1
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Protective HLA-B57: T cell and natural killer cell recognition in HIV infection. Biochem Soc Trans 2022; 50:1329-1339. [DOI: 10.1042/bst20220244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Understanding the basis of the immune determinants controlling disease outcome is critical to provide better care to patients and could be exploited for therapeutics and vaccine design. The discovery of the human immunodeficiency virus (HIV) virus as the causing agent of acquired immunodeficiency syndrome (AIDS) decades ago, led to a tremendous amount of research. Among the findings, it was discovered that some rare HIV+ individuals, called HIV controllers (HICs), had the ability to control the virus and keep a low viral load without the need of treatment. This ability allows HICs to delay or avoid progression to AIDS. HIV control is strongly associated with the expression of human leukocyte antigen (HLA) alleles in HICs. From the HIV protective HLAs described, HLA-B57 is the most frequent in HIC patients. HLA-B57 can present a large range of highly conserved Gag-derived HIV peptides to CD8+ T cells and natural killer (NK) cells, both the focus of this review. So far there are limited differences in the immune response strength, magnitude, or receptor repertoire towards HIV epitopes that could explain viral control in HICs. Interestingly, some studies revealed that during early infection the large breadth of the immune response towards HIV mutants in HLA-B57+ HIC patients, might in turn influence the disease outcome.
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2
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A transformer-based model to predict peptide–HLA class I binding and optimize mutated peptides for vaccine design. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00459-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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3
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Pymm P, Tenzer S, Wee E, Weimershaus M, Burgevin A, Kollnberger S, Gerstoft J, Josephs TM, Ladell K, McLaren JE, Appay V, Price DA, Fugger L, Bell JI, Schild H, van Endert P, Harkiolaki M, Iversen AKN. Epitope length variants balance protective immune responses and viral escape in HIV-1 infection. Cell Rep 2022; 38:110449. [PMID: 35235807 PMCID: PMC9631117 DOI: 10.1016/j.celrep.2022.110449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/31/2021] [Accepted: 02/07/2022] [Indexed: 11/21/2022] Open
Abstract
Cytotoxic T lymphocyte (CTL) and natural killer (NK) cell responses to a single optimal 10-mer epitope (KK10) in the human immunodeficiency virus type-1 (HIV-1) protein p24Gag are associated with enhanced immune control in patients expressing human leukocyte antigen (HLA)-B∗27:05. We find that proteasomal activity generates multiple length variants of KK10 (4-14 amino acids), which bind TAP and HLA-B∗27:05. However, only epitope forms ≥8 amino acids evoke peptide length-specific and cross-reactive CTL responses. Structural analyses reveal that all epitope forms bind HLA-B∗27:05 via a conserved N-terminal motif, and competition experiments show that the truncated epitope forms outcompete immunogenic epitope forms for binding to HLA-B∗27:05. Common viral escape mutations abolish (L136M) or impair (R132K) production of KK10 and longer epitope forms. Peptide length influences how well the inhibitory NK cell receptor KIR3DL1 binds HLA-B∗27:05 peptide complexes and how intraepitope mutations affect this interaction. These results identify a viral escape mechanism from CTL and NK responses based on differential antigen processing and peptide competition.
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Affiliation(s)
- Phillip Pymm
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK; Walter and Eliza Hall Institute of Medical Research, University of Melbourne, 1G Royalparade, Parkville, VIC 3052, Australia
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Edmund Wee
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Mirjana Weimershaus
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Anne Burgevin
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Simon Kollnberger
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - Jan Gerstoft
- Department of Infectious Diseases, Rigshospitalet, The National University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Tracy M Josephs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK
| | - Victor Appay
- Institut National de la Santé et de la Recherche Médicale, Unité 1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Boulevard de l'Hopital, 75013 Paris, France; International Research Center of Medical Sciences, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto City 860-0811, Japan
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, CF14 4XN Cardiff, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Tenovus Building, CF14 4XN Cardiff, UK
| | - Lars Fugger
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK; Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, OX3 9DS Oxford, UK
| | - John I Bell
- Office of the Regius Professor of Medicine, The Richard Doll Building, University of Oxford, Old Road Campus, OX3 7LF Oxford, UK
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University of Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker, 149 Rue de Severs, 75015 Paris, France
| | - Maria Harkiolaki
- Structural Biology Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Old Road Campus, OX3 7LF Oxford, UK; Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, OX11 0DE Didcot, UK
| | - Astrid K N Iversen
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK.
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4
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Luo Y, Kanai M, Choi W, Li X, Sakaue S, Yamamoto K, Ogawa K, Gutierrez-Arcelus M, Gregersen PK, Stuart PE, Elder JT, Forer L, Schönherr S, Fuchsberger C, Smith AV, Fellay J, Carrington M, Haas DW, Guo X, Palmer ND, Chen YDI, Rotter JI, Taylor KD, Rich SS, Correa A, Wilson JG, Kathiresan S, Cho MH, Metspalu A, Esko T, Okada Y, Han B, McLaren PJ, Raychaudhuri S. A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response. Nat Genet 2021; 53:1504-1516. [PMID: 34611364 PMCID: PMC8959399 DOI: 10.1038/s41588-021-00935-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/02/2021] [Indexed: 02/08/2023]
Abstract
Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particularly in the MHC, which has population-specific structure. To enable such studies, we constructed a large (n = 21,546) HLA reference panel spanning five global populations based on whole-genome sequences. Despite population-specific long-range haplotypes, we demonstrated accurate imputation at G-group resolution (94.2%, 93.7%, 97.8% and 93.7% in admixed African (AA), East Asian (EAS), European (EUR) and Latino (LAT) populations). Applying HLA imputation to genome-wide association study data for HIV-1 viral load in three populations (EUR, AA and LAT), we obviated effects of previously reported associations from population-specific HIV studies and discovered a novel association at position 156 in HLA-B. We pinpointed the MHC association to three amino acid positions (97, 67 and 156) marking three consecutive pockets (C, B and D) within the HLA-B peptide-binding groove, explaining 12.9% of trait variance.
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Affiliation(s)
- Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Masahiro Kanai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Wanson Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Xinyi Li
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Maria Gutierrez-Arcelus
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter K Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research,North Short LIJ Health System, Manhasset, NY, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, USA
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Fuchsberger
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Albert V Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - David W Haas
- Vanderbilt University Medical Center, Nashville, TN, USA
- Meharry Medical College, Nashville, TN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Adolfo Correa
- Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - James G Wilson
- Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiology Division of the Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tonu Esko
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Paul J McLaren
- J.C. Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Immunology, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK.
