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Brackenridge S, John N, Früh K, Borrow P, McMichael AJ. The antibodies 3D12 and 4D12 recognise distinct epitopes and conformations of HLA-E. Front Immunol 2024; 15:1329032. [PMID: 38571959 PMCID: PMC10987726 DOI: 10.3389/fimmu.2024.1329032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
The commonly used antibodies 3D12 and 4D12 recognise the human leukocyte antigen E (HLA-E) protein. These antibodies bind distinct epitopes on HLA-E and differ in their ability to bind alleles of the major histocompatibility complex E (MHC-E) proteins of rhesus and cynomolgus macaques. We confirmed that neither antibody cross-reacts with classical HLA alleles, and used hybrids of different MHC-E alleles to map the regions that are critical for their binding. 3D12 recognises a region on the alpha 3 domain, with its specificity for HLA-E resulting from the amino acids present at three key positions (219, 223 and 224) that are unique to HLA-E, while 4D12 binds to the start of the alpha 2 domain, adjacent to the C terminus of the presented peptide. 3D12 staining is increased by incubation of cells at 27°C, and by addition of the canonical signal sequence peptide presented by HLA-E peptide (VL9, VMAPRTLVL). This suggests that 3D12 may bind peptide-free forms of HLA-E, which would be expected to accumulate at the cell surface when cells are incubated at lower temperatures, as well as HLA-E with peptide. Therefore, additional studies are required to determine exactly what forms of HLA-E can be recognised by 3D12. In contrast, while staining with 4D12 was also increased when cells were incubated at 27°C, it was decreased when the VL9 peptide was added. We conclude that 4D12 preferentially binds to peptide-free HLA-E, and, although not suitable for measuring the total cell surface levels of MHC-E, may putatively identify peptide-receptive forms.
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Affiliation(s)
- Simon Brackenridge
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nessy John
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Klaus Früh
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Persephone Borrow
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J. McMichael
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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2
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Huisman BD, Guan N, Rückert T, Garner L, Singh NK, McMichael AJ, Gillespie GM, Romagnani C, Birnbaum ME. Publisher Correction: High-throughput characterization of HLA-E-presented CD94/NKG2x ligands reveals peptides which modulate NK cell activation. Nat Commun 2023; 14:5264. [PMID: 37644057 PMCID: PMC10465582 DOI: 10.1038/s41467-023-40946-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Affiliation(s)
- Brooke D Huisman
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Ning Guan
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Timo Rückert
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
| | - Lee Garner
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nishant K Singh
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Andrew J McMichael
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chiara Romagnani
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael E Birnbaum
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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3
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Huisman BD, Guan N, Rückert T, Garner L, Singh NK, McMichael AJ, Gillespie GM, Romagnani C, Birnbaum ME. High-throughput characterization of HLA-E-presented CD94/NKG2x ligands reveals peptides which modulate NK cell activation. Nat Commun 2023; 14:4809. [PMID: 37558657 PMCID: PMC10412585 DOI: 10.1038/s41467-023-40220-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/13/2023] [Indexed: 08/11/2023] Open
Abstract
HLA-E is a non-classical class I MHC protein involved in innate and adaptive immune recognition. While recent studies have shown HLA-E can present diverse peptides to NK cells and T cells, the HLA-E repertoire recognized by CD94/NKG2x has remained poorly defined, with only a limited number of peptide ligands identified. Here we screen a yeast-displayed peptide library in the context of HLA-E to identify 500 high-confidence unique peptides that bind both HLA-E and CD94/NKG2A or CD94/NKG2C. Utilizing the sequences identified via yeast display selections, we train prediction algorithms and identify human and cytomegalovirus (CMV) proteome-derived, HLA-E-presented peptides capable of binding and signaling through both CD94/NKG2A and CD94/NKG2C. In addition, we identify peptides which selectively activate NKG2C+ NK cells. Taken together, characterization of the HLA-E-binding peptide repertoire and identification of NK activity-modulating peptides present opportunities for studies of NK cell regulation in health and disease, in addition to vaccine and therapeutic design.
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Affiliation(s)
- Brooke D Huisman
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Ning Guan
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Timo Rückert
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
| | - Lee Garner
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nishant K Singh
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Andrew J McMichael
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Old Road Campus Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chiara Romagnani
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael E Birnbaum
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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4
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He W, Gea-Mallorquí E, Colin-York H, Fritzsche M, Gillespie GM, Brackenridge S, Borrow P, McMichael AJ. Intracellular trafficking of HLA-E and its regulation. J Exp Med 2023; 220:214089. [PMID: 37140910 PMCID: PMC10165540 DOI: 10.1084/jem.20221941] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/13/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Interest in MHC-E-restricted CD8+ T cell responses has been aroused by the discovery of their efficacy in controlling simian immunodeficiency virus (SIV) infection in a vaccine model. The development of vaccines and immunotherapies utilizing human MHC-E (HLA-E)-restricted CD8+ T cell response requires an understanding of the pathway(s) of HLA-E transport and antigen presentation, which have not been clearly defined previously. We show here that, unlike classical HLA class I, which rapidly exits the endoplasmic reticulum (ER) after synthesis, HLA-E is largely retained because of a limited supply of high-affinity peptides, with further fine-tuning by its cytoplasmic tail. Once at the cell surface, HLA-E is unstable and is rapidly internalized. The cytoplasmic tail plays a crucial role in facilitating HLA-E internalization, which results in its enrichment in late and recycling endosomes. Our data reveal distinctive transport patterns and delicate regulatory mechanisms of HLA-E, which help to explain its unusual immunological functions.
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Affiliation(s)
- Wanlin He
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Ester Gea-Mallorquí
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Huw Colin-York
- Kennedy Institute of Rheumatology, University of Oxford , Oxford, UK
| | - Marco Fritzsche
- Kennedy Institute of Rheumatology, University of Oxford , Oxford, UK
| | - Geraldine M Gillespie
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Simon Brackenridge
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Persephone Borrow
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
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5
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Lin Z, Bashirova AA, Viard M, Garner L, Quastel M, Beiersdorfer M, Kasprzak WK, Akdag M, Yuki Y, Ojeda P, Das S, Andresson T, Naranbhai V, Horowitz A, McMichael AJ, Hoelzemer A, Gillespie GM, Garcia-Beltran WF, Carrington M. HLA class I signal peptide polymorphism determines the level of CD94/NKG2-HLA-E-mediated regulation of effector cell responses. Nat Immunol 2023; 24:1087-1097. [PMID: 37264229 PMCID: PMC10690437 DOI: 10.1038/s41590-023-01523-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
Human leukocyte antigen (HLA)-E binds epitopes derived from HLA-A, HLA-B, HLA-C and HLA-G signal peptides (SPs) and serves as a ligand for CD94/NKG2A and CD94/NKG2C receptors expressed on natural killer and T cell subsets. We show that among 16 common classical HLA class I SP variants, only 6 can be efficiently processed to generate epitopes that enable CD94/NKG2 engagement, which we term 'functional SPs'. The single functional HLA-B SP, known as HLA-B/-21M, induced high HLA-E expression, but conferred the lowest receptor recognition. Consequently, HLA-B/-21M SP competes with other SPs for providing epitope to HLA-E and reduces overall recognition of target cells by CD94/NKG2A, calling for reassessment of previous disease models involving HLA-B/-21M. Genetic population data indicate a positive correlation between frequencies of functional SPs in humans and corresponding cytomegalovirus mimics, suggesting a means for viral escape from host responses. The systematic, quantitative approach described herein will facilitate development of prediction algorithms for accurately measuring the impact of CD94/NKG2-HLA-E interactions in disease resistance/susceptibility.
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Affiliation(s)
- Zhansong Lin
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Lee Garner
- Centre for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Max Quastel
- Centre for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Maya Beiersdorfer
- Leibniz Institute of Virology, Hamburg, Germany
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marjan Akdag
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Pedro Ojeda
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sudipto Das
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thorkell Andresson
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Angelique Hoelzemer
- Leibniz Institute of Virology, Hamburg, Germany
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | | | | | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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6
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Yang H, Sun H, Brackenridge S, Zhuang X, Wing PAC, Quastel M, Walters L, Garner L, Wang B, Yao X, Felce SL, Peng Y, Moore S, Peeters BWA, Rei M, Canto Gomes J, Tomas A, Davidson A, Semple MG, Turtle LCW, Openshaw PJM, Baillie JK, Mentzer AJ, Klenerman P, Borrow P, Dong T, McKeating JA, Gillespie GM, McMichael AJ. HLA-E-restricted SARS-CoV-2-specific T cells from convalescent COVID-19 patients suppress virus replication despite HLA class Ia down-regulation. Sci Immunol 2023; 8:eabl8881. [PMID: 37390223 DOI: 10.1126/sciimmunol.abl8881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/07/2023] [Indexed: 07/02/2023]
Abstract
Pathogen-specific CD8+ T cell responses restricted by the nonpolymorphic nonclassical class Ib molecule human leukocyte antigen E (HLA-E) are rarely reported in viral infections. The natural HLA-E ligand is a signal peptide derived from classical class Ia HLA molecules that interact with the NKG2/CD94 receptors to regulate natural killer cell functions, but pathogen-derived peptides can also be presented by HLA-E. Here, we describe five peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that elicited HLA-E-restricted CD8+ T cell responses in convalescent patients with coronavirus disease 2019. These T cell responses were identified in the blood at frequencies similar to those reported for classical HLA-Ia-restricted anti-SARS-CoV-2 CD8+ T cells. HLA-E peptide-specific CD8+ T cell clones, which expressed diverse T cell receptors, suppressed SARS-CoV-2 replication in Calu-3 human lung epithelial cells. SARS-CoV-2 infection markedly down-regulated classical HLA class I expression in Calu-3 cells and primary reconstituted human airway epithelial cells, whereas HLA-E expression was not affected, enabling T cell recognition. Thus, HLA-E-restricted T cells could contribute to the control of SARS-CoV-2 infection alongside classical T cells.
