID: 38092513 PMCID: PMC10994539 DOI: 10.1093/brain/awad419] [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: 07/20/2023] [Revised: 10/25/2023] [Accepted: 11/27/2023] [Indexed: 04/06/2024] Open
Abstract
Herpes simplex virus encephalitis (HSE) is the leading cause of non-epidemic encephalitis in the developed world and, despite antiviral therapy, mortality and morbidity is high. The emergence of post-HSE autoimmune encephalitis reveals a new immunological paradigm in autoantibody-mediated disease. A reductionist evaluation of the immunobiological mechanisms in HSE is crucial to dissect the origins of post-viral autoimmunity and supply rational approaches to the selection of immunotherapeutics. Herein, we review the latest evidence behind the phenotypic progression and underlying immunobiology of HSE including the cytokine/chemokine environment, the role of pathogen-recognition receptors, T- and B-cell immunity and relevant inborn errors of immunity. Second, we provide a contemporary review of published patients with post-HSE autoimmune encephalitis from a combined cohort of 110 patients. Third, we integrate novel mechanisms of autoimmunization in deep cervical lymph nodes to explore hypotheses around post-HSE autoimmune encephalitis and challenge these against mechanisms of molecular mimicry and others. Finally, we explore translational concepts where neuroglial surface autoantibodies have been observed with other neuroinfectious diseases and those that generate brain damage including traumatic brain injury, ischaemic stroke and neurodegenerative disease. Overall, the clinical and immunological landscape of HSE is an important and evolving field, from which precision immunotherapeutics could soon emerge.
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Affiliation(s)
- Jonathan Cleaver
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, OX3 9DU, UK
| | - Katie Jeffery
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Ming Lim
- Children’s Neurosciences, Evelina London Children’s Hospital at Guy’s and St Thomas’ NHS Foundation Trust, London, SE1 7EH, UK
- Department Women and Children’s Health, School of Life Course Sciences, King’s College London, London, WC2R 2LS, UK
| | - Lahiru Handunnetthi
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, OX3 9DU, UK
| | - Adam Handel
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, OX3 9DU, UK
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7
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Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86. Nat Commun 2024; 15:2734. [PMID: 38548763 PMCID: PMC10978878 DOI: 10.1038/s41467-024-46982-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.
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Affiliation(s)
- Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Muneeswaran Selvaraj
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-Noi, Bangkok, 10700, Thailand
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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8
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Luo J, Chen W, Liu W, Jiang S, Ye Y, Shrimanker R, Hynes G, Klenerman P, Pavord ID, Xue L. IL-5 antagonism reverses priming and activation of eosinophils in severe eosinophilic asthma. Mucosal Immunol 2024:S1933-0219(24)00024-2. [PMID: 38493955 DOI: 10.1016/j.mucimm.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
Eosinophils are key effector cells mediating airway inflammation and exacerbation in patients with severe eosinophilic asthma. They are present in increased numbers and activation states in the airway mucosa and lumen. Interleukin-5 (IL-5) is the key eosinophil growth factor that is thought to play a role in eosinophil priming and activation. However, the mechanism of these effects is still not fully understood. The anti-IL-5 antibody mepolizumab reduces eosinophil counts in the airway modestly but has a large beneficial effect on the frequency of exacerbations of severe eosinophilic asthma, suggesting that reduction in eosinophil priming and activation is of central mechanistic importance. In this study, we used the therapeutic effect of mepolizumab and single-cell ribonucleic acid sequencing to investigate the mechanism of eosinophil priming and activation by IL-5. We demonstrated that IL-5 is a dominant driver of eosinophil priming and plays multifaceted roles in eosinophil function. It enhances eosinophil responses to other stimulators of migration, survival, and activation by activating phosphatidylinositol-3-kinases, extracellular signal-regulated kinases, and p38 mitogen-activated protein kinases signaling pathways. It also enhances the pro-fibrotic roles of eosinophils in airway remodeling via transforming growth factor-β pathway. These findings provide a mechanistic understanding of eosinophil priming in severe eosinophilic asthma and the therapeutic effect of anti-IL-5 approaches in the disease.
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Affiliation(s)
- Jian Luo
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.
| | - Wentao Chen
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Wei Liu
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom; Division of Pulmonary Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Jiang
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom; Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuan Ye
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Rahul Shrimanker
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Gareth Hynes
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Translational Gastroenterology Unit and Peter Medawar Building, University of Oxford, Oxford, United Kingdom
| | - Ian D Pavord
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Luzheng Xue
- Respiratory Medicine Unit and NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.
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9
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Sampson OL, Jay C, Adland E, Csala A, Lim N, Ebbrecht SM, Gilligan LC, Taylor AE, George SS, Longet S, Jones LC, Barnes E, Frater J, Klenerman P, Dunachie S, Carrol M, Hawley J, Arlt W, Groll A, Goulder P. Gonadal androgens are associated with decreased type I interferon production by plasmacytoid dendritic cells and increased IgG titres to BNT162b2 following co-vaccination with live attenuated influenza vaccine in adolescents. Front Immunol 2024; 15:1329805. [PMID: 38481993 PMCID: PMC10933029 DOI: 10.3389/fimmu.2024.1329805] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 04/09/2024] Open
Abstract
mRNA vaccine technologies introduced following the SARS-CoV-2 pandemic have highlighted the need to better understand the interaction of adjuvants and the early innate immune response. Type I interferon (IFN-I) is an integral part of this early innate response that primes several components of the adaptive immune response. Women are widely reported to respond better than men to tri- and quadrivalent influenza vaccines. Plasmacytoid dendritic cells (pDCs) are the primary cell type responsible for IFN-I production, and female pDCs produce more IFN-I than male pDCs since the upstream pattern recognition receptor Toll-like receptor 7 (TLR7) is encoded by X chromosome and is biallelically expressed by up to 30% of female immune cells. Additionally, the TLR7 promoter contains several putative androgen response elements, and androgens have been reported to suppress pDC IFN-I in vitro. Unexpectedly, therefore, we recently observed that male adolescents mount stronger antibody responses to the Pfizer BNT162b2 mRNA vaccine than female adolescents after controlling for natural SARS-CoV-2 infection. We here examined pDC behaviour in this same cohort to determine the impact of IFN-I on anti-spike and anti-receptor-binding domain IgG titres to BNT162b2. Through flow cytometry and least absolute shrinkage and selection operator (LASSO) modelling, we determined that serum-free testosterone was associated with reduced pDC IFN-I, but contrary to the well-described immunosuppressive role for androgens, the most bioactive androgen dihydrotestosterone was associated with increased IgG titres to BNT162b2. Also unexpectedly, we observed that co-vaccination with live attenuated influenza vaccine boosted the magnitude of IgG responses to BNT162b2. Together, these data support a model where systemic IFN-I increases vaccine-mediated immune responses, yet for vaccines with intracellular stages, modulation of the local IFN-I response may alter antigen longevity and consequently improve vaccine-driven immunity.
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Affiliation(s)
- Oliver L. Sampson
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Cecilia Jay
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Emily Adland
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Anna Csala
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Nicholas Lim
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Stella M. Ebbrecht
- Department of Statistics, Technical University of Dortmund, Dortmund, Germany
| | - Lorna C. Gilligan
- Steroid Metabolome Analysis Core, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Angela E. Taylor
- Steroid Metabolome Analysis Core, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Sherley Sherafin George
- Biochemistry Department, Clinical Science Building, Wythenshawe Hospital, Manchester, United Kingdom
| | - Stephanie Longet
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lucy C. Jones
- Department of Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Ellie Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - John Frater
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Susie Dunachie
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Miles Carrol
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James Hawley
- Biochemistry Department, Clinical Science Building, Wythenshawe Hospital, Manchester, United Kingdom
| | - Wiebke Arlt
- Steroid Metabolome Analysis Core, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
- Medical Research Council London Institute of Medical Sciences (MRC LMS), Imperial College London, London, United Kingdom
| | - Andreas Groll
- Department of Statistics, Technical University of Dortmund, Dortmund, Germany
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
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10
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Ng MTH, Borst R, Gacaferi H, Davidson S, Ackerman JE, Johnson PA, Machado CC, Reekie I, Attar M, Windell D, Kurowska-Stolarska M, MacDonald L, Alivernini S, Garvilles M, Jansen K, Bhalla A, Lee A, Charlesworth J, Chowdhury R, Klenerman P, Powell K, Hackstein CP, Furniss D, Rees J, Gilroy D, Coles M, Carr AJ, Sansom SN, Buckley CD, Dakin SG. A single cell atlas of frozen shoulder capsule identifies features associated with inflammatory fibrosis resolution. Nat Commun 2024; 15:1394. [PMID: 38374174 PMCID: PMC10876649 DOI: 10.1038/s41467-024-45341-9] [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: 03/31/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
Frozen shoulder is a spontaneously self-resolving chronic inflammatory fibrotic human disease, which distinguishes the condition from most fibrotic diseases that are progressive and irreversible. Using single-cell analysis, we identify pro-inflammatory MERTKlowCD48+ macrophages and MERTK + LYVE1 + MRC1+ macrophages enriched for negative regulators of inflammation which co-exist in frozen shoulder capsule tissues. Micro-cultures of patient-derived cells identify integrin-mediated cell-matrix interactions between MERTK+ macrophages and pro-resolving DKK3+ and POSTN+ fibroblasts, suggesting that matrix remodelling plays a role in frozen shoulder resolution. Cross-tissue analysis reveals a shared gene expression cassette between shoulder capsule MERTK+ macrophages and a respective population enriched in synovial tissues of rheumatoid arthritis patients in disease remission, supporting the concept that MERTK+ macrophages mediate resolution of inflammation and fibrosis. Single-cell transcriptomic profiling and spatial analysis of human foetal shoulder tissues identify MERTK + LYVE1 + MRC1+ macrophages and DKK3+ and POSTN+ fibroblast populations analogous to those in frozen shoulder, suggesting that the template to resolve fibrosis is established during shoulder development. Crosstalk between MerTK+ macrophages and pro-resolving DKK3+ and POSTN+ fibroblasts could facilitate resolution of frozen shoulder, providing a basis for potential therapeutic resolution of persistent fibrotic diseases.
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Affiliation(s)
| | | | | | | | | | | | - Caio C Machado
- University of Oxford, Oxford, UK
- University of Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | - Lucy MacDonald
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, UK
| | - Stefano Alivernini
- Fondazione Policlinico Universitario Agostino Gemelli - IRCCS, Rome, Italy
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11
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Mulroney TE, Pöyry T, Yam-Puc JC, Rust M, Harvey RF, Kalmar L, Horner E, Booth L, Ferreira AP, Stoneley M, Sawarkar R, Mentzer AJ, Lilley KS, Smales CM, von der Haar T, Turtle L, Dunachie S, Klenerman P, Thaventhiran JED, Willis AE. N 1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting. Nature 2024; 625:189-194. [PMID: 38057663 PMCID: PMC10764286 DOI: 10.1038/s41586-023-06800-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 01/25/2023] [Accepted: 10/31/2023] [Indexed: 12/08/2023]
Abstract
In vitro-transcribed (IVT) mRNAs are modalities that can combat human disease, exemplified by their use as vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IVT mRNAs are transfected into target cells, where they are translated into recombinant protein, and the biological activity or immunogenicity of the encoded protein exerts an intended therapeutic effect1,2. Modified ribonucleotides are commonly incorporated into therapeutic IVT mRNAs to decrease their innate immunogenicity3-5, but their effects on mRNA translation fidelity have not been fully explored. Here we demonstrate that incorporation of N1-methylpseudouridine into mRNA results in +1 ribosomal frameshifting in vitro and that cellular immunity in mice and humans to +1 frameshifted products from BNT162b2 vaccine mRNA translation occurs after vaccination. The +1 ribosome frameshifting observed is probably a consequence of N1-methylpseudouridine-induced ribosome stalling during IVT mRNA translation, with frameshifting occurring at ribosome slippery sequences. However, we demonstrate that synonymous targeting of such slippery sequences provides an effective strategy to reduce the production of frameshifted products. Overall, these data increase our understanding of how modified ribonucleotides affect the fidelity of mRNA translation, and although there are no adverse outcomes reported from mistranslation of mRNA-based SARS-CoV-2 vaccines in humans, these data highlight potential off-target effects for future mRNA-based therapeutics and demonstrate the requirement for sequence optimization.
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Affiliation(s)
| | - Tuija Pöyry
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Maria Rust
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Lajos Kalmar
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Emily Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Lucy Booth
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Mark Stoneley
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | | | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - C Mark Smales
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
- National Institute for Bioprocessing Research and Training, University College Dublin, Foster Avenue, Mount Merrion, Dublin, Ireland
| | - Tobias von der Haar
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Susanna Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK.
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12
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Murray SM, Pose E, Wittner M, Londoño MC, Schaub G, Cook J, Dimitriadis S, Meacham G, Irwin S, Lim Z, Duengelhoef P, Sterneck M, Lohse AW, Perez V, Trivedi P, Bhandal K, Mullish BH, Manousou P, Provine NM, Avitabile E, Carroll M, Tipton T, Healy S, Burra P, Klenerman P, Dunachie S, Kronsteiner B, Maciola AK, Pasqual G, Hernandez-Gea V, Garcia-Pagan JC, Lampertico P, Iavarone M, Gines P, Lütgehetmann M, Schulze Zur Wiesch J, Russo FP, Barnes E, Marjot T. Immune responses and clinical outcomes after COVID-19 vaccination in patients with liver disease and liver transplant recipients. J Hepatol 2024; 80:109-123. [PMID: 37863203 PMCID: PMC10914634 DOI: 10.1016/j.jhep.2023.10.009] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023]
Abstract
BACKGROUND & AIMS Comparative assessments of immunogenicity following different COVID-19 vaccines in patients with distinct liver diseases are lacking. SARS-CoV-2-specific T-cell and antibody responses were evaluated longitudinally after one to three vaccine doses, with long-term follow-up for COVID-19-related clinical outcomes. METHODS A total of 849 participants (355 with cirrhosis, 74 with autoimmune hepatitis [AIH], 36 with vascular liver disease [VLD], 257 liver transplant recipients [LTRs] and 127 healthy controls [HCs]) were recruited from four countries. Standardised immune assays were performed pre and post three vaccine doses (V1-3). RESULTS In the total cohort, there were incremental increases in antibody titres after each vaccine dose (p <0.0001). Factors associated with reduced antibody responses were age and LT, whereas heterologous vaccination, prior COVID-19 and mRNA platforms were associated with greater responses. Although antibody titres decreased between post-V2 and pre-V3 (p = 0.012), patients with AIH, VLD, and cirrhosis had equivalent antibody responses to HCs post-V3. LTRs had lower and more heterogenous antibody titres than other groups, including post-V3 where 9% had no detectable antibodies; this was heavily influenced by intensity of immunosuppression. Vaccination increased T-cell IFNγ responses in all groups except LTRs. Patients with liver disease had lower functional antibody responses against nine Omicron subvariants and reduced T-cell responses to Omicron BA.1-specific peptides compared to wild-type. 122 cases of breakthrough COVID-19 were reported of which 5/122 (4%) were severe. Of the severe cases, 4/5 (80%) occurred in LTRs and 2/5 (40%) had no serological response post-V2. CONCLUSION After three COVID-19 vaccines, patients with liver disease generally develop robust antibody and T-cell responses to vaccination and have mild COVID-19. However, LTRs have sustained no/low antibody titres and appear most vulnerable to severe disease. IMPACT AND IMPLICATIONS Standardised assessments of the immune response to different COVID-19 vaccines in patients with liver disease are lacking. We performed antibody and T-cell assays at multiple timepoints following up to three vaccine doses in a large cohort of patients with a range of liver conditions. Overall, the three most widely available vaccine platforms were immunogenic and appeared to protect against severe breakthrough COVID-19. This will provide reassurance to patients with chronic liver disease who were deemed at high risk of severe COVID-19 during the pre-vaccination era, however, liver transplant recipients had the lowest antibody titres and remained vulnerable to severe breakthrough infection. We also characterise the immune response to multiple SARS-CoV-2 variants and describe the interaction between disease type, severity, and vaccine platform. These insights may prove useful in the event of future viral infections which also require rapid vaccine development and delivery to patients with liver disease.