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5
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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] [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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6
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Mohamed YS, Borthwick NJ, Moyo N, Murakoshi H, Akahoshi T, Siliquini F, Hannoun Z, Crook A, Hayes P, Fast PE, Mutua G, Jaoko W, Silva-Arrieta S, Llano A, Brander C, Takiguchi M, Hanke T. Specificity of CD8 + T-Cell Responses Following Vaccination with Conserved Regions of HIV-1 in Nairobi, Kenya. Vaccines (Basel) 2020; 8:E260. [PMID: 32485938 PMCID: PMC7349992 DOI: 10.3390/vaccines8020260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 01/08/2023] Open
Abstract
Sub-Saharan Africa carries the biggest burden of the human immunodeficiency virus type 1 (HIV-1)/AIDS epidemic and is in an urgent need of an effective vaccine. CD8+ T cells are an important component of the host immune response to HIV-1 and may need to be harnessed if a vaccine is to be effective. CD8+ T cells recognize human leukocyte antigen (HLA)-associated viral epitopes and the HLA alleles vary significantly among different ethnic groups. It follows that definition of HIV-1-derived peptides recognized by CD8+ T cells in the geographically relevant regions will critically guide vaccine development. Here, we study fine details of CD8+ T-cell responses elicited in HIV-1/2-uninfected individuals in Nairobi, Kenya, who received a candidate vaccine delivering conserved regions of HIV-1 proteins called HIVconsv. Using 10-day cell lines established by in vitro peptide restimulation of cryopreserved PBMC and stably HLA-transfected 721.221/C1R cell lines, we confirm experimentally many already defined epitopes, for a number of epitopes we define the restricting HLA molecule(s) and describe four novel HLA-epitope pairs. We also identify specific dominance patterns, a promiscuous T-cell epitope and a rescue of suboptimal T-cell epitope induction in vivo by its functional variant, which all together inform vaccine design.
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Affiliation(s)
- Yehia S. Mohamed
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11823, Egypt
| | - Nicola J. Borthwick
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Nathifa Moyo
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Hayato Murakoshi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Tomohiro Akahoshi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Francesca Siliquini
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Zara Hannoun
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Alison Crook
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Peter Hayes
- International AIDS Vaccine Initiative IAVI-Human Immunology Laboratory, Imperial College London, London SW10 9NH, UK;
| | - Patricia E. Fast
- International AIDS Vaccine Initiative-New York, New York, NY 10004, USA;
| | - Gaudensia Mutua
- KAVI-Institute of Clinical Research, University of Nairobi, Nairobi 19676 00202, Kenya; (G.M.); (W.J.)
| | - Walter Jaoko
- KAVI-Institute of Clinical Research, University of Nairobi, Nairobi 19676 00202, Kenya; (G.M.); (W.J.)
| | - Sandra Silva-Arrieta
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
| | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
- Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
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7
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Hu Y, Wang Z, Hu H, Wan F, Chen L, Xiong Y, Wang X, Zhao D, Huang W, Zeng J. ACME: pan-specific peptide–MHC class I binding prediction through attention-based deep neural networks. Bioinformatics 2019; 35:4946-4954. [PMID: 31120490 DOI: 10.1093/bioinformatics/btz427] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/12/2019] [Accepted: 05/19/2019] [Indexed: 12/30/2022] Open
Abstract
Abstract
Motivation
Prediction of peptide binding to the major histocompatibility complex (MHC) plays a vital role in the development of therapeutic vaccines for the treatment of cancer. Algorithms with improved correlations between predicted and actual binding affinities are needed to increase precision and reduce the number of false positive predictions.
Results
We present ACME (Attention-based Convolutional neural networks for MHC Epitope binding prediction), a new pan-specific algorithm to accurately predict the binding affinities between peptides and MHC class I molecules, even for those new alleles that are not seen in the training data. Extensive tests have demonstrated that ACME can significantly outperform other state-of-the-art prediction methods with an increase of the Pearson correlation coefficient between predicted and measured binding affinities by up to 23 percentage points. In addition, its ability to identify strong-binding peptides has been experimentally validated. Moreover, by integrating the convolutional neural network with attention mechanism, ACME is able to extract interpretable patterns that can provide useful and detailed insights into the binding preferences between peptides and their MHC partners. All these results have demonstrated that ACME can provide a powerful and practically useful tool for the studies of peptide–MHC class I interactions.
Availability and implementation
ACME is available as an open source software at https://github.com/HYsxe/ACME.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yan Hu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Ziqiang Wang
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Hailin Hu
- School of Medicine, Tsinghua University, Beijing, China
| | - Fangping Wan
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Lin Chen
- Turing AI Institute of Nanjing, Nanjing, China
| | - Yuanpeng Xiong
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
- Bioinformatics Division, BNRIST/Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Xiaoxia Wang
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
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8
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Abels WC, Manandhar T, Kunze-Schumacher H, Blasczyk R, Bade-Döding C. The polymorphism at residue 156 determines the HLA-B*35 restricted peptide repertoire during HCMV infection. Immunogenetics 2018; 70:639-646. [PMID: 30128813 PMCID: PMC6182399 DOI: 10.1007/s00251-018-1077-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/16/2018] [Indexed: 12/27/2022]
Abstract
Peptide selection in infected cells is not fully understood yet, but several indications point to the fact that there are differences to uninfected cells, especially in productive HCMV infection, since HCMV evolved various strategies to disable the hosts immune system, including presentation of peptide-HLA complexes to immune effector cells. Therefore, peptide predictions for specific HLA alleles are limited in these cases and the naturally presented peptide repertoire of HCMV-infected cells is of major interest to optimize adoptive T cell therapies. The allotypes HLA-B*35:01 and B*35:08 differ at a single amino acid at position 156 and have been described to differ in their peptide features and in their association with the peptide loading complex. Virus specific T cells recognizing the allelic pHLA-B*35 complexes could be detected, indicating a significant role of this HLA subtypes in viral immunity. However, naturally selected and presented viral peptides have not been described so far. In this study, we analyzed the peptide binding repertoire for HLA-B*35:01 and HLA-B*35:08 in HCMV-infected cells. The isolated peptides from both allelic subtypes were of extraordinary length, however differed in their features, origin, and sequence. For these HCMV-originated peptides, no overlap in the peptide repertoire could be observed between the two allelic subtypes. These findings reveal the discrepancies between predicted and naturally presented immunogenic epitopes and support the need of comprehensive peptide recruitment data for personalized and effective cellular therapies.
