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Wellington D, Yin Z, Yu Z, Heilig R, Davis S, Fischer R, Felce SL, Antoun E, Hublitz P, Beveridge R, Dong D, Liu G, Yao X, Peng Y, Kessler BM, Dong T. SARS-CoV-2 mutations affect antigen processing by the proteasome to alter CD8 + T cell responses. Heliyon 2023; 9:e20076. [PMID: 37842619 PMCID: PMC10570596 DOI: 10.1016/j.heliyon.2023.e20076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Mutations within viral epitopes can result in escape from T cells, but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two SARS-CoV-2 nucleoprotein CD8+ epitopes, we investigated the contribution of these flanking mutations to proteasomal processing and T cell activation. We found decreased NP9-17-B*27:05 CD8+ T cell responses to the NP-Q7K mutation, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103 N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+ T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on proteasomal processing, either contributing to T cell escape or enhancement that may be exploited for future vaccine design.
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Affiliation(s)
- Dannielle Wellington
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zixi Yin
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zhanru Yu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Simon Davis
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Elie Antoun
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Ryan Beveridge
- Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Yanchun Peng
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Benedikt M. Kessler
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
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2
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Yin Z, Chen JL, Lu Y, Wang B, Godfrey L, Mentzer AJ, Yao X, Liu G, Wellington D, Zhao Y, Wing PAC, Dejnirattisa W, Supasa P, Liu C, Hublitz P, Beveridge R, Waugh C, Clark SA, Clark K, Sopp P, Rostron T, Mongkolsapaya J, Screaton GR, Ogg G, Ewer K, Pollard AJ, Gilbert S, Knight JC, Lambe T, Smith GL, Dong T, Peng Y. Evaluation of T cell responses to naturally processed variant SARS-CoV-2 spike antigens in individuals following infection or vaccination. Cell Rep 2023; 42:112470. [PMID: 37141092 PMCID: PMC10121105 DOI: 10.1016/j.celrep.2023.112470] [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: 01/19/2023] [Revised: 03/20/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Most existing studies characterizing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell responses are peptide based. This does not allow evaluation of whether tested peptides are processed and presented canonically. In this study, we use recombinant vaccinia virus (rVACV)-mediated expression of SARS-CoV-2 spike protein and SARS-CoV-2 infection of angiotensin-converting enzyme (ACE)-2-transduced B cell lines to evaluate overall T cell responses in a small cohort of recovered COVID-19 patients and uninfected donors vaccinated with ChAdOx1 nCoV-19. We show that rVACV expression of SARS-CoV-2 antigen can be used as an alternative to SARS-CoV-2 infection to evaluate T cell responses to naturally processed spike antigens. In addition, the rVACV system can be used to evaluate the cross-reactivity of memory T cells to variants of concern (VOCs) and to identify epitope escape mutants. Finally, our data show that both natural infection and vaccination could induce multi-functional T cell responses with overall T cell responses remaining despite the identification of escape mutations.
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Affiliation(s)
- Zixi Yin
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ji-Li Chen
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Beibei Wang
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
| | - Leila Godfrey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Xuan Yao
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
| | - Guihai Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Beijing You'an Hospital, Capital Medical University, Beijing 100069, China
| | - Dannielle Wellington
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
| | - Yiqi Zhao
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Peter A C Wing
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Wanwisa Dejnirattisa
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ryan Beveridge
- Screening Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Craig Waugh
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Timothy Rostron
- Sequencing Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Graham Ogg
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Katie Ewer
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK; National Institute for Health Research Oxford Biomedical Research Center, Oxford, UK
| | - Sarah Gilbert
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Julian C Knight
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK.
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.
| | - Tao Dong
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Yanchun Peng
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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3
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Abstract
In this issue of Cell Host & Microbe, Grifoni et al. provide reassuring evidence that the majority of epitopes induced by vaccinia virus vaccines are conserved in monkeypox virus and can elicit memory T cell responses, while also providing an extensive list of potential T cell epitopes.
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Affiliation(s)
- Dannielle Wellington
- Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tao Dong
- Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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4
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Clement M, Forbester JL, Marsden M, Sabberwal P, Sommerville MS, Wellington D, Dimonte S, Clare S, Harcourt K, Yin Z, Nobre L, Antrobus R, Jin B, Chen M, Makvandi-Nejad S, Lindborg JA, Strittmatter SM, Weekes MP, Stanton RJ, Dong T, Humphreys IR. IFITM3 restricts virus-induced inflammatory cytokine production by limiting Nogo-B mediated TLR responses. Nat Commun 2022; 13:5294. [PMID: 36075894 PMCID: PMC9454482 DOI: 10.1038/s41467-022-32587-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 08/08/2022] [Indexed: 11/20/2022] Open
Abstract
Interferon-induced transmembrane protein 3 (IFITM3) is a restriction factor that limits viral pathogenesis and exerts poorly understood immunoregulatory functions. Here, using human and mouse models, we demonstrate that IFITM3 promotes MyD88-dependent, TLR-mediated IL-6 production following exposure to cytomegalovirus (CMV). IFITM3 also restricts IL-6 production in response to influenza and SARS-CoV-2. In dendritic cells, IFITM3 binds to the reticulon 4 isoform Nogo-B and promotes its proteasomal degradation. We reveal that Nogo-B mediates TLR-dependent pro-inflammatory cytokine production and promotes viral pathogenesis in vivo, and in the case of TLR2 responses, this process involves alteration of TLR2 cellular localization. Nogo-B deletion abrogates inflammatory cytokine responses and associated disease in virus-infected IFITM3-deficient mice. Thus, we uncover Nogo-B as a driver of viral pathogenesis and highlight an immunoregulatory pathway in which IFITM3 fine-tunes the responsiveness of myeloid cells to viral stimulation.
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Affiliation(s)
- M Clement
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - J L Forbester
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - M Marsden
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - P Sabberwal
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - M S Sommerville
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - D Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - S Dimonte
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - S Clare
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - K Harcourt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Z Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - L Nobre
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - R Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - B Jin
- Fourth Military Medical University, Xian, China
| | - M Chen
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - S Makvandi-Nejad
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - J A Lindborg
- Departments of Neurology and Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - S M Strittmatter
- Departments of Neurology and Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - M P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - R J Stanton
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - T Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - I R Humphreys
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, CF14 4XN, UK.
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5
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Peng Y, Felce SL, Dong D, Penkava F, Mentzer AJ, Yao X, Liu G, Yin Z, Chen JL, Lu Y, Wellington D, Wing PAC, Dominey-Foy DCC, Jin C, Wang W, Hamid MA, Fernandes RA, Wang B, Fries A, Zhuang X, Ashley N, Rostron T, Waugh C, Sopp P, Hublitz P, Beveridge R, Tan TK, Dold C, Kwok AJ, Rich-Griffin C, Dejnirattisa W, Liu C, Kurupati P, Nassiri I, Watson RA, Tong O, Taylor CA, Kumar Sharma P, Sun B, Curion F, Revale S, Garner LC, Jansen K, Ferreira RC, Attar M, Fry JW, Russell RA, Stauss HJ, James W, Townsend A, Ho LP, Klenerman P, Mongkolsapaya J, Screaton GR, Dendrou C, Sansom SN, Bashford-Rogers R, Chain B, Smith GL, McKeating JA, Fairfax BP, Bowness P, McMichael AJ, Ogg G, Knight JC, Dong T. An immunodominant NP 105-113-B*07:02 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease. Nat Immunol 2022; 23:50-61. [PMID: 34853448 PMCID: PMC8709787 DOI: 10.1038/s41590-021-01084-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/26/2021] [Indexed: 11/11/2022]
Abstract
NP105-113-B*07:02-specific CD8+ T cell responses are considered among the most dominant in SARS-CoV-2-infected individuals. We found strong association of this response with mild disease. Analysis of NP105-113-B*07:02-specific T cell clones and single-cell sequencing were performed concurrently, with functional avidity and antiviral efficacy assessed using an in vitro SARS-CoV-2 infection system, and were correlated with T cell receptor usage, transcriptome signature and disease severity (acute n = 77, convalescent n = 52). We demonstrated a beneficial association of NP105-113-B*07:02-specific T cells in COVID-19 disease progression, linked with expansion of T cell precursors, high functional avidity and antiviral effector function. Broad immune memory pools were narrowed postinfection but NP105-113-B*07:02-specific T cells were maintained 6 months after infection with preserved antiviral efficacy to the SARS-CoV-2 Victoria strain, as well as Alpha, Beta, Gamma and Delta variants. Our data show that NP105-113-B*07:02-specific T cell responses associate with mild disease and high antiviral efficacy, pointing to inclusion for future vaccine design.