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Affiliation(s)
- Sam M Murray
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Elisa Pose
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain; CIBERehd (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Spain
| | - Melanie Wittner
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maria-Carlota Londoño
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain; CIBERehd (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Spain
| | - Golda Schaub
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonathan Cook
- Centre for Statistics in Medicine, University of Oxford, Oxford, UK
| | - Stavros Dimitriadis
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Georgina Meacham
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie Irwin
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zixiang Lim
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Duengelhoef
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martina Sterneck
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ansgar W Lohse
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Valeria Perez
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain; CIBERehd (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Spain; Health Care Provider of the European Reference Network on Rare Liver Disorders (ERN-Liver), Germany
| | - Palak Trivedi
- National Institute for Health Research Birmingham Biomedical Research Centre, Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, UK; Liver Unit, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Birmingham, UK
| | - Khush Bhandal
- Liver Unit, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Birmingham, UK
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK; Department of Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Pinelopi Manousou
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK; Department of Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emma Avitabile
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain; CIBERehd (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Spain
| | - Miles Carroll
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tom Tipton
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Saoirse Healy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Patrizia Burra
- University of Padova, Department of Surgery, Oncology and Gastroenterology DISCOG, Italy
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK; The Oxford NIHR Biomedical Research Centre, Oxford University Hospital NHS Trust, Oxford, UK
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; The Oxford NIHR Biomedical Research Centre, Oxford University Hospital NHS Trust, Oxford, UK; Mahidol Oxford Tropical Medicine Research Unit, University of Mahidol, Bangkok, Thailand
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; The Oxford NIHR Biomedical Research Centre, Oxford University Hospital NHS Trust, Oxford, UK; Mahidol Oxford Tropical Medicine Research Unit, University of Mahidol, Bangkok, Thailand
| | - Agnieszka Katarzyna Maciola
- Laboratory of Synthetic Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Giulia Pasqual
- Laboratory of Synthetic Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy; Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Virginia Hernandez-Gea
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain; CIBERehd (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Spain; Health Care Provider of the European Reference Network on Rare Liver Disorders (ERN-Liver), Germany
| | - Juan Carlos Garcia-Pagan
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain; CIBERehd (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Spain; Health Care Provider of the European Reference Network on Rare Liver Disorders (ERN-Liver), Germany
| | - Pietro Lampertico
- Division of Gastroenterology and Hepatology, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; CRC "A. M. and A. Migliavacca" Center for Liver Disease, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Massimo Iavarone
- Division of Gastroenterology and Hepatology, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Pere Gines
- Liver Unit, Hospital Clínic, Institut de Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain; CIBERehd (Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas), Spain
| | - Marc Lütgehetmann
- Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Schulze Zur Wiesch
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Francesco Paolo Russo
- University of Padova, Department of Surgery, Oncology and Gastroenterology DISCOG, Italy
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; The Oxford NIHR Biomedical Research Centre, Oxford University Hospital NHS Trust, Oxford, UK.
| | - Thomas Marjot
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, University of Oxford, Oxford, UK; Oxford Liver Unit, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.
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13
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Ratcliffe H, Tiley KS, Longet S, Tonry C, Roarty C, Watson C, Amirthalingam G, Vichos I, Morey E, Douglas NL, Marinou S, Plested E, Aley PK, Galiza E, Faust SN, Hughes S, Murray C, Roderick MR, Shackley F, Oddie S, Lee TW, Turner DP, Raman M, Owens S, Turner PJ, Cockerill H, Lopez Bernal J, Ijaz S, Poh J, Shute J, Linley E, Borrow R, Hoschler K, Brown KE, Carroll MW, Klenerman P, Dunachie SJ, Ramsay M, Voysey M, Waterfield T, Snape MD. Serum HCoV-spike specific antibodies do not protect against subsequent SARS-CoV-2 infection in children and adolescents. iScience 2023; 26:108500. [PMID: 38089581 PMCID: PMC10711458 DOI: 10.1016/j.isci.2023.108500] [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: 03/30/2023] [Revised: 09/17/2023] [Accepted: 11/17/2023] [Indexed: 02/15/2024] Open
Abstract
SARS-CoV-2 infections in children are generally asymptomatic or mild and rarely progress to severe disease and hospitalization. Why this is so remains unclear. Here we explore the potential for protection due to pre-existing cross-reactive seasonal coronavirus antibodies and compare the rate of antibody decline for nucleocapsid and spike protein in serum and oral fluid against SARS-CoV-2 within the pediatric population. No differences in seasonal coronaviruses antibody concentrations were found at baseline between cases and controls, suggesting no protective effect from pre-existing immunity against seasonal coronaviruses. Antibodies against seasonal betacoronaviruses were boosted in response to SARS-CoV-2 infection. In serum, anti-nucleocapsid antibodies fell below the threshold of positivity more quickly than anti-spike protein antibodies. These findings add to our understanding of protection against infection with SARS-CoV-2 within the pediatric population, which is important when considering pediatric SARS-CoV-2 immunization policies.
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Affiliation(s)
- Helen Ratcliffe
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Karen S. Tiley
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claire Tonry
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast- School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
| | - Cathal Roarty
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast- School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
| | - Chris Watson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast- School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
| | | | - Iason Vichos
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Ella Morey
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Naomi L. Douglas
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Spyridoula Marinou
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Emma Plested
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Parvinder K. Aley
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Eva Galiza
- St Georges Hospital NHS Foundation Trust
| | - Saul N. Faust
- NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust and Faculty of Medicine and Institute of Life Sciences, University of Southampton
- National Immunisation Schedule Evaluation Consortium
| | - Stephen Hughes
- Manchester University NHS Foundation Trust, NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
| | - Clare Murray
- Manchester University NHS Foundation Trust, NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, UK
| | | | | | - Sam Oddie
- Bradford Teaching Hospitals NHS Foundation Trust
| | | | - David P.J. Turner
- School of Life Sciences, University of Nottingham
- Nottingham University Hospitals NHS Trust
| | | | - Stephen Owens
- The Newcastle Upon Tyne Hospitals NHS Foundation Trust
| | - Paul J. Turner
- National Heart & Lung Institute, Imperial College London
| | | | | | | | | | | | | | | | | | | | - Miles W. Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Oxford BRC
| | - Susanna J. Dunachie
- National Institute for Health Research (NIHR) Oxford BRC
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Merryn Voysey
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Thomas Waterfield
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast- School of Medicine, Dentistry and Biomedical Sciences, Belfast, UK
| | - Matthew D. Snape
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
- National Immunisation Schedule Evaluation Consortium
- West Suffolk NHS Foundation Trust
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14
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Fowler A, FitzPatrick M, Shanmugarasa A, Ibrahim ASF, Kockelbergh H, Yang HC, Williams-Walker A, Luu Hoang KN, Evans S, Provine N, Klenerman P, Soilleux EJ. An Interpretable Classification Model Using Gluten-Specific TCR Sequences Shows Diagnostic Potential in Coeliac Disease. Biomolecules 2023; 13:1707. [PMID: 38136579 PMCID: PMC10742135 DOI: 10.3390/biom13121707] [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: 10/03/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Coeliac disease (CeD) is a T-cell mediated enteropathy triggered by dietary gluten which remains substantially under-diagnosed around the world. The diagnostic gold-standard requires histological assessment of intestinal biopsies taken at endoscopy while consuming a gluten-containing diet. However, there is a lack of concordance between pathologists in histological assessment, and both endoscopy and gluten challenge are burdensome and unpleasant for patients. Identification of gluten-specific T-cell receptors (TCRs) in the TCR repertoire could provide a less subjective diagnostic test, and potentially remove the need to consume gluten. We review published gluten-specific TCR sequences, and develop an interpretable machine learning model to investigate their diagnostic potential. To investigate this, we sequenced the TCR repertoires of mucosal CD4+ T cells from 20 patients with and without CeD. These data were used as a training dataset to develop the model, then an independently published dataset of 20 patients was used as the testing dataset. We determined that this model has a training accuracy of 100% and testing accuracy of 80% for the diagnosis of CeD, including in patients on a gluten-free diet (GFD). We identified 20 CD4+ TCR sequences with the highest diagnostic potential for CeD. The sequences identified here have the potential to provide an objective diagnostic test for CeD, which does not require the consumption of gluten.
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Affiliation(s)
- Anna Fowler
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK
| | - Michael FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; (M.F.); (P.K.)
| | | | - Amro Sayed Fadel Ibrahim
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Hannah Kockelbergh
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK
| | - Han-Chieh Yang
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Amelia Williams-Walker
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Kim Ngan Luu Hoang
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Shelley Evans
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
| | - Nicholas Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; (M.F.); (P.K.)
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; (M.F.); (P.K.)
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Elizabeth J. Soilleux
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (A.S.F.I.); (H.-C.Y.); (A.W.-W.); (K.N.L.H.); (S.E.); (E.J.S.)
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15
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Wang L, Nicols A, Turtle L, Richter A, Duncan CJA, Dunachie SJ, Klenerman P, Payne RP. T cell immune memory after covid-19 and vaccination. BMJ Med 2023; 2:e000468. [PMID: 38027416 PMCID: PMC10668147 DOI: 10.1136/bmjmed-2022-000468] [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] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains.
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Affiliation(s)
- Lulu Wang
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Alex Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Christopher JA Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susanna J Dunachie
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University Faculty of Science, Bangkok, Thailand
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
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16
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Weeratunga P, Denney L, Bull JA, Repapi E, Sergeant M, Etherington R, Vuppussetty C, Turner GDH, Clelland C, Woo J, Cross A, Issa F, de Andrea CE, Melero Bermejo I, Sims D, McGowan S, Zurke YX, Ahern DJ, Gamez EC, Whalley J, Richards D, Klenerman P, Monaco C, Udalova IA, Dong T, Antanaviciute A, Ogg G, Knight JC, Byrne HM, Taylor S, Ho LP. Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs. Nat Commun 2023; 14:7216. [PMID: 37940670 PMCID: PMC10632491 DOI: 10.1038/s41467-023-42421-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Single cell spatial interrogation of the immune-structural interactions in COVID -19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we develop a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method reveals a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and CD8 T cells, is found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings offer further insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline [Spatial Omics Oxford Pipeline (SpOOx)] and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.
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Affiliation(s)
- Praveen Weeratunga
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Laura Denney
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joshua A Bull
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Emmanouela Repapi
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Martin Sergeant
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rachel Etherington
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chaitanya Vuppussetty
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gareth D H Turner
- Department of Cellular Pathology and Radcliffe Department of Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Colin Clelland
- Anatomic Pathology, Weill Cornell Medical College, Doha, Qatar
| | - Jeongmin Woo
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Amy Cross
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | | | - David Sims
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Simon McGowan
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - David J Ahern
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Eddie C Gamez
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Justin Whalley
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Duncan Richards
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Diseases, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claudia Monaco
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Irina A Udalova
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Agne Antanaviciute
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Graham Ogg
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Stephen Taylor
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Ling-Pei Ho
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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17
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Cargill T, Cicconi P, Brown A, Holland L, Karanth B, Rutkowski K, Ashwin E, Mehta R, Chinnakannan S, Sebastian S, Bussey L, Sorensen H, Klenerman P, Evans T, Barnes E. HBV001: Phase I study evaluating the safety and immunogenicity of the therapeutic vaccine ChAdOx1-HBV. JHEP Rep 2023; 5:100885. [PMID: 37791379 PMCID: PMC10543776 DOI: 10.1016/j.jhepr.2023.100885] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/23/2023] [Accepted: 07/22/2023] [Indexed: 10/05/2023] Open
Abstract
Background & Aims Millions of people worldwide are infected chronically with HBV, which results in significant morbidity and mortality. Therapeutic vaccination is a strategy that aims to induce functional cure by restoring cellular immunity to HBV. Previously we have shown the candidate HBV immunotherapeutic vaccine ChAdOx1-HBV, encoding all major HBV antigens and a genetic adjuvant (shark invariant chain), is highly immunogenic in mice. Methods Here we report the results of HBV001, a first-in-human, phase I, non-randomised, dose-escalation trial of ChAdOx1-HBV assessed in healthy volunteers and patients with chronic HBV (CHB). Results Vaccination with a single dose of ChAdOx1-HBV was safe and well tolerated in both healthy and CHB cohorts. Vaccination induced high magnitude HBV-specific T cell responses against all major HBV antigens (core, polymerase, and surface) in healthy volunteers. Responses were detected but lower in patients with CHB. T cells generated by vaccination were cross-reactive between HBV C and D genotypes. Conclusions ChAdOx1-HBV is safe and immunogenic in healthy volunteers and patients with CHB. In further studies, ChAdOx1-HBV will be used in combination with other therapeutic strategies with an aim to overcome the attenuated immunogenicity in patients with CHB. Impact and implications Therapeutic vaccine ChAdOx1-HBV, a novel treatment for chronic hepatitis B infection (CHB), has been shown to be immunogenic in preclinical studies. In HBV001, a first-in-human phase I study, we show vaccination with ChAdOx1-HBV is safe and generates high magnitude T cell responses in healthy volunteers and lower levels of responses in patients with CHB. This is an important first step in the development of ChAdOx1-HBV as part of a wider therapeutic strategy to induce hepatitis B functional cure, and is of great interest to patients CHB and clinicians treating the condition. Clinical Trials Registration This study is registered at ClinicalTrials.gov (NCT04297917).