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Affiliation(s)
- Wiebke C Abels
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Trishna Manandhar
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | | | - Rainer Blasczyk
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
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9
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Ramsbottom KA, Carr DF, Jones AR, Rigden DJ. Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions. Mol Immunol 2018; 101:488-499. [PMID: 30125869 PMCID: PMC6148408 DOI: 10.1016/j.molimm.2018.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/27/2018] [Accepted: 08/03/2018] [Indexed: 01/11/2023]
Abstract
All software assessed could dock Abacavir back into the risk allele structure but not always predict the exact binding mode. Most docking software assessed can distinguish between risk and control alleles. Docking performance can be degraded by using a homology model. Receptor flexibility can negatively affect the docking performance for complex HLA examples. Using AutoDockFR cannot compensate for the added difficulty of docking to the unbound target.
Adverse drug reactions have been linked with genetic polymorphisms in HLA genes in numerous different studies. HLA proteins have an essential role in the presentation of self and non-self peptides, as part of the adaptive immune response. Amongst the associated drugs-allele combinations, anti-HIV drug Abacavir has been shown to be associated with the HLA-B*57:01 allele, and anti-epilepsy drug Carbamazepine with B*15:02, in both cases likely following the altered peptide repertoire model of interaction. Under this model, the drug binds directly to the antigen presentation region, causing different self peptides to be presented, which trigger an unwanted immune response. There is growing interest in searching for evidence supporting this model for other ADRs using bioinformatics techniques. In this study, in silico docking was used to assess the utility and reliability of well-known docking programs when addressing these challenging HLA-drug situations. The overall aim was to address the uncertainty of docking programs giving different results by completing a detailed comparative study of docking software, grounded in the MHC-ligand experimental structural data – for Abacavir and to a lesser extent Carbamazepine - in order to assess their performance. Four docking programs: SwissDock, ROSIE, AutoDock Vina and AutoDockFR, were used to investigate if each software could accurately dock the Abacavir back into the crystal structure for the protein arising from the known risk allele, and if they were able to distinguish between the HLA-associated and non-HLA-associated (control) alleles. The impact of using homology models on the docking performance and how using different parameters, such as including receptor flexibility, affected the docking performance were also investigated to simulate the approach where a crystal structure for a given HLA allele may be unavailable. The programs that were best able to predict the binding position of Abacavir were then used to recreate the docking seen for Carbamazepine with B*15:02 and controls alleles. It was found that the programs investigated were sometimes able to correctly predict the binding mode of Abacavir with B*57:01 but not always. Each of the software packages that were assessed could predict the binding of Abacavir and Carbamazepine within the correct sub-pocket and, with the exception of ROSIE, was able to correctly distinguish between risk and control alleles. We found that docking to homology models could produce poorer quality predictions, especially when sequence differences impact the architecture of predicted binding pockets. Caution must therefore be used as inaccurate structures may lead to erroneous docking predictions. Incorporating receptor flexibility was found to negatively affect the docking performance for the examples investigated. Taken together, our findings help characterise the potential but also the limitations of computational prediction of drug-HLA interactions. These docking techniques should therefore always be used with care and alongside other methods of investigation, in order to be able to draw strong conclusions from the given results.
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Affiliation(s)
- Kerry A Ramsbottom
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel F Carr
- MRC Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
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10
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Martin MP, Naranbhai V, Shea PR, Qi Y, Ramsuran V, Vince N, Gao X, Thomas R, Brumme ZL, Carlson JM, Wolinsky SM, Goedert JJ, Walker BD, Segal FP, Deeks SG, Haas DW, Migueles SA, Connors M, Michael N, Fellay J, Gostick E, Llewellyn-Lacey S, Price DA, Lafont BA, Pymm P, Saunders PM, Widjaja J, Wong SC, Vivian JP, Rossjohn J, Brooks AG, Carrington M. Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1. J Clin Invest 2018; 128:1903-1912. [PMID: 29461980 PMCID: PMC5919796 DOI: 10.1172/jci98463] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 01/11/2023] Open
Abstract
HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57+ individuals. Using whole-genome sequencing of untreated B*57+ HIV-1-infected controllers and noncontrollers, we identified a single variant (rs643347A/G) encoding an isoleucine-to-valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor KIR3DL1 as the only significant modifier of B*57 protection. The association was replicated in an independent cohort and across multiple outcomes. The modifying effect of I47V was confined to B*57:01 and was not observed for the closely related B*57:03. Positions 2, 47, and 54 tracked one another nearly perfectly, and 2 KIR3DL1 allotypes differing only at these 3 positions showed significant differences in binding B*57:01 tetramers, whereas the protective allotype showed lower binding. Thus, variation in an immune NK cell receptor that binds B*57:01 modifies its protection. These data highlight the exquisite specificity of KIR-HLA interactions in human health and disease.