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Affiliation(s)
- Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Danning Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, Urumqi, China
| | - Frank Penkava
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guihai Liu
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ji-Li Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Peter A C Wing
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Delaney C C Dominey-Foy
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chen Jin
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wenbo Wang
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Megat Abd Hamid
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ricardo A Fernandes
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anastasia Fries
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Neil Ashley
- Single Cell Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Timothy Rostron
- Sequencing Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Craig Waugh
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ryan Beveridge
- Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, and NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Andrew J Kwok
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Wanwisa Dejnirattisa
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Prathiba Kurupati
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Isar Nassiri
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert A Watson
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Orion Tong
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chelsea A Taylor
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Piyush Kumar Sharma
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bo Sun
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fabiola Curion
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Helmholtz Center Munich-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Santiago Revale
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lucy C Garner
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kathrin Jansen
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | | | - Moustafa Attar
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | | | - Rebecca A Russell
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Hans J Stauss
- Institute of Immunity and Transplantation, University College London, London, UK
| | - William James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alain Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Ling-Pei Ho
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe 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
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriaj Hospital, Mahidol Unviversity, Bangkok, Thailand
| | - Gavin R Screaton
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Calliope Dendrou
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen N Sansom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | | | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
| | | | - Jane A McKeating
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benjamin P Fairfax
- Department of Oncology, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Andrew J McMichael
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Graham Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | - Julian C Knight
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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6
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de Silva TI, Liu G, Lindsey BB, Dong D, Moore SC, Hsu NS, Shah D, Wellington D, Mentzer AJ, Angyal A, Brown R, Parker MD, Ying Z, Yao X, Turtle L, Dunachie S, Maini MK, Ogg G, Knight JC, Peng Y, Rowland-Jones SL, Dong T. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. iScience 2021; 24:103353. [PMID: 34729465 PMCID: PMC8552693 DOI: 10.1016/j.isci.2021.103353] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 10/28/2022] Open
Abstract
We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.
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Affiliation(s)
- Thushan I. de Silva
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Benjamin B. Lindsey
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
- CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, China
| | - Shona C. Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
| | - Nienyun Sharon Hsu
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
| | - Dhruv Shah
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Dannielle Wellington
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Alexander J. Mentzer
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrienn Angyal
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Rebecca Brown
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Matthew D. Parker
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
- Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield S10 2JF, UK
| | - Zixi Ying
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
- Tropical & Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (Member of Liverpool Health Partners), Liverpool L7 8XP, UK
| | - Susanna Dunachie
- Centre For Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Mala K. Maini
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Graham Ogg
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Julian C. Knight
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Yanchun Peng
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sarah L. Rowland-Jones
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK
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7
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Wellington D, Yin Z, Kessler BM, Dong T. Immunodominance complexity: lessons yet to be learned from dominant T cell responses to SARS-COV-2. Curr Opin Virol 2021; 50:183-191. [PMID: 34534732 PMCID: PMC8424056 DOI: 10.1016/j.coviro.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022]
Abstract
Immunodominance is a complex and highly debated topic of T cell biology. The current SARS-CoV-2 pandemic has provided the opportunity to profile adaptive immune responses and determine molecular factors contributing to emerging responses towards immunodominant viral epitopes. Here, we discuss parameters that alter the dynamics of CD8 viral epitope processing, generation and T-cell responses, and how immunodominance counteracts viral immune escape mechanisms that develop in the context of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Benedikt M Kessler
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Target Discovery Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
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8
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Wellington D, Yin Z, Abdel-Haq A, Zhang L, Forbester J, Kite K, Rajapaksa U, Laurenson-Schafer H, Makvandi-Nejad S, Jin B, Bowes E, Manoharan K, Maldonado-Perez D, Verrill C, Humphreys IR, Dong T. IFITM3-specific antibody reveals IFN preferences and slow IFN induction of the antiviral factor IFITM3 in humans. Eur J Immunol 2021; 51:742-745. [PMID: 33125710 PMCID: PMC7983929 DOI: 10.1002/eji.202048706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/01/2020] [Accepted: 10/22/2020] [Indexed: 01/09/2023]
Abstract
Using a specific antibody, we found that expression of the viral restriction factor IFITM3 differs across cell types within the immune compartment with higher expression in myeloid rather than lymphoid cells. IFITM3 expression was increased following IFN stimulation, mostly type I, in immune cells, with the exception of T cells.
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Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK.,Nuffield Department of Medicine, Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Oxford University, Oxford, UK
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK.,Nuffield Department of Medicine, Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Oxford University, Oxford, UK
| | - Adi Abdel-Haq
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK.,Charles Tanford-Proteinzentrum, Martin-Luther-Universität Halle-Wittenberg, Institut für Molekulare Medizin, Kurt-Mothes-Straße 3a, Halle, Germany
| | - Liwei Zhang
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK
| | - Jessica Forbester
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK.,Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, UK
| | - Kerry Kite
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK
| | - Ushani Rajapaksa
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK
| | - Henry Laurenson-Schafer
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK
| | - Shokouh Makvandi-Nejad
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK
| | - Boquan Jin
- Fourth Military Medical University, Xian, China
| | - Emma Bowes
- Oxford Radcliffe Biobank, Nuffield Department of Surgical Sciences, Oxford University, Oxford, UK
| | - Krishnageetha Manoharan
- Oxford Radcliffe Biobank, Nuffield Department of Surgical Sciences, Oxford University, Oxford, UK
| | - David Maldonado-Perez
- Oxford Radcliffe Biobank, Nuffield Department of Surgical Sciences, Oxford University, Oxford, UK
| | - Clare Verrill
- Oxford Radcliffe Biobank, Nuffield Department of Surgical Sciences, Oxford University, Oxford, UK
| | - Ian R Humphreys
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Cardiff, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK.,Nuffield Department of Medicine, Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Oxford University, Oxford, UK
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9
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Peng Y, Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, López-Camacho C, Slon-Campos J, Zhao Y, Stuart DI, Paesen GC, Grimes JM, Antson AA, Bayfield OW, Hawkins DEDP, Ker DS, Wang B, Turtle L, Subramaniam K, Thomson P, Zhang P, Dold C, Ratcliff J, Simmonds P, de Silva T, Sopp P, Wellington D, Rajapaksa U, Chen YL, Salio M, Napolitani G, Paes W, Borrow P, Kessler BM, Fry JW, Schwabe NF, Semple MG, Baillie JK, Moore SC, Openshaw PJM, Ansari MA, Dunachie S, Barnes E, Frater J, Kerr G, Goulder P, Lockett T, Levin R, Zhang Y, Jing R, Ho LP, Cornall RJ, Conlon CP, Klenerman P, Screaton GR, Mongkolsapaya J, McMichael A, Knight JC, Ogg G, Dong T. Broad and strong memory CD4 + and CD8 + T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat Immunol 2020; 21:1336-1345. [PMID: 32887977 PMCID: PMC7611020 DOI: 10.1038/s41590-020-0782-6] [Citation(s) in RCA: 826] [Impact Index Per Article: 206.5] [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: 06/02/2020] [Accepted: 08/11/2020] [Indexed: 01/08/2023]
Abstract
The development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and therapeutics will depend on understanding viral immunity. We studied T cell memory in 42 patients following recovery from COVID-19 (28 with mild disease and 14 with severe disease) and 16 unexposed donors, using interferon-γ-based assays with peptides spanning SARS-CoV-2 except ORF1. The breadth and magnitude of T cell responses were significantly higher in severe as compared with mild cases. Total and spike-specific T cell responses correlated with spike-specific antibody responses. We identified 41 peptides containing CD4+ and/or CD8+ epitopes, including six immunodominant regions. Six optimized CD8+ epitopes were defined, with peptide-MHC pentamer-positive cells displaying the central and effector memory phenotype. In mild cases, higher proportions of SARS-CoV-2-specific CD8+ T cells were observed. The identification of T cell responses associated with milder disease will support an understanding of protective immunity and highlights the potential of including non-spike proteins within future COVID-19 vaccine design.