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Affiliation(s)
- Hongbing Yang
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Hong Sun
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Key Laboratory of AIDS Immunology, Department of Laboratory Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Simon Brackenridge
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Peter A C Wing
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Max Quastel
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lucy Walters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Lee Garner
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Beibei Wang
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Shona Moore
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bas W A Peeters
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Margarida Rei
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Oxford, UK
| | - Joao Canto Gomes
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga, Portugal
| | - Ana Tomas
- Unidada de Investigacao em Patobiologia Molecular, Instituto Portugues de Oncologia de Lisboa Francisco Gentil, EPE Lisbon, Portugal
- Chronic Diseases Research Centre, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Malcolm G Semple
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Unit, Alder Hey Children's Hospital, Eaton Road, Liverpool L12 2AP, UK
| | - Lance C W Turtle
- Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust (member of Liverpool Health Partners), Liverpool, UK
| | | | | | - Alexander J Mentzer
- Welcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Persephone Borrow
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jane A McKeating
- Chinese Academy of Medical Sciences Oxford Institute, Old Road Campus, Oxford, UK
- Nuffield Depertment of Clinical Medicine, NDM Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Andrew J McMichael
- Centre for Immuno-Oncology, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
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7
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Haynes BF, Wiehe K, Borrow P, Saunders KO, Korber B, Wagh K, McMichael AJ, Kelsoe G, Hahn BH, Alt F, Shaw GM. Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies. Nat Rev Immunol 2023; 23:142-158. [PMID: 35962033 PMCID: PMC9372928 DOI: 10.1038/s41577-022-00753-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 75.0] [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] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
After nearly four decades of research, a safe and effective HIV-1 vaccine remains elusive. There are many reasons why the development of a potent and durable HIV-1 vaccine is challenging, including the extraordinary genetic diversity of HIV-1 and its complex mechanisms of immune evasion. HIV-1 envelope glycoproteins are poorly recognized by the immune system, which means that potent broadly neutralizing antibodies (bnAbs) are only infrequently induced in the setting of HIV-1 infection or through vaccination. Thus, the biology of HIV-1-host interactions necessitates novel strategies for vaccine development to be designed to activate and expand rare bnAb-producing B cell lineages and to select for the acquisition of critical improbable bnAb mutations. Here we discuss strategies for the induction of potent and broad HIV-1 bnAbs and outline the steps that may be necessary for ultimate success.
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Affiliation(s)
- Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA. .,Department of Medicine, Duke University School of Medicine, Durham, NC, USA. .,Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.,New Mexico Consortium, Los Alamos, NM, USA
| | - Kshitij Wagh
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.,New Mexico Consortium, Los Alamos, NM, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederick Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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8
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Affiliation(s)
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
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9
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Yang X, Garner LI, Zvyagin IV, Paley MA, Komech EA, Jude KM, Zhao X, Fernandes RA, Hassman LM, Paley GL, Savvides CS, Brackenridge S, Quastel MN, Chudakov DM, Bowness P, Yokoyama WM, McMichael AJ, Gillespie GM, Garcia KC. Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Nature 2022; 612:771-777. [PMID: 36477533 PMCID: PMC10511244 DOI: 10.1038/s41586-022-05501-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 06/05/2021] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Human leucocyte antigen B*27 (HLA-B*27) is strongly associated with inflammatory diseases of the spine and pelvis (for example, ankylosing spondylitis (AS)) and the eye (that is, acute anterior uveitis (AAU))1. How HLA-B*27 facilitates disease remains unknown, but one possible mechanism could involve presentation of pathogenic peptides to CD8+ T cells. Here we isolated orphan T cell receptors (TCRs) expressing a disease-associated public β-chain variable region-complementary-determining region 3β (BV9-CDR3β) motif2-4 from blood and synovial fluid T cells from individuals with AS and from the eye in individuals with AAU. These TCRs showed consistent α-chain variable region (AV21) chain pairing and were clonally expanded in the joint and eye. We used HLA-B*27:05 yeast display peptide libraries to identify shared self-peptides and microbial peptides that activated the AS- and AAU-derived TCRs. Structural analysis revealed that TCR cross-reactivity for peptide-MHC was rooted in a shared binding motif present in both self-antigens and microbial antigens that engages the BV9-CDR3β TCRs. These findings support the hypothesis that microbial antigens and self-antigens could play a pathogenic role in HLA-B*27-associated disease.
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Affiliation(s)
- Xinbo Yang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lee I Garner
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ivan V Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Michael A Paley
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Ekaterina A Komech
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiang Zhao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ricardo A Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn M Hassman
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Grace L Paley
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Christina S Savvides
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Brackenridge
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Max N Quastel
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dmitriy M Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Paul Bowness
- Nuffield Department of Orthopaedics Rheumatology and Muscuoskeletal Science (NDORMS), Botnar Research Center, University of Oxford, Oxford, UK
| | - Wayne M Yokoyama
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Andrew J McMichael
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Geraldine M Gillespie
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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10
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Walters LC, Rozbesky D, Harlos K, Quastel M, Sun H, Springer S, Rambo RP, Mohammed F, Jones EY, McMichael AJ, Gillespie GM. Primary and secondary functions of HLA-E are determined by stability and conformation of the peptide-bound complexes. Cell Rep 2022; 39:110959. [PMID: 35705051 PMCID: PMC9380258 DOI: 10.1016/j.celrep.2022.110959] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/11/2022] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
MHC-E regulates NK cells by displaying MHC class Ia signal peptides (VL9) to NKG2A:CD94 receptors. MHC-E can also present sequence-diverse, lower-affinity, pathogen-derived peptides to T cell receptors (TCRs) on CD8+ T cells. To understand these affinity differences, human MHC-E (HLA-E)-VL9 versus pathogen-derived peptide structures are compared. Small-angle X-ray scatter (SAXS) measures biophysical parameters in solution, allowing comparison with crystal structures. For HLA-E-VL9, there is concordance between SAXS and crystal parameters. In contrast, HLA-E-bound pathogen-derived peptides produce larger SAXS dimensions that reduce to their crystallographic dimensions only when excess peptide is supplied. Further crystallographic analysis demonstrates three amino acids, exclusive to MHC-E, that not only position VL9 close to the α2 helix, but also allow non-VL9 peptide binding with re-configuration of a key TCR-interacting α2 region. Thus, non-VL9-bound peptides introduce an alternative peptide-binding motif and surface recognition landscape, providing a likely basis for VL9- and non-VL9-HLA-E immune discrimination.
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Affiliation(s)
- Lucy C Walters
- Nuffield Department of Medicine Research Building, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Daniel Rozbesky
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Max Quastel
- Nuffield Department of Medicine Research Building, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Hong Sun
- Nuffield Department of Medicine Research Building, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Robert P Rambo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Fiyaz Mohammed
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
| | - Geraldine M Gillespie
- Nuffield Department of Medicine Research Building, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
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11
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Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
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Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
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12
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Li D, Brackenridge S, Walters LC, Swanson O, Harlos K, Rozbesky D, Cain DW, Wiehe K, Scearce RM, Barr M, Mu Z, Parks R, Quastel M, Edwards RJ, Wang Y, Rountree W, Saunders KO, Ferrari G, Borrow P, Jones EY, Alam SM, Azoitei ML, Gillespie GM, McMichael AJ, Haynes BF. Mouse and human antibodies bind HLA-E-leader peptide complexes and enhance NK cell cytotoxicity. Commun Biol 2022; 5:271. [PMID: 35347236 PMCID: PMC8960791 DOI: 10.1038/s42003-022-03183-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/17/2022] [Indexed: 12/16/2022] Open
Abstract
The non-classical class Ib molecule human leukocyte antigen E (HLA-E) has limited polymorphism and can bind HLA class Ia leader peptides (VL9). HLA-E-VL9 complexes interact with the natural killer (NK) cell receptors NKG2A-C/CD94 and regulate NK cell-mediated cytotoxicity. Here we report the isolation of 3H4, a murine HLA-E-VL9-specific IgM antibody that enhances killing of HLA-E-VL9-expressing cells by an NKG2A+ NK cell line. Structural analysis reveal that 3H4 acts by preventing CD94/NKG2A docking on HLA-E-VL9. Upon in vitro maturation, an affinity-optimized IgG form of 3H4 showes enhanced NK killing of HLA-E-VL9-expressing cells. HLA-E-VL9-specific IgM antibodies similar in function to 3H4 are also isolated from naïve B cells of cytomegalovirus (CMV)-negative, healthy humans. Thus, HLA-E-VL9-targeting mouse and human antibodies isolated from the naïve B cell antibody pool have the capacity to enhance NK cell cytotoxicity.
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Affiliation(s)
- Dapeng Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Lucy C Walters
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Olivia Swanson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Daniel Rozbesky
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Cell Biology, Charles University, Prague, 12800, Czech Republic
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Richard M Scearce
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Zekun Mu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Max Quastel
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Guido Ferrari
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Mihai L Azoitei
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Geraldine M Gillespie
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA.
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13
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Ruibal P, Franken KLMC, van Meijgaarden KE, Walters LC, McMichael AJ, Gillespie GM, Joosten SA, Ottenhoff THM. Discovery of HLA-E-Presented Epitopes: MHC-E/Peptide Binding and T-Cell Recognition. Methods Mol Biol 2022; 2574:15-30. [PMID: 36087196 PMCID: PMC10508831 DOI: 10.1007/978-1-0716-2712-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding the interactions involved during the immunological synapse between peptide, HLA-E molecules, and TCR is crucial to effectively target protective HLA-E-restricted T-cell responses in humans. Here we describe three techniques based on the generation of MHC-E/peptide complexes (MHC-E generically includes HLA-E-like molecules in human and nonhuman species, while HLA-E specifically refers to human molecules), which allow to investigate MHC-E/peptide binding at the molecular level through binding assays and by using peptide loaded HLA-E tetramers, to detect, isolate, and study peptide-specific HLA-E-restricted human T-cells.
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Affiliation(s)
- Paula Ruibal
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Kees L M C Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Lucy C Walters
- Nuffield Department of Medicine Research Building, Old Road Campus, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Old Road Campus, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Geraldine M Gillespie
- Nuffield Department of Medicine Research Building, Old Road Campus, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.
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14
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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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15
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Brenna E, McMichael AJ. The Importance of Cellular Immune Response to HIV: Implications for Antibody Production and Vaccine Design. DNA Cell Biol 2022; 41:38-42. [PMID: 34664991 PMCID: PMC8787704 DOI: 10.1089/dna.2021.0520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 12/04/2022] Open
Abstract
Despite many years from the discovery of human immunodeficiency virus (HIV), a prophylactic vaccine against HIV is still needed. The failure of most of the vaccine clinical trials in the field has different causes, mainly due by the difficulties to identify the correct antigen able to prime the optimal B cell lineage and then make the series of somatic mutations necessary to generate broadly neutralizing antibodies (bNAbs). B cells are responsible for the bNAbs production; however, their function is strongly influenced by the presence of a population of CD4+ T lymphocytes, mainly present in the lymphoid organs, the T follicular helper cells (Tfh). In this review, the importance of the contribution of Tfh cells in HIV response is highlighted and future therapy perspectives based on these observations are described. The advanced technology available nowadays and the wide knowledge built over the past years for HIV may eventually create the best scenario for the generation of an effective vaccine.