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Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Vivek Naranbhai
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Patrick R. Shea
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Veron Ramsuran
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas Vince
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- ATIP-Avenir, Centre de Recherche en Transplantation et Immunologie, UMR 1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - Steven M. Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | | | - Steven G. Deeks
- San Francisco General Hospital Medical Center, San Francisco, California, USA
| | - David W. Haas
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Stephen A. Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Nelson Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Jacques Fellay
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Emma Gostick
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom
- Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
| | - Sian Llewellyn-Lacey
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom
- Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
| | - David A. Price
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Bernard A. Lafont
- Viral Immunology Section, Office of the Scientific Director, NIAID, NIH, Bethesda, Maryland, USA
| | - Phillip Pymm
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Philippa M. Saunders
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Jacqueline Widjaja
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Shu Cheng Wong
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Julian P. Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom
- Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Andrew G. Brooks
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
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11
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Yang C, Wu J, Zhang X, Wen L, Sun J, Cheng Y, Tang X, Liang B, Chen G, Zhou F, Cui Y, Zhang A, Zhang X, Zheng X, Yang S, Sun L. Fine-mapping analysis of the MHC region for vitiligo based on a new Han-MHC reference panel. Gene 2018; 648:76-81. [DOI: 10.1016/j.gene.2018.01.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/30/2017] [Accepted: 01/16/2018] [Indexed: 11/26/2022]
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12
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Gao C, He X, Quan J, Jiang Q, Lin H, Chen H, Qu L. Specificity Characterization of SLA Class I Molecules Binding to Swine-Origin Viral Cytotoxic T Lymphocyte Epitope Peptides in Vitro. Front Microbiol 2017; 8:2524. [PMID: 29326671 PMCID: PMC5741678 DOI: 10.3389/fmicb.2017.02524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/05/2017] [Indexed: 02/03/2023] Open
Abstract
Swine leukocyte antigen (SLA) class I molecules play a crucial role in generating specific cellular immune responses against viruses and other intracellular pathogens. They mainly bind and present antigens of intracellular origin to circulating MHC I-restricted cytotoxic T lymphocytes (CTLs). Binding of an appropriate epitope to an SLA class I molecule is the single most selective event in antigen presentation and the first step in the killing of infected cells by CD8+ CTLs. Moreover, the antigen epitopes are strictly restricted to specific SLA molecules. In this study, we constructed SLA class I complexes in vitro comprising viral epitope peptides, the extracellular region of the SLA-1 molecules, and β2-microglobulin (β2m) using splicing overlap extension polymerase chain reaction (SOE-PCR). The protein complexes were induced and expressed in an Escherichia coli prokaryotic expression system and subsequently purified and refolded. Specific binding of seven SLA-1 proteins to one classical swine fever virus (CSFV) and four porcine reproductive and respiratory syndrome virus (PRRSV) epitope peptides was detected by enzyme-linked immunosorbent assay (ELISA)-based method. The SLA-1∗13:01, SLA-1∗11:10, and SLA-1∗11:01:02 proteins were able to bind specifically to different CTL epitopes of CSFV and PRRSV and the MHC restrictions of the five epitopes were identified. The fixed combination of Asn151Val152 residues was identified as the potentially key amino acid residues influencing the binding of viral several CTL epitope peptides to SLA-1∗13:01 and SLA-1∗04:01:01 proteins. The more flexible pocket E in the SLA-1∗13:01 protein might have fewer steric limitations and therefore be able to accommodate more residues of viral CTL epitope peptides, and may thus play a critical biochemical role in determining the peptide-binding motif of SLA-1∗13:01. Characterization of the binding specificity of peptides to SLA class I molecules provides an important basis for epitope studies of infectious diseases in swine, and for the rational development of novel porcine vaccines, as well as for detailed studies of CTL responses in pigs used as animal models.
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Affiliation(s)
- Caixia Gao
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiwen He
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinqiang Quan
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Qian Jiang
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huan Lin
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongyan Chen
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Liandong Qu
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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13
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Bassani-Sternberg M, Chong C, Guillaume P, Solleder M, Pak H, Gannon PO, Kandalaft LE, Coukos G, Gfeller D. Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity. PLoS Comput Biol 2017; 13:e1005725. [PMID: 28832583 PMCID: PMC5584980 DOI: 10.1371/journal.pcbi.1005725] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/05/2017] [Accepted: 08/17/2017] [Indexed: 01/01/2023] Open
Abstract
The precise identification of Human Leukocyte Antigen class I (HLA-I) binding motifs plays a central role in our ability to understand and predict (neo-)antigen presentation in infectious diseases and cancer. Here, by exploiting co-occurrence of HLA-I alleles across ten newly generated as well as forty public HLA peptidomics datasets comprising more than 115,000 unique peptides, we show that we can rapidly and accurately identify many HLA-I binding motifs and map them to their corresponding alleles without any a priori knowledge of HLA-I binding specificity. Our approach recapitulates and refines known motifs for 43 of the most frequent alleles, uncovers new motifs for 9 alleles that up to now had less than five known ligands and provides a scalable framework to incorporate additional HLA peptidomics studies in the future. The refined motifs improve neo-antigen and cancer testis antigen predictions, indicating that unbiased HLA peptidomics data are ideal for in silico predictions of neo-antigens from tumor exome sequencing data. The new motifs further reveal distant modulation of the binding specificity at P2 for some HLA-I alleles by residues in the HLA-I binding site but outside of the B-pocket and we unravel the underlying mechanisms by protein structure analysis, mutagenesis and in vitro binding assays. Predicting the differences between cancer and normal cells that are visible to the immune system is of central importance for cancer immunotherapy. Here we introduce a novel computational framework to harness the wealth of data from in-depth HLA peptidomics studies, including ten novel high quality (<1% FDR) datasets generated for this work, to improve predictions of peptides displayed on HLA-I molecules. These high-throughput and unbiased data enable us to refine models of HLA-I binding specificity for many alleles (including some that had no ligand until this study) and improve predictions of neo-antigens from exome sequencing data in melanoma and lung cancer samples. Moreover, the refined description of HLA-I binding specificity reveals cases of allosteric modulation of HLA-I binding specificity at the second amino acid position (P2) of their ligands by residues that are part of the HLA-I binding site but outside of the B pocket.
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Affiliation(s)
- Michal Bassani-Sternberg
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
- * E-mail: (DG); (MBS)
| | - Chloé Chong
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Marthe Solleder
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Philippe O. Gannon
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Lana E. Kandalaft
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- * E-mail: (DG); (MBS)
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14
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Josephs TM, Grant EJ, Gras S. Molecular challenges imposed by MHC-I restricted long epitopes on T cell immunity. Biol Chem 2017; 398:1027-1036. [PMID: 28141543 DOI: 10.1515/hsz-2016-0305] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/25/2017] [Indexed: 11/15/2022]
Abstract
It has widely been accepted that major histocompatibility complex class I molecules (MHC-I) are limited to binding small peptides of 8-10 residues in length. However, this consensus has recently been challenged with the identification of longer peptides (≥11 residues) that can also elicit cytotoxic CD8+ T cell responses. Indeed, a growing number of studies demonstrate that these non-canonical epitopes are important targets for the immune system. As long epitopes represent up to 10% of the peptide repertoire bound to MHC-I molecules, here we review their impact on antigen presentation by MHC-I, TCR recognition, and T cell immunity.