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Affiliation(s)
- Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Xuan Yao
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, Xinjiang, China
| | | | - Timothy Rostron
- Sequencing and Flow Cytometry Facility, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - César López-Camacho
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jose Slon-Campos
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yuguang Zhao
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David I Stuart
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Diamond Light Source, Didcot, UK
| | - Guido C Paesen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan M Grimes
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Diamond Light Source, Didcot, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Beibei Wang
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lance Turtle
- Tropical and Infectious Diseases Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Krishanthi Subramaniam
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Paul Thomson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Ping Zhang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thushan de Silva
- The Florey Institute for Host-Pathogen Interactions, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Paul Sopp
- Sequencing and Flow Cytometry Facility, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Ushani Rajapaksa
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yi-Ling Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Wayne Paes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Benedikt M Kessler
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Institute in The Park, Alder Hey Children's Hospital, Liverpool, UK
| | - J Kenneth Baillie
- Anaesthesia, Critical Care and Pain Medicine Division of Health Sciences, University of Edinburgh, Edinburgh, 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
| | - Peter J M Openshaw
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - M Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Georgina Kerr
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip Goulder
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Teresa Lockett
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Yonghong Zhang
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Ronghua Jing
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Ling-Pei Ho
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Richard J Cornall
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christopher P Conlon
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Gavin R Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Dengue Hemorrhagic Fever Research Unit, Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Andrew McMichael
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C Knight
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Graham Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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10
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Peng Y, Mentzer AJ, Liu G, Yao X, Yin Z, Dong D, Dejnirattisai W, Rostron T, Supasa P, Liu C, Lopez-Camacho C, Slon-Campos J, Zhao Y, Stuart D, Paeson G, Grimes J, Antson F, Bayfield OW, Hawkins DE, Ker DS, Turtle L, Subramaniam K, Thomson P, Zhang P, Dold C, Ratcliff J, Simmonds P, de Silva T, Sopp P, Wellington D, Rajapaksa U, Chen YL, Salio M, Napolitani G, Paes W, Borrow P, Kessler B, Fry JW, Schwabe NF, Semple MG, Baillie KJ, Moore S, Openshaw PJ, Ansari A, Dunachie S, Barnes E, Frater J, Kerr G, Goulder P, Lockett T, Levin R, Cornall RJ, Conlon C, Klenerman P, McMichael A, Screaton G, Mongkolsapaya J, Knight JC, Ogg G, Dong T. Broad and strong memory CD4 + and CD8 + T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients. bioRxiv 2020. [PMID: 32577665 DOI: 10.1101/2020.06.05.134551] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
COVID-19 is an ongoing global crisis in which the development of effective vaccines and therapeutics will depend critically on understanding the natural immunity to the virus, including the role of SARS-CoV-2-specific T cells. We have conducted a study of 42 patients following recovery from COVID-19, including 28 mild and 14 severe cases, comparing their T cell responses to those of 16 control donors. We assessed the immune memory of T cell responses using IFNγ based assays with overlapping peptides spanning SARS-CoV-2 apart from ORF1. We found the breadth, magnitude and frequency of memory T cell responses from COVID-19 were significantly higher in severe compared to mild COVID-19 cases, and this effect was most marked in response to spike, membrane, and ORF3a proteins. Total and spike-specific T cell responses correlated with the anti-Spike, anti-Receptor Binding Domain (RBD) as well as anti-Nucleoprotein (NP) endpoint antibody titre (p<0.001, <0.001 and =0.002). We identified 39 separate peptides containing CD4 + and/or CD8 + epitopes, which strikingly included six immunodominant epitope clusters targeted by T cells in many donors, including 3 clusters in spike (recognised by 29%, 24%, 18% donors), two in the membrane protein (M, 32%, 47%) and one in the nucleoprotein (Np, 35%). CD8+ responses were further defined for their HLA restriction, including B*4001-restricted T cells showing central memory and effector memory phenotype. In mild cases, higher frequencies of multi-cytokine producing M- and NP-specific CD8 + T cells than spike-specific CD8 + T cells were observed. They furthermore showed a higher ratio of SARS-CoV-2-specific CD8 + to CD4 + T cell responses. Immunodominant epitope clusters and peptides containing T cell epitopes identified in this study will provide critical tools to study the role of virus-specific T cells in control and resolution of SARS-CoV-2 infections. The identification of T cell specificity and functionality associated with milder disease, highlights the potential importance of including non-spike proteins within future COVID-19 vaccine design.
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11
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Mbiribindi B, Mukherjee S, Wellington D, Das J, Khakoo SI. Corrigendum: Spatial Clustering of Receptors and Signaling Molecules Regulates NK Cell Response to Peptide Repertoire Changes. Front Immunol 2019; 10:2370. [PMID: 31660057 PMCID: PMC6804635 DOI: 10.3389/fimmu.2019.02370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022] Open
Affiliation(s)
- Berenice Mbiribindi
- Department of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sayak Mukherjee
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Dannielle Wellington
- Department of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, Wexner College of Medicine, The Ohio State University, Columbus, OH, United States.,Biophysics Program, The Ohio State University, Columbus, OH, United States
| | - Salim I Khakoo
- Department of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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12
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Mbiribindi B, Mukherjee S, Wellington D, Das J, Khakoo SI. Spatial Clustering of Receptors and Signaling Molecules Regulates NK Cell Response to Peptide Repertoire Changes. Front Immunol 2019; 10:605. [PMID: 31024524 PMCID: PMC6460049 DOI: 10.3389/fimmu.2019.00605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/07/2019] [Indexed: 11/13/2022] Open
Abstract
Natural Killer (NK) cell activation requires integration of inhibitory and activating signaling. Inhibitory signals are determined by members of the killer cell immunoglobulin-like receptor (KIR) family, which have major histocompatibility complex (MHC) class I ligands. Loss of this inhibitory signal leads to NK cell activation. Thus, down-regulation of MHC I during viral infection or cancer induces NK cell activation. However, NK cell activation in the presence of MHC-I has been demonstrated for HLA-C*0102 through changes in its peptide content: "peptide antagonism." Here we identify an antagonist peptide for HLA-C*0304 suggesting that peptide antagonism is a generalizable phenomenon and, using a combination of mathematical modeling, confocal imaging, and immune-assays, we quantitatively determine mechanisms that underlie peptide antagonism in inhibitory KIR2DL2/3 signaling. These data provide a mechanism for NK cell activation based on a reduction of inhibitory signaling in the presence of preserved levels of MHC class I.
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Affiliation(s)
- Berenice Mbiribindi
- Department of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sayak Mukherjee
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Dannielle Wellington
- Department of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, Wexner College of Medicine, The Ohio State University, Columbus, OH, United States.,Biophysics Program, The Ohio State University, Columbus, OH, United States
| | - Salim I Khakoo
- Department of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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Wellington D, Laurenson-Schafer H, Abdel-Haq A, Dong T. IFITM3: How genetics influence influenza infection demographically. Biomed J 2019; 42:19-26. [PMID: 30987701 PMCID: PMC6468115 DOI: 10.1016/j.bj.2019.01.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/06/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022] Open
Abstract
The role of host genetics in influenza infection is unclear despite decades of interest. Confounding factors such as age, sex, ethnicity and environmental factors have made it difficult to assess the role of genetics without influence. In recent years a single nucleotide polymorphism, interferon-induced transmembrane protein 3 (IFITM3) rs12252, has been shown to alter the severity of influenza infection in Asian populations. In this review we investigate this polymorphism as well as several others suggested to alter the host's defence against influenza infection. In addition, we highlight the open questions surrounding the viral restriction protein IFITM3 with the hope that by answering some of these questions we can elucidate the mechanism of IFITM3 viral restriction and therefore how this restriction is altered due to the rs12252 polymorphism.
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Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK.
| | - Henry Laurenson-Schafer
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK
| | - Adi Abdel-Haq
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; Martin-Luther-University, Halle-Wittenberg, Germany
| | - Tao Dong
- MRC Human Immunology Unit, WIMM, University of Oxford, OX3 9DS, UK; CAMS Oxford Institute, Nuffield Department of Medicine, Oxford University, OX3 9FZ, UK.