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Affiliation(s)
- Elena Brenna
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J. McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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16
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Campion SL, Brenna E, Thomson E, Fischer W, Ladell K, McLaren JE, Price DA, Frahm N, McElrath JM, Cohen KW, Maenza JR, Walsh SR, Baden LR, Haynes BF, Korber B, Borrow P, McMichael AJ. Preexisting memory CD4+ T cells contribute to the primary response in an HIV-1 vaccine trial. J Clin Invest 2021; 131:e150823. [PMID: 34850742 PMCID: PMC8631594 DOI: 10.1172/jci150823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/07/2021] [Indexed: 11/17/2022] Open
Abstract
Naive and memory CD4+ T cells reactive with human immunodeficiency virus type 1 (HIV-1) are detectable in unexposed, unimmunized individuals. The contribution of preexisting CD4+ T cells to a primary immune response was investigated in 20 HIV-1-seronegative volunteers vaccinated with an HIV-1 envelope (Env) plasmid DNA prime and recombinant modified vaccinia virus Ankara (MVA) boost in the HVTN 106 vaccine trial (clinicaltrials.gov NCT02296541). Prevaccination naive or memory CD4+ T cell responses directed against peptide epitopes in Env were identified in 14 individuals. After priming with DNA, 40% (8/20) of the elicited responses matched epitopes detected in the corresponding preimmunization memory repertoires, and clonotypes were shared before and after vaccination in 2 representative volunteers. In contrast, there were no shared epitope specificities between the preimmunization memory compartment and responses detected after boosting with recombinant MVA expressing a heterologous Env. Preexisting memory CD4+ T cells therefore shape the early immune response to vaccination with a previously unencountered HIV-1 antigen.
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Affiliation(s)
- Suzanne L. Campion
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Elena Brenna
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Elaine Thomson
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Will Fischer
- Los Alamos National Laboratory, Santa Fe, New Mexico, USA
| | | | | | - David A. Price
- Division of Infection and Immunity and
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Nicole Frahm
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Juliana M. McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Janine R. Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Stephen R. Walsh
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Lindsey R. Baden
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Barton F. Haynes
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Bette Korber
- Los Alamos National Laboratory, Santa Fe, New Mexico, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J. McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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17
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McMichael AJ, Zafeiridi E, Ryan M, Cunningham EL, Passmore AP, McGuinness B. Anticholinergic drug use and risk of mortality for people with dementia in Northern Ireland. Aging Ment Health 2021; 25:1475-1482. [PMID: 33073601 DOI: 10.1080/13607863.2020.1830028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Indexed: 10/23/2022]
Abstract
OBJECTIVE Anticholinergic burden refers to the cumulative effect of medications which contain anticholinergic properties. We assessed how anticholinergic burden and different types of anticholinergic medications influence mortality rates among people with dementia in Northern Ireland. Our secondary aim was to determine what demographic characteristics predict the anticholinergic burden of people with dementia. METHODS Data were extracted from the Enhanced Prescribing database for 25,418 people who were prescribed at least one dementia management medication between 2010 and 2016. Information was also extracted on the number of times each available anticholinergic drug was prescribed between 2010 and 2016, allowing the calculation of an overall anticholinergic burden. Cox proportional hazard models were used to determine how anticholinergic burden influenced mortality whilst multilevel model regression determined what demographic characteristics influence overall anticholinergic burden. RESULTS Of the 25,418 people with dementia, only 15% (n = 3880) had no anticholinergic burden. Diazepam (42%) and risperidone (18%) were the two most commonly prescribed drugs. Unadjusted Cox proportional hazard models indicated that higher anticholinergic burden was associated with significantly higher mortality rates in comparison to people with dementia who had no anticholinergic burden (HR = 1.59: 95% CI = 1.07-2.36). In particular, urological (HR = 1.20: 95% CI = 1.05-1.38) and respiratory (HR = 1.17: 95% CI = 1.08-1.27) drugs significantly increased mortality rates. People with dementia living in areas with low levels of deprivation had significantly lower anticholinergic burden (HR=-.39: 95% CI=-.47:-30). CONCLUSIONS Reducing anticholinergic burden is essential for people with dementia. Further research should address the unfavourable prognosis of people living with dementia in highly deprived areas.
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Affiliation(s)
- A J McMichael
- Centre for Public Health, Institute for Clinical Sciences Block B, Queens University Belfast, Belfast, Northern Ireland
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18
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Yang H, Rei M, Brackenridge S, Brenna E, Sun H, Abdulhaqq S, Liu MKP, Ma W, Kurupati P, Xu X, Cerundolo V, Jenkins E, Davis SJ, Sacha JB, Früh K, Picker LJ, Borrow P, Gillespie GM, McMichael AJ. HLA-E-restricted, Gag-specific CD8 + T cells can suppress HIV-1 infection, offering vaccine opportunities. Sci Immunol 2021; 6:eabg1703. [PMID: 33766848 PMCID: PMC8258078 DOI: 10.1126/sciimmunol.abg1703] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 12/15/2020] [Accepted: 02/18/2021] [Indexed: 12/26/2022]
Abstract
Human leukocyte antigen-E (HLA-E) normally presents an HLA class Ia signal peptide to the NKG2A/C-CD94 regulatory receptors on natural killer (NK) cells and T cell subsets. Rhesus macaques immunized with a cytomegalovirus-vectored simian immunodeficiency virus (SIV) vaccine generated Mamu-E (HLA-E homolog)-restricted T cell responses that mediated post-challenge SIV replication arrest in >50% of animals. However, HIV-1-specific, HLA-E-restricted T cells have not been observed in HIV-1-infected individuals. Here, HLA-E-restricted, HIV-1-specific CD8 + T cells were primed in vitro. These T cell clones and allogeneic CD8 + T cells transduced with their T cell receptors suppressed HIV-1 replication in CD4 + T cells in vitro. Vaccine induction of efficacious HLA-E-restricted HIV-1-specific T cells should therefore be possible.
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MESH Headings
- Amino Acid Sequence
- Biomarkers
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cell Line, Tumor
- Cytokines/metabolism
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- HIV Infections/immunology
- HIV Infections/metabolism
- HIV Infections/prevention & control
- HIV Infections/virology
- HIV-1/immunology
- Histocompatibility Antigens Class I/immunology
- Host-Pathogen Interactions/immunology
- Humans
- Immunophenotyping
- Jurkat Cells
- Lymphocyte Activation/genetics
- Lymphocyte Activation/immunology
- Peptides/chemistry
- Peptides/immunology
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Cell Antigen Receptor Specificity/immunology
- gag Gene Products, Human Immunodeficiency Virus/immunology
- HLA-E Antigens
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Affiliation(s)
- Hongbing Yang
- NDM Research Building, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK
| | - Margarida Rei
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Simon Brackenridge
- NDM Research Building, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK
| | - Elena Brenna
- NDM Research Building, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK
| | - Hong Sun
- NDM Research Building, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK
- Key Laboratory of AIDS Immunology, Department of Laboratory Medicine, First Affiliated Hospital of China Medical University, Shenyang, China
- Chinese Academy of Medical Sciences Oxford Institute, NDM, Oxford University, Oxford, UK
| | - Shaheed Abdulhaqq
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Michael K P Liu
- Centre For Immunology and Vaccinology, Chelsea and Westminster Hospital, Imperial College, London, UK
| | - Weiwei Ma
- Centre For Immunology and Vaccinology, Chelsea and Westminster Hospital, Imperial College, London, UK
| | - Prathiba Kurupati
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Xiaoning Xu
- Centre For Immunology and Vaccinology, Chelsea and Westminster Hospital, Imperial College, London, UK
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Edward Jenkins
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Simon J Davis
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Klaus Früh
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Persephone Borrow
- NDM Research Building, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK
| | - Geraldine M Gillespie
- NDM Research Building, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK
| | - Andrew J McMichael
- NDM Research Building, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK.
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19
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Brenna E, Davydov AN, Ladell K, McLaren JE, Bonaiuti P, Metsger M, Ramsden JD, Gilbert SC, Lambe T, Price DA, Campion SL, Chudakov DM, Borrow P, McMichael AJ. CD4 + T Follicular Helper Cells in Human Tonsils and Blood Are Clonally Convergent but Divergent from Non-Tfh CD4 + Cells. Cell Rep 2021; 30:137-152.e5. [PMID: 31914381 PMCID: PMC7029615 DOI: 10.1016/j.celrep.2019.12.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/16/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022] Open
Abstract
T follicular helper (Tfh) cells are fundamental for B cell selection and antibody maturation in germinal centers. Circulating Tfh (cTfh) cells constitute a minor proportion of the CD4+ T cells in peripheral blood, but their clonotypic relationship to Tfh populations resident in lymph nodes and the extent to which they differ from non-Tfh CD4+ cells have been unclear. Using donor-matched blood and tonsil samples, we investigate T cell receptor (TCR) sharing between tonsillar Tfh cells and peripheral Tfh and non-Tfh cell populations. TCR transcript sequencing reveals considerable clonal overlap between peripheral and tonsillar Tfh cell subsets as well as a clear distinction between Tfh and non-Tfh cells. Furthermore, influenza-specific cTfh cell clones derived from blood can be found in the repertoire of tonsillar Tfh cells. Therefore, human blood samples can be used to gain insight into the specificity of Tfh responses occurring in lymphoid tissues, provided that cTfh subsets are studied.
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Affiliation(s)
- Elena Brenna
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK.
| | - Alexey N Davydov
- Central European Institute of Technology, Brno 601 77, Czech Republic
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Paolo Bonaiuti
- Istituto Firc di Oncologia Molecolare, Milano 20139, Italy
| | - Maria Metsger
- Central European Institute of Technology, Brno 601 77, Czech Republic
| | | | - Sarah C Gilbert
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Teresa Lambe
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Suzanne L Campion
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Dmitriy M Chudakov
- Central European Institute of Technology, Brno 601 77, Czech Republic; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russia
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK.
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK.
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20
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Walters LC, McMichael AJ, Gillespie GM. Detailed and atypical HLA-E peptide binding motifs revealed by a novel peptide exchange binding assay. Eur J Immunol 2020; 50:2075-2091. [PMID: 32716529 DOI: 10.1002/eji.202048719] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/23/2020] [Indexed: 11/05/2022]
Abstract
Diverse SIV and HIV epitopes that bind the rhesus homolog of HLA-E, Mamu-E, have recently been identified in SIVvaccine studies using a recombinant Rhesus cytomegalovirus (RhCMV 68-1) vector, where unprecedented protection against SIV challenge was achieved. Additionally, several Mycobacterial peptides identified both algorithmically and following elution from infected cells, are presented to CD8+ T cells by HLA-E in humans. Yet, a comparative and comprehensive analysis of relative HLA-E peptide binding strength via a reliable, high throughput in vitro assay is currently lacking. To address this, we developed and optimized a novel, highly sensitive peptide exchange ELISA-based assay that relatively quantitates peptide binding to HLA-E. Using this approach, we screened multiple peptides, including peptide panels derived from HIV, SIV, and Mtb predicted to bind HLA-E. Our results indicate that although HLA-E preferentially accommodates canonical MHC class I leader peptides, many non-canonical, sequence diverse, pathogen-derived peptides also bind HLA-E, albeit generally with lower relative binding strength. Additionally, our screens demonstrate that the majority of peptides tested, including some key Mtb and SIV epitopes that have been shown to elicit strong Mamu-E-restricted T cell responses, either bind HLA-E extremely weakly or give signals that are indistinguishable from the negative, peptide-free controls.