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15
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Saunders PM, Vivian JP, O'Connor GM, Sullivan LC, Pymm P, Rossjohn J, Brooks AG. A bird's eye view of NK cell receptor interactions with their MHC class I ligands. Immunol Rev 2016; 267:148-66. [PMID: 26284476 DOI: 10.1111/imr.12319] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The surveillance of target cells by natural killer (NK) cells utilizes an ensemble of inhibitory and activating receptors, many of which interact with major histocompatibility complex (MHC) class I molecules. NK cell recognition of MHC class I proteins is important developmentally for the acquisition of full NK cell effector capacity and during target cell recognition, where the engagement of inhibitory receptors and MHC class I molecules attenuates NK cell activation. Human NK cells have evolved two broad strategies for recognition of human leukocyte antigen (HLA) class I molecules: (i) direct recognition of polymorphic classical HLA class I proteins by diverse receptor families such as the killer cell immunoglobulin-like receptors (KIRs), and (ii) indirect recognition of conserved sets of HLA class I-derived peptides displayed on the non-classical HLA-E for recognition by CD94-NKG2 receptors. In this review, we assess the structural basis for the interaction between these NK receptors and their HLA class I ligands and, using the suite of published KIR and CD94-NKG2 ternary complexes, highlight the features that allow NK cells to orchestrate the recognition of a range of different HLA class I proteins.
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Affiliation(s)
- Philippa M Saunders
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Julian P Vivian
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Geraldine M O'Connor
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Lucy C Sullivan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Phillip Pymm
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Andrew G Brooks
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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16
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Ho SS, McLachlan AJ, Chen TF, Hibbs DE, Fois RA. Relationships Between Pharmacovigilance, Molecular, Structural, and Pathway Data: Revealing Mechanisms for Immune-Mediated Drug-Induced Liver Injury. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2015; 4:426-41. [PMID: 26312166 PMCID: PMC4544056 DOI: 10.1002/psp4.56] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/08/2015] [Indexed: 11/18/2022]
Abstract
Immune-mediated drug-induced liver injury (IMDILI) can be devastating, irreversible, and fatal in the absence of successful transplantation surgery. We present a novel approach that combines the methods of pharmacoepidemiology with in silico molecular modeling to identify specific features in toxic ligands that are associated with clinical features of IMDILI. Specifically, from pharmacovigilance data multivariate logistic regression identified 18 drugs associated with IMDILI (P < 0.00015). Eleven of these drugs, along with their known and proposed metabolites, constituted a training set used to develop a four-point pharmacophore model (sensitivity 75%; specificity 85%). Subsequently, this information was combined with information from immune-pathway reviews and genetic-association studies and complemented with ligand-protein docking simulations to support a hypothesis implicating two putative targets within separate, possibly interacting, immune-system pathways: the major histocompatibility complex within the adaptive immune system and Toll-like receptors (TLRs), in particular TLR-7, which represent pattern recognition receptors of the innate immune system.
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Affiliation(s)
- S S Ho
- Faculty of Pharmacy (A15), University of Sydney Sydney, NSW, Australia
| | - A J McLachlan
- Faculty of Pharmacy (A15), University of Sydney Sydney, NSW, Australia
| | - T F Chen
- Faculty of Pharmacy (A15), University of Sydney Sydney, NSW, Australia
| | - D E Hibbs
- Faculty of Pharmacy (A15), University of Sydney Sydney, NSW, Australia
| | - R A Fois
- Faculty of Pharmacy (A15), University of Sydney Sydney, NSW, Australia
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17
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Okada Y, Han B, Tsoi L, Stuart P, Ellinghaus E, Tejasvi T, Chandran V, Pellett F, Pollock R, Bowcock A, Krueger G, Weichenthal M, Voorhees J, Rahman P, Gregersen P, Franke A, Nair R, Abecasis G, Gladman D, Elder J, de Bakker P, Raychaudhuri S. Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes. Am J Hum Genet 2014; 95:162-72. [PMID: 25087609 PMCID: PMC4129407 DOI: 10.1016/j.ajhg.2014.07.002] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 07/07/2014] [Indexed: 02/08/2023] Open
Abstract
Psoriasis vulgaris (PsV) risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but its genetic architecture has yet to be fully elucidated. Here, we conducted a large-scale fine-mapping study of PsV risk in the MHC region in 9,247 PsV-affected individuals and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) genes from SNP genotype data. In addition, we imputed sequence variants for MICA, an MHC HLA-like gene that has been associated with PsV, to evaluate association at that locus as well. We observed that HLA-C∗06:02 demonstrated the lowest p value for overall PsV risk (p = 1.7 × 10−364). Stepwise analysis revealed multiple HLA-C∗06:02-independent risk variants in both class I and class II HLA genes for PsV susceptibility (HLA-C∗12:03, HLA-B amino acid positions 67 and 9, HLA-A amino acid position 95, and HLA-DQα1 amino acid position 53; p < 5.0 × 10−8), but no apparent risk conferred by MICA. We further evaluated risk of two major clinical subtypes of PsV, psoriatic arthritis (PsA; n = 3,038) and cutaneous psoriasis (PsC; n = 3,098). We found that risk heterogeneity between PsA and PsC might be driven by HLA-B amino acid position 45 (pomnibus = 2.2 × 10−11), indicating that different genetic factors underlie the overall risk of PsV and the risk of specific PsV subphenotypes. Our study illustrates the value of high-resolution HLA and MICA imputation for fine mapping causal variants in the MHC.
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Sun X, Fujiwara M, Shi Y, Kuse N, Gatanaga H, Appay V, Gao GF, Oka S, Takiguchi M. Superimposed epitopes restricted by the same HLA molecule drive distinct HIV-specific CD8+ T cell repertoires. THE JOURNAL OF IMMUNOLOGY 2014; 193:77-84. [PMID: 24899498 DOI: 10.4049/jimmunol.1400375] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Superimposed epitopes, in which a shorter epitope is embedded within a longer one, can be presented by the same HLA class I molecule. CD8(+) CTL responses against such epitopes and the contribution of this phenomenon to immune control are poorly characterized. In this study, we examined HLA-A*24:02-restricted CTLs specific for the superimposed HIV Nef epitopes RYPLTFGWCF (RF10) and RYPLTFGW (RW8). Unexpectedly, RF10-specific and RW8-specific CTLs from HIV-1-infected HLA-A*24:02+ individuals had no overlapping Ag reactivity or clonotypic compositions. Single-cell TCR sequence analyses demonstrated that RF10-specific T cells had a more diverse TCR repertoire than did RW8-specific T cells. Furthermore, RF10-specific CTLs presented a higher Ag sensitivity and HIV suppressive capacity compared with RW8-specific CTLs. Crystallographic analyses revealed important structural differences between RF10- and RW8-HLA-A*24:02 complexes as well, with featured and featureless conformations, respectively, providing an explanation for the induction of distinct T cell responses against these epitopes. The present study shows that a single viral sequence containing superimposed epitopes restricted by the same HLA molecule could elicit distinct CD8+ T cell responses, therefore enhancing the control of HIV replication. This study also showed that a featured epitope (e.g., RF10) could drive the induction of T cells with high TCR diversity and affinity.