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14
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Qin L, Wang D, Li D, Zhao Y, Peng Y, Wellington D, Dai Y, Sun H, Sun J, Liu G, McMichael A, Dong T, Zhang Y. High Level Antibody Response to Pandemic Influenza H1N1/09 Virus Is Associated With Interferon-Induced Transmembrane Protein-3 rs12252-CC in Young Adults. Front Cell Infect Microbiol 2018; 8:134. [PMID: 29868492 PMCID: PMC5962690 DOI: 10.3389/fcimb.2018.00134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/18/2018] [Indexed: 01/27/2023] Open
Abstract
Background: The C allele of the interferon-induced transmembrane protein-3 (IFITM3) SNP rs12252, a common allele in South East Asia and China, is strongly associated with severe influenza infection. However, despite the high occurrence of rs12252-CC genotype in Chinese population (~25%), severe influenza infection is rare. The aim of study is to determine whether rs12252-CC individuals have pre-existing antibody responses to previous seasonal influenza infections. Cohort and Method: A total 99 young healthy volunteers (18-20 years) were recruited and received an influenza seasonal Vaccination [A/Switzerland/9715293/2013(H3N2), A/California/7/2009 (pdm09H1N1) and B/Jeep/3073/2013-like virus (Flu-B)]. Plasma and gDNA was isolated from each volunteer before, and 14, 28, 180, 360, and 540 days after vaccination. Additionally, 68 elderlies (>65 years) were also recruited as a control group to compare the levels of antibodies at baseline between the young adults and the elderly. For each sample IFITM3 rs12252 genotype was determined and antibody levels in response to pdmH1N1, H3N2 and Influenza B infection were measured for each time point. Results: We found a significantly higher level of pre-existing antibodies to pandemic influenza H1N1/09 virus (pdm09H1N1) but not to H3N2 or FluB in CC donors in comparison with CT/TT donors prior to vaccination. No impact of IFITM3 genotype in boosting influenza specific antibodies in young adults within 1 year after receiving seasonal influenza vaccination was observed. In addition, there was no difference in pdm09H1N1 specific antibody levels observed in the elderly cohort between volunteers carrying different IFITM3 genotypes. Higher levels of antibodies to pdmH1N1 were observed in elderly CC carriers when compared to the young CC carriers, but this trend was not replicated in TT carriers. Conclusion:IFITM3-rs12252 CC carriers exhibit a high level of pre-existing immunity to pdm09H1N1 compared to TT carriers in the young cohort. This suggests that compensatory mechanisms exist which might contribute to viral control in patients carrying the rs12252-CC genotype who do not become sick after flu infection. However, such a potential compensatory effect appears to be lost overtime, as evidenced in the elderly cohort. If this compensatory mechanism is lost, it may make the CC carrying elderly more susceptible to severe influenza infection.
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Affiliation(s)
- Ling Qin
- Beijing Youan Hospital, Capital Medical University, Beijing, China.,Nuffield Department of Medicine, CAMS-Oxford Center for Translational Immunology, Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Dayan Wang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, China Centre for Disease Control (China CDC), Beijing, China
| | - Dongfu Li
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yan Zhao
- Beijing Youan Hospital, Capital Medical University, Beijing, China.,Nuffield Department of Medicine, CAMS-Oxford Center for Translational Immunology, Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Yanchun Peng
- Nuffield Department of Medicine, CAMS-Oxford Center for Translational Immunology, Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, United Kingdom.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Dannielle Wellington
- Nuffield Department of Medicine, CAMS-Oxford Center for Translational Immunology, Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, United Kingdom.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Yanchao Dai
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Huanqin Sun
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jinping Sun
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Guihai Liu
- Beijing Youan Hospital, Capital Medical University, Beijing, China.,Nuffield Department of Medicine, CAMS-Oxford Center for Translational Immunology, Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, United Kingdom.,Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, China Centre for Disease Control (China CDC), Beijing, China
| | - Andrew McMichael
- Nuffield Department of Medicine, CAMS-Oxford Center for Translational Immunology, Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, United Kingdom.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Tao Dong
- Beijing Youan Hospital, Capital Medical University, Beijing, China.,Nuffield Department of Medicine, CAMS-Oxford Center for Translational Immunology, Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, United Kingdom.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Yonghong Zhang
- Beijing Youan Hospital, Capital Medical University, Beijing, China.,Nuffield Department of Medicine, CAMS-Oxford Center for Translational Immunology, Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, United Kingdom
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15
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Makvandi-Nejad S, Laurenson-Schafer H, Wang L, Wellington D, Zhao Y, Jin B, Qin L, Kite K, Moghadam HK, Song C, Clark K, Hublitz P, Townsend AR, Wu H, McMichael AJ, Zhang Y, Dong T. Lack of Truncated IFITM3 Transcripts in Cells Homozygous for the rs12252-C Variant That is Associated With Severe Influenza Infection. J Infect Dis 2017; 217:257-262. [DOI: 10.1093/infdis/jix512] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/26/2017] [Indexed: 01/19/2023] Open
Affiliation(s)
- Shokouh Makvandi-Nejad
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University
| | - Henry Laurenson-Schafer
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University
| | - LiLi Wang
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University
| | - Dannielle Wellington
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University
| | - Yan Zhao
- Chinese Academy of Medical Sciences-Oxford Center for Translational Immunology, Nuffield Department of Medicine, Oxford University, United Kingdom
- Beijing You’an Hospital, Capital Medical University, Beijing, China
| | - Boquan Jin
- Fourth Military Medical University, Xian, China
| | - Ling Qin
- Chinese Academy of Medical Sciences-Oxford Center for Translational Immunology, Nuffield Department of Medicine, Oxford University, United Kingdom
- Beijing You’an Hospital, Capital Medical University, Beijing, China
| | - Kerry Kite
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University
| | | | | | - Kevin Clark
- Flow Cytometry Facility, Oxford University, United Kingdom
| | - Philip Hublitz
- Genome Engineering Department, Weatherall Institute of Molecular Medicine, Oxford University, United Kingdom
| | - Alain R Townsend
- Chinese Academy of Medical Sciences-Oxford Center for Translational Immunology, Nuffield Department of Medicine, Oxford University, United Kingdom
| | - Hao Wu
- Beijing You’an Hospital, Capital Medical University, Beijing, China
| | - Andrew J McMichael
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University
- Chinese Academy of Medical Sciences-Oxford Center for Translational Immunology, Nuffield Department of Medicine, Oxford University, United Kingdom
| | - YongHong Zhang
- Chinese Academy of Medical Sciences-Oxford Center for Translational Immunology, Nuffield Department of Medicine, Oxford University, United Kingdom
- Beijing You’an Hospital, Capital Medical University, Beijing, China
| | - Tao Dong
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University
- Chinese Academy of Medical Sciences-Oxford Center for Translational Immunology, Nuffield Department of Medicine, Oxford University, United Kingdom
- Beijing You’an Hospital, Capital Medical University, Beijing, China
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16
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Barker R, Ashby EL, Wellington D, Barrow VM, Palmer JC, Kehoe PG, Esiri MM, Love S. Pathophysiology of white matter perfusion in Alzheimer's disease and vascular dementia. ACTA ACUST UNITED AC 2014; 137:1524-32. [PMID: 24618270 PMCID: PMC3999715 DOI: 10.1093/brain/awu040] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The pathophysiology of white matter hypoperfusion is poorly understood. Barker et al. quantify ante-mortem hypoperfusion by measuring myelin proteins differentially susceptible to ischaemia, and assess the extent to which vasoregulatory factors protect from or contribute to ischaemic white matter injury in Alzheimer’s disease and vascular dementia. Little is known about the contributors and physiological responses to white matter hypoperfusion in the human brain. We previously showed the ratio of myelin-associated glycoprotein to proteolipid protein 1 in post-mortem human brain tissue correlates with the degree of ante-mortem ischaemia. In age-matched post-mortem cohorts of Alzheimer’s disease (n = 49), vascular dementia (n = 17) and control brains (n = 33) from the South West Dementia Brain Bank (Bristol), we have now examined the relationship between the ratio of myelin-associated glycoprotein to proteolipid protein 1 and several other proteins involved in regulating white matter vascularity and blood flow. Across the three cohorts, white matter perfusion, indicated by the ratio of myelin-associated glycoprotein to proteolipid protein 1, correlated positively with the concentration of the vasoconstrictor, endothelin 1 (P = 0.0005), and negatively with the concentration of the pro-angiogenic protein, vascular endothelial growth factor (P = 0.0015). The activity of angiotensin-converting enzyme, which catalyses production of the vasoconstrictor angiotensin II was not altered. In samples of frontal white matter from an independent (Oxford, UK) cohort of post-mortem brains (n = 74), we confirmed the significant correlations between the ratio of myelin-associated glycoprotein to proteolipid protein 1 and both endothelin 1 and vascular endothelial growth factor. We also assessed microvessel density in the Bristol (UK) samples, by measurement of factor VIII-related antigen, which we showed to correlate with immunohistochemical measurements of vessel density, and found factor VIII-related antigen levels to correlate with the level of vascular endothelial growth factor (P = 0.0487), suggesting that upregulation of vascular endothelial growth factor tends to increase vessel density in the white matter. We propose that downregulation of endothelin 1 and upregulation of vascular endothelial growth factor in the context of reduced ratio of myelin-associated glycoprotein to proteolipid protein 1 are likely to be protective physiological responses to reduced white matter perfusion. Further analysis of the Bristol cohort showed that endothelin 1 was reduced in the white matter in Alzheimer’s disease (P < 0.05) compared with control subjects, but not in vascular dementia, in which endothelin 1 tended to be elevated, perhaps reflecting abnormal regulation of white matter perfusion in vascular dementia. Our findings demonstrate the potential of post-mortem measurement of myelin proteins and mediators of vascular function, to assess physiological and pathological processes involved in the regulation of cerebral perfusion in Alzheimer’s disease and vascular dementia.