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Affiliation(s)
- Tamsin Cargill
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Paola Cicconi
- Jenner Vaccine Trials Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Louise Holland
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Jenner Vaccine Trials Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | | | | | - Emily Ashwin
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Jenner Vaccine Trials Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Senthil Chinnakannan
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Oxford NIHR Biomedical Research Centre, University of Oxford, The Joint Research Office, OUH Cowley, Oxford, UK
| | | | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Oxford NIHR Biomedical Research Centre, University of Oxford, The Joint Research Office, OUH Cowley, Oxford, UK
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Raman B, McCracken C, Cassar MP, Moss AJ, Finnigan L, Samat AHA, Ogbole G, Tunnicliffe EM, Alfaro-Almagro F, Menke R, Xie C, Gleeson F, Lukaschuk E, Lamlum H, McGlynn K, Popescu IA, Sanders ZB, Saunders LC, Piechnik SK, Ferreira VM, Nikolaidou C, Rahman NM, Ho LP, Harris VC, Shikotra A, Singapuri A, Pfeffer P, Manisty C, Kon OM, Beggs M, O'Regan DP, Fuld J, Weir-McCall JR, Parekh D, Steeds R, Poinasamy K, Cuthbertson DJ, Kemp GJ, Semple MG, Horsley A, Miller CA, O'Brien C, Shah AM, Chiribiri A, Leavy OC, Richardson M, Elneima O, McAuley HJC, Sereno M, Saunders RM, Houchen-Wolloff L, Greening NJ, Bolton CE, Brown JS, Choudhury G, Diar Bakerly N, Easom N, Echevarria C, Marks M, Hurst JR, Jones MG, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Howard LS, Jacob J, Man WDC, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Singh SJ, Thomas DC, Toshner M, Lewis KE, Heaney LG, Harrison EM, Kerr S, Docherty AB, Lone NI, Quint J, Sheikh A, Zheng B, Jenkins RG, Cox E, Francis S, Halling-Brown M, Chalmers JD, Greenwood JP, Plein S, Hughes PJC, Thompson AAR, Rowland-Jones SL, Wild JM, Kelly M, Treibel TA, Bandula S, Aul R, Miller K, Jezzard P, Smith S, Nichols TE, McCann GP, Evans RA, Wain LV, Brightling CE, Neubauer S, Baillie JK, Shaw A, Hairsine B, Kurasz C, Henson H, Armstrong L, Shenton L, Dobson H, Dell A, Lucey A, Price A, Storrie A, Pennington C, Price C, Mallison G, Willis G, Nassa H, Haworth J, Hoare M, Hawkings N, Fairbairn S, Young S, Walker S, Jarrold I, Sanderson A, David C, Chong-James K, Zongo O, James WY, Martineau A, King B, Armour C, McAulay D, Major E, McGinness J, McGarvey L, Magee N, Stone R, Drain S, Craig T, Bolger A, Haggar A, Lloyd A, Subbe C, Menzies D, Southern D, McIvor E, Roberts K, Manley R, Whitehead V, Saxon W, Bularga A, Mills NL, El-Taweel H, Dawson J, Robinson L, Saralaya D, Regan K, Storton K, Brear L, Amoils S, Bermperi A, Elmer A, Ribeiro C, Cruz I, Taylor J, Worsley J, Dempsey K, Watson L, Jose S, Marciniak S, Parkes M, McQueen A, Oliver C, Williams J, Paradowski K, Broad L, Knibbs L, Haynes M, Sabit R, Milligan L, Sampson C, Hancock A, Evenden C, Lynch C, Hancock K, Roche L, Rees M, Stroud N, Thomas-Woods T, Heller S, Robertson E, Young B, Wassall H, Babores M, Holland M, Keenan N, Shashaa S, Price C, Beranova E, Ramos H, Weston H, Deery J, Austin L, Solly R, Turney S, Cosier T, Hazelton T, Ralser M, Wilson A, Pearce L, Pugmire S, Stoker W, McCormick W, Dewar A, Arbane G, Kaltsakas G, Kerslake H, Rossdale J, Bisnauthsing K, Aguilar Jimenez LA, Martinez LM, Ostermann M, Magtoto MM, Hart N, Marino P, Betts S, Solano TS, Arias AM, Prabhu A, Reed A, Wrey Brown C, Griffin D, Bevan E, Martin J, Owen J, Alvarez Corral M, Williams N, Payne S, Storrar W, Layton A, Lawson C, Mills C, Featherstone J, Stephenson L, Burdett T, Ellis Y, Richards A, Wright C, Sykes DL, Brindle K, Drury K, Holdsworth L, Crooks MG, Atkin P, Flockton R, Thackray-Nocera S, Mohamed A, Taylor A, Perkins E, Ross G, McGuinness H, Tench H, Phipps J, Loosley R, Wolf-Roberts R, Coetzee S, Omar Z, Ross A, Card B, Carr C, King C, Wood C, Copeland D, Calvelo E, Chilvers ER, Russell E, Gordon H, Nunag JL, Schronce J, March K, Samuel K, Burden L, Evison L, McLeavey L, Orriss-Dib L, Tarusan L, Mariveles M, Roy M, Mohamed N, Simpson N, Yasmin N, Cullinan P, Daly P, Haq S, Moriera S, Fayzan T, Munawar U, Nwanguma U, Lingford-Hughes A, Altmann D, Johnston D, Mitchell J, Valabhji J, Price L, Molyneaux PL, Thwaites RS, Walsh S, Frankel A, Lightstone L, Wilkins M, Willicombe M, McAdoo S, Touyz R, Guerdette AM, Warwick K, Hewitt M, Reddy R, White S, McMahon A, Hoare A, Knighton A, Ramos A, Te A, Jolley CJ, Speranza F, Assefa-Kebede H, Peralta I, Breeze J, Shevket K, Powell N, Adeyemi O, Dulawan P, Adrego R, Byrne S, Patale S, Hayday A, Malim M, Pariante C, Sharpe C, Whitney J, Bramham K, Ismail K, Wessely S, Nicholson T, Ashworth A, Humphries A, Tan AL, Whittam B, Coupland C, Favager C, Peckham D, Wade E, Saalmink G, Clarke J, Glossop J, Murira J, Rangeley J, Woods J, Hall L, Dalton M, Window N, Beirne P, Hardy T, Coakley G, Turtle L, Berridge A, Cross A, Key AL, Rowe A, Allt AM, Mears C, Malein F, Madzamba G, Hardwick HE, Earley J, Hawkes J, Pratt J, Wyles J, Tripp KA, Hainey K, Allerton L, Lavelle-Langham L, Melling L, Wajero LO, Poll L, Noonan MJ, French N, Lewis-Burke N, Williams-Howard SA, Cooper S, Kaprowska S, Dobson SL, Marsh S, Highett V, Shaw V, Beadsworth M, Defres S, Watson E, Tiongson GF, Papineni P, Gurram S, Diwanji SN, Quaid S, Briggs A, Hastie C, Rogers N, Stensel D, Bishop L, McIvor K, Rivera-Ortega P, Al-Sheklly B, Avram C, Faluyi D, Blaikely J, Piper Hanley K, Radhakrishnan K, Buch M, Hanley NA, Odell N, Osbourne R, Stockdale S, Felton T, Gorsuch T, Hussell T, Kausar Z, Kabir T, McAllister-Williams H, Paddick S, Burn D, Ayoub A, Greenhalgh A, Sayer A, Young A, Price D, Burns G, MacGowan G, Fisher H, Tedd H, Simpson J, Jiwa K, Witham M, Hogarth P, West S, Wright S, McMahon MJ, Neill P, Dougherty A, Morrow A, Anderson D, Grieve D, Bayes H, Fallon K, Mangion K, Gilmour L, Basu N, Sykes R, Berry C, McInnes IB, Donaldson A, Sage EK, Barrett F, Welsh B, Bell M, Quigley J, Leitch K, Macliver L, Patel M, Hamil R, Deans A, Furniss J, Clohisey S, Elliott A, Solstice AR, Deas C, Tee C, Connell D, Sutherland D, George J, Mohammed S, Bunker J, Holmes K, Dipper A, Morley A, Arnold D, Adamali H, Welch H, Morrison L, Stadon L, Maskell N, Barratt S, Dunn S, Waterson S, Jayaraman B, Light T, Selby N, Hosseini A, Shaw K, Almeida P, Needham R, Thomas AK, Matthews L, Gupta A, Nikolaidis A, Dupont C, Bonnington J, Chrystal M, Greenhaff PL, Linford S, Prosper S, Jang W, Alamoudi A, Bloss A, Megson C, Nicoll D, Fraser E, Pacpaco E, Conneh F, Ogg G, McShane H, Koychev I, Chen J, Pimm J, Ainsworth M, Pavlides M, Sharpe M, Havinden-Williams M, Petousi N, Talbot N, Carter P, Kurupati P, Dong T, Peng Y, Burns A, Kanellakis N, Korszun A, Connolly B, Busby J, Peto T, Patel B, Nolan CM, Cristiano D, Walsh JA, Liyanage K, Gummadi M, Dormand N, Polgar O, George P, Barker RE, Patel S, Price L, Gibbons M, Matila D, Jarvis H, Lim L, Olaosebikan O, Ahmad S, Brill S, Mandal S, Laing C, Michael A, Reddy A, Johnson C, Baxendale H, Parfrey H, Mackie J, Newman J, Pack J, Parmar J, Paques K, Garner L, Harvey A, Summersgill C, Holgate D, Hardy E, Oxton J, Pendlebury J, McMorrow L, Mairs N, Majeed N, Dark P, Ugwuoke R, Knight S, Whittaker S, Strong-Sheldrake S, Matimba-Mupaya W, Chowienczyk P, Pattenadk D, Hurditch E, Chan F, Carborn H, Foot H, Bagshaw J, Hockridge J, Sidebottom J, Lee JH, Birchall K, Turner K, Haslam L, Holt L, Milner L, Begum M, Marshall M, Steele N, Tinker N, Ravencroft P, Butcher R, Misra S, Walker S, Coburn Z, Fairman A, Ford A, Holbourn A, Howell A, Lawrie A, Lye A, Mbuyisa A, Zawia A, Holroyd-Hind B, Thamu B, Clark C, Jarman C, Norman C, Roddis C, Foote D, Lee E, Ilyas F, Stephens G, Newell H, Turton H, Macharia I, Wilson I, Cole J, McNeill J, Meiring J, Rodger J, Watson J, Chapman K, Harrington K, Chetham L, Hesselden L, Nwafor L, Dixon M, Plowright M, Wade P, Gregory R, Lenagh R, Stimpson R, Megson S, Newman T, Cheng Y, Goodwin C, Heeley C, Sissons D, Sowter D, Gregory H, Wynter I, Hutchinson J, Kirk J, Bennett K, Slack K, Allsop L, Holloway L, Flynn M, Gill M, Greatorex M, Holmes M, Buckley P, Shelton S, Turner S, Sewell TA, Whitworth V, Lovegrove W, Tomlinson J, Warburton L, Painter S, Vickers C, Redwood D, Tilley J, Palmer S, Wainwright T, Breen G, Hotopf M, Dunleavy A, Teixeira J, Ali M, Mencias M, Msimanga N, Siddique S, Samakomva T, Tavoukjian V, Forton D, Ahmed R, Cook A, Thaivalappil F, Connor L, Rees T, McNarry M, Williams N, McCormick J, McIntosh J, Vere J, Coulding M, Kilroy S, Turner V, Butt AT, Savill H, Fraile E, Ugoji J, Landers G, Lota H, Portukhay S, Nasseri M, Daniels A, Hormis A, Ingham J, Zeidan L, Osborne L, Chablani M, Banerjee A, David A, Pakzad A, Rangelov B, Williams B, Denneny E, Willoughby J, Xu M, Mehta P, Batterham R, Bell R, Aslani S, Lilaonitkul W, Checkley A, Bang D, Basire D, Lomas D, Wall E, Plant H, Roy K, Heightman M, Lipman M, Merida Morillas M, Ahwireng N, Chambers RC, Jastrub R, Logan S, Hillman T, Botkai A, Casey A, Neal A, Newton-Cox A, Cooper B, Atkin C, McGee C, Welch C, Wilson D, Sapey E, Qureshi H, Hazeldine J, Lord JM, Nyaboko J, Short J, Stockley J, Dasgin J, Draxlbauer K, Isaacs K, Mcgee K, Yip KP, Ratcliffe L, Bates M, Ventura M, Ahmad Haider N, Gautam N, Baggott R, Holden S, Madathil S, Walder S, Yasmin S, Hiwot T, Jackson T, Soulsby T, Kamwa V, Peterkin Z, Suleiman Z, Chaudhuri N, Wheeler H, Djukanovic R, Samuel R, Sass T, Wallis T, Marshall B, Childs C, Marouzet E, Harvey M, Fletcher S, Dickens C, Beckett P, Nanda U, Daynes E, Charalambou A, Yousuf AJ, Lea A, Prickett A, Gooptu B, Hargadon B, Bourne C, Christie C, Edwardson C, Lee D, Baldry E, Stringer E, Woodhead F, Mills G, Arnold H, Aung H, Qureshi IN, Finch J, Skeemer J, Hadley K, Khunti K, Carr L, Ingram L, Aljaroof M, Bakali M, Bakau M, Baldwin M, Bourne M, Pareek M, Soares M, Tobin M, Armstrong N, Brunskill N, Goodman N, Cairns P, Haldar P, McCourt P, Dowling R, Russell R, Diver S, Edwards S, Glover S, Parker S, Siddiqui S, Ward TJC, Mcnally T, Thornton T, Yates T, Ibrahim W, Monteiro W, Thickett D, Wilkinson D, Broome M, McArdle P, Upthegrove R, Wraith D, Langenberg C, Summers C, Bullmore E, Heeney JL, Schwaeble W, Sudlow CL, Adeloye D, Newby DE, Rudan I, Shankar-Hari M, Thorpe M, Pius R, Walmsley S, McGovern A, Ballard C, Allan L, Dennis J, Cavanagh J, Petrie J, O'Donnell K, Spears M, Sattar N, MacDonald S, Guthrie E, Henderson M, Guillen Guio B, Zhao B, Lawson C, Overton C, Taylor C, Tong C, Mukaetova-Ladinska E, Turner E, Pearl JE, Sargant J, Wormleighton J, Bingham M, Sharma M, Steiner M, Samani N, Novotny P, Free R, Allen RJ, Finney S, Terry S, Brugha T, Plekhanova T, McArdle A, Vinson B, Spencer LG, Reynolds W, Ashworth M, Deakin B, Chinoy H, Abel K, Harvie M, Stanel S, Rostron A, Coleman C, Baguley D, Hufton E, Khan F, Hall I, Stewart I, Fabbri L, Wright L, Kitterick P, Morriss R, Johnson S, Bates A, Antoniades C, Clark D, Bhui K, Channon KM, Motohashi K, Sigfrid L, Husain M, Webster M, Fu X, Li X, Kingham L, Klenerman P, Miiler K, Carson G, Simons G, Huneke N, Calder PC, Baldwin D, Bain S, Lasserson D, Daines L, Bright E, Stern M, Crisp P, Dharmagunawardena R, Reddington A, Wight A, Bailey L, Ashish A, Robinson E, Cooper J, Broadley A, Turnbull A, Brookes C, Sarginson C, Ionita D, Redfearn H, Elliott K, Barman L, Griffiths L, Guy Z, Gill R, Nathu R, Harris E, Moss P, Finnigan J, Saunders K, Saunders P, Kon S, Kon SS, O'Brien L, Shah K, Shah P, Richardson E, Brown V, Brown M, Brown J, Brown J, Brown A, Brown A, Brown M, Choudhury N, Jones S, Jones H, Jones L, Jones I, Jones G, Jones H, Jones D, Davies F, Davies E, Davies K, Davies G, Davies GA, Howard K, Porter J, Rowland J, Rowland A, Scott K, Singh S, Singh C, Thomas S, Thomas C, Lewis V, Lewis J, Lewis D, Harrison P, Francis C, Francis R, Hughes RA, Hughes J, Hughes AD, Thompson T, Kelly S, Smith D, Smith N, Smith A, Smith J, Smith L, Smith S, Evans T, Evans RI, Evans D, Evans R, Evans H, Evans J. Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study. Lancet Respir Med 2023; 11:1003-1019. [PMID: 37748493 PMCID: PMC7615263 DOI: 10.1016/s2213-2600(23)00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. METHODS In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. FINDINGS Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. INTERPRETATION After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification. FUNDING UK Research and Innovation and National Institute for Health Research.