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Affiliation(s)
- Lucy C Walters
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Geraldine M Gillespie
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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21
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Mendoza JL, Fischer S, Gee MH, Lam LH, Brackenridge S, Powrie FM, Birnbaum M, McMichael AJ, Garcia KC, Gillespie GM. Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity. eLife 2020; 9:58128. [PMID: 32716298 PMCID: PMC7384859 DOI: 10.7554/elife.58128] [Citation(s) in RCA: 4] [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: 04/21/2020] [Accepted: 07/01/2020] [Indexed: 11/20/2022] Open
Abstract
T cell cross-reactivity ensures that diverse pathogen-derived epitopes encountered during a lifetime are recognized by the available TCR repertoire. A feature of cross-reactivity where previous exposure to one microbe can alter immunity to subsequent, non-related pathogens has been mainly explored for viruses. Yet cross-reactivity to additional microbes is important to consider, especially in HIV infection where gut-intestinal barrier dysfunction could facilitate T cell exposure to commensal/pathogenic microbes. Here we evaluated the cross-reactivity of a ‘public’, HIV-specific, CD8 T cell-derived TCR (AGA1 TCR) using MHC class I yeast display technology. Via screening of MHC-restricted libraries comprising ~2×108 sequence-diverse peptides, AGA1 TCR specificity was mapped to a central peptide di-motif. Using the top TCR-enriched library peptides to probe the non-redundant protein database, bacterial peptides that elicited functional responses by AGA1-expressing T cells were identified. The possibility that in context-specific settings, MHC class I proteins presenting microbial peptides influence virus-specific T cell populations in vivo is discussed.
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Affiliation(s)
- Juan L Mendoza
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Suzanne Fischer
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Marvin H Gee
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Lilian H Lam
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom.,Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Old Road Campus, Headington, Oxford, United Kingdom
| | - Fiona M Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom.,Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Michael Birnbaum
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Koch Institute at MIT, Cambridge, United States
| | - Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Old Road Campus, Headington, Oxford, United Kingdom
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
| | - Geraldine M Gillespie
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Old Road Campus, Headington, Oxford, United Kingdom
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22
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Paes W, Leonov G, Partridge T, Chikata T, Murakoshi H, Frangou A, Brackenridge S, Nicastri A, Smith AG, Learn GH, Li Y, Parker R, Oka S, Pellegrino P, Williams I, Haynes BF, McMichael AJ, Shaw GM, Hahn BH, Takiguchi M, Ternette N, Borrow P. Contribution of proteasome-catalyzed peptide cis-splicing to viral targeting by CD8 + T cells in HIV-1 infection. Proc Natl Acad Sci U S A 2019; 116:24748-24759. [PMID: 31748275 PMCID: PMC6900506 DOI: 10.1073/pnas.1911622116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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] [Indexed: 01/15/2023] Open
Abstract
Peptides generated by proteasome-catalyzed splicing of noncontiguous amino acid sequences have been shown to constitute a source of nontemplated human leukocyte antigen class I (HLA-I) epitopes, but their role in pathogen-specific immunity remains unknown. CD8+ T cells are key mediators of HIV type 1 (HIV-1) control, and identification of novel epitopes to enhance targeting of infected cells is a priority for prophylactic and therapeutic strategies. To explore the contribution of proteasome-catalyzed peptide splicing (PCPS) to HIV-1 epitope generation, we developed a broadly applicable mass spectrometry-based discovery workflow that we employed to identify spliced HLA-I-bound peptides on HIV-infected cells. We demonstrate that HIV-1-derived spliced peptides comprise a relatively minor component of the HLA-I-bound viral immunopeptidome. Although spliced HIV-1 peptides may elicit CD8+ T cell responses relatively infrequently during infection, CD8+ T cells primed by partially overlapping contiguous epitopes in HIV-infected individuals were able to cross-recognize spliced viral peptides, suggesting a potential role for PCPS in restricting HIV-1 escape pathways. Vaccine-mediated priming of responses to spliced HIV-1 epitopes could thus provide a novel means of exploiting epitope targets typically underutilized during natural infection.
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Affiliation(s)
- Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom;
| | - German Leonov
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Takayuki Chikata
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hayato Murakoshi
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Anna Frangou
- Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Andrew G Smith
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert Parker
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Shinichi Oka
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
- AIDS Clinical Centre, National Centre for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Pierre Pellegrino
- Centre for Sexual Health and HIV Research, University College London, London WC1E 6JB, United Kingdom
| | - Ian Williams
- Centre for Sexual Health and HIV Research, University College London, London WC1E 6JB, United Kingdom
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom;
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23
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Marks DH, Hagigeorges D, Okhovat JP, Manatis-Lornell AJ, McMichael AJ, Senna MM. Association of cicatricial alopecia with chemical hair straightening. Br J Dermatol 2019; 181:1317-1319. [PMID: 31206604 DOI: 10.1111/bjd.18217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- D H Marks
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, U.S.A
| | - D Hagigeorges
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, U.S.A
| | - J-P Okhovat
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, U.S.A
| | - A J Manatis-Lornell
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, U.S.A
| | - A J McMichael
- Department of Dermatology, Wake Forest School of Medicine, Winston-Salem, NC, U.S.A
| | - M M Senna
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, U.S.A.,Harvard Medical School, Boston, MA, U.S.A
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24
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Ogg G, Cerundolo V, McMichael AJ. Capturing the antigen landscape: HLA-E, CD1 and MR1. Curr Opin Immunol 2019; 59:121-129. [PMID: 31445404 DOI: 10.1016/j.coi.2019.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/12/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022]
Abstract
T cell receptor (TCR) recognition of antigens presented by relatively non-polymorphic MHC-like molecules is emerging as a significant contributor to health and disease. These evolutionarily ancient pathways have been inappropriately labelled 'non-conventional' because their roles were discovered after viral-specific peptide presentation by polymorphic MHC class I molecules. We suggest that these pathways are complementary to mainstream peptide presentation. HLA-E, CD1 and MR1 can present diverse self and foreign antigens to TCRs and therefore contribute to tissue homeostasis, pathogen defence, inflammation and immune responses to cancer. Despite presenting different classes of antigens, they share many features and are under common selective pressures. Through understanding their roles in disease, therapeutic manipulation for disease prevention and treatment should become possible.
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Affiliation(s)
- Graham Ogg
- MRC Human Immunology Unit, and Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | | | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, University of Oxford, UK.
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25
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Affiliation(s)
- Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Old Road Campus, Oxford OX3 7FZ, UK.
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
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26
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Peng BJ, Carlson JM, Liu MKP, Gao F, Goonetilleke N, McMichael AJ, Borrow P, Gilmour J, Heath SL, Hunter E, Bansal A, Goepfert PA. Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection. J Virol 2018; 92:e00711-18. [PMID: 30021907 PMCID: PMC6146806 DOI: 10.1128/jvi.00711-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/31/2023] Open
Abstract
While prior studies have demonstrated that CD8 T cell responses to cryptic epitopes (CE) are readily detectable during HIV-1 infection, their ability to drive escape mutations following acute infection is unknown. We predicted 66 CE in a Zambian acute infection cohort based on escape mutations occurring within or near the putatively predicted HLA-I-restricted epitopes. The CE were evaluated for CD8 T cell responses for patients with chronic and acute HIV infections. Of the 66 predicted CE, 10 were recognized in 8/32 and 4/11 patients with chronic and acute infections, respectively. The immunogenic CE were all derived from a single antisense reading frame within pol However, when these CE were tested using longitudinal study samples, CE-specific T cell responses were detected but did not consistently select for viral escape mutations. Thus, while we demonstrated that CE are immunogenic in acute infection, the immune responses to CE are not major drivers of viral escape in the initial stages of HIV infection. The latter finding may be due to either the subdominant nature of CE-specific responses, the low antigen sensitivity, or the magnitude of CE responses during acute infections.IMPORTANCE Although prior studies demonstrated that cryptic epitopes of HIV-1 induce CD8 T cell responses, evidence that targeting these epitopes drives HIV escape mutations has been substantially limited, and no studies have addressed this question following acute infection. In this comprehensive study, we utilized longitudinal viral sequencing data obtained from three separate acute infection cohorts to predict potential cryptic epitopes based on HLA-I-associated viral escape. Our data show that cryptic epitopes are immunogenic during acute infection and that many of the responses they elicit are toward translation products of HIV-1 antisense reading frames. However, despite cryptic epitope targeting, our study did not find any evidence of early CD8-mediated immune escape. Nevertheless, improving cryptic epitope-specific CD8 T cell responses may still be beneficial in both preventative and therapeutic HIV-1 vaccines.
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Affiliation(s)
- Binghao J Peng
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Michael K P Liu
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Feng Gao
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Nilu Goonetilleke
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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27
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Abstract
The influenza virus was instrumental in unravelling critical aspects of the antiviral T lymphocyte mediated immune response. A major finding was the demonstration that CD8 T lymphocytes recognize short viral peptides presented by class I molecules of the major histocompatibility complex. Studies of influenza specific T cells have also led to an understanding of their important role in recovery from influenza virus infection in humans.
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Affiliation(s)
- Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Old Road Campus, Oxford, OX3 7FZ, UK.
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28
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McMichael AJ. Is a Human CD8 T-Cell Vaccine Possible, and if So, What Would It Take? Could a CD8 + T-Cell Vaccine Prevent Persistent HIV Infection? Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a029124. [PMID: 29254977 DOI: 10.1101/cshperspect.a029124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Vaccines that stimulate CD8+ T cells could clear early virus infection or control ongoing infection and prevent disease. This could be valuable to combat human immunodeficiency virus type 1 (HIV-1) where it has not yet been possible to generate broadly reacting neutralizing antibodies with a vaccine. However, HIV-1 vaccines aimed at stimulating CD8+ T cells have had no success. In contrast, a cytomegalovirus vectored simian immunodeficiency virus (SIV) vaccine enabled clearance of early SIV infection. This may open the door to the design of an effective HIV vaccine.