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Affiliation(s)
- Rachel Barker
- 1 Dementia Research Group, Institute of Clinical Neurosciences, School of Clinical Sciences, University of Bristol, Bristol, UK
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17
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Grotzinger JP, Sumner DY, Kah LC, Stack K, Gupta S, Edgar L, Rubin D, Lewis K, Schieber J, Mangold N, Milliken R, Conrad PG, DesMarais D, Farmer J, Siebach K, Calef F, Hurowitz J, McLennan SM, Ming D, Vaniman D, Crisp J, Vasavada A, Edgett KS, Malin M, Blake D, Gellert R, Mahaffy P, Wiens RC, Maurice S, Grant JA, Wilson S, Anderson RC, Beegle L, Arvidson R, Hallet B, Sletten RS, Rice M, Bell J, Griffes J, Ehlmann B, Anderson RB, Bristow TF, Dietrich WE, Dromart G, Eigenbrode J, Fraeman A, Hardgrove C, Herkenhoff K, Jandura L, Kocurek G, Lee S, Leshin LA, Leveille R, Limonadi D, Maki J, McCloskey S, Meyer M, Minitti M, Newsom H, Oehler D, Okon A, Palucis M, Parker T, Rowland S, Schmidt M, Squyres S, Steele A, Stolper E, Summons R, Treiman A, Williams R, Yingst A, Team MS, Kemppinen O, Bridges N, Johnson JR, Cremers D, Godber A, Wadhwa M, Wellington D, McEwan I, Newman C, Richardson M, Charpentier A, Peret L, King P, Blank J, Weigle G, Li S, Robertson K, Sun V, Baker M, Edwards C, Farley K, Miller H, Newcombe M, Pilorget C, Brunet C, Hipkin V, Leveille R, Marchand G, Sanchez PS, Favot L, Cody G, Fluckiger L, Lees D, Nefian A, Martin M, Gailhanou M, Westall F, Israel G, Agard C, Baroukh J, Donny C, Gaboriaud A, Guillemot P, Lafaille V, Lorigny E, Paillet A, Perez R, Saccoccio M, Yana C, Armiens-Aparicio C, Rodriguez JC, Blazquez IC, Gomez FG, Gomez-Elvira J, Hettrich S, Malvitte AL, Jimenez MM, Martinez-Frias J, Martin-Soler J, Martin-Torres FJ, Jurado AM, Mora-Sotomayor L, Caro GM, Lopez SN, Peinado-Gonzalez V, Pla-Garcia J, Manfredi JAR, Romeral-Planello JJ, Fuentes SAS, Martinez ES, Redondo JT, Urqui-O'Callaghan R, Mier MPZ, Chipera S, Lacour JL, Mauchien P, Sirven JB, Manning H, Fairen A, Hayes A, Joseph J, Sullivan R, Thomas P, Dupont A, Lundberg A, Melikechi N, Mezzacappa A, DeMarines J, Grinspoon D, Reitz G, Prats B, Atlaskin E, Genzer M, Harri AM, Haukka H, Kahanpaa H, Kauhanen J, Paton M, Polkko J, Schmidt W, Siili T, Fabre C, Wray J, Wilhelm MB, Poitrasson F, Patel K, Gorevan S, Indyk S, Paulsen G, Bish D, Gondet B, Langevin Y, Geffroy C, Baratoux D, Berger G, Cros A, d'Uston C, Forni O, Gasnault O, Lasue J, Lee QM, Meslin PY, Pallier E, Parot Y, Pinet P, Schroder S, Toplis M, Lewin E, Brunner W, Heydari E, Achilles C, Sutter B, Cabane M, Coscia D, Szopa C, Robert F, Sautter V, Le Mouelic S, Nachon M, Buch A, Stalport F, Coll P, Francois P, Raulin F, Teinturier S, Cameron J, Clegg S, Cousin A, DeLapp D, Dingler R, Jackson RS, Johnstone S, Lanza N, Little C, Nelson T, Williams RB, Jones A, Kirkland L, Baker B, Cantor B, Caplinger M, Davis S, Duston B, Fay D, Harker D, Herrera P, Jensen E, Kennedy MR, Krezoski G, Krysak D, Lipkaman L, McCartney E, McNair S, Nixon B, Posiolova L, Ravine M, Salamon A, Saper L, Stoiber K, Supulver K, Van Beek J, Van Beek T, Zimdar R, French KL, Iagnemma K, Miller K, Goesmann F, Goetz W, Hviid S, Johnson M, Lefavor M, Lyness E, Breves E, Dyar MD, Fassett C, Edwards L, Haberle R, Hoehler T, Hollingsworth J, Kahre M, Keely L, McKay C, Bleacher L, Brinckerhoff W, Choi D, Dworkin JP, Floyd M, Freissinet C, Garvin J, Glavin D, Harpold D, Martin DK, McAdam A, Pavlov A, Raaen E, Smith MD, Stern J, Tan F, Trainer M, Posner A, Voytek M, Aubrey A, Behar A, Blaney D, Brinza D, Christensen L, DeFlores L, Feldman J, Feldman S, Flesch G, Jun I, Keymeulen D, Mischna M, Morookian JM, Pavri B, Schoppers M, Sengstacken A, Simmonds JJ, Spanovich N, Juarez MDLT, Webster CR, Yen A, Archer PD, Cucinotta F, Jones JH, Morris RV, Niles P, Rampe E, Nolan T, Fisk M, Radziemski L, Barraclough B, Bender S, Berman D, Dobrea EN, Tokar R, Cleghorn T, Huntress W, Manhes G, Hudgins J, Olson T, Stewart N, Sarrazin P, Vicenzi E, Bullock M, Ehresmann B, Hamilton V, Hassler D, Peterson J, Rafkin S, Zeitlin C, Fedosov F, Golovin D, Karpushkina N, Kozyrev A, Litvak M, Malakhov A, Mitrofanov I, Mokrousov M, Nikiforov S, Prokhorov V, Sanin A, Tretyakov V, Varenikov A, Vostrukhin A, Kuzmin R, Clark B, Wolff M, Botta O, Drake D, Bean K, Lemmon M, Schwenzer SP, Lee EM, Sucharski R, Hernandez MADP, Avalos JJB, Ramos M, Kim MH, Malespin C, Plante I, Muller JP, Navarro-Gonzalez R, Ewing R, Boynton W, Downs R, Fitzgibbon M, Harshman K, Morrison S, Kortmann O, Williams A, Lugmair G, Wilson MA, Jakosky B, Balic-Zunic T, Frydenvang J, Jensen JK, Kinch K, Koefoed A, Madsen MB, Stipp SLS, Boyd N, Campbell JL, Perrett G, Pradler I, VanBommel S, Jacob S, Owen T, Savijarvi H, Boehm E, Bottcher S, Burmeister S, Guo J, Kohler J, Garcia CM, Mueller-Mellin R, Wimmer-Schweingruber R, Bridges JC, McConnochie T, Benna M, Franz H, Bower H, Brunner A, Blau H, Boucher T, Carmosino M, Atreya S, Elliott H, Halleaux D, Renno N, Wong M, Pepin R, Elliott B, Spray J, Thompson L, Gordon S, Ollila A, Williams J, Vasconcelos P, Bentz J, Nealson K, Popa R, Moersch J, Tate C, Day M, Francis R, McCullough E, Cloutis E, ten Kate IL, Scholes D, Slavney S, Stein T, Ward J, Berger J, Moores JE. A Habitable Fluvio-Lacustrine Environment at Yellowknife Bay, Gale Crater, Mars. Science 2013; 343:1242777. [DOI: 10.1126/science.1242777] [Citation(s) in RCA: 578] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Vaniman DT, Bish DL, Ming DW, Bristow TF, Morris RV, Blake DF, Chipera SJ, Morrison SM, Treiman AH, Rampe EB, Rice M, Achilles CN, Grotzinger JP, McLennan SM, Williams J, Bell JF, Newsom HE, Downs RT, Maurice S, Sarrazin P, Yen AS, Morookian JM, Farmer JD, Stack K, Milliken RE, Ehlmann BL, Sumner