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Neale I, Ali M, Kronsteiner B, Longet S, Abraham P, Deeks AS, Brown A, Moore SC, Stafford L, Dobson SL, Plowright M, Newman TAH, Wu MY, Carr EJ, Beale R, Otter AD, Hopkins S, Hall V, Tomic A, Payne RP, Barnes E, Richter A, Duncan CJA, Turtle L, de Silva TI, Carroll M, Lambe T, Klenerman P, Dunachie S. CD4+ and CD8+ T cells and antibodies are associated with protection against Delta vaccine breakthrough infection: a nested case-control study within the PITCH study. mBio 2023; 14:e0121223. [PMID: 37655880 PMCID: PMC10653804 DOI: 10.1128/mbio.01212-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Defining correlates of protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine breakthrough infection informs vaccine policy for booster doses and future vaccine designs. Existing studies demonstrate humoral correlates of protection, but the role of T cells in protection is still unclear. In this study, we explore antibody and T cell immune responses associated with protection against Delta variant vaccine breakthrough infection in a well-characterized cohort of UK Healthcare Workers (HCWs). We demonstrate evidence to support a role for CD4+ and CD8+ T cells as well as antibodies against Delta vaccine breakthrough infection. In addition, our results suggest a potential role for cross-reactive T cells in vaccine breakthrough.
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Affiliation(s)
- Isabel Neale
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephanie Longet
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Priyanka Abraham
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Alexandra S. Deeks
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Shona C. Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Lizzie Stafford
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Susan L. Dobson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Thomas A. H. Newman
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Mary Y. Wu
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
| | - Crick COVID Immunity Pipeline
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- UCL Department of Renal Medicine, Royal Free Hospital, London, United Kingdom
| | | | | | | | - Adriana Tomic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Rebecca P. Payne
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Christopher J. A. Duncan
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Thushan I. de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Miles Carroll
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Teresa Lambe
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - On behalf of the PITCH Consortium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- UCL Department of Renal Medicine, Royal Free Hospital, London, United Kingdom
- UK Health Security Agency, Porton Down, United Kingdom
- UK Health Security Agency, London, United Kingdom
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
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Jay C, Adland E, Csala A, Lim N, Longet S, Ogbe A, Ratcliff J, Sampson O, Thompson CP, Turtle L, Barnes E, Dunachie S, Klenerman P, Carroll M, Goulder P. Age- and sex-specific differences in immune responses to BNT162b2 COVID-19 and live-attenuated influenza vaccines in UK adolescents. Front Immunol 2023; 14:1248630. [PMID: 37942333 PMCID: PMC10627794 DOI: 10.3389/fimmu.2023.1248630] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/15/2023] [Indexed: 11/10/2023] Open
Abstract
Introduction The key to understanding the COVID-19 correlates of protection is assessing vaccine-induced immunity in different demographic groups. Young people are at a lower risk of COVID-19 mortality, females are at a lower risk than males, and females often generate stronger immune responses to vaccination. Methods We studied immune responses to two doses of BNT162b2 Pfizer COVID-19 vaccine in an adolescent cohort (n = 34, ages 12-16), an age group previously shown to elicit significantly greater immune responses to the same vaccine than young adults. Adolescents were studied with the aim of comparing their response to BNT162b2 to that of adults; and to assess the impacts of other factors such as sex, ongoing SARS-CoV-2 infection in schools, and prior exposure to endemic coronaviruses that circulate at high levels in young people. At the same time, we were able to evaluate immune responses to the co-administered live attenuated influenza vaccine. Blood samples from 34 adolescents taken before and after vaccination with COVID-19 and influenza vaccines were assayed for SARS-CoV-2-specific IgG and neutralising antibodies and cellular immunity specific for SARS-CoV-2 and endemic betacoronaviruses. The IgG targeting influenza lineages contained in the influenza vaccine were also assessed. Results Robust neutralising responses were identified in previously infected adolescents after one dose, and two doses were required in infection-naïve adolescents. As previously demonstrated, total IgG responses to SARS-CoV-2 Spike were significantly higher among vaccinated adolescents than among adults (aged 32-52) who received the BNT162b2 vaccine (comparing infection-naïve, 49,696 vs. 33,339; p = 0.03; comparing SARS-CoV-2 previously infected, 743,691 vs. 269,985; p <0.0001) by the MSD v-plex assay. There was no evidence of a stronger vaccine-induced immunity in females compared than in males. Discussion These findings may result from the introduction of novel mRNA vaccination platforms, generating patterns of immunity divergent from established trends and providing new insights into what might be protective following COVID-19 vaccination.
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Affiliation(s)
- Cecilia Jay
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Anna Csala
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Nicholas Lim
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ane Ogbe
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oliver Sampson
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Craig P. Thompson
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Warwick, United Kingdom
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Susanna Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Miles Carroll
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
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21
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López-Rodríguez JC, Hancock SJ, Li K, Crotta S, Barrington C, Suárez-Bonnet A, Priestnall SL, Aubé J, Wack A, Klenerman P, Bengoechea JA, Barral P. Type I interferons drive MAIT cell functions against bacterial pneumonia. J Exp Med 2023; 220:e20230037. [PMID: 37516912 PMCID: PMC10373297 DOI: 10.1084/jem.20230037] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/31/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are abundant in the lung and contribute to host defense against infections. During bacterial infections, MAIT cell activation has been proposed to require T cell receptor (TCR)-mediated recognition of antigens derived from the riboflavin synthesis pathway presented by the antigen-presenting molecule MR1. MAIT cells can also be activated by cytokines in an MR1-independent manner, yet the contribution of MR1-dependent vs. -independent signals to MAIT cell functions in vivo remains unclear. Here, we use Klebsiella pneumoniae as a model of bacterial pneumonia and demonstrate that MAIT cell activation is independent of MR1 and primarily driven by type I interferons (IFNs). During Klebsiella infection, type I IFNs stimulate activation of murine and human MAIT cells, induce a Th1/cytotoxic transcriptional program, and modulate MAIT cell location within the lungs. Consequently, adoptive transfer or boosting of pulmonary MAIT cells protect mice from Klebsiella infection, with protection being dependent on direct type I IFN signaling on MAIT cells. These findings reveal type I IFNs as new molecular targets to manipulate MAIT cell functions during bacterial infections.
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Affiliation(s)
- Juan Carlos López-Rodríguez
- The Peter Gorer Department of Immunobiology, King’s College London, London, UK
- The Francis Crick Institute, London, UK
| | - Steven J. Hancock
- Wellcome-Wolfson Institute for Experimental Medicine. School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Alejandro Suárez-Bonnet
- The Francis Crick Institute, London, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Simon L. Priestnall
- The Francis Crick Institute, London, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Oxford, UK
| | - Jose A. Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine. School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Patricia Barral
- The Peter Gorer Department of Immunobiology, King’s College London, London, UK
- The Francis Crick Institute, London, UK
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22
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Garner LC, Amini A, FitzPatrick MEB, Lett MJ, Hess GF, Filipowicz Sinnreich M, Provine NM, Klenerman P. Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity. Nat Immunol 2023; 24:1565-1578. [PMID: 37580605 PMCID: PMC10457204 DOI: 10.1038/s41590-023-01575-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/26/2023] [Indexed: 08/16/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells that recognize microbial metabolites through a semi-invariant T cell receptor (TCR). Major questions remain regarding the extent of human MAIT cell functional and clonal diversity. To address these, we analyzed the single-cell transcriptome and TCR repertoire of blood and liver MAIT cells and developed functional RNA-sequencing, a method to integrate function and TCR clonotype at single-cell resolution. MAIT cell clonal diversity was comparable to conventional memory T cells, with private TCR repertoires shared across matched tissues. Baseline functional diversity was low and largely related to tissue site. MAIT cells showed stimulus-specific transcriptional responses in vitro, with cells positioned along gradients of activation. Clonal identity influenced resting and activated transcriptional profiles but intriguingly was not associated with the capacity to produce IL-17. Overall, MAIT cells show phenotypic and functional diversity according to tissue localization, stimulation environment and clonotype.
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Affiliation(s)
- Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Ali Amini
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michael E B FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Martin J Lett
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Gabriel F Hess
- Division of Visceral Surgery, Clarunis University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Magdalena Filipowicz Sinnreich
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
- Gastroenterology and Hepatology, University Department of Medicine, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.
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23
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Kurioka A, Klenerman P. Aging unconventionally: γδ T cells, iNKT cells, and MAIT cells in aging. Semin Immunol 2023; 69:101816. [PMID: 37536148 PMCID: PMC10804939 DOI: 10.1016/j.smim.2023.101816] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
Unconventional T cells include γδ T cells, invariant Natural Killer T cells (iNKT) cells and Mucosal Associated Invariant T (MAIT) cells, which are distinguished from conventional T cells by their recognition of non-peptide ligands presented by non-polymorphic antigen presenting molecules and rapid effector functions that are pre-programmed during their development. Here we review current knowledge of the effect of age on unconventional T cells, from early life to old age, in both mice and humans. We then discuss the role of unconventional T cells in age-associated diseases and infections, highlighting the similarities between members of the unconventional T cell family in the context of aging.
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Affiliation(s)
- Ayako Kurioka
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
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24
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Jay C, Adland E, Csala A, Dold C, Edmans M, Hackstein CP, Jamsen A, Lim N, Longet S, Ogbe A, Sampson O, Skelly D, Spiller OB, Stafford L, Thompson CP, Turtle L, Barnes E, Dunachie S, Carroll M, Klenerman P, Conlon C, Goulder P, Jones LC. Cellular immunity to SARS-CoV-2 following intrafamilial exposure in seronegative family members. Front Immunol 2023; 14:1248658. [PMID: 37711627 PMCID: PMC10497976 DOI: 10.3389/fimmu.2023.1248658] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Family studies of antiviral immunity provide an opportunity to assess virus-specific immunity in infected and highly exposed individuals, as well as to examine the dynamics of viral infection within families. Transmission of SARS-CoV-2 between family members represented a major route for viral spread during the early stages of the pandemic, due to the nature of SARS-CoV-2 transmission through close contacts. Methods Here, humoral and cellular immunity is explored in 264 SARS-CoV-2 infected, exposed or unexposed individuals from 81 families in the United Kingdom sampled in the winter of 2020 before widespread vaccination and infection. Results We describe robust cellular and humoral immunity into COVID-19 convalescence, albeit with marked heterogeneity between families and between individuals. T-cell response magnitude is associated with male sex and older age by multiple linear regression. SARS-CoV-2-specific T-cell responses in seronegative individuals are widespread, particularly in adults and in individuals exposed to SARS-CoV-2 through an infected family member. The magnitude of this response is associated with the number of seropositive family members, with a greater number of seropositive individuals within a family leading to stronger T-cell immunity in seronegative individuals. Discussion These results support a model whereby exposure to SARS-CoV-2 promotes T-cell immunity in the absence of an antibody response. The source of these seronegative T-cell responses to SARS-CoV-2 has been suggested as cross-reactive immunity to endemic coronaviruses that is expanded upon SARS-CoV-2 exposure. However, in this study, no association between HCoV-specific immunity and seronegative T-cell immunity to SARS-CoV-2 is identified, suggesting that de novo T-cell immunity may be generated in seronegative SARS-CoV-2 exposed individuals.
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Affiliation(s)
- Cecilia Jay
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Anna Csala
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Christina Dold
- Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Matthew Edmans
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Anni Jamsen
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicholas Lim
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ane Ogbe
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oliver Sampson
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Donal Skelly
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals, University of Oxford, Oxford, United Kingdom
| | - Owen B. Spiller
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Lizzie Stafford
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Craig P. Thompson
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ellie Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Susanna Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Miles Carroll
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Chris Conlon
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Lucy C. Jones
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
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25
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Hornsby H, Nicols AR, Longet S, Liu C, Tomic A, Angyal A, Kronsteiner B, Tyerman JK, Tipton T, Zhang P, Gallis M, Supasa P, Selvaraj M, Abraham P, Neale I, Ali M, Barratt NA, Nell JM, Gustafsson L, Strickland S, Grouneva I, Rostron T, Moore SC, Hering LM, Dobson SL, Bibi S, Mongkolsapaya J, Lambe T, Wootton D, Hall V, Hopkins S, Dong T, Barnes E, Screaton G, Richter A, Turtle L, Rowland-Jones SL, Carroll M, Duncan CJA, Klenerman P, Dunachie SJ, Payne RP, de Silva TI. Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history. Nat Commun 2023; 14:5065. [PMID: 37604803 PMCID: PMC10442364 DOI: 10.1038/s41467-023-40592-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 02/17/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023] Open
Abstract
Pronounced immune escape by the SARS-CoV-2 Omicron variant has resulted in many individuals possessing hybrid immunity, generated through a combination of vaccination and infection. Concerns have been raised that omicron breakthrough infections in triple-vaccinated individuals result in poor induction of omicron-specific immunity, and that prior SARS-CoV-2 infection is associated with immune dampening. Taking a broad and comprehensive approach, we characterize mucosal and blood immunity to spike and non-spike antigens following BA.1/BA.2 infections in triple mRNA-vaccinated individuals, with and without prior SARS-CoV-2 infection. We find that most individuals increase BA.1/BA.2/BA.5-specific neutralizing antibodies following infection, but confirm that the magnitude of increase and post-omicron titres are higher in the infection-naive. In contrast, significant increases in nasal responses, including neutralizing activity against BA.5 spike, are seen regardless of infection history. Spike-specific T cells increase only in infection-naive vaccinees; however, post-omicron T cell responses are significantly higher in the previously-infected, who display a maximally induced response with a highly cytotoxic CD8+ phenotype following their 3rd mRNA vaccine dose. Responses to non-spike antigens increase significantly regardless of prior infection status. These findings suggest that hybrid immunity induced by omicron breakthrough infections is characterized by significant immune enhancement that can help protect against future omicron variants.