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Affiliation(s)
- Xiaoming Sun
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mamoru Fujiwara
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yi Shi
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; and
| | - Victor Appay
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan; INSERM, Unité Mixte de Recherche 1135, Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Centre d'Immunologie et des Maladies Infectieuses-Paris, 75013, Paris, France
| | - George F Gao
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; and
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan;
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Vaidya SA, Streeck H, Beckwith N, Ghebremichael M, Pereyra F, Kwon DS, Addo MM, Rychert J, Routy JP, Jessen H, Kelleher AD, Hecht F, Sekaly RP, Carrington M, Walker BD, Allen TM, Rosenberg ES, Altfeld M. Temporal effect of HLA-B*57 on viral control during primary HIV-1 infection. Retrovirology 2013; 10:139. [PMID: 24245727 PMCID: PMC3874665 DOI: 10.1186/1742-4690-10-139] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/28/2013] [Indexed: 01/17/2023] Open
Abstract
Background HLA-B alleles are associated with viral control in chronic HIV-1 infection, however, their role in primary HIV-1 disease is unclear. This study sought to determine the role of HLA-B alleles in viral control during the acute phase of HIV-1 infection and establishment of the early viral load set point (VLSP). Findings Individuals identified during primary HIV-1 infection were HLA class I typed and followed longitudinally. Associations between HLA-B alleles and HIV-1 viral replication during acute infection and VLSP were analyzed in untreated subjects. The results showed that neither HLA-B*57 nor HLA-B*27 were significantly associated with viral control during acute HIV-1 infection (Fiebig stage I-IV, n=171). HLA-B*57 was however significantly associated with a subsequent lower VLSP (p<0.001, n=135) with nearly 1 log10 less median viral load. Analysis of a known polymorphism at position 97 of HLA-B showed significant associations with both lower initial viral load (p<0.01) and lower VLSP (p<0.05). However, this association was dependent on different amino acids at this position for each endpoint. Conclusions The effect of HLA-B*57 on viral control is more pronounced during the later stages of primary HIV-1 infection, which suggests the underlying mechanism of control occurs at a critical period in the first several months after HIV-1 acquisition. The risk profile of polymorphisms at position 97 of HLA-B are more broadly associated with HIV-1 viral load during primary infection and may serve as a focal point in further studies of HLA-B function.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marcus Altfeld
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Boston, MA, USA.
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Raposo RAS, Abdel-Mohsen M, Holditch SJ, Kuebler PJ, Cheng RG, Eriksson EM, Liao W, Pillai SK, Nixon DF. Increased expression of intrinsic antiviral genes in HLA-B*57-positive individuals. J Leukoc Biol 2013; 94:1051-9. [PMID: 23929683 DOI: 10.1189/jlb.0313150] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The genetic background of HIV-1-infected subjects, particularly the HLA class I haplotype, appears to be critical in determining disease progression rates, thought to be a result of the role of HIV-1-specific CD8(+) T cell responses. The HLA-B*57 allele is strongly associated with viremic suppression and slower disease progression. However, there is considerable heterogeneity in HIV-1 disease progression rates among HLA-B*57-positive subjects, suggesting that additional factors may help to contain viral replication. In this report, we investigated the association between host restriction factors, other established immunological parameters, and HLA type in HIV-1-seronegative individuals. Our results demonstrate that healthy, uninfected HLA-B*57-positive individuals exhibit significantly higher gene-expression levels of host restriction factors, such as APOBEC3A, APOBEC3B, BST-2/tetherin, and ISG15. Interestingly, HLA-B*57 individuals have significantly lower CD4(+) T cell frequencies but harbor slightly more activated CD4(+) T cells compared with their HLA-B*35 counterparts. We detected significant correlations between CD4(+) T cell activation and expression of several APOBEC3 family members, BST-2/tetherin, SAMHD1, and TRIM5α in HLA-B*57-positive individuals. To our knowledge, this is the first report showing distinct associations between host restriction factors and HLA class I genotype. Our results provide insights into natural protection mechanisms and immunity against HIV-1 that fall outside of classical HLA-mediated effects.
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Affiliation(s)
- Rui André Saraiva Raposo
- 2.Division of Experimental Medicine, 1001 Potrero Ave., Bldg. 3, Room 603, Box 1234, San Francisco, CA 94110, USA.
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21
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Rist MJ, Theodossis A, Croft NP, Neller MA, Welland A, Chen Z, Sullivan LC, Burrows JM, Miles JJ, Brennan RM, Gras S, Khanna R, Brooks AG, McCluskey J, Purcell AW, Rossjohn J, Burrows SR. HLA peptide length preferences control CD8+ T cell responses. THE JOURNAL OF IMMUNOLOGY 2013; 191:561-71. [PMID: 23749632 DOI: 10.4049/jimmunol.1300292] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Class I HLAs generally present peptides of 8-10 aa in length, although it is unclear whether peptide length preferences are affected by HLA polymorphism. In this study, we investigated the CD8(+) T cell response to the BZLF1 Ag of EBV, which includes overlapping sequences of different size that nevertheless conform to the binding motif of the large and abundant HLA-B*44 supertype. Whereas HLA-B*18:01(+) individuals responded strongly and exclusively to the octamer peptide (173)SELEIKRY(180), HLA-B*44:03(+) individuals responded to the atypically large dodecamer peptide (169)EECDSELEIKRY(180), which encompasses the octamer peptide. Moreover, the octamer peptide bound more stably to HLA-B*18:01 than did the dodecamer peptide, whereas, conversely, HLA-B*44:03 bound only the longer peptide. Furthermore, crystal structures of these viral peptide-HLA complexes showed that the Ag-binding cleft of HLA-B*18:01 was more ideally suited to bind shorter peptides, whereas HLA-B*44:03 exhibited characteristics that favored the presentation of longer peptides. Mass spectrometric identification of > 1000 naturally presented ligands revealed that HLA-B*18:01 was more biased toward presenting shorter peptides than was HLA-B*44:03. Collectively, these data highlight a mechanism through which polymorphism within an HLA class I supertype can diversify determinant selection and immune responses by varying peptide length preferences.