DY, Berger G, Crisp JA, Hurowitz JA, Anderson R, Des Marais DJ, Stolper EM, Edgett KS, Gupta S, Spanovich N, Agard C, Alves Verdasca JA, Anderson R, Archer D, Armiens-Aparicio C, Arvidson R, Atlaskin E, Atreya S, Aubrey A, Baker B, Baker M, Balic-Zunic T, Baratoux D, Baroukh J, Barraclough B, Bean K, Beegle L, Behar A, Bender S, Benna M, Bentz J, Berger J, Berman D, Blanco Avalos JJ, Blaney D, Blank J, Blau H, Bleacher L, Boehm E, Botta O, Bottcher S, Boucher T, Bower H, Boyd N, Boynton B, Breves E, Bridges J, Bridges N, Brinckerhoff W, Brinza D, Brunet C, Brunner A, Brunner W, Buch A, Bullock M, Burmeister S, Cabane M, Calef F, Cameron J, Campbell JI, Cantor B, Caplinger M, Caride Rodriguez J, Carmosino M, Carrasco Blazquez I, Charpentier A, Choi D, Clark B, Clegg S, Cleghorn T, Cloutis E, Cody G, Coll P, Conrad P, Coscia D, Cousin A, Cremers D, Cros A, Cucinotta F, d'Uston C, Davis S, Day MK, de la Torre Juarez M, DeFlores L, DeLapp D, DeMarines J, Dietrich W, Dingler R, Donny C, Drake D, Dromart G, Dupont A, Duston B, Dworkin J, Dyar MD, Edgar L, Edwards C, Edwards L, Ehresmann B, Eigenbrode J, Elliott B, Elliott H, Ewing R, Fabre C, Fairen A, Farley K, Fassett C, Favot L, Fay D, Fedosov F, Feldman J, Feldman S, Fisk M, Fitzgibbon M, Flesch G, Floyd M, Fluckiger L, Forni O, Fraeman A, Francis R, Francois P, Franz H, Freissinet C, French KL, Frydenvang J, Gaboriaud A, Gailhanou M, Garvin J, Gasnault O, Geffroy C, Gellert R, Genzer M, Glavin D, Godber A, Goesmann F, Goetz W, Golovin D, Gomez Gomez F, Gomez-Elvira J, Gondet B, Gordon S, Gorevan S, Grant J, Griffes J, Grinspoon D, Guillemot P, Guo J, Guzewich S, Haberle R, Halleaux D, Hallet B, Hamilton V, Hardgrove C, Harker D, Harpold D, Harri AM, Harshman K, Hassler D, Haukka H, Hayes A, Herkenhoff K, Herrera P, Hettrich S, Heydari E, Hipkin V, Hoehler T, Hollingsworth J, Hudgins J, Huntress W, Hviid S, Iagnemma K, Indyk S, Israel G, Jackson R, Jacob S, Jakosky B, Jensen E, Jensen JK, Johnson J, Johnson M, Johnstone S, Jones A, Jones J, Joseph J, Jun I, Kah L, Kahanpaa H, Kahre M, Karpushkina N, Kasprzak W, Kauhanen J, Keely L, Kemppinen O, Keymeulen D, Kim MH, Kinch K, King P, Kirkland L, Kocurek G, Koefoed A, Kohler J, Kortmann O, Kozyrev A, Krezoski J, Krysak D, Kuzmin R, Lacour JL, Lafaille V, Langevin Y, Lanza N, Lasue J, Le Mouelic S, Lee EM, Lee QM, Lees D, Lefavor M, Lemmon M, Malvitte AL, Leshin L, Leveille R, Lewin-Carpintier E, Lewis K, Li S, Lipkaman L, Little C, Litvak M, Lorigny E, Lugmair G, Lundberg A, Lyness E, Madsen M, Mahaffy P, Maki J, Malakhov A, Malespin C, Malin M, Mangold N, Manhes G, Manning H, Marchand G, Marin Jimenez M, Martin Garcia C, Martin D, Martin M, Martinez-Frias J, Martin-Soler J, Martin-Torres FJ, Mauchien P, McAdam A, McCartney E, McConnochie T, McCullough E, McEwan I, McKay C, McNair S, Melikechi N, Meslin PY, Meyer M, Mezzacappa A, Miller H, Miller K, Minitti M, Mischna M, Mitrofanov I, Moersch J, Mokrousov M, Molina Jurado A, Moores J, Mora-Sotomayor L, Mueller-Mellin R, Muller JP, Munoz Caro G, Nachon M, Navarro Lopez S, Navarro-Gonzalez R, Nealson K, Nefian A, Nelson T, Newcombe M, Newman C, Nikiforov S, Niles P, Nixon B, Noe Dobrea E, Nolan T, Oehler D, Ollila A, Olson T, Owen T, de Pablo Hernandez MA, Paillet A, Pallier E, Palucis M, Parker T, Parot Y, Patel K, Paton M, Paulsen G, Pavlov A, Pavri B, Peinado-Gonzalez V, Pepin R, Peret L, Perez R, Perrett G, Peterson J, Pilorget C, Pinet P, Pla-Garcia J, Plante I, Poitrasson F, Polkko J, Popa R, Posiolova L, Posner A, Pradler I, Prats B, Prokhorov V, Purdy SW, Raaen E, Radziemski L, Rafkin S, Ramos M, Raulin F, Ravine M, Reitz G, Renno N, Richardson M, Robert F, Robertson K, Rodriguez Manfredi JA, Romeral-Planello JJ, Rowland S, Rubin D, Saccoccio M, Salamon A, Sandoval J, Sanin A, Sans Fuentes SA, Saper L, Sautter V, Savijarvi H, Schieber J, Schmidt M, Schmidt W, Scholes DD, Schoppers M, Schroder S, Schwenzer S, Sebastian Martinez E, Sengstacken A, Shterts R, Siebach K, Siili T, Simmonds J, Sirven JB, Slavney S, Sletten R, Smith M, Sobron Sanchez P, Spray J, Squyres S, Stalport F, Steele A, Stein T, Stern J, Stewart N, Stipp SLS, Stoiber K, Sucharski B, Sullivan R, Summons R, Sun V, Supulver K, Sutter B, Szopa C, Tan F, Tate C, Teinturier S, ten Kate I, Thomas P, Thompson L, Tokar R, Toplis M, Torres Redondo J, Trainer M, Tretyakov V, Urqui-O'Callaghan R, Van Beek J, Van Beek T, VanBommel S, Varenikov A, Vasavada A, Vasconcelos P, Vicenzi E, Vostrukhin A, Voytek M, Wadhwa M, Ward J, Webster C, Weigle E, Wellington D, Westall F, Wiens RC, Wilhelm MB, Williams A, Williams R, Williams RBM, Wilson M, Wimmer-Schweingruber R, Wolff M, Wong M, Wray J, Wu M, Yana C, Yingst A, Zeitlin C, Zimdar R, Zorzano Mier MP. Mineralogy of a Mudstone at Yellowknife Bay, Gale Crater, Mars. Science 2013; 343:1243480. [DOI: 10.1126/science.1243480] [Citation(s) in RCA: 433] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Leshin LA, Mahaffy PR, Webster CR, Cabane M, Coll P, Conrad PG, Archer PD, Atreya SK, Brunner AE, Buch A, Eigenbrode JL, Flesch GJ, Franz HB, Freissinet C, Glavin DP, McAdam AC, Miller KE, Ming DW, Morris RV, Navarro-Gonzalez R, Niles PB, Owen T, Pepin RO, Squyres S, Steele A, Stern JC, Summons RE, Sumner DY, Sutter B, Szopa C, Teinturier S, Trainer MG, Wray JJ, Grotzinger JP, Kemppinen O, Bridges N, Johnson JR, Minitti M, Cremers D, Bell JF, Edgar L, Farmer J, Godber A, Wadhwa M, Wellington D, McEwan I, Newman C, Richardson M, Charpentier A, Peret L, King P, Blank J, Weigle G, Schmidt M, Li S, Milliken R, Robertson K, Sun V, Baker M, Edwards C, Ehlmann B, Farley K, Griffes J, Miller H, Newcombe M, Pilorget C, Rice M, Siebach K, Stack K, Stolper E, Brunet C, Hipkin V, Leveille R, Marchand G, Sanchez PS, Favot L, Cody