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Affiliation(s)
- Hailey Hornsby
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Alexander R Nicols
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Stephanie Longet
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adriana Tomic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Adrienn Angyal
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Jessica K Tyerman
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Tom Tipton
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peijun Zhang
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Marta Gallis
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Priyanka Abraham
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Isabel Neale
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
| | - Natalie A Barratt
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Jeremy M Nell
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Lotta Gustafsson
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Scarlett Strickland
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Irina Grouneva
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Timothy Rostron
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Luisa M Hering
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Susan L Dobson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Dan Wootton
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Victoria Hall
- UK Health Security Agency, London, UK
- Faculty of Medicine, Department of Infectious Disease, Imperial College London, London, UK
| | - Susan Hopkins
- UK Health Security Agency, London, UK
- Faculty of Medicine, Department of Infectious Disease, Imperial College London, London, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre and Oxford University NHS Foundation Trust, Oxford, UK
| | - Gavin Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alex Richter
- Institute for Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical & Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), Liverpool, UK
| | - Sarah L Rowland-Jones
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Miles Carroll
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christopher J A Duncan
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre and Oxford University NHS Foundation Trust, Oxford, UK.
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre and Oxford University NHS Foundation Trust, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity, and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Thushan I de Silva
- Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Sheffield, UK.
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia.
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26
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Hackstein CP, Klenerman P. MAITs and their mates: "Innate-like" behaviors in conventional and unconventional T cells. Clin Exp Immunol 2023; 213:1-9. [PMID: 37256718 PMCID: PMC10324555 DOI: 10.1093/cei/uxad058] [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: 03/02/2023] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Most CD4 and CD8 T cells are restricted by conventional major histocompatibility complex (MHC) molecules and mount TCR-dependent adaptive immune responses. In contrast, MAIT, iNKT, and certain γδ TCR bearing cells are characterized by their abilities to recognize antigens presented by unconventional antigen-presenting molecules and to mount cytokine-mediated TCR-independent responses in an "innate-like" manner. In addition, several more diverse T-cell subsets have been described that in a similar manner are restricted by unconventional antigen-presenting molecules but mainly depend on their TCRs for activation. Vice versa, innate-like behaviour was reported in defined subpopulations of conventional T cells, particularly in barrier sites, showing that these two features are not necessarily linked. The abilities to recognize antigens presented by unconventional antigen-presenting molecules or to mount TCR-independent responses creates unique niches for these T cells and is linked to wide range of functional capabilities. This is especially exemplified by unconventional and innate-like T cells present at barrier sites where they are involved in pathogen defense, tissue homeostasis as well as in pathologic processes.
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Affiliation(s)
- Carl-Philipp Hackstein
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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27
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Barnes E, Goodyear CS, Willicombe M, Gaskell C, Siebert S, I de Silva T, Murray SM, Rea D, Snowden JA, Carroll M, Pirrie S, Bowden SJ, Dunachie SJ, Richter A, Lim Z, Satsangi J, Cook G, Pope A, Hughes A, Harrison M, Lim SH, Miller P, Klenerman P, Basu N, Gilmour A, Irwin S, Meacham G, Marjot T, Dimitriadis S, Kelleher P, Prendecki M, Clarke C, Mortimer P, McIntyre S, Selby R, Meardon N, Nguyen D, Tipton T, Longet S, Laidlaw S, Orchard K, Ireland G, Thomas D, Kearns P, Kirkham A, McInnes IB. SARS-CoV-2-specific immune responses and clinical outcomes after COVID-19 vaccination in patients with immune-suppressive disease. Nat Med 2023; 29:1760-1774. [PMID: 37414897 PMCID: PMC10353927 DOI: 10.1038/s41591-023-02414-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [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: 08/05/2022] [Accepted: 05/23/2023] [Indexed: 07/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune responses and infection outcomes were evaluated in 2,686 patients with varying immune-suppressive disease states after administration of two Coronavirus Disease 2019 (COVID-19) vaccines. Overall, 255 of 2,204 (12%) patients failed to develop anti-spike antibodies, with an additional 600 of 2,204 (27%) patients generating low levels (<380 AU ml-1). Vaccine failure rates were highest in ANCA-associated vasculitis on rituximab (21/29, 72%), hemodialysis on immunosuppressive therapy (6/30, 20%) and solid organ transplant recipients (20/81, 25% and 141/458, 31%). SARS-CoV-2-specific T cell responses were detected in 513 of 580 (88%) patients, with lower T cell magnitude or proportion in hemodialysis, allogeneic hematopoietic stem cell transplantation and liver transplant recipients (versus healthy controls). Humoral responses against Omicron (BA.1) were reduced, although cross-reactive T cell responses were sustained in all participants for whom these data were available. BNT162b2 was associated with higher antibody but lower cellular responses compared to ChAdOx1 nCoV-19 vaccination. We report 474 SARS-CoV-2 infection episodes, including 48 individuals with hospitalization or death from COVID-19. Decreased magnitude of both the serological and the T cell response was associated with severe COVID-19. Overall, we identified clinical phenotypes that may benefit from targeted COVID-19 therapeutic strategies.
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Affiliation(s)
- Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Carl S Goodyear
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Charlotte Gaskell
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Stefan Siebert
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Sheffield, UK
| | - Sam M Murray
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Rea
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - John A Snowden
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
| | - Miles Carroll
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah Pirrie
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Sarah J Bowden
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Susanna J Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alex Richter
- Clinical Immunology Service, University of Birmingham, Edgbaston, Birmingham, UK
| | - Zixiang Lim
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jack Satsangi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gordon Cook
- National Institute for Health Research, Leeds MIC, University of Leeds, Leeds, UK
| | - Ann Pope
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Ana Hughes
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Molly Harrison
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Sean H Lim
- Centre for Cancer Immunology, University of Southampton, Southampton, UK
| | - Paul Miller
- British Society of Blood and Marrow Transplantation and Cellular Therapy, Guy's Hospital, London, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Neil Basu
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Ashley Gilmour
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Sophie Irwin
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Georgina Meacham
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Marjot
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Peter Kelleher
- Department of Infectious Diseases, Imperial College London, School of Medicine Chelsea and Westminster Hospital, London, UK
| | - Maria Prendecki
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Candice Clarke
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Paige Mortimer
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Stacey McIntyre
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Rachael Selby
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
| | - Naomi Meardon
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Sheffield, UK
| | - Dung Nguyen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tom Tipton
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen Laidlaw
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kim Orchard
- Department of Haematology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Georgina Ireland
- UK Health Security Agency (UKHSA), Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, UK
| | - David Thomas
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Pamela Kearns
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
- National Institute for Health Research Birmingham Biomedical Research Centre, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Amanda Kirkham
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Edgbaston, Birmingham, UK
| | - Iain B McInnes
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.
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28
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Yang H, Sun H, Brackenridge S, Zhuang X, Wing PAC, Quastel M, Walters L, Garner L, Wang B, Yao X, Felce SL, Peng Y, Moore S, Peeters BWA, Rei M, Canto Gomes J, Tomas A, Davidson A, Semple MG, Turtle LCW, Openshaw PJM, Baillie JK, Mentzer AJ, Klenerman P, Borrow P, Dong T, McKeating JA, Gillespie GM, McMichael AJ. HLA-E-restricted SARS-CoV-2-specific T cells from convalescent COVID-19 patients suppress virus replication despite HLA class Ia down-regulation. Sci Immunol 2023; 8:eabl8881. [PMID: 37390223 DOI: 10.1126/sciimmunol.abl8881] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Pathogen-specific CD8+ T cell responses restricted by the nonpolymorphic nonclassical class Ib molecule human leukocyte antigen E (HLA-E) are rarely reported in viral infections. The natural HLA-E ligand is a signal peptide derived from classical class Ia HLA molecules that interact with the NKG2/CD94 receptors to regulate natural killer cell functions, but pathogen-derived peptides can also be presented by HLA-E. Here, we describe five peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that elicited HLA-E-restricted CD8+ T cell responses in convalescent patients with coronavirus disease 2019. These T cell responses were identified in the blood at frequencies similar to those reported for classical HLA-Ia-restricted anti-SARS-CoV-2 CD8+ T cells. HLA-E peptide-specific CD8+ T cell clones, which expressed diverse T cell receptors, suppressed SARS-CoV-2 replication in Calu-3 human lung epithelial cells. SARS-CoV-2 infection markedly down-regulated classical HLA class I expression in Calu-3 cells and primary reconstituted human airway epithelial cells, whereas HLA-E expression was not affected, enabling T cell recognition. Thus, HLA-E-restricted T cells could contribute to the control of SARS-CoV-2 infection alongside classical T cells.
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Affiliation(s)
- Hongbing Yang
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Hong Sun
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Key Laboratory of AIDS Immunology, Department of Laboratory Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Simon Brackenridge
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Peter A C Wing
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Max Quastel
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lucy Walters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lee Garner
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Beibei Wang
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Shona Moore
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bas W A Peeters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Margarida Rei
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Oxford, UK
| | - Joao Canto Gomes
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga, Portugal
| | - Ana Tomas
- Unidada de Investigacao em Patobiologia Molecular, Instituto Portugues de Oncologia de Lisboa Francisco Gentil, EPE Lisbon, Portugal
- Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Unit, Alder Hey Children's Hospital, Eaton Road, Liverpool L12 2AP, UK
| | - Lance C W Turtle
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), Liverpool, UK
| | | | | | - Alexander J Mentzer
- Welcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Persephone Borrow
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jane A McKeating
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Andrew J McMichael
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
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29
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Ragonnet-Cronin M, Nutalai R, Huo J, Dijokaite-Guraliuc A, Das R, Tuekprakhon A, Supasa P, Liu C, Selvaraj M, Groves N, Hartman H, Ellaby N, Mark Sutton J, Bahar MW, Zhou D, Fry E, Ren J, Brown C, Klenerman P, Dunachie SJ, Mongkolsapaya J, Hopkins S, Chand M, Stuart DI, Screaton GR, Rokadiya S. Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy. Nat Commun 2023; 14:3334. [PMID: 37286554 PMCID: PMC10246534 DOI: 10.1038/s41467-023-37826-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 10/06/2022] [Accepted: 04/03/2023] [Indexed: 06/09/2023] Open
Abstract
COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the antibody epitopes and for casirivimab+imdevimab multiple mutations are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum.
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Affiliation(s)
- Manon Ragonnet-Cronin
- Genomics Public Health Analysis, UK Health Security Agency, London, UK.
- Centre for Global Infectious Disease Analysis, Imperial College London, London, England.
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie Groves
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Hassan Hartman
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Nicholas Ellaby
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - J Mark Sutton
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Mohammad W Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Elizabeth Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Colin Brown
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford, UK
| | - Susan Hopkins
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Meera Chand
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Sakib Rokadiya
- Genomics Public Health Analysis, UK Health Security Agency, London, UK.
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30
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Johnson SA, Phillips E, Adele S, Longet S, Malone T, Mason C, Stafford L, Jamsen A, Gardiner S, Deeks A, Neo J, Blurton EJ, White J, Ali M, Kronsteiner B, Wilson JD, Skelly DT, Jeffery K, Conlon CP, Goulder P, Consortium PITCH, Carroll M, Barnes E, Klenerman P, Dunachie SJ. Evaluation of QuantiFERON SARS-CoV-2 interferon-γ release assay following SARS-CoV-2 infection and vaccination. Clin Exp Immunol 2023; 212:249-261. [PMID: 36807499 PMCID: PMC10243914 DOI: 10.1093/cei/uxad027] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 09/27/2022] [Revised: 01/18/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023] Open
Abstract
T cells are important in preventing severe disease from SARS-CoV-2, but scalable and field-adaptable alternatives to expert T-cell assays are needed. The interferon-gamma release assay QuantiFERON platform was developed to detect T-cell responses to SARS-CoV-2 from whole blood with relatively basic equipment and flexibility of processing timelines. Forty-eight participants with different infection and vaccination backgrounds were recruited. Whole blood samples were analysed using the QuantiFERON SARS-CoV-2 assay in parallel with the well-established 'Protective Immunity from T Cells in Healthcare workers' (PITCH) ELISpot, which can evaluate spike-specific T-cell responses. The primary aims of this cross-sectional observational cohort study were to establish if the QuantiFERON SARS-Co-V-2 assay could discern differences between specified groups and to assess the sensitivity of the assay compared with the PITCH ELISpot. The QuantiFERON SARS-CoV-2 distinguished acutely infected individuals (12-21 days post positive PCR) from naïve individuals (P < 0.0001) with 100% sensitivity and specificity for SARS-CoV-2 T cells, whilst the PITCH ELISpot had reduced sensitivity (62.5%) for the acute infection group. Sensitivity with QuantiFERON for previous infection was 12.5% (172-444 days post positive test) and was inferior to the PITCH ELISpot (75%). Although the QuantiFERON assay could discern differences between unvaccinated and vaccinated individuals (55-166 days since second vaccination), the latter also had reduced sensitivity (44.4%) compared to the PITCH ELISpot (66.6%). The QuantiFERON SARS-CoV-2 assay showed potential as a T- cell evaluation tool soon after SARS-CoV-2 infection but has lower sensitivity for use in reliable evaluation of vaccination or more distant infection.
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Affiliation(s)
- Síle A Johnson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- University of Oxford Medical School, University of Oxford, Oxford, UK
- University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK
| | - Eloise Phillips
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Stephanie Longet
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tom Malone
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Chris Mason
- University of Oxford Medical School, University of Oxford, Oxford, UK
| | - Lizzie Stafford
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Experimental Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Anni Jamsen
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Experimental Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Siobhan Gardiner
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Experimental Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Alexandra Deeks
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Department of Experimental Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Janice Neo
- University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK
| | - Emily J Blurton
- University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK
| | - Jemima White
- University of Oxford Medical School, University of Oxford, Oxford, UK
| | - Muhammed Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Joseph D Wilson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- King’s College Hospital NHS Foundation Trust, London, UK
| | - Dónal T Skelly
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Christopher P Conlon
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, UK
| | - PITCH Consortium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED. Accelerated waning of the humoral response to COVID-19 vaccines in obesity. Nat Med 2023; 29:1146-1154. [PMID: 37169862 PMCID: PMC10202802 DOI: 10.1038/s41591-023-02343-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 08/09/2022] [Accepted: 04/07/2023] [Indexed: 05/13/2023]
Abstract
Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI > 40 kg/m2) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9 kg/m2). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P = 0.0003) 6 months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.