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Affiliation(s)
- Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
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29
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Walters LC, Harlos K, Brackenridge S, Rozbesky D, Barrett JR, Jain V, Walter TS, O'Callaghan CA, Borrow P, Toebes M, Hansen SG, Sacha JB, Abdulhaqq S, Greene JM, Früh K, Marshall E, Picker LJ, Jones EY, McMichael AJ, Gillespie GM. Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding. Nat Commun 2018; 9:3137. [PMID: 30087334 PMCID: PMC6081459 DOI: 10.1038/s41467-018-05459-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/04/2018] [Indexed: 12/31/2022] Open
Abstract
Through major histocompatibility complex class Ia leader sequence-derived (VL9) peptide binding and CD94/NKG2 receptor engagement, human leucocyte antigen E (HLA-E) reports cellular health to NK cells. Previous studies demonstrated a strong bias for VL9 binding by HLA-E, a preference subsequently supported by structural analyses. However, Mycobacteria tuberculosis (Mtb) infection and Rhesus cytomegalovirus-vectored SIV vaccinations revealed contexts where HLA-E and the rhesus homologue, Mamu-E, presented diverse pathogen-derived peptides to CD8+ T cells, respectively. Here we present crystal structures of HLA-E in complex with HIV and Mtb-derived peptides. We show that despite the presence of preferred primary anchor residues, HLA-E-bound peptides can adopt alternative conformations within the peptide binding groove. Furthermore, combined structural and mutagenesis analyses illustrate a greater tolerance for hydrophobic and polar residues in the primary pockets than previously appreciated. Finally, biochemical studies reveal HLA-E peptide binding and exchange characteristics with potential relevance to its alternative antigen presenting function in vivo.
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Affiliation(s)
- Lucy C Walters
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, UK
| | - Simon Brackenridge
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Daniel Rozbesky
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, UK
| | - Jordan R Barrett
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Vitul Jain
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, UK
| | - Thomas S Walter
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, UK
| | - Chris A O'Callaghan
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Persephone Borrow
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Mireille Toebes
- Department Molecular Oncology and Immunology, B6 Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Shaheed Abdulhaqq
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Justin M Greene
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Klaus Früh
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Emily Marshall
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Geraldine M Gillespie
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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30
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Song H, Giorgi EE, Ganusov VV, Cai F, Athreya G, Yoon H, Carja O, Hora B, Hraber P, Romero-Severson E, Jiang C, Li X, Wang S, Li H, Salazar-Gonzalez JF, Salazar MG, Goonetilleke N, Keele BF, Montefiori DC, Cohen MS, Shaw GM, Hahn BH, McMichael AJ, Haynes BF, Korber B, Bhattacharya T, Gao F. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat Commun 2018; 9:1928. [PMID: 29765018 PMCID: PMC5954121 DOI: 10.1038/s41467-018-04217-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 04/10/2018] [Indexed: 11/29/2022] Open
Abstract
Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of within-host diversification is less understood. Here we develop a novel computational tool (RAPR (Recombination Analysis PRogram)) to enable a detailed view of in vivo viral recombination during early infection, and we apply it to near-full-length HIV-1 genome sequences from longitudinal samples. Recombinant genomes rapidly replace transmitted/founder (T/F) lineages, with a median half-time of 27 days, increasing the genetic complexity of the viral population. We identify recombination hot and cold spots that differ from those observed in inter-subtype recombinants. Furthermore, RAPR analysis of longitudinal samples from an individual with well-characterized neutralizing antibody responses shows that recombination helps carry forward resistance-conferring mutations in the diversifying quasispecies. These findings provide insight into molecular mechanisms by which viral recombination contributes to HIV-1 persistence and immunopathogenesis and have implications for studies of HIV transmission and evolution in vivo. Recombination contributes to HIV evolution in patients, but its identification can be difficult. Here, the authors develop a computational tool called RAPR to track recombination in patients, identify recombination hot spots, and show contribution of recombination to antibody escape.
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Affiliation(s)
- Hongshuo Song
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.,United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Elena E Giorgi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Fangping Cai
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Gayathri Athreya
- Office for Research & Discovery, University of Arizona, Tucson, AZ, 85721, USA
| | - Hyejin Yoon
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Oana Carja
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Peter Hraber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | | | - Chunlai Jiang
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, 130012, China
| | - Xiaojun Li
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jesus F Salazar-Gonzalez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,MRC/UVRI and LSHTM Uganda Research Unit, Plot 51-57, Nakiwogo Road, Entebbe, Uganda
| | - Maria G Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Nilu Goonetilleke
- Departments of Microbiology and Immunology & Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - David C Montefiori
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Myron S Cohen
- Departments of Microbiology and Immunology & Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew J McMichael
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Barton F Haynes
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Bette Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA.,Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Feng Gao
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA. .,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, 130012, China.
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31
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Wu HL, Wiseman RW, Hughes CM, Webb GM, Abdulhaqq SA, Bimber BN, Hammond KB, Reed JS, Gao L, Burwitz BJ, Greene JM, Ferrer F, Legasse AW, Axthelm MK, Park BS, Brackenridge S, Maness NJ, McMichael AJ, Picker LJ, O'Connor DH, Hansen SG, Sacha JB. The Role of MHC-E in T Cell Immunity Is Conserved among Humans, Rhesus Macaques, and Cynomolgus Macaques. J Immunol 2018; 200:49-60. [PMID: 29150562 PMCID: PMC5736429 DOI: 10.4049/jimmunol.1700841] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022]
Abstract
MHC-E is a highly conserved nonclassical MHC class Ib molecule that predominantly binds and presents MHC class Ia leader sequence-derived peptides for NK cell regulation. However, MHC-E also binds pathogen-derived peptide Ags for presentation to CD8+ T cells. Given this role in adaptive immunity and its highly monomorphic nature in the human population, HLA-E is an attractive target for novel vaccine and immunotherapeutic modalities. Development of HLA-E-targeted therapies will require a physiologically relevant animal model that recapitulates HLA-E-restricted T cell biology. In this study, we investigated MHC-E immunobiology in two common nonhuman primate species, Indian-origin rhesus macaques (RM) and Mauritian-origin cynomolgus macaques (MCM). Compared to humans and MCM, RM expressed a greater number of MHC-E alleles at both the population and individual level. Despite this difference, human, RM, and MCM MHC-E molecules were expressed at similar levels across immune cell subsets, equivalently upregulated by viral pathogens, and bound and presented identical peptides to CD8+ T cells. Indeed, SIV-specific, Mamu-E-restricted CD8+ T cells from RM recognized antigenic peptides presented by all MHC-E molecules tested, including cross-species recognition of human and MCM SIV-infected CD4+ T cells. Thus, MHC-E is functionally conserved among humans, RM, and MCM, and both RM and MCM represent physiologically relevant animal models of HLA-E-restricted T cell immunobiology.
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Affiliation(s)
- Helen L Wu
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53706
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Gabriela M Webb
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Shaheed A Abdulhaqq
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - Katherine B Hammond
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Jason S Reed
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Lina Gao
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239
| | - Benjamin J Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - Justin M Greene
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Fidel Ferrer
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Alfred W Legasse
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - Michael K Axthelm
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - Byung S Park
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
- School of Public Health, Oregon Health and Science University, Portland, OR 97239
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Nicholas J Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433
- Department of Microbiology and Immunology, School of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70118; and
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53706
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006;
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
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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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33
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Liu D, Wang C, Hora B, Zuo T, Goonetilleke N, Liu MKP, Berrong M, Ferrari G, McMichael AJ, Bhattacharya T, Perelson AS, Gao F. A strongly selected mutation in the HIV-1 genome is independent of T cell responses and neutralizing antibodies. Retrovirology 2017; 14:46. [PMID: 29017536 PMCID: PMC5634943 DOI: 10.1186/s12977-017-0371-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 06/23/2017] [Accepted: 10/03/2017] [Indexed: 01/19/2023] Open
Abstract
Background Mutations rapidly accumulate in the HIV-1 genome after infection. Some of those mutations are selected by host immune responses and often cause viral fitness losses. This study is to investigate whether strongly selected mutations that are not associated with immune responses result in fitness losses. Results Strongly selected mutations were identified by analyzing 5′-half HIV-1 genome (gag/pol) sequences from longitudinal samples of subject CH0131. The K43R mutation in the gag gene was first detected at day 91 post screening and was fixed in the viral population at day 273 while the synonymous N323tc mutation was first detected at day 177 and fixed at day 670. No conventional or cryptic T cell responses were detected against either mutation sites by ELISpot analysis. However, when fitness costs of both mutations were measured by introducing each mutation into their cognate transmitted/founder (T/F) viral genome, the K43R mutation caused a significant fitness loss while the N323tc mutation had little impact on viral fitness. Conclusions The rapid fixation, the lack of detectable immune responses and the significant fitness cost of the K43R mutation suggests that it was strongly selected by host factors other than T cell responses and neutralizing antibodies.
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Affiliation(s)
- Donglai Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China.,Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA.,Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China.,Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA
| | - Bhavna Hora
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA
| | - Tao Zuo
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China.,Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA
| | - Nilu Goonetilleke
- Department of Microbiology, Immunology and Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael K P Liu
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, England, UK
| | - Mark Berrong
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Andrew J McMichael
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, England, UK
| | | | - Alan S Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China. .,Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA.
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34
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Wee EG, Ondondo B, Berglund P, Archer J, McMichael AJ, Baltimore D, Ter Meulen JH, Hanke T. HIV-1 Conserved Mosaics Delivered by Regimens with Integration-Deficient DC-Targeting Lentiviral Vector Induce Robust T Cells. Mol Ther 2017; 25:494-503. [PMID: 28153096 PMCID: PMC5368423 DOI: 10.1016/j.ymthe.2016.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 06/22/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/19/2022] Open
Abstract
To be effective against HIV type 1 (HIV-1), vaccine-induced T cells must selectively target epitopes, which are functionally conserved (present in the majority of currently circulating and reactivated HIV-1 strains) and, at the same time, beneficial (responses to which are associated with better clinical status and control of HIV-1 replication), and rapidly reach protective frequencies upon exposure to the virus. Heterologous prime-boost regimens using virally vectored vaccines are currently the most promising vaccine strategies; nevertheless, induction of robust long-term memory remains challenging. To this end, lentiviral vectors induce high frequencies of memory cells due to their low-inflammatory nature, while typically inducing only low anti-vector immune responses. Here, we describe construction of novel candidate vaccines ZVex.tHIVconsv1 and ZVex.tHIVconsv2, which are based on an integration-deficient lentiviral vector platform with preferential transduction of human dendritic cells and express a bivalent mosaic of conserved-region T cell immunogens with a high global HIV-1 match. Each of the two mosaic vaccines was individually immunogenic. When administered together in heterologous prime-boost regimens with chimpanzee adenovirus and/or poxvirus modified vaccinia virus Ankara (MVA) vaccines to BALB/c and outbred CD1-Swiss mice, they induced a median frequency of over 6,000 T cells/106 splenocytes, which were plurifunctional, broadly specific, and cross-reactive. These results support further development of this vaccine concept.
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Affiliation(s)
- Edmund G Wee
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | | | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-8555, Japan.
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35
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McMichael AJ, Picker LJ. Unusual antigen presentation offers new insight into HIV vaccine design. Curr Opin Immunol 2017; 46:75-81. [PMID: 28505602 DOI: 10.1016/j.coi.2017.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/21/2017] [Accepted: 04/17/2017] [Indexed: 11/29/2022]
Abstract
Recent findings with a rhesus monkey cytomegalovirus based simian immunodeficiency virus vaccine have identified strong CD8+ T cell responses that are restricted by MHC-E. Also mycobacteria specific CD8+ T cells, that are MHC-E restricted, have been identified. MHC-E therefore can present a wide range of epitope peptides to CD8+ T cells, alongside its well defined role in presenting a conserved MHC-class I signal peptide to the NKG2A/C-CD94 receptor on natural killer cells. Here we explore the antigen processing pathways involved in these atypical T cell responses.