G, Fluckiger L, Lees D, Nefian A, Martin M, Gailhanou M, Westall F, Israel G, Agard C, Baroukh J, Donny C, Gaboriaud A, Guillemot P, Lafaille V, Lorigny E, Paillet A, Perez R, Saccoccio M, Yana C, Armiens-Aparicio C, Rodriguez JC, Blazquez IC, Gomez FG, Gomez-Elvira J, Hettrich S, Malvitte AL, Jimenez MM, Martinez-Frias J, Martin-Soler J, Martin-Torres FJ, Jurado AM, Mora-Sotomayor L, Caro GM, Lopez SN, Peinado-Gonzalez V, Pla-Garcia J, Manfredi JAR, Romeral-Planello JJ, Fuentes SAS, Martinez ES, Redondo JT, Urqui-O'Callaghan R, Mier MPZ, Chipera S, Lacour JL, Mauchien P, Sirven JB, Manning H, Fairen A, Hayes A, Joseph J, Sullivan R, Thomas P, Dupont A, Lundberg A, Melikechi N, Mezzacappa A, DeMarines J, Grinspoon D, Reitz G, Prats B, Atlaskin E, Genzer M, Harri AM, Haukka H, Kahanpaa H, Kauhanen J, Kemppinen O, Paton M, Polkko J, Schmidt W, Siili T, Fabre C, Wilhelm MB, Poitrasson F, Patel K, Gorevan S, Indyk S, Paulsen G, Gupta S, Bish D, Schieber J, Gondet B, Langevin Y, Geffroy C, Baratoux D, Berger G, Cros A, d'Uston C, Forni O, Gasnault O, Lasue J, Lee QM, Maurice S, Meslin PY, Pallier E, Parot Y, Pinet P, Schroder S, Toplis M, Lewin E, Brunner W, Heydari E, Achilles C, Oehler D, Coscia D, Israel G, Dromart G, Robert F, Sautter V, Le Mouelic S, Mangold N, Nachon M, Stalport F, Francois P, Raulin F, Cameron J, Clegg S, Cousin A, DeLapp D, Dingler R, Jackson RS, Johnstone S, Lanza N, Little C, Nelson T, Wiens RC, Williams RB, Jones A, Kirkland L, Treiman A, Baker B, Cantor B, Caplinger M, Davis S, Duston B, Edgett K, Fay D, Hardgrove C, Harker D, Herrera P, Jensen E, Kennedy MR, Krezoski G, Krysak D, Lipkaman L, Malin M, McCartney E, McNair S, Nixon B, Posiolova L, Ravine M, Salamon A, Saper L, Stoiber K, Supulver K, Van Beek J, Van Beek T, Zimdar R, French KL, Iagnemma K, Goesmann F, Goetz W, Hviid S, Johnson M, Lefavor M, Lyness E, Breves E, Dyar MD, Fassett C, Blake DF, Bristow T, DesMarais D, Edwards L, Haberle R, Hoehler T, Hollingsworth J, Kahre M, Keely L, McKay C, Wilhelm MB, Bleacher L, Brinckerhoff W, Choi D, Dworkin JP, Floyd M, Garvin J, Harpold D, Jones A, Martin DK, Pavlov A, Raaen E, Smith MD, Tan F, Meyer M, Posner A, Voytek M, Anderson RC, Aubrey A, Beegle LW, Behar A, Blaney D, Brinza D, Calef F, Christensen L, Crisp JA, DeFlores L, Ehlmann B, Feldman J, Feldman S, Hurowitz J, Jun I, Keymeulen D, Maki J, Mischna M, Morookian JM, Parker T, Pavri B, Schoppers M, Sengstacken A, Simmonds JJ, Spanovich N, Juarez MDLT, Vasavada AR, Yen A, Cucinotta F, Jones JH, Rampe E, Nolan T, Fisk M, Radziemski L, Barraclough B, Bender S, Berman D, Dobrea EN, Tokar R, Vaniman D, Williams RME, Yingst A, Lewis K, Cleghorn T, Huntress W, Manhes G, Hudgins J, Olson T, Stewart N, Sarrazin P, Grant J, Vicenzi E, Wilson SA, Bullock M, Ehresmann B, Hamilton V, Hassler D, Peterson J, Rafkin S, Zeitlin C, Fedosov F, Golovin D, Karpushkina N, Kozyrev A, Litvak M, Malakhov A, Mitrofanov I, Mokrousov M, Nikiforov S, Prokhorov V, Sanin A, Tretyakov V, Varenikov A, Vostrukhin A, Kuzmin R, Clark B, Wolff M, McLennan S, Botta O, Drake D, Bean K, Lemmon M, Schwenzer SP, Anderson RB, Herkenhoff K, Lee EM, Sucharski R, Hernandez MADP, Avalos JJB, Ramos M, Kim MH, Malespin C, Plante I, Muller JP, Ewing R, Boynton W, Downs R, Fitzgibbon M, Harshman K, Morrison S, Dietrich W, Kortmann O, Palucis M, Williams A, Lugmair G, Wilson MA, Rubin D, Jakosky B, Balic-Zunic T, Frydenvang J, Jensen JK, Kinch K, Koefoed A, Madsen MB, Stipp SLS, Boyd N, Campbell JL, Gellert R, Perrett G, Pradler I, VanBommel S, Jacob S, Rowland S, Atlaskin E, Savijarvi H, Boehm E, Bottcher S, Burmeister S, Guo J, Kohler J, Garcia CM, Mueller-Mellin R, Wimmer-Schweingruber R, Bridges JC, McConnochie T, Benna M, Bower H, Blau H, Boucher T, Carmosino M, Elliott H, Halleaux D, Renno N, Wong M, Elliott B, Spray J, Thompson L, Gordon S, Newsom H, Ollila A, Williams J, Vasconcelos P, Bentz J, Nealson K, Popa R, Kah LC, Moersch J, Tate C, Day M, Kocurek G, Hallet B, Sletten R, Francis R, McCullough E, Cloutis E, ten Kate IL, Kuzmin R, Arvidson R, Fraeman A, Scholes D, Slavney S, Stein T, Ward J, Berger J, Moores JE. Volatile, Isotope, and Organic Analysis of Martian Fines with the Mars Curiosity Rover. Science 2013; 341:1238937. [DOI: 10.1126/science.1238937] [Citation(s) in RCA: 327] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Mahaffy PR, Webster CR, Atreya SK, Franz H, Wong M, Conrad PG, Harpold D, Jones JJ, Leshin LA, Manning H, Owen T, Pepin RO, Squyres S, Trainer M, Kemppinen O, Bridges N, Johnson JR, Minitti M, Cremers D, Bell JF, Edgar L, Farmer J, Godber A, Wadhwa M, Wellington D, McEwan I, Newman C, Richardson M, Charpentier A, Peret L, King P, Blank J, Weigle G, Schmidt M, Li S, Milliken R, Robertson K, Sun V, Baker M, Edwards C, Ehlmann B, Farley K, Griffes J, Grotzinger J, Miller H, Newcombe M, Pilorget C, Rice M, Siebach K, Stack K, Stolper E, Brunet C, Hipkin V, Leveille R, Marchand G, Sanchez PS, Favot L, Cody G, Steele A, Fluckiger L, Lees D, Nefian A, Martin M, Gailhanou M, Westall F, Israel G, Agard C, Baroukh J, Donny C, Gaboriaud A, Guillemot P, Lafaille V, Lorigny E, Paillet A, Perez R, Saccoccio M, Yana C, Armiens-Aparicio C, Rodriguez JC, Blazquez IC, Gomez FG, Gomez-Elvira J, Hettrich S, Malvitte AL, Jimenez MM, Martinez-Frias J, Martin-Soler J, Martin-Torres FJ, Jurado AM, Mora-Sotomayor L, Caro GM, Lopez SN, Peinado-Gonzalez V, Pla-Garcia J, Manfredi JAR, Romeral-Planello JJ, Fuentes SAS, Martinez ES, Redondo JT, Urqui-O'Callaghan R, Mier MPZ, Chipera S, Lacour JL, Mauchien P, Sirven JB, Fairen A, Hayes A, Joseph J, Sullivan R, Thomas P, Dupont A, Lundberg A, Melikechi N, Mezzacappa A, DeMarines J, Grinspoon D, Reitz G, Prats B, Atlaskin E, Genzer M, Harri AM, Haukka H, Kahanpaa H, Kauhanen J, Kemppinen