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Affiliation(s)
- Agatha A van der Klaauw
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Emily C Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Utkarsh Agrawal
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Sarah Spencer
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Bensi Vergese
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Miriam Smith
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Isobel D Ramsay
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jack A Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Iain M Hay
- Babraham Institute, Babraham Research Campus, Cambridge, UK
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Sam Thompson
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Lucy H Booth
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Chris Robertson
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Colin McCowan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Steven Kerr
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | | | - Maria A Rust
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Alex Ferreira
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Soraya Ebrahimi
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lourdes Ceron-Gutierrez
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacopo Scotucci
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Adrian J Park
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Francesco Rubino
- Department of Diabetes, King's College London and King's College Hospital NHS Foundation Trust, London, UK
| | - Abigail A Lamikanra
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah Stark
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lise Estcourt
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - David J Roberts
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Rainer Doffinger
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Aziz Sheikh
- Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
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Marchi E, Ramamurthy N, Ansari MA, Harrer CE, Barnes E, Klenerman P. Defining the key intrahepatic gene networks in HCV infection driven by sex. Gut 2023; 72:984-994. [PMID: 35613843 PMCID: PMC10086281 DOI: 10.1136/gutjnl-2021-326314] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/30/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The transcriptional response in the liver during HCV infection is critical for determining clinical outcomes. This issue remains relatively unexplored as tissue access to address this at scale is usually limited. We aimed to profile the transcriptomics of HCV-infected livers to describe the expression networks involved and assess the effect on them of major predictors of clinical outcome such as IFNL4 (interferon lambda 4) host genotype and sex. DESIGN We took advantage of a large clinical study of HCV therapy accompanied by baseline liver biopsy to examine the drivers of transcription in tissue samples in 195 patients also genotyped genome-wide for host and viral single nucleotide polymorphisms. We addressed the role of host factors (disease status, sex, genotype, age) and viral factors (load, mutation) on transcriptional responses. RESULTS We observe key modules of transcription which can be impacted differentially by host and viral factors. Underlying cirrhotic state had the most substantial impact, even in a stable, compensated population. Notably, sex had a major impact on antiviral responses in concert with IL28B (interleukin 28B)/IFNL4 genotype, with stronger interferon and humoral responses in females. Males tended towards a dominant cellular immune response. In both sexes, there was a strong influence of the underlying host disease status and of specific viral mutations, and sex-specific expression quantitative trait loci were also observed. CONCLUSION These features help define the major influences on tissue responses in HCV infection, impacting on the response to treatment and with broader implications for responses in other sex-biased infections.
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Affiliation(s)
- Emanuele Marchi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - M Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
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33
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Murray SM, Ansari AM, Frater J, Klenerman P, Dunachie S, Barnes E, Ogbe A. The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses. Nat Rev Immunol 2023; 23:304-316. [PMID: 36539527 PMCID: PMC9765363 DOI: 10.1038/s41577-022-00809-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
Pre-existing cross-reactive immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in infection-naive subjects have been described by several studies. In particular, regions of high homology between SARS-CoV-2 and common cold coronaviruses have been highlighted as a likely source of this cross-reactivity. However, the role of such cross-reactive responses in the outcome of SARS-CoV-2 infection and vaccination is currently unclear. Here, we review evidence regarding the impact of pre-existing humoral and T cell immune responses to outcomes of SARS-CoV-2 infection and vaccination. Furthermore, we discuss the importance of conserved coronavirus epitopes for the rational design of pan-coronavirus vaccines and consider cross-reactivity of immune responses to ancestral SARS-CoV-2 and SARS-CoV-2 variants, as well as their impact on COVID-19 vaccination.
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Affiliation(s)
- Sam M Murray
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Azim M Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
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Dijokaite-Guraliuc A, Das R, Zhou D, Ginn HM, Liu C, Duyvesteyn HME, Huo J, Nutalai R, Supasa P, Selvaraj M, de Silva TI, Plowright M, Newman TAH, Hornsby H, Mentzer AJ, Skelly D, Ritter TG, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Roemer C, Peacock TP, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Cell Rep 2023; 42:112271. [PMID: 36995936 PMCID: PMC9988707 DOI: 10.1016/j.celrep.2023.112271] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 01/09/2023] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.
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Key Words
- CP: Immunology
- CP: Microbiology
- SARS-CoV-2, BA.2, variant, mutation, RBD, antibodies, binding site, breakthrough, neutralizing, structure, COVID-19
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Affiliation(s)
- Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Megan Plowright
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas A H Newman
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Hailey Hornsby
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Department of Medicine, University of Oxford, Oxford, UK
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Neil G Paterson
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
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Green C, McGinley J, Sande C, Capone S, Makvandi-Nejad S, Vitelli A, Silva-Reyes L, Bibi S, Otasowie C, Sheerin D, Thompson A, Dold C, Klenerman P, Barnes E, Dorrell L, Rollier C, Pollard A, O’Connor D. Transcriptomic response and immunological responses to chimpanzee adenovirus- and MVA viral-vectored vaccines for RSV in healthy adults. Clin Exp Immunol 2023; 211:269-279. [PMID: 36622786 PMCID: PMC10038321 DOI: 10.1093/cei/uxad003] [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: 05/03/2022] [Revised: 10/30/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Cohorts of healthy younger adults (18-50yrs) and healthy older adults (60-75yrs) were immunized intramuscularly or intranasally with an adenovirus-vectored RSV vaccine (PanAd3-RSV) as a prime dose and boosted with PanAd3-RSV or a poxvirus-vectored vaccine (MVA-RSV) encoding the same insert. Whole blood gene expression was measured at baseline, 3- and 7-days post vaccination. Intramuscular prime vaccination with PanAd3-RSV induced differential expression of 643 genes (DEGs, FDR < 0.05). Intranasal prime vaccination with PanAd3-RSV did not induce any differentially expressed genes (DEGs) in blood samples at 3 days post vaccination. Intranasally primed participants showed greater numbers of DEGS on boosting than intramuscularly primed participants. The most highly enriched biological processes related to DEGs after both prime and boost vaccination were type-1 interferon related pathways, lymphocytic and humoral immune responses.
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Affiliation(s)
- C Green
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Institute of Microbiology & Infection, University of Birmingham, Birmingham, UK
| | - J McGinley
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - C Sande
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - S Capone
- Experimental Vaccinology Department, ReiThera Srl, Roma, Italy
| | - S Makvandi-Nejad
- Nuffield Department of Medicine, University of Oxford NDM Research Building, Oxford, UK
| | - A Vitelli
- Experimental Vaccinology Department, ReiThera Srl, Roma, Italy
| | - L Silva-Reyes
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - S Bibi
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - C Otasowie
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - D Sheerin
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - A Thompson
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - C Dold
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - P Klenerman
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - E Barnes
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - L Dorrell
- Nuffield Department of Medicine, University of Oxford NDM Research Building, Oxford, UK
| | - C Rollier
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - A Pollard
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - D O’Connor
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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36
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Moore SC, Kronsteiner B, Longet S, Adele S, Deeks AS, Liu C, Dejnirattisai W, Reyes LS, Meardon N, Faustini S, Al-Taei S, Tipton T, Hering LM, Angyal A, Brown R, Nicols AR, Dobson SL, Supasa P, Tuekprakhon A, Cross A, Tyerman JK, Hornsby H, Grouneva I, Plowright M, Zhang P, Newman TAH, Nell JM, Abraham P, Ali M, Malone T, Neale I, Phillips E, Wilson JD, Murray SM, Zewdie M, Shields A, Horner EC, Booth LH, Stafford L, Bibi S, Wootton DG, Mentzer AJ, Conlon CP, Jeffery K, Matthews PC, Pollard AJ, Brown A, Rowland-Jones SL, Mongkolsapaya J, Payne RP, Dold C, Lambe T, Thaventhiran JED, Screaton G, Barnes E, Hopkins S, Hall V, Duncan CJA, Richter A, Carroll M, de Silva TI, Klenerman P, Dunachie S, Turtle L. Evolution of long-term vaccine-induced and hybrid immunity in healthcare workers after different COVID-19 vaccine regimens. Med 2023; 4:191-215.e9. [PMID: 36863347 PMCID: PMC9933851 DOI: 10.1016/j.medj.2023.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 01/30/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
BACKGROUND Both infection and vaccination, alone or in combination, generate antibody and T cell responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the maintenance of such responses-and hence protection from disease-requires careful characterization. In a large prospective study of UK healthcare workers (HCWs) (Protective Immunity from T Cells in Healthcare Workers [PITCH], within the larger SARS-CoV-2 Immunity and Reinfection Evaluation [SIREN] study), we previously observed that prior infection strongly affected subsequent cellular and humoral immunity induced after long and short dosing intervals of BNT162b2 (Pfizer/BioNTech) vaccination. METHODS Here, we report longer follow-up of 684 HCWs in this cohort over 6-9 months following two doses of BNT162b2 or AZD1222 (Oxford/AstraZeneca) vaccination and up to 6 months following a subsequent mRNA booster vaccination. FINDINGS We make three observations: first, the dynamics of humoral and cellular responses differ; binding and neutralizing antibodies declined, whereas T and memory B cell responses were maintained after the second vaccine dose. Second, vaccine boosting restored immunoglobulin (Ig) G levels; broadened neutralizing activity against variants of concern, including Omicron BA.1, BA.2, and BA.5; and boosted T cell responses above the 6-month level after dose 2. Third, prior infection maintained its impact driving larger and broader T cell responses compared with never-infected people, a feature maintained until 6 months after the third dose. CONCLUSIONS Broadly cross-reactive T cell responses are well maintained over time-especially in those with combined vaccine and infection-induced immunity ("hybrid" immunity)-and may contribute to continued protection against severe disease. FUNDING Department for Health and Social Care, Medical Research Council.
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Affiliation(s)
- Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Stephanie Longet
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Alexandra S Deeks
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Division of Emerging Infectious Disease, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Laura Silva Reyes
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Naomi Meardon
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Sian Faustini
- Institute for Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Saly Al-Taei
- Institute for Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Tom Tipton
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luisa M Hering
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Adrienn Angyal
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Rebecca Brown
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Alexander R Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Susan L Dobson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Cross
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Jessica K Tyerman
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Hailey Hornsby
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Irina Grouneva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Peijun Zhang
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Thomas A H Newman
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Jeremy M Nell
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Priyanka Abraham
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Tom Malone
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Isabel Neale
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Eloise Phillips
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Joseph D Wilson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford University Medical School, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Sam M Murray
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Martha Zewdie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Adrian Shields
- Institute for Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Emily C Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Lucy H Booth
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Lizzie Stafford
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel G Wootton
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christopher P Conlon
- Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Philippa C Matthews
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; The Francis Crick Institute, London, UK; Division of Infection and Immunity, University College London, London, UK; Department of Infectious Diseases, University College London Hospital NHS Foundation Trust, London, UK
| | - Andrew J Pollard
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sarah L Rowland-Jones
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | | | - Gavin Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susan Hopkins
- UK Health Security Agency, London, UK; Faculty of Medicine, Department of Infectious Disease, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Victoria Hall
- UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Christopher J A Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle, UK; Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Alex Richter
- Institute for Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Miles Carroll
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK.
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Mehta H, Tasin I, Hackstein CP, Willberg C, Klenerman P. Prostaglandins differentially modulate mucosal-associated invariant T-cell activation and function according to stimulus. Immunol Cell Biol 2023; 101:262-272. [PMID: 36541521 PMCID: PMC10152717 DOI: 10.1111/imcb.12617] [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: 11/24/2021] [Revised: 05/29/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are an innate-like T-cell type conserved in many mammals and especially abundant in humans. Their semi-invariant T-cell receptor (TCR) recognizes the major histocompatibility complex-like molecule MR1 presenting riboflavin intermediates associated with microbial metabolism. Full MAIT cell triggering requires costimulation via cytokines, and the cells can also be effectively triggered in a TCR-independent manner by cytokines [e.g. interleukin (IL)-12 and IL-18 in combination]. Thus, triggering of MAIT cells is highly sensitive to local soluble mediators. Suppression of MAIT cell activation has not been well explored and could be very relevant to their roles in infection, inflammation and cancer. Prostaglandins (PG) are major local mediators of these microenvironments which can have regulatory roles for T cells. Here, we explored whether prostaglandins suppressed MAIT cell activation in response to TCR-dependent and TCR-independent signals. We found that protaglandin E2 (PGE2 ) and to a lesser extent protaglandin D2 (PGD2 ), but not leukotrienes, suppressed MAIT cell responses to Escherichia coli or TCR triggers. However, there was no impact on cytokine-induced triggering. The inhibition was blocked by targeting the signaling mediated via PG receptor 2 (PTGER2) and 4 (PTGER4) receptors in combination. These data indicate that prostaglandins can potentially modulate local MAIT cell functions in vivo and indicate distinct regulation of the TCR-dependent and TCR-independent pathways of MAIT cell activation.