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Affiliation(s)
- Andrew J McMichael
- Nuffield Deparment of Medicine, Oxford University, Old Road Campus, Oxford OX37FZ, UK.
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006-3448, United States
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36
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Cole SL, Dunning J, Kok WL, Benam KH, Benlahrech A, Repapi E, Martinez FO, Drumright L, Powell TJ, Bennett M, Elderfield R, Thomas C, Dong T, McCauley J, Liew FY, Taylor S, Zambon M, Barclay W, Cerundolo V, Openshaw PJ, McMichael AJ, Ho LP. M1-like monocytes are a major immunological determinant of severity in previously healthy adults with life-threatening influenza. JCI Insight 2017; 2:e91868. [PMID: 28405622 PMCID: PMC5374077 DOI: 10.1172/jci.insight.91868] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In each influenza season, a distinct group of young, otherwise healthy individuals with no risk factors succumbs to life-threatening infection. To better understand the cause for this, we analyzed a broad range of immune responses in blood from a unique cohort of patients, comprising previously healthy individuals hospitalized with and without respiratory failure during one influenza season, and infected with one specific influenza A strain. This analysis was compared with similarly hospitalized influenza patients with known risk factors (total of n = 60 patients recruited). We found a sustained increase in a specific subset of proinflammatory monocytes, with high TNF-α expression and an M1-like phenotype (independent of viral titers), in these previously healthy patients with severe disease. The relationship between M1-like monocytes and immunopathology was strengthened using murine models of influenza, in which severe infection generated using different models (including the high-pathogenicity H5N1 strain) was also accompanied by high levels of circulating M1-like monocytes. Additionally, a raised M1/M2 macrophage ratio in the lungs was observed. These studies identify a specific subtype of monocytes as a modifiable immunological determinant of disease severity in this subgroup of severely ill, previously healthy patients, offering potential novel therapeutic avenues. In a cohort of influenza patients, previously healthy and young patients who succumbed to life-threatening disease were defined by high levels of circulating M1-like, TNF-αhi monocytes.
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Affiliation(s)
- Suzanne L Cole
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Jake Dunning
- National Heart and Lung Division, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Wai Ling Kok
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Kambez Hajipouran Benam
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adel Benlahrech
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Emmanouela Repapi
- Computational Biology Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Fernando O Martinez
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Lydia Drumright
- National Heart and Lung Division, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Timothy J Powell
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Ruth Elderfield
- Section of Virology, Faculty of Medicine, Wright Fleming Institute, Imperial College London, London, United Kingdom
| | - Catherine Thomas
- National Infection Service, Public Health England, Colindale, London, United Kingdom
| | | | - Tao Dong
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Foo Y Liew
- Division of Immunology, Infection and Inflammation, University of Glasgow, Glasgow, United Kingdom.,School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Stephen Taylor
- Computational Biology Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Maria Zambon
- National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Wendy Barclay
- Section of Virology, Faculty of Medicine, Wright Fleming Institute, Imperial College London, London, United Kingdom
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter J Openshaw
- National Heart and Lung Division, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Andrew J McMichael
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ling-Pei Ho
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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37
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Demers KR, Makedonas G, Buggert M, Eller MA, Ratcliffe SJ, Goonetilleke N, Li CK, Eller LA, Rono K, Maganga L, Nitayaphan S, Kibuuka H, Routy JP, Slifka MK, Haynes BF, McMichael AJ, Bernard NF, Robb ML, Betts MR. Temporal Dynamics of CD8+ T Cell Effector Responses during Primary HIV Infection. PLoS Pathog 2016; 12:e1005805. [PMID: 27486665 PMCID: PMC4972399 DOI: 10.1371/journal.ppat.1005805] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/11/2016] [Indexed: 01/12/2023] Open
Abstract
The loss of HIV-specific CD8+ T cell cytolytic function is a primary factor underlying progressive HIV infection, but whether HIV-specific CD8+ T cells initially possess cytolytic effector capacity, and when and why this may be lost during infection, is unclear. Here, we assessed CD8+ T cell functional evolution from primary to chronic HIV infection. We observed a profound expansion of perforin+ CD8+ T cells immediately following HIV infection that quickly waned after acute viremia resolution. Selective expression of the effector-associated transcription factors T-bet and eomesodermin in cytokine-producing HIV-specific CD8+ T cells differentiated HIV-specific from bulk memory CD8+ T cell effector expansion. As infection progressed expression of perforin was maintained in HIV-specific CD8+ T cells with high levels of T-bet, but not necessarily in the population of T-betLo HIV-specific CD8+ T cells that expand as infection progresses. Together, these data demonstrate that while HIV-specific CD8+ T cells in acute HIV infection initially possess cytolytic potential, progressive transcriptional dysregulation leads to the reduced CD8+ T cell perforin expression characteristic of chronic HIV infection. Previous studies have demonstrated that HIV-specific CD8+ T cells are critical for the initial control of HIV infection. However, this control is typically incomplete, being able to neither clear infection nor maintain plasma viremia below undetectable levels. Mounting evidence has implicated CD8+ T cell cytotoxic capacity as a critical component of the HIV-specific response associated with spontaneous long-term control of HIV replication. CD8+ T cell cytotoxic responses are largely absent in the vast majority of HIV chronically infected individuals and it is unclear when or why this functionality is lost. In this study we show that HIV-specific CD8+ T cells readily express the cytolytic protein perforin during the acute phase of chronic progressive HIV infection but rapidly lose the ability to upregulate this molecule following resolution of peak viremia. Maintenance of perforin expression by HIV-specific CD8+ T cells appears to be associated with the expression level of the transcription factor T-bet, but not with the T-bet paralogue, Eomes. These findings further delineate qualitative attributes of CD8+ T cell-mediated immunity that may serve as targets for future HIV vaccine and therapeutic research.
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Affiliation(s)
- Korey R. Demers
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George Makedonas
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marcus Buggert
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute, Karolinksa University Hospital Huddinge, Stockholm, Sweden
| | - Michael A. Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Sarah J. Ratcliffe
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nilu Goonetilleke
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, England
| | - Chris K. Li
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, England
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kathleen Rono
- Walter Reed Project-Kenya, Kenya Medical Research Institute, Kericho, Kenya
| | | | - Sorachai Nitayaphan
- Department of Retrovirology, United States Army Medical Component, Armed Forces Research Institute of Medical Sciences (USAMC-AFRIMS), Bangkok, Thailand
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Makerere University Medical School, Kampala, Uganda
| | - Jean-Pierre Routy
- Division of Hematology & Chronic Viral Illness Service, McGill University Health Centre, Montréal, Québec, Canada
| | - Mark K. Slifka
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Andrew J. McMichael
- NDM Research Building, Old Road Campus, University of Oxford, Oxford, United Kingdom
| | - Nicole F. Bernard
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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38
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Moody MA, Pedroza-Pacheco I, Vandergrift NA, Chui C, Lloyd KE, Parks R, Soderberg KA, Ogbe AT, Cohen MS, Liao HX, Gao F, McMichael AJ, Montefiori DC, Verkoczy L, Kelsoe G, Huang J, Shea PR, Connors M, Borrow P, Haynes BF. Immune perturbations in HIV-1-infected individuals who make broadly neutralizing antibodies. Sci Immunol 2016; 1:aag0851. [PMID: 28783677 DOI: 10.1126/sciimmunol.aag0851] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 06/05/2016] [Indexed: 12/16/2022]
Abstract
Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. bnAbs occur in some HIV-1-infected individuals and frequently have characteristics of autoantibodies. We have studied cohorts of HIV-1-infected individuals who made bnAbs and compared them with those who did not do so, and determined immune traits associated with the ability to produce bnAbs. HIV-1-infected individuals with bnAbs had a higher frequency of blood autoantibodies, a lower frequency of regulatory CD4+ T cells, a higher frequency of circulating memory T follicular helper CD4+ cells, and a higher T regulatory cell level of programmed cell death-1 expression compared with HIV-1-infected individuals without bnAbs. Thus, induction of HIV-1 bnAbs may require vaccination regimens that transiently mimic immunologic perturbations in HIV-1-infected individuals.
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Affiliation(s)
- M Anthony Moody
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. .,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Nathan A Vandergrift
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cecilia Chui
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Krissey E Lloyd
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kelly A Soderberg
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ane T Ogbe
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Myron S Cohen
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hua-Xin Liao
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Feng Gao
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laurent Verkoczy
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Garnett Kelsoe
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jinghe Huang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK.
| | - Barton F Haynes
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. .,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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39
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Barton JP, Goonetilleke N, Butler TC, Walker BD, McMichael AJ, Chakraborty AK. Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable. Nat Commun 2016; 7:11660. [PMID: 27212475 PMCID: PMC4879252 DOI: 10.1038/ncomms11660] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 04/18/2016] [Indexed: 12/05/2022] Open
Abstract
Human immunodeficiency virus (HIV) evolves within infected persons to escape being destroyed by the host immune system, thereby preventing effective immune control of infection. Here, we combine methods from evolutionary dynamics and statistical physics to simulate in vivo HIV sequence evolution, predicting the relative rate of escape and the location of escape mutations in response to T-cell-mediated immune pressure in a cohort of 17 persons with acute HIV infection. Predicted and clinically observed times to escape immune responses agree well, and we show that the mutational pathways to escape depend on the viral sequence background due to epistatic interactions. The ability to predict escape pathways and the duration over which control is maintained by specific immune responses open the door to rational design of immunotherapeutic strategies that might enable long-term control of HIV infection. Our approach enables intra-host evolution of a human pathogen to be predicted in a probabilistic framework.