O, Paton M, Polkko J, Schmidt W, Siili T, Fabre C, Wray J, Wilhelm MB, Poitrasson F, Patel K, Gorevan S, Indyk S, Paulsen G, Gupta S, Bish D, Schieber J, Gondet B, Langevin Y, Geffroy C, Baratoux D, Berger G, Cros A, d'Uston C, Forni O, Gasnault O, Lasue J, Lee QM, Maurice S, Meslin PY, Pallier E, Parot Y, Pinet P, Schroder S, Toplis M, Lewin E, Brunner W, Heydari E, Achilles C, Oehler D, Sutter B, Cabane M, Coscia D, Israel G, Szopa C, Dromart G, Robert F, Sautter V, Le Mouelic S, Mangold N, Nachon M, Buch A, Stalport F, Coll P, Francois P, Raulin F, Teinturier S, Cameron J, Clegg S, Cousin A, DeLapp D, Dingler R, Jackson RS, Johnstone S, Lanza N, Little C, Nelson T, Wiens RC, Williams RB, Jones A, Kirkland L, Treiman A, Baker B, Cantor B, Caplinger M, Davis S, Duston B, Edgett K, Fay D, Hardgrove C, Harker D, Herrera P, Jensen E, Kennedy MR, Krezoski G, Krysak D, Lipkaman L, Malin M, McCartney E, McNair S, Nixon B, Posiolova L, Ravine M, Salamon A, Saper L, Stoiber K, Supulver K, Van Beek J, Van Beek T, Zimdar R, French KL, Iagnemma K, Miller K, Summons R, Goesmann F, Goetz W, Hviid S, Johnson M, Lefavor M, Lyness E, Breves E, Dyar MD, Fassett C, Blake DF, Bristow T, DesMarais D, Edwards L, Haberle R, Hoehler T, Hollingsworth J, Kahre M, Keely L, McKay C, Wilhelm MB, Bleacher L, Brinckerhoff W, Choi D, Dworkin JP, Eigenbrode J, Floyd M, Freissinet C, Garvin J, Glavin D, Jones A, Martin DK, McAdam A, Pavlov A, Raaen E, Smith MD, Stern J, Tan F, Meyer M, Posner A, Voytek M, Anderson RC, Aubrey A, Beegle LW, Behar A, Blaney D, Brinza D, Calef F, Christensen L, Crisp JA, DeFlores L, Ehlmann B, Feldman J, Feldman S, Flesch G, Hurowitz J, Jun I, Keymeulen D, Maki J, Mischna M, Morookian JM, Parker T, Pavri B, Schoppers M, Sengstacken A, Simmonds JJ, Spanovich N, Juarez MDLT, Vasavada AR, Yen A, Archer PD, Cucinotta F, Ming D, Morris RV, Niles P, Rampe E, Nolan T, Fisk M, Radziemski L, Barraclough B, Bender S, Berman D, Dobrea EN, Tokar R, Vaniman D, Williams RME, Yingst A, Lewis K, Cleghorn T, Huntress W, Manhes G, Hudgins J, Olson T, Stewart N, Sarrazin P, Grant J, Vicenzi E, Wilson SA, Bullock M, Ehresmann B, Hamilton V, Hassler D, Peterson J, Rafkin S, Zeitlin C, Fedosov F, Golovin D, Karpushkina N, Kozyrev A, Litvak M, Malakhov A, Mitrofanov I, Mokrousov M, Nikiforov S, Prokhorov V, Sanin A, Tretyakov V, Varenikov A, Vostrukhin A, Kuzmin R, Clark B, Wolff M, McLennan S, Botta O, Drake D, Bean K, Lemmon M, Schwenzer SP, Anderson RB, Herkenhoff K, Lee EM, Sucharski R, Hernandez MADP, Avalos JJB, Ramos M, Kim MH, Malespin C, Plante I, Muller JP, Navarro-Gonzalez R, Ewing R, Boynton W, Downs R, Fitzgibbon M, Harshman K, Morrison S, Dietrich W, Kortmann O, Palucis M, Sumner DY, Williams A, Lugmair G, Wilson MA, Rubin D, Jakosky B, Balic-Zunic T, Frydenvang J, Jensen JK, Kinch K, Koefoed A, Madsen MB, Stipp SLS, Boyd N, Campbell JL, Gellert R, Perrett G, Pradler I, VanBommel S, Jacob S, Rowland S, Atlaskin E, Savijarvi H, Boehm E, Bottcher S, Burmeister S, Guo J, Kohler J, Garcia CM, Mueller-Mellin R, Wimmer-Schweingruber R, Bridges JC, McConnochie T, Benna M, Bower H, Brunner A, Blau H, Boucher T, Carmosino M, Elliott H, Halleaux D, Renno N, Elliott B, Spray J, Thompson L, Gordon S, Newsom H, Ollila A, Williams J, Vasconcelos P, Bentz J, Nealson K, Popa R, Kah LC, Moersch J, Tate C, Day M, Kocurek G, Hallet B, Sletten R, Francis R, McCullough E, Cloutis E, ten Kate IL, Kuzmin R, Arvidson R, Fraeman A, Scholes D, Slavney S, Stein T, Ward J, Berger J, Moores JE. Abundance and Isotopic Composition of Gases in the Martian Atmosphere from the Curiosity Rover. Science 2013; 341:263-6. [PMID: 23869014 DOI: 10.1126/science.1237966] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Barker R, Wellington D, Esiri MM, Love S. Assessing white matter ischemic damage in dementia patients by measurement of myelin proteins. J Cereb Blood Flow Metab 2013; 33:1050-7. [PMID: 23532085 PMCID: PMC3705431 DOI: 10.1038/jcbfm.2013.46] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/11/2013] [Accepted: 03/04/2013] [Indexed: 11/09/2022]
Abstract
White matter ischemia is difficult to quantify histologically. Myelin-associated glycoprotein (MAG) is highly susceptible to ischemia, being expressed only adaxonally, far from the oligodendrocyte cell body. Myelin-basic protein (MBP) and proteolipid protein (PLP) are expressed throughout the myelin sheath. We compared MAG, MBP, and PLP levels in parietal white matter homogenates from 17 vascular dementia (VaD), 49 Alzheimer's disease (AD), and 33 control brains, after assessing the post-mortem stability of these proteins. Small vessel disease (SVD) and cerebral amyloid angiopathy (CAA) severity had been assessed in paraffin sections. The concentration of MAG remained stable post-mortem, declined with increasing SVD, and was significantly lower in VaD than controls. The concentration of MBP fell progressively post-mortem, limiting its diagnostic utility in this context. Proteolipid protein was stable post-mortem and increased significantly with SVD severity. The MAG/PLP ratio declined significantly with SVD and CAA severity. The MAG and PLP levels and MAG/PLP did not differ significantly between AD and control brains. We validated the utility of MAG and MAG/PLP measurements on analysis of 74 frontal white matter samples from an Oxford cohort in which SVD had previously been scored. MAG concentration and the MAG/PLP ratio are useful post-mortem measures of ante-mortem white matter ischemia.
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Affiliation(s)
- Rachel Barker
- Dementia Research Group, Institute of Clinical Neurosciences, School of Clinical Sciences, University of Bristol, Bristol, UK
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