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Affiliation(s)
- Hema Mehta
- The Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
| | - Irene Tasin
- The Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
| | | | - Christian Willberg
- The Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
| | - Paul Klenerman
- The Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
- NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
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38
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Wang T, Smith DA, Campbell C, Freeman O, Moysova Z, Noble T, Várnai KA, Harris S, Salih H, Roadknight G, Little S, Glampson B, Mercuri L, Papadimitriou D, Jones CR, Taylor V, Chaudhry A, Phan H, Borca F, Olza J, Warricker F, Romão L, Ramlakhan D, English L, Klenerman P, Andersson M, Collier J, Stockdale AJ, Todd S, McIntyre K, Frankland A, Nastouli E, Khakoo SI, Gelson W, Cooke GS, Woods K, Davies J, Barnes E, Matthews PC. Cohort Profile: The National Institute for Health Research Health Informatics Collaborative: Hepatitis B Virus (NIHR HIC HBV) research dataset. Int J Epidemiol 2023; 52:e27-e37. [PMID: 35708657 PMCID: PMC9908046 DOI: 10.1093/ije/dyac127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 06/03/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tingyan Wang
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David A Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Informatics Collaborative, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Cori Campbell
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Oliver Freeman
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Zuzana Moysova
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- NIHR Health Informatics Collaborative, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Theresa Noble
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- NIHR Health Informatics Collaborative, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kinga A Várnai
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- NIHR Health Informatics Collaborative, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Steve Harris
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Hizni Salih
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | | | - Ben Glampson
- NIHR Health Informatics Collaborative, Imperial College Healthcare NHS Trust, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | - Luca Mercuri
- NIHR Health Informatics Collaborative, Imperial College Healthcare NHS Trust, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | - Dimitri Papadimitriou
- NIHR Health Informatics Collaborative, Imperial College Healthcare NHS Trust, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | - Christopher R Jones
- NIHR Imperial Biomedical Research Centre, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Vince Taylor
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Afzal Chaudhry
- Department of Nephrology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hang Phan
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Clinical Informatics Research Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Florina Borca
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Clinical Informatics Research Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Josune Olza
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Frazer Warricker
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Luis Romão
- NIHR University College London Hospitals Biomedical Research Centre, London, UK
| | - David Ramlakhan
- NIHR University College London Hospitals Biomedical Research Centre, London, UK
| | - Louise English
- NIHR University College London Hospitals Biomedical Research Centre, London, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Monique Andersson
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jane Collier
- Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alexander J Stockdale
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical Infectious Diseases Unit, Royal Liverpool Hospital, Liverpool University Hospitals NHS Trust, Liverpool, UK
| | - Stacy Todd
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Karl McIntyre
- Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Trust, Liverpool, UK
| | - Andrew Frankland
- Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Trust, Liverpool, UK
| | - Eleni Nastouli
- Department of Clinical Virology, University College London Hospital, London, UK
- Department of Infection, Immunity and Inflammation, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Salim I Khakoo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - William Gelson
- Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Graham S Cooke
- NIHR Health Informatics Collaborative, Imperial College Healthcare NHS Trust, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
- Faculty of Medicine, Department of Infectious Disease, Imperial College London, London, UK
| | - Kerrie Woods
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- NIHR Health Informatics Collaborative, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jim Davies
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Informatics Collaborative, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Informatics Collaborative, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Francis Crick Institute, London, UK
- Division of Infection and Immunity, University College London, London, UK
- Department of Infectious Diseases, University College London Hospital, London, UK
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39
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Huo J, Dijokaite-Guraliuc A, Liu C, Zhou D, Ginn HM, Das R, Supasa P, Selvaraj M, Nutalai R, Tuekprakhon A, Duyvesteyn HME, Mentzer AJ, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Paterson NG, Williams MA, Hall DR, Plowright M, Newman TAH, Hornsby H, de Silva TI, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Pollard AJ, Lambe T, Goulder P, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75. Cell Rep 2023; 42:111903. [PMID: 36586406 PMCID: PMC9747698 DOI: 10.1016/j.celrep.2022.111903] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [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: 09/14/2022] [Revised: 11/05/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have caused successive global waves of infection. These variants, with multiple mutations in the spike protein, are thought to facilitate escape from natural and vaccine-induced immunity and often increase in affinity for ACE2. The latest variant to cause concern is BA.2.75, identified in India where it is now the dominant strain, with evidence of wider dissemination. BA.2.75 is derived from BA.2 and contains four additional mutations in the receptor-binding domain (RBD). Here, we perform an antigenic and biophysical characterization of BA.2.75, revealing an interesting balance between humoral evasion and ACE2 receptor affinity. ACE2 affinity for BA.2.75 is increased 9-fold compared with BA.2; there is also evidence of escape of BA.2.75 from immune serum, particularly that induced by Delta infection, which may explain the rapid spread in India, where where there is a high background of Delta infection. ACE2 affinity appears to be prioritized over greater escape.
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Affiliation(s)
- Jiandong Huo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK; Guangzhou Laboratory, Bio-island, Guangzhou 510320, China.
| | - Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sandra Adele
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Neil G Paterson
- Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Megan Plowright
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas A H Newman
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Hailey Hornsby
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, the Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source, Ltd., Harwell Science and Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
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40
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Cross AR, de Andrea CE, Villalba-Esparza M, Landecho MF, Cerundolo L, Weeratunga P, Etherington RE, Denney L, Ogg G, Ho LP, Roberts IS, Hester J, Klenerman P, Melero I, Sansom SN, Issa F. Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury. JCI Insight 2023; 8:e157837. [PMID: 36472908 PMCID: PMC9977306 DOI: 10.1172/jci.insight.157837] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 12/21/2021] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Severe lung damage resulting from COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways, and genes present across the spectrum of histopathological damage in COVID-19-affected lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from 46 areas of interest covering more than 62,000 cells within well-preserved lung samples from 3 patients. Despite substantial interpatient heterogeneity, we discovered evidence for a common immune-cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines, including CXCL9, CXCL10, and CXCL11, which are known to promote the recruitment of CXCR3+ immune cells. The TNF superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were consistently upregulated in the areas with severe tissue damage. We used published spatial and single-cell SARS-CoV-2 data sets to validate our findings in the lung tissue from additional cohorts of patients with COVID-19. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies.
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Affiliation(s)
- Amy R. Cross
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Manuel F. Landecho
- Department of Internal Medicine, and
- Department of Immunology and Immunotherapy, Clínica de la Universidad de Navarra, Pamplona, Spain
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Praveen Weeratunga
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Rachel E. Etherington
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Laura Denney
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ling-Pei Ho
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ian S.D. Roberts
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joanna Hester
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ignacio Melero
- Department of Immunology and Immunotherapy, Clínica de la Universidad de Navarra, Pamplona, Spain
- CIBERONC, Madrid, Spain
- Center for Applied Medical Research, Pamplona, Spain
| | - Stephen N. Sansom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
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Fidler S, Fox J, Tipoe T, Longet S, Tipton T, Abeywickrema M, Adele S, Alagaratnam J, Ali M, Aley PK, Aslam S, Balasubramanian A, Bara A, Bawa T, Brown A, Brown H, Cappuccini F, Davies S, Fowler J, Godfrey L, Goodman AL, Hilario K, Hackstein CP, Mathew M, Mujadidi YF, Packham A, Petersen C, Plested E, Pollock KM, Ramasamy MN, Robinson H, Robinson N, Rongkard P, Sanders H, Serafimova T, Spence N, Waters A, Woods D, Zacharopoulou P, Barnes E, Dunachie S, Goulder P, Klenerman P, Winston A, Hill AVS, Gilbert SC, Carroll M, Pollard AJ, Lambe T, Ogbe A, Frater J. Booster Vaccination Against SARS-CoV-2 Induces Potent Immune Responses in People With Human Immunodeficiency Virus. Clin Infect Dis 2023; 76:201-209. [PMID: 36196614 PMCID: PMC9619587 DOI: 10.1093/cid/ciac796] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/23/2022] [Accepted: 09/28/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND People with human immunodeficiency virus (HIV) on antiretroviral therapy (ART) with good CD4 T-cell counts make effective immune responses following vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are few data on longer term responses and the impact of a booster dose. METHODS Adults with HIV were enrolled into a single arm open label study. Two doses of ChAdOx1 nCoV-19 were followed 12 months later by a third heterologous vaccine dose. Participants had undetectable viraemia on ART and CD4 counts >350 cells/µL. Immune responses to the ancestral strain and variants of concern were measured by anti-spike immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA), MesoScale Discovery (MSD) anti-spike platform, ACE-2 inhibition, activation induced marker (AIM) assay, and T-cell proliferation. FINDINGS In total, 54 participants received 2 doses of ChAdOx1 nCoV-19. 43 received a third dose (42 with BNT162b2; 1 with mRNA-1273) 1 year after the first dose. After the third dose, total anti-SARS-CoV-2 spike IgG titers (MSD), ACE-2 inhibition, and IgG ELISA results were significantly higher compared to Day 182 titers (P < .0001 for all 3). SARS-CoV-2 specific CD4+ T-cell responses measured by AIM against SARS-CoV-2 S1 and S2 peptide pools were significantly increased after a third vaccine compared to 6 months after a first dose, with significant increases in proliferative CD4+ and CD8+ T-cell responses to SARS-CoV-2 S1 and S2 after boosting. Responses to Alpha, Beta, Gamma, and Delta variants were boosted, although to a lesser extent for Omicron. CONCLUSIONS In PWH receiving a third vaccine dose, there were significant increases in B- and T-cell immunity, including to known variants of concern (VOCs).
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Affiliation(s)
- Sarah Fidler
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of HIV Medicine, St Mary's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
- National Institute for Health and Care Research (NIHR) Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Julie Fox
- NIHR Guy's and St Thomas’ Biomedical Research Centre, London, United Kingdom
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Timothy Tipoe
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Stephanie Longet
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tom Tipton
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Movin Abeywickrema
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Sandra Adele
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Jasmini Alagaratnam
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of HIV Medicine, St Mary's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
| | - Mohammad Ali
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | - Suhail Aslam
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Anbhu Balasubramanian
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Anna Bara
- National Institute for Health and Care Research (NIHR) Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Tanveer Bawa
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Anthony Brown
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Helen Brown
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Federica Cappuccini
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Sophie Davies
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Jamie Fowler
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Leila Godfrey
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Anna L Goodman
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
- Medical Research Council Clinical Trials Unit, University College London, London, United Kingdom
| | - Kathrine Hilario
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Carl-Philipp Hackstein
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Moncy Mathew
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Yama F Mujadidi
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Alice Packham
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Claire Petersen
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of HIV Medicine, St Mary's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
| | - Emma Plested
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Katrina M Pollock
- National Institute for Health and Care Research (NIHR) Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Maheshi N Ramasamy
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Hannah Robinson
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | - Nicola Robinson
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Patpong Rongkard
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Helen Sanders
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Teona Serafimova
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Niamh Spence
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Anele Waters
- Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas’ NHS Trust, London, United Kingdom
| | - Danielle Woods
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Panagiota Zacharopoulou
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Department of HIV Medicine, St Mary's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Susanna Dunachie
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Philip Goulder
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Alan Winston
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of HIV Medicine, St Mary's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
| | - Adrian V S Hill
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Sarah C Gilbert
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Miles Carroll
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Public Health England, Porton Down, Salisbury, United Kingdom
| | - Andrew J Pollard
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, Oxford, United Kingdom
| | - Ane Ogbe
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - John Frater
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
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42
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Jay C, Ratcliff J, Turtle L, Goulder P, Klenerman P. Exposed seronegative: Cellular immune responses to SARS-CoV-2 in the absence of seroconversion. Front Immunol 2023; 14:1092910. [PMID: 36776841 PMCID: PMC9909393 DOI: 10.3389/fimmu.2023.1092910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
The factors determining whether infection will occur following exposure to SARS-CoV-2 remain elusive. Certain SARS-CoV-2-exposed individuals mount a specific T-cell response but fail to seroconvert, representing a population that may provide further clarity on the nature of infection susceptibility and correlates of protection against SARS-CoV-2. Exposed seronegative individuals have been reported in patients exposed to the blood-borne pathogens Human Immunodeficiency virus and Hepatitis C virus and the sexually transmitted viruses Hepatitis B virus and Herpes Simplex virus. By comparing the quality of seronegative T-cell responses to SARS-CoV-2 with seronegative cellular immunity to these highly divergent viruses, common patterns emerge that offer insights on the role of cellular immunity against infection. For both SARS-CoV-2 and Hepatitis C, T-cell responses in exposed seronegatives are consistently higher than in unexposed individuals, but lower than in infected, seropositive patients. Durability of T-cell responses to Hepatitis C is dependent upon repeated exposure to antigen - single exposures do not generate long-lived memory T-cells. Finally, exposure to SARS-CoV-2 induces varying degrees of immune activation, suggesting that exposed seronegative individuals represent points on a spectrum rather than a discrete group. Together, these findings paint a complex landscape of the nature of infection but provide clues as to what may be protective early on in SARS-CoV-2 disease course. Further research on this phenomenon, particularly through cohort studies, is warranted.
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Affiliation(s)
- Cecilia Jay
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jeremy Ratcliff
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lance Turtle
- National Institute for Health and Care Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, United Kingdom
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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43
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Moseley P, Klenerman P, Kadambari S. Indirect effects of cytomegalovirus infection: Implications for vaccine development. Rev Med Virol 2023; 33:e2405. [PMID: 36378563 PMCID: PMC10078107 DOI: 10.1002/rmv.2405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/12/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022]
Abstract
Development of a cytomegalovirus (CMV) vaccine is a high priority due to its significant global impact-contributing to mortality in immunosuppressed individuals, neurodevelopmental delay in infected neonates and non-genetic sensorineural hearing loss. The impact of CMV on the general population has been less well studied; however, a wide range of evidence indicates that CMV may increase the risk of atherosclerosis, cancer, immunosenescence, and progression of tuberculosis (TB) and human immunodeficiency virus. Due to the high seroprevalence of CMV worldwide, any modulation of risk by CMV is likely to have a significant impact on the epidemiology of these diseases. This review will evaluate how CMV may cause morbidity and mortality outside of the neonatal and immunosuppressed populations and consider the potential impact of a CMV vaccine on these outcomes.
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Affiliation(s)
- Philip Moseley
- Department of Paediatrics, Horton General Hospital, Oxford University Hospitals, Banbury, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Seilesh Kadambari
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK.,Department of Paediatric Infectious Diseases, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Great Ormond Street Institute of Child Health, University College London, London, UK
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44
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Kandasamy M, Gileadi U, Rijal P, Tan TK, Lee LN, Chen J, Prota G, Klenerman P, Townsend A, Cerundolo V. Recombinant single-cycle influenza virus with exchangeable pseudotypes allows repeated immunization to augment anti-tumour immunity with immune checkpoint inhibitors. eLife 2023; 12:76414. [PMID: 36626205 PMCID: PMC9831609 DOI: 10.7554/elife.76414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/08/2022] [Indexed: 01/11/2023] Open
Abstract
Virus-based tumour vaccines offer many advantages compared to other antigen-delivering systems. They generate concerted innate and adaptive immune response, and robust CD8+ T cell responses. We engineered a non-replicating pseudotyped influenza virus (S-FLU) to deliver the well-known cancer testis antigen, NY-ESO-1 (NY-ESO-1 S-FLU). Intranasal or intramuscular immunization of NY-ESO-1 S-FLU virus in mice elicited a strong NY-ESO-1-specific CD8+ T cell response in lungs and spleen that resulted in the regression of NY-ESO-1-expressing lung tumour and subcutaneous tumour, respectively. Combined administration with anti-PD-1 antibody, NY-ESO-1 S-FLU virus augmented the tumour protection by reducing the tumour metastasis. We propose that the antigen delivery through S-FLU is highly efficient in inducing antigen-specific CD8+ T cell response and protection against tumour development in combination with PD-1 blockade.