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Affiliation(s)
- Melissa J Rist
- Centre for Immunotherapy and Vaccine Development, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
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Selection and phylogenetics of salmonid MHC class I: wild brown trout (Salmo trutta) differ from a non-native introduced strain. PLoS One 2013; 8:e63035. [PMID: 23667568 PMCID: PMC3646885 DOI: 10.1371/journal.pone.0063035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 03/29/2013] [Indexed: 01/29/2023] Open
Abstract
We tested how variation at a gene of adaptive importance, MHC class I (UBA), in a wild, endemic Salmo trutta population compared to that in both a previously studied non-native S. trutta population and a co-habiting Salmo salar population (a sister species). High allelic diversity is observed and allelic divergence is much higher than that noted previously for co-habiting S. salar. Recombination was found to be important to population-level divergence. The α1 and α2 domains of UBA demonstrate ancient lineages but novel lineages are also identified at both domains in this work. We also find examples of recombination between UBA and the non-classical locus, ULA. Evidence for strong diversifying selection was found at a discrete suite of S. trutta UBA amino acid sites. The pattern was found to contrast with that found in re-analysed UBA data from an artificially stocked S. trutta population.
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Abstract
Natural killer (NK) cells are key components of innate immune responses, providing surveillance against cells undergoing tumorigenesis or infection, by viruses or internal pathogens. NK cells can directly eliminate compromised cells and regulate downstream responses of the innate and acquired immune systems through the release of immune modulators (cytokines, interferons). The importance of the role NK cells play in immune defense was demonstrated originally in herpes viral infections, usually mild or localized, which become severe and life threatening in NK-deficient patients . NK cell effector functions are governed by balancing opposing signals from a diverse array of activating and inhibitory receptors. Many NK receptors occur in paired activating and inhibitory isoforms and recognize major histocompatibility complex (MHC) class I proteins with varying degrees of peptide specificity. Structural studies have made considerable inroads into understanding the molecular mechanisms employed to broadly recognize multiple MHC ligands or specific pathogen-associated antigens and the strategies employed by viruses to thwart these defenses. Although many details of NK development, signaling, and integration remain mysterious, it is clear that NK receptors are key components of a system exquisitely tuned to sense any dysregulation in MHC class I expression, or the expression of certain viral antigens, resulting in the elimination of affected cells.
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Affiliation(s)
- Kathryn A Finton
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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24
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Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms. Proc Natl Acad Sci U S A 2012; 109:E3483-92. [PMID: 23161907 DOI: 10.1073/pnas.1207896109] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polymorphic differences distinguishing MHC class I subtypes often permit the presentation of shared epitopes in conformationally identical formats but can affect T-cell repertoire selection, differentially impacting autoimmune susceptibilities and viral clearance in vivo. The molecular mechanisms underlying this effect are not well understood. We performed structural, thermodynamic, and functional analyses of a conserved T-cell receptor (TCR) which is frequently expanded in response to a HIV-1 epitope when presented by HLA-B*5701 but is not selected by HLA-B*5703, which differs from HLA-B*5701 by two concealed polymorphisms. Our findings illustrate that although both HLA-B*57 subtypes display the epitope in structurally conserved formats, the impact of their polymorphic differences occurs directly as a consequence of TCR ligation, primarily because of peptide adjustments required for TCR binding, which involves the interplay of polymorphic residues and water molecules. These minor differences culminate in subtype-specific differential TCR-binding kinetics and cellular function. Our data demonstrate a potential mechanism whereby the most subtle MHC class I micropolymorphisms can influence TCR use and highlight their implications for disease outcomes.
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The potential role of epitope-specific T-cell receptor diversity in the control of HIV replication. Curr Opin HIV AIDS 2012; 2:177-82. [PMID: 19372884 DOI: 10.1097/coh.0b013e3280ef692f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to assess the influence of T-cell receptor clonotype diversity on the recognition and control of chronic viral infections, and specifically in the case of HIV infection. RECENT FINDINGS The latest publications have examined the role of T-cell receptor repertoires specific for dominant epitopes in the ability to recognize variants and control viremia in chronic viral infections. In the hepatitis C virus and SIV models, diverse T-cell receptor repertoires appear to limit immune escape. In HIV infection, circulating clonotypes may have different functional abilities, showing another potential advantage of diverse clonotypic repertoires. A recent study suggests that at times narrow repertoires against a conserved epitope may be effective, perhaps through the ability to cross-recognize potential epitope variants. SUMMARY The studies discussed in this review have identified T-cell receptor diversity as an important factor for understanding the immune recognition of highly variable viruses. Further studies are needed to determine whether T-cell receptor repertoire analysis of HIV epitope-specific immune responses will provide a more accurate correlate for the control of viremia than conventional immune function assays.
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Abstract
Successful vaccine development for infectious diseases has largely been achieved in settings where natural immunity to the pathogen results in clearance in at least some individuals. HIV presents an additional challenge in that natural clearance of infection does not occur, and the correlates of immune protection are still uncertain. However, partial control of viremia and markedly different outcomes of disease are observed in HIV-infected persons. Here, we examine the antiviral mechanisms implicated by one variable that has been consistently associated with extremes of outcome, namely HLA class I alleles, and in particular HLA-B, and examine the mechanisms by which this modulation is likely to occur and the impact of these interactions on evolution of the virus and the host. Studies to date provide evidence for both HLA-dependent and epitope-dependent influences on viral control and viral evolution and have important implications for the continued quest for an effective HIV vaccine.