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Affiliation(s)
- John P. Barton
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nilu Goonetilleke
- Department of Microbiology, Immunology and Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Thomas C. Butler
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Andrew J. McMichael
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Arup K. Chakraborty
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Ondondo B, Murakoshi H, Clutton G, Abdul-Jawad S, Wee EGT, Gatanaga H, Oka S, McMichael AJ, Takiguchi M, Korber B, Hanke T. Novel Conserved-region T-cell Mosaic Vaccine With High Global HIV-1 Coverage Is Recognized by Protective Responses in Untreated Infection. Mol Ther 2016; 24:832-42. [PMID: 26743582 PMCID: PMC4886941 DOI: 10.1038/mt.2016.3] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [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: 07/06/2015] [Accepted: 12/31/2015] [Indexed: 12/12/2022] Open
Abstract
An effective human immunodeficiency virus type 1 (HIV-1) vaccine is the best solution for halting the acquired immune deficiency syndrome epidemic. Here, we describe the design and preclinical immunogenicity of T-cell vaccine expressing novel immunogens tHIVconsvX, vectored by DNA, simian (chimpanzee) adenovirus, and poxvirus modified vaccinia virus Ankara (MVA), a combination highly immunogenic in humans. The tHIVconsvX immunogens combine the three leading strategies for elicitation of effective CD8(+) T cells: use of regions of HIV-1 proteins functionally conserved across all M group viruses (to make HIV-1 escape costly on viral fitness), inclusion of bivalent complementary mosaic immunogens (to maximize global epitope matching and breadth of responses, and block common escape paths), and inclusion of epitopes known to be associated with low viral load in infected untreated people (to induce field-proven protective responses). tHIVconsvX was highly immunogenic in two strains of mice. Furthermore, the magnitude and breadth of CD8(+) T-cell responses to tHIVconsvX-derived peptides in treatment-naive HIV-1(+) patients significantly correlated with high CD4(+) T-cell count and low viral load. Overall, the tHIVconsvX design, combining the mosaic and conserved-region approaches, provides an indisputably better coverage of global HIV-1 variants than previous T-cell vaccines. These immunogens delivered in a highly immunogenic framework of adenovirus prime and MVA boost are ready for clinical development.
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Affiliation(s)
- Beatrice Ondondo
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
| | | | - Genevieve Clutton
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
- Current address: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Edmund G-T Wee
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Bette Korber
- Los Alamo National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, USA
- The New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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Haynes BF, Shaw GM, Korber B, Kelsoe G, Sodroski J, Hahn BH, Borrow P, McMichael AJ. HIV-Host Interactions: Implications for Vaccine Design. Cell Host Microbe 2016; 19:292-303. [PMID: 26922989 DOI: 10.1016/j.chom.2016.02.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Development of an effective AIDS vaccine is a global priority. However, the extreme diversity of HIV type 1 (HIV-1), which is a consequence of its propensity to mutate to escape immune responses, along with host factors that prevent the elicitation of protective immune responses, continue to hinder vaccine development. Breakthroughs in understanding of the biology of the transmitted virus, the structure and nature of its envelope trimer, vaccine-induced CD8 T cell control in primates, and host control of broadly neutralizing antibody elicitation have given rise to new vaccine strategies. Despite this promise, emerging data from preclinical trials reinforce the need for additional insight into virus-host biology in order to facilitate the development of a successful vaccine.
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Affiliation(s)
- Barton F Haynes
- Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Duke University Human Vaccine Institute, Duke University, Durham, NC 27710, USA.
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC 27710, USA; Duke University Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Joseph Sodroski
- Dana Farber-Cancer Institute, Harvard Medical School, Harvard University, Boston, MA 02215, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
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Hansen SG, Wu HL, Burwitz BJ, Hughes CM, Hammond KB, Ventura AB, Reed JS, Gilbride RM, Ainslie E, Morrow DW, Ford JC, Selseth AN, Pathak R, Malouli D, Legasse AW, Axthelm MK, Nelson JA, Gillespie GM, Walters LC, Brackenridge S, Sharpe HR, López CA, Früh K, Korber BT, McMichael AJ, Gnanakaran S, Sacha JB, Picker LJ. Broadly targeted CD8⁺ T cell responses restricted by major histocompatibility complex E. Science 2016; 351:714-20. [PMID: 26797147 PMCID: PMC4769032 DOI: 10.1126/science.aac9475] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [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: 07/02/2015] [Accepted: 01/06/2016] [Indexed: 12/22/2022]
Abstract
Major histocompatibility complex E (MHC-E) is a highly conserved, ubiquitously expressed, nonclassical MHC class Ib molecule with limited polymorphism that is primarily involved in the regulation of natural killer (NK) cells. We found that vaccinating rhesus macaques with rhesus cytomegalovirus vectors in which genes Rh157.5 and Rh157.4 are deleted results in MHC-E-restricted presentation of highly varied peptide epitopes to CD8αβ(+) T cells, at ~4 distinct epitopes per 100 amino acids in all tested antigens. Computational structural analysis revealed that MHC-E provides heterogeneous chemical environments for diverse side-chain interactions within a stable, open binding groove. Because MHC-E is up-regulated to evade NK cell activity in cells infected with HIV, simian immunodeficiency virus, and other persistent viruses, MHC-E-restricted CD8(+) T cell responses have the potential to exploit pathogen immune-evasion adaptations, a capability that might endow these unconventional responses with superior efficacy.
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Affiliation(s)
- Scott G. Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Helen L. Wu
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Benjamin J. Burwitz
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Colette M. Hughes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Katherine B. Hammond
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Abigail B. Ventura
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Jason S. Reed
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Roxanne M. Gilbride
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Emily Ainslie
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - David W. Morrow
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Julia C. Ford
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Andrea N. Selseth
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Reesab Pathak
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Alfred W. Legasse
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Michael K. Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Jay A. Nelson
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | | | - Lucy C. Walters
- Nuffield Department of Medicine, University of Oxford, OX37FZ, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Medicine, University of Oxford, OX37FZ, United Kingdom
| | - Hannah R. Sharpe
- Nuffield Department of Medicine, University of Oxford, OX37FZ, United Kingdom
| | - César A. López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory
| | - Klaus Früh
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Bette T. Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory
- The New Mexico Consortium, Los Alamos, NM 87545
| | - Andrew J. McMichael
- Nuffield Department of Medicine, University of Oxford, OX37FZ, United Kingdom
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory
| | - Jonah B. Sacha
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
| | - Louis J. Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006
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Hayward AC, Wang L, Goonetilleke N, Fragaszy EB, Bermingham A, Copas A, Dukes O, Millett ERC, Nazareth I, Nguyen-Van-Tam JS, Watson JM, Zambon M, Johnson AM, McMichael AJ. Natural T Cell-mediated Protection against Seasonal and Pandemic Influenza. Results of the Flu Watch Cohort Study. Am J Respir Crit Care Med 2015; 191:1422-31. [PMID: 25844934 DOI: 10.1164/rccm.201411-1988oc] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE A high proportion of influenza infections are asymptomatic. Animal and human challenge studies and observational studies suggest T cells protect against disease among those infected, but the impact of T-cell immunity at the population level is unknown. OBJECTIVES To investigate whether naturally preexisting T-cell responses targeting highly conserved internal influenza proteins could provide cross-protective immunity against pandemic and seasonal influenza. METHODS We quantified influenza A(H3N2) virus-specific T cells in a population cohort during seasonal and pandemic periods between 2006 and 2010. Follow-up included paired serology, symptom reporting, and polymerase chain reaction (PCR) investigation of symptomatic cases. MEASUREMENTS AND MAIN RESULTS A total of 1,414 unvaccinated individuals had baseline T-cell measurements (1,703 participant observation sets). T-cell responses to A(H3N2) virus nucleoprotein (NP) dominated and strongly cross-reacted with A(H1N1)pdm09 NP (P < 0.001) in participants lacking antibody to A(H1N1)pdm09. Comparison of paired preseason and post-season sera (1,431 sets) showed 205 (14%) had evidence of infection based on fourfold influenza antibody titer rises. The presence of NP-specific T cells before exposure to virus correlated with less symptomatic, PCR-positive influenza A (overall adjusted odds ratio, 0.27; 95% confidence interval, 0.11-0.68; P = 0.005, during pandemic [P = 0.047] and seasonal [P = 0.049] periods). Protection was independent of baseline antibodies. Influenza-specific T-cell responses were detected in 43%, indicating a substantial population impact. CONCLUSIONS Naturally occurring cross-protective T-cell immunity protects against symptomatic PCR-confirmed disease in those with evidence of infection and helps to explain why many infections do not cause symptoms. Vaccines stimulating T cells may provide important cross-protective immunity.
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Affiliation(s)
- Andrew C Hayward
- 1 Department of Infectious Disease Informatics, Farr Institute of Health Informatics Research
| | - Lili Wang
- 2 Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Nilu Goonetilleke
- 2 Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,3 Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ellen B Fragaszy
- 1 Department of Infectious Disease Informatics, Farr Institute of Health Informatics Research.,4 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Alison Bermingham
- 5 Respiratory Virus Unit, Centre for Infections, Public Health England, Colindale, United Kingdom
| | - Andrew Copas
- 6 Research Department of Infection and Population Health, and
| | - Oliver Dukes
- 1 Department of Infectious Disease Informatics, Farr Institute of Health Informatics Research
| | - Elizabeth R C Millett
- 6 Research Department of Infection and Population Health, and.,4 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Irwin Nazareth
- 7 Department of Primary Care and Population Health, University College London, London, United Kingdom
| | - Jonathan S Nguyen-Van-Tam
- 8 Health Protection and Influenza Research Group, Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom; and
| | | | - Maria Zambon
- 5 Respiratory Virus Unit, Centre for Infections, Public Health England, Colindale, United Kingdom
| | | | - Anne M Johnson
- 6 Research Department of Infection and Population Health, and
| | - Andrew J McMichael
- 2 Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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McMichael AJ, Butler CD, Dixon J. Climate change, food systems and population health risks in their eco-social context. Public Health 2015; 129:1361-8. [PMID: 25896548 DOI: 10.1016/j.puhe.2014.11.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 04/05/2013] [Accepted: 11/17/2014] [Indexed: 11/29/2022]
Abstract
The establishment of ecological public health as crucial to modern public health is overdue. While the basic concepts have been gestating for decades, receptivity within broader public health has been limited. This position is changing, not least as the population-level impacts of climate change and, more broadly, of limits to growth are emerging from theory and forecasting into daily reality. This paper describes several key elements of ecological public health thinking. These include the 'environmental' risks to human health (often systemic and disruptive, rather than local and toxic) posed by climate change and other forms of adverse global environmental change. Closer recognition of the links between social and environmental factors has been urged--an 'eco-social' approach--and, relatedly, for greater co-operation between social and natural sciences. The authors revisit critics of capitalism who foresaw the global capture and transformation of ecosystems for material human ends, and their resultant despoliation. The perennial call within public health to reduce vulnerability by lessening poverty is more important than ever, given the multifactored threat to the health of the poor which is anticipated, assuming no radical strategies to alleviate these pressures. But enhanced health security for the poor requires more than the reconfiguring of social determinants; it also requires, as the overarching frame, ecological public health.