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Affiliation(s)
- Matheswaran Kandasamy
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Uzi Gileadi
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Pramila Rijal
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Lian N Lee
- Nuffield Department of Medicine and Translational Gastroenterology Unit, Peter Medawar Building, University of OxfordOxfordUnited Kingdom
| | - Jili Chen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Gennaro Prota
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine and Translational Gastroenterology Unit, Peter Medawar Building, University of OxfordOxfordUnited Kingdom
| | - Alain Townsend
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
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45
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Phalora P, Klenerman P. MR1: An unconventional twist in the tail. J Cell Biol 2022; 221:e202211016. [PMID: 36374222 PMCID: PMC9665901 DOI: 10.1083/jcb.202211016] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
MR1 is a conserved molecule that binds microbial vitamin B metabolites and presents them to unconventional T cells. Lim and colleagues (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202110125) uncover the role of AP2 in ensuring MR1 surface presentation, which relies on an atypical motif within the MR1 cytoplasmic tail.
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Affiliation(s)
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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46
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Hackstein CP, Costigan D, Drexhage L, Pearson C, Bullers S, Ilott N, Akther HD, Gu Y, FitzPatrick MEB, Harrison OJ, Garner LC, Mann EH, Pandey S, Friedrich M, Provine NM, Uhlig HH, Marchi E, Powrie F, Klenerman P, Thornton EE. A conserved population of MHC II-restricted, innate-like, commensal-reactive T cells in the gut of humans and mice. Nat Commun 2022; 13:7472. [PMID: 36463279 PMCID: PMC9719512 DOI: 10.1038/s41467-022-35126-3] [Citation(s) in RCA: 4] [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: 02/24/2022] [Accepted: 11/20/2022] [Indexed: 12/05/2022] Open
Abstract
Interactions with commensal microbes shape host immunity on multiple levels and play a pivotal role in human health and disease. Tissue-dwelling, antigen-specific T cells are poised to respond to local insults, making their phenotype important in the relationship between host and microbes. Here we show that MHC-II restricted, commensal-reactive T cells in the colon of both humans and mice acquire transcriptional and functional characteristics associated with innate-like T cells. This cell population is abundant and conserved in the human and murine colon and endowed with polyfunctional effector properties spanning classic Th1- and Th17-cytokines, cytotoxic molecules, and regulators of epithelial homeostasis. T cells with this phenotype are increased in ulcerative colitis patients, and their presence aggravates pathology in dextran sodium sulphate-treated mice, pointing towards a pathogenic role in colitis. Our findings add to the expanding spectrum of innate-like immune cells positioned at the frontline of intestinal immune surveillance, capable of acting as sentinels of microbes and the local cytokine milieu.
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Affiliation(s)
- Carl-Philipp Hackstein
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dana Costigan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Linnea Drexhage
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Claire Pearson
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Samuel Bullers
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Nicholas Ilott
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Hossain Delowar Akther
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yisu Gu
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Michael E B FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Oliver J Harrison
- Center for Fundamental Immunology, Benaroya Research Institute, 1201 9th Ave, Seattle, WA, 98101, USA
- Department of Immunology, University of Washington, 750 Republican St, Seattle, WA, 98108, USA
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth H Mann
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Sumeet Pandey
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthias Friedrich
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, and Biomedical Research Centre, and Department of Paediatrics, University of Oxford, Oxford, OX39DU, UK
| | - Emanuele Marchi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Emily E Thornton
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Lett MJ, Mehta H, Keogh A, Jaeger T, Jacquet M, Powell K, Meier MA, Fofana I, Melhem H, Vosbeck J, Cathomas G, Heigl A, Heim MH, Burri E, Mertz KD, Niess JH, Kollmar O, Zech CJ, Ivanek R, Duthaler U, Klenerman P, Stroka D, Filipowicz Sinnreich M. Stimulatory MAIT cell antigens reach the circulation and are efficiently metabolised and presented by human liver cells. Gut 2022; 71:2526-2538. [PMID: 35058274 PMCID: PMC9664123 DOI: 10.1136/gutjnl-2021-324478] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 01/08/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Mucosal-associated invariant T (MAIT) cells are the most abundant T cells in human liver. They respond to bacterial metabolites presented by major histocompatibility complex-like molecule MR1. MAIT cells exert regulatory and antimicrobial functions and are implicated in liver fibrogenesis. It is not well understood which liver cells function as antigen (Ag)-presenting cells for MAIT cells, and under which conditions stimulatory Ags reach the circulation. DESIGN We used different types of primary human liver cells in Ag-presentation assays to blood-derived and liver-derived MAIT cells. We assessed MAIT cell stimulatory potential of serum from healthy subjects and patients with portal hypertension undergoing transjugular intrahepatic portosystemic shunt stent, and patients with inflammatory bowel disease (IBD). RESULTS MAIT cells were dispersed throughout healthy human liver and all tested liver cell types stimulated MAIT cells, hepatocytes being most efficient. MAIT cell activation by liver cells occurred in response to bacterial lysate and pure Ag, and was prevented by non-activating MR1 ligands. Serum derived from peripheral and portal blood, and from patients with IBD stimulated MAIT cells in MR1-dependent manner. CONCLUSION Our findings reveal previously unrecognised roles of liver cells in Ag metabolism and activation of MAIT cells, repression of which creates an opportunity to design antifibrotic therapies. The presence of MAIT cell stimulatory Ags in serum rationalises the observed activated MAIT cell phenotype in liver. Increased serum levels of gut-derived MAIT cell stimulatory ligands in patients with impaired intestinal barrier function indicate that intrahepatic Ag-presentation may represent an important step in the development of liver disease.
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Affiliation(s)
- Martin J Lett
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Hema Mehta
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adrian Keogh
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Tina Jaeger
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Maxime Jacquet
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Kate Powell
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marie-Anne Meier
- Department of Biomedicine, Hepatology, University Hospital Basel and University of Basel, Basel, Switzerland,Division of Gastroenterology and Hepatology, Clarunis University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Isabel Fofana
- Department of Biomedicine, Hepatology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Hassan Melhem
- Department of Biomedicine, Gastroenterology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jürg Vosbeck
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Gieri Cathomas
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Andres Heigl
- Department of Surgery, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Markus H Heim
- Department of Biomedicine, Hepatology, University Hospital Basel and University of Basel, Basel, Switzerland,Division of Gastroenterology and Hepatology, Clarunis University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Emanuel Burri
- Gastroenterology and Hepatology, University Department of Medicine, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Kirsten D Mertz
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Jan Hendrik Niess
- Division of Gastroenterology and Hepatology, Clarunis University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland,Department of Biomedicine, Gastroenterology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Otto Kollmar
- Division of Visceral Surgery, Clarunis University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Christoph J Zech
- Radiology and Nuclear Medicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Robert Ivanek
- Department of Biomedicine, Bioinformatics Core Facility, University Hospital Basel and University of Basel, Basel, Switzerland,DBM Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Urs Duthaler
- Department of Biomedicine, Clinical Pharmacology and Toxicology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Magdalena Filipowicz Sinnreich
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland .,Gastroenterology and Hepatology, University Department of Medicine, Cantonal Hospital Baselland, Liestal, Switzerland
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Provine NM, Klenerman P. Adenovirus vector and mRNA vaccines: Mechanisms regulating their immunogenicity. Eur J Immunol 2022:10.1002/eji.202250022. [PMID: 36330560 PMCID: PMC9877955 DOI: 10.1002/eji.202250022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/05/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
Replication-incompetent adenovirus (Ad) vector and mRNA-lipid nanoparticle (LNP) constructs represent two modular vaccine platforms that have attracted substantial interest over the past two decades. Due to the COVID-19 pandemic and the rapid development of multiple successful vaccines based on these technologies, there is now clear real-world evidence of the utility and efficacy of these platforms. Considerable optimization and refinement efforts underpin the successful application of these technologies. Despite this, our understanding of the specific pathways and processes engaged by these vaccines to stimulate the immune response remains incomplete. This review will synthesize our current knowledge of the specific mechanisms by which CD8+ T cell and antibody responses are induced by each of these vaccine platforms, and how this can be impacted by specific vaccine construction techniques. Key gaps in our knowledge are also highlighted, which can hopefully focus future studies.
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Affiliation(s)
- Nicholas M. Provine
- Translational Gastroenterology UnitNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Paul Klenerman
- Translational Gastroenterology UnitNuffield Department of MedicineUniversity of OxfordOxfordUK,Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
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49
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Melero I, Villalba-Esparza M, Recalde-Zamacona B, Jiménez-Sánchez D, Teijeira Á, Argueta A, García-Tobar L, Álvarez-Gigli L, Sainz C, Garcia-Ros D, Toledo E, Abengozar-Muela M, Fernández-Alonso M, Rodríguez-Mateos M, Reina G, Carmona-Torre F, Quiroga JA, Del Pozo JL, Cross A, López-Janeiro Á, Hardisson D, Echeveste JI, Lozano MD, Ho LP, Klenerman P, Issa F, Landecho MF, de Andrea CE. Neutrophil Extracellular Traps, Local IL-8 Expression, and Cytotoxic T-Lymphocyte Response in the Lungs of Patients With Fatal COVID-19. Chest 2022; 162:1006-1016. [PMID: 35714708 PMCID: PMC9197577 DOI: 10.1016/j.chest.2022.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Excessive inflammation is pathogenic in the pneumonitis associated with severe COVID-19. Neutrophils are among the most abundantly present leukocytes in the inflammatory infiltrates and may form neutrophil extracellular traps (NETs) under the local influence of cytokines. NETs constitute a defense mechanism against bacteria, but have also been shown to mediate tissue damage in a number of diseases. RESEARCH QUESTION Could NETs and their tissue-damaging properties inherent to neutrophil-associated functions play a role in the respiratory failure seen in patients with severe COVID-19, and how does this relate to the SARS-CoV-2 viral loads, IL-8 (CXCL8) chemokine expression, and cytotoxic T-lymphocyte infiltrates? STUDY DESIGN AND METHODS Sixteen lung biopsy samples obtained immediately after death were analyzed methodically as exploratory and validation cohorts. NETs were analyzed quantitatively by multiplexed immunofluorescence and were correlated with local levels of IL-8 messenger RNA (mRNA) and the density of CD8+ T-cell infiltration. SARS-CoV-2 presence in tissue was quantified by reverse-transcriptase polymerase chain reaction and immunohistochemistry analysis. RESULTS NETs were found in the lung interstitium and surrounding the bronchiolar epithelium with interindividual and spatial heterogeneity. NET density did not correlate with SARS-CoV-2 tissue viral load. NETs were associated with local IL-8 mRNA levels. NETs were also detected in pulmonary thrombi and in only one of eight liver tissues. NET focal presence correlated negatively with CD8+ T-cell infiltration in the lungs. INTERPRETATION Abundant neutrophils undergoing NETosis are found in the lungs of patients with fatal COVID-19, but no correlation was found with viral loads. The strong association between NETs and IL-8 points to this chemokine as a potentially causative factor. The function of cytotoxic T-lymphocytes in the immune responses against SARS-CoV-2 may be interfered with by the presence of NETs.
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Affiliation(s)
- Ignacio Melero
- Division of Immunology and Immunotherapy, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - María Villalba-Esparza
- Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain; Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
| | | | | | - Álvaro Teijeira
- Division of Immunology and Immunotherapy, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Alan Argueta
- Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Laura García-Tobar
- Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Cristina Sainz
- Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
| | - David Garcia-Ros
- Department of Anatomy, Physiology and Pathology, University of Navarra, Pamplona, Spain
| | - Estefanía Toledo
- Department of Preventive Medicine and Public Health, IdiSNA, University of Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición, Institute of Health Carlos III, Madrid, Spain
| | | | - Mirian Fernández-Alonso
- Navarra Institute for Health Research, Pamplona, Spain; Department of Microbiology and Infectious Diseases, Clínica Universidad de Navarra, Pamplona, Spain
| | - Mariano Rodríguez-Mateos
- Department of Microbiology and Infectious Diseases, Clínica Universidad de Navarra, Pamplona, Spain
| | - Gabriel Reina
- Navarra Institute for Health Research, Pamplona, Spain; Department of Microbiology and Infectious Diseases, Clínica Universidad de Navarra, Pamplona, Spain
| | - Francisco Carmona-Torre
- Navarra Institute for Health Research, Pamplona, Spain; Department of Microbiology and Infectious Diseases, Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Jose L Del Pozo
- Navarra Institute for Health Research, Pamplona, Spain; Department of Microbiology and Infectious Diseases, Clínica Universidad de Navarra, Pamplona, Spain
| | - Amy Cross
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, England
| | | | - David Hardisson
- Department of Pathology, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - José I Echeveste
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain; Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain; Department of Anatomy, Physiology and Pathology, University of Navarra, Pamplona, Spain
| | - Maria D Lozano
- Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain; Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain; Department of Anatomy, Physiology and Pathology, University of Navarra, Pamplona, Spain
| | - Ling-Pei Ho
- MRC Human Immunology Unit, University of Oxford, Oxford, England
| | - Paul Klenerman
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, Oxford, England
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, England
| | - Manuel F Landecho
- Department of Internal Medicine, Clínica Universidad de Navarra, Pamplona, Spain
| | - Carlos E de Andrea
- Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain; Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain; Department of Anatomy, Physiology and Pathology, University of Navarra, Pamplona, Spain.
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50
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Hackstein CP, Klenerman P. Emerging features of MAIT cells and other unconventional T cell populations in human viral disease and vaccination. Semin Immunol 2022; 61-64:101661. [PMID: 36374780 PMCID: PMC10933818 DOI: 10.1016/j.smim.2022.101661] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 12/14/2022]
Abstract
MAIT cells are one representative of a group of related unconventional or pre-set T cells, and are particularly abundant in humans. While these unconventional T cell types, which also include populations of Vδ2 cells and iNKT cells, recognise quite distinct ligands, they share functional features including the ability to sense "danger" by integration of cytokine signals. Since such signals are common to many human pathologies, activation of MAIT cells in particular has been widely observed. In this review we will discuss recent trends in these data, for example the findings from patients with Covid-19 and responses to novel vaccines. Covid-19 is an example where MAIT cell activation has been correlated with disease severity by several groups, and the pathways leading to activation are being clarified, but the overall role of the cells in vivo requires further exploration. Given the potential wide functional responsiveness of these cells, which ranges from tissue repair to cytotoxicity, and likely impacts on the activity of many other cell populations, defining the role of these cells - not only as sensitive biomarkers but also as mediators - across human disease remains an important task.
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Affiliation(s)
- Carl-Philipp Hackstein
- Peter Medawar Building for Pathogen Research, Nuffield Dept of Medicine, University of Oxford, Oxford OX1 3SY, UK; Translational Gastroenterology Unit, Nuffield Dept of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Dept of Medicine, University of Oxford, Oxford OX1 3SY, UK; Translational Gastroenterology Unit, Nuffield Dept of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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