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Affiliation(s)
- A J McMichael
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
| | - C D Butler
- Faculty of Health, University of Canberra, Canberra, Australia.
| | - J Dixon
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
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45
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Townsend AR, McMichael AJ. Specificity of cytotoxic T lymphocytes stimulated with influenza virus. Studies in mice and humans. Prog Allergy 2015; 36:10-43. [PMID: 3881777 DOI: 10.1159/000409860] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Smith NMG, Mlcochova P, Watters SA, Aasa-Chapman MMI, Rabin N, Moore S, Edwards SG, Garson JA, Grant PR, Ferns RB, Kashuba A, Mayor NP, Schellekens J, Marsh SGE, McMichael AJ, Perelson AS, Pillay D, Goonetilleke N, Gupta RK. Proof-of-Principle for Immune Control of Global HIV-1 Reactivation In Vivo. Clin Infect Dis 2015; 61:120-8. [PMID: 25778749 PMCID: PMC4463006 DOI: 10.1093/cid/civ219] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 01/18/2015] [Accepted: 02/09/2015] [Indexed: 12/22/2022] Open
Abstract
It is unclear whether the human immune response is sufficiently potent to clear human immunodeficiency virus (HIV) type 1 latently infected cells globally reactivated by drug treatment. We report an elite controller who, following myeloablation and full HIV reactivation, achieved sustained control of viremia. Background. Emerging data relating to human immunodeficiency virus type 1 (HIV-1) cure suggest that vaccination to stimulate the host immune response, particularly cytotoxic cells, may be critical to clearing of reactivated HIV-1–infected cells. However, evidence for this approach in humans is lacking, and parameters required for a vaccine are unknown because opportunities to study HIV-1 reactivation are rare. Methods. We present observations from a HIV-1 elite controller, not treated with combination antiretroviral therapy, who experienced viral reactivation following treatment for myeloma with melphalan and autologous stem cell transplantation. Mathematical modeling was performed using a standard viral dynamic model. Enzyme-linked immunospot, intracellular cytokine staining, and tetramer staining were performed on peripheral blood mononuclear cells; in vitro CD8 T-cell–mediated control of virion production by autologous CD4 T cells was quantified; and neutralizing antibody titers were measured. Results. Viral rebound was measured at 28 000 copies/mL on day 13 post-transplant before rapid decay to <50 copies/mL in 2 distinct phases with t1/2 of 0.71 days and 4.1 days. These kinetics were consistent with an expansion of cytotoxic effector cells and killing of productively infected CD4 T cells. Following transplantation, innate immune cells, including natural killer cells, recovered with virus rebound. However, most striking was the expansion of highly functional HIV-1–specific cytotoxic CD8 T cells, at numbers consistent with those applied in modeling, as virus control was regained. Conclusions. These observations provide evidence that the human immune response is capable of controlling coordinated global HIV-1 reactivation, remarkably with potency equivalent to combination antiretroviral therapy. These data will inform design of vaccines for use in HIV-1 curative interventions.
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Affiliation(s)
| | - Petra Mlcochova
- Department of Infection, Division of Infection and Immunity, University College London
| | - Sarah A Watters
- Department of Infection, Division of Infection and Immunity, University College London
| | | | - Neil Rabin
- University College London Hospitals National Health Service (NHS) Foundation Trust
| | - Sally Moore
- University College London Hospitals National Health Service (NHS) Foundation Trust
| | - Simon G Edwards
- Mortimer Market Centre, Central and North West London NHS Foundation Trust, United Kingdom
| | - Jeremy A Garson
- Department of Infection, Division of Infection and Immunity, University College London
| | - Paul R Grant
- University College London Hospitals National Health Service (NHS) Foundation Trust
| | - R Bridget Ferns
- Department of Infection, Division of Infection and Immunity, University College London
| | - Angela Kashuba
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
| | - Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital Cancer Institute, University College London, United Kingdom
| | - Jennifer Schellekens
- Anthony Nolan Research Institute, Royal Free Hospital Cancer Institute, University College London, United Kingdom
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital Cancer Institute, University College London, United Kingdom
| | | | | | - Deenan Pillay
- Department of Infection, Division of Infection and Immunity, University College London Africa Centre for Health and Population Sciences, University of KwaZulu Natal, South Africa
| | - Nilu Goonetilleke
- Nuffield Department of Medicine, University of Oxford Department of Microbiology & Immunology, University of North Carolina at Chapel Hill
| | - Ravindra K Gupta
- Department of Infection, Division of Infection and Immunity, University College London
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47
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Bowles EJ, Schiffner T, Rosario M, Needham GA, Ramaswamy M, McGouran J, Kessler B, LaBranche C, McMichael AJ, Montefiori D, Sattentau QJ, Hanke T, Stewart-Jones GBE. Comparison of neutralizing antibody responses elicited from highly diverse polyvalent heterotrimeric HIV-1 gp140 cocktail immunogens versus a monovalent counterpart in rhesus macaques. PLoS One 2014; 9:e114709. [PMID: 25490553 PMCID: PMC4260879 DOI: 10.1371/journal.pone.0114709] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 11/12/2014] [Indexed: 12/22/2022] Open
Abstract
Eliciting neutralizing antibodies capable of inactivating a broad spectrum of HIV-1 strains is a major goal of HIV-1 vaccine design. The challenge is that envelopes (Envs) of circulating viruses are almost certainly different from any Env used in a vaccine. A novel immunogen composed of a highly diverse set of gp140 Envs including subtypes A, B, C, D and F was developed to stimulate a more cross-neutralizing antibody response. Env heterotrimers composed of up to 54 different gp140s were produced with the aim of focusing the response to the conserved regions of Env while reducing the dominance of any individual hypervariable region. Heterotrimeric gp140 Envs of inter- and intra-subtype combinations were shown to bind CD4 and a panel of neutralizing monoclonal antibodies with similar affinity to monovalent UG37 gp140. Macaques immunized with six groups of heterotrimer mixtures showed slightly more potent neutralizing antibody responses in TZM-BL tier 1 and A3R5 tier 2 pseudovirus assays than macaques immunized with monovalent Env gp140, and exhibited a marginally greater focus on the CD4-binding site. Carbopol enhanced neutralization when used as an adjuvant instead of RIBI in combination with UG37 gp140. These data indicate that cross-subtype heterotrimeric gp140 Envs may elicit some improvement of the neutralizing antibody response in macaques compared to monovalent gp140 Env.
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Affiliation(s)
- Emma J. Bowles
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
- * E-mail: (EJB); (GSJ)
| | - Torben Schiffner
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Maximillian Rosario
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
| | - Gemma A. Needham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Meghna Ramaswamy
- Division of Retrovirology, Centre for AIDS Reagents, National Institute of Biological Standards and Control, South Mimms, Potters Bar, Herts, United Kingdom
| | - Joanna McGouran
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt Kessler
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Celia LaBranche
- Division of Surgical Sciences, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Andrew J. McMichael
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
| | - David Montefiori
- Division of Surgical Sciences, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Quentin J. Sattentau
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Tomáš Hanke
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, United Kingdom
| | - Guillaume B. E. Stewart-Jones
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
- * E-mail: (EJB); (GSJ)
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48
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Liu D, Zuo T, Hora B, Song H, Kong W, Yu X, Goonetilleke N, Bhattacharya T, Perelson AS, Haynes BF, McMichael AJ, Gao F. Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation. Retrovirology 2014; 11:101. [PMID: 25407514 PMCID: PMC4264250 DOI: 10.1186/s12977-014-0101-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fitness costs and slower disease progression are associated with a cytolytic T lymphocyte (CTL) escape mutation T242N in Gag in HIV-1-infected individuals carrying HLA-B*57/5801 alleles. However, the impact of different context in diverse HIV-1 strains on the fitness costs due to the T242N mutation has not been well characterized. To better understand the extent of fitness costs of the T242N mutation and the repair of fitness loss through compensatory amino acids, we investigated its fitness impact in different transmitted/founder (T/F) viruses. RESULTS The T242N mutation resulted in various levels of fitness loss in four different T/F viruses. However, the fitness costs were significantly compromised by preexisting compensatory amino acids in (Isoleucine at position 247) or outside (glutamine at position 219) the CTL epitope. Moreover, the transmitted T242N escape mutant in subject CH131 was as fit as the revertant N242T mutant and the elimination of the compensatory amino acid I247 in the T/F viral genome resulted in significant fitness cost, suggesting the fitness loss caused by the T242N mutation had been fully repaired in the donor at transmission. Analysis of the global circulating HIV-1 sequences in the Los Alamos HIV Sequence Database showed a high prevalence of compensatory amino acids for the T242N mutation and other T cell escape mutations. CONCLUSIONS Our results show that the preexisting compensatory amino acids in the majority of circulating HIV-1 strains could significantly compromise the fitness loss due to CTL escape mutations and thus increase challenges for T cell based vaccines.
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Affiliation(s)
- Donglai Liu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA. .,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
| | - Tao Zuo
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA. .,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Hongshuo Song
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Wei Kong
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
| | - Xianghui Yu
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
| | - Nilu Goonetilleke
- Department of Microbiology, Immunology and Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National laboratory, Los Alamos, NM, 87545, USA.
| | - Alan S Perelson
- Theoretical Division, Los Alamos National laboratory, Los Alamos, NM, 87545, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Andrew J McMichael
- Weatherall Institute of molecular Medicine, University of Oxford, Oxford, OX3 9DS, England, UK.
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA. .,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
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Abstract
The influenza virus behaves unpredictably and can cause devastating pandemics. Nearly 50 years after its first isolation it is probably the most infectious agent known that we cannot yet control. Why? The answer lies in the virus's unique capacity to alter antigenically and in the inability of the host's immune system to respond satisfactorily to the vaccines currently available. What follows is a record, prepared exclusively for Immunology Today, of a conference held in Oxford on March 21-24 this year, to discuss problems relating to protection against influenza.
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Affiliation(s)
- A J McMichael
- A. J. McMichael is in the Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, U.K
| | - B A Askonas
- B. A. Askonas is in the Immunology Division, National Institute for Medical Research, Mill Hill, London, U.K
| | - R G Webster
- R. G. Webster is in the St Judes Children's Research Hospital, Memphis, Tennessee, USA
| | - W G Laver
- W. G. Laver is in the Department of Microbiology, John Curtin School of Medical Research, Australian National University, Canberra City, Australia
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Ritchie AJ, Cai F, Smith NMG, Chen S, Song H, Brackenridge S, Abdool Karim SS, Korber BT, McMichael AJ, Gao F, Goonetilleke N. Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection. Retrovirology 2014; 11:69. [PMID: 25212771 PMCID: PMC4180588 DOI: 10.1186/s12977-014-0069-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 07/31/2014] [Indexed: 12/02/2022] Open
Abstract
Background A major immune evasion mechanism of HIV-1 is the accumulation of non-synonymous mutations in and around T cell epitopes, resulting in loss of T cell recognition and virus escape. Results Here we analyze primary CD8+ T cell responses and virus escape in a HLA B*81 expressing subject who was infected with two T/F viruses from a single donor. In addition to classic escape through non-synonymous mutation/s, we also observed rapid selection of multiple recombinant viruses that conferred escape from T cells specific for two epitopes in Nef. Conclusions Our study shows that recombination between multiple T/F viruses provide greater options for acute escape from CD8+ T cell responses than seen in cases of single T/F virus infection. This process may contribute to the rapid disease progression in patients infected by multiple T/F viruses. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0069-9) contains supplementary material, which is available to authorized users.
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