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27
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McLaren PJ, Ripke S, Pelak K, Weintrob AC, Patsopoulos NA, Jia X, Erlich RL, Lennon NJ, Kadie CM, Heckerman D, Gupta N, Haas DW, Deeks SG, Pereyra F, Walker BD, de Bakker PIW. Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans. Hum Mol Genet 2012; 21:4334-47. [PMID: 22718199 DOI: 10.1093/hmg/dds226] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed HIV-1 controllers, suppress viral replication to very low levels in the absence of therapy. Genetic investigations of this phenotype have strongly implicated variation in the class I major histocompatibility complex (MHC) region as key to HIV-1 control. We collected sequence-based classical class I HLA genotypes at 4-digit resolution in HIV-1-infected African American controllers and progressors (n = 1107), and tested them for association with host control using genome-wide single nucleotide polymorphism data to account for population structure. Several classical alleles at HLA-B were associated with host control, including B*57:03 [odds ratio (OR) = 5.1; P= 3.4 × 10(-18)] and B*81:01 (OR = 4.8; P= 1.3 × 10(-9)). Analysis of variable amino acid positions demonstrates that HLA-B position 97 is the most significant association with host control in African Americans (omnibus P = 1.2 × 10(-21)) and explains the signal of several HLA-B alleles, including B*57:03. Within HLA-B, we also identified independent effects at position 116 (omnibus P= 2.8 × 10(-15)) in the canonical F pocket, position 63 in the B pocket (P= 1.5 × 10(-3)) and the non-pocket position 245 (P= 8.8 × 10(-10)), which is thought to influence CD8-binding kinetics. Adjusting for these HLA-B effects, there is evidence for residual association in the MHC region. These results underscore the key role of HLA-B in affecting HIV-1 replication, likely through the molecular interaction between HLA-B and viral peptides presented by infected cells, and suggest that sites outside the peptide-binding pocket also influence HIV-1 control.
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Affiliation(s)
- Paul J McLaren
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Wu Y, Gao F, Liu J, Qi J, Gostick E, Price DA, Gao GF. Structural Basis of Diverse Peptide Accommodation by the Rhesus Macaque MHC Class I Molecule Mamu-B*17: Insights into Immune Protection from Simian Immunodeficiency Virus. THE JOURNAL OF IMMUNOLOGY 2011; 187:6382-92. [DOI: 10.4049/jimmunol.1101726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Crystal structure of swine major histocompatibility complex class I SLA-1 0401 and identification of 2009 pandemic swine-origin influenza A H1N1 virus cytotoxic T lymphocyte epitope peptides. J Virol 2011; 85:11709-24. [PMID: 21900158 DOI: 10.1128/jvi.05040-11] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The presentation of viral epitopes to cytotoxic T lymphocytes (CTLs) by swine leukocyte antigen class I (SLA I) is crucial for swine immunity. To illustrate the structural basis of swine CTL epitope presentation, the first SLA crystal structures, SLA-1 0401, complexed with peptides derived from either 2009 pandemic H1N1 (pH1N1) swine-origin influenza A virus (S-OIV(NW9); NSDTVGWSW) or Ebola virus (Ebola(AY9); ATAAATEAY) were determined in this study. The overall peptide-SLA-1 0401 structures resemble, as expected, the general conformations of other structure-solved peptide major histocompatibility complexes (pMHC). The major distinction of SLA-1 0401 is that Arg(156) has a "one-ballot veto" function in peptide binding, due to its flexible side chain. S-OIV(NW9) and Ebola(AY9) bind SLA-1 0401 with similar conformations but employ different water molecules to stabilize their binding. The side chain of P7 residues in both peptides is exposed, indicating that the epitopes are "featured" peptides presented by this SLA. Further analyses showed that SLA-1 0401 and human leukocyte antigen (HLA) class I HLA-A 0101 can present the same peptides, but in different conformations, demonstrating cross-species epitope presentation. CTL epitope peptides derived from 2009 pandemic S-OIV were screened and evaluated by the in vitro refolding method. Three peptides were identified as potential cross-species influenza virus (IV) CTL epitopes. The binding motif of SLA-1 0401 was proposed, and thermostabilities of key peptide-SLA-1 0401 complexes were analyzed by circular dichroism spectra. Our results not only provide the structural basis of peptide presentation by SLA I but also identify some IV CTL epitope peptides. These results will benefit both vaccine development and swine organ-based xenotransplantation.
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HLA-B57 and gender influence the occurrence of tuberculosis in HIV infected people of south India. Clin Dev Immunol 2011; 2011:549023. [PMID: 21876708 PMCID: PMC3162975 DOI: 10.1155/2011/549023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 06/02/2011] [Indexed: 11/17/2022]
Abstract
BACKGROUND Substantial evidence exists for HLA and other host genetic factors being determinants of susceptibility or resistance to infectious diseases. However, very little information is available on the role of host genetic factors in HIV-TB coinfection. Hence, a longitudinal study was undertaken to investigate HLA associations in a cohort of HIV seropositive individuals with and without TB in Bangalore, South India. METHODS A cohort of 238 HIV seropositive subjects were typed for HLA-A, B, and DR by PCR-SSP and followed up for 5 years or till manifestation of Tuberculosis. HLA data of 682 HIV Negative healthy renal donors was used as control. RESULTS The ratio of males and females in HIV cohort was comparable (50.4% and 49.6%). But the incidence of TB was markedly lower in females (12.6%,) than males (25.6%). Further, HLA-B*57 frequency in HIV cohort was significantly higher among females without TB (21.6%, 19/88) than males (1.7%, 1/59); P = 0.0046; OR = 38. CD4 counts also were higher among females in this cohort. CONCLUSION This study suggests that HIV positive women with HLA-B*57 have less occurrence of TB as compared to males.
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Orlova M, Di Pietrantonio T, Schurr E. Genetics of infectious diseases: hidden etiologies and common pathways. Clin Chem Lab Med 2011; 49:1427-37. [PMID: 21619464 DOI: 10.1515/cclm.2011.620] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Since the completion of the human genome sequence, the study of common genetic polymorphisms in complex human diseases has become a main activity of human genetics. Employing genome-wide association studies, hundreds of modest genetic risk factors have been identified. In infectious diseases the identification of common risk factors has been varied and as in other common diseases it seems likely that important genetic risk factors remain to be discovered. Nevertheless, the identification of disease-specific genetic risk factors revealed an unexpected overlap in susceptibility genes of diverse inflammatory and infectious diseases. Analysis of the multi-disease susceptibility genes has allowed the definition of shared key pathways of inflammatory dysregulation and suggested unexpected infectious etiologies for other "non-infectious" common diseases.
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Affiliation(s)
- Marianna Orlova
- McGill Centre for the Study of Host Resistance, The Research Institute of the McGill University Health Centre, Montreal, PQ, Canada
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Diverse peptide presentation of rhesus macaque major histocompatibility complex class I Mamu-A 02 revealed by two peptide complex structures and insights into immune escape of simian immunodeficiency virus. J Virol 2011; 85:7372-83. [PMID: 21561910 DOI: 10.1128/jvi.00350-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major histocompatibility complex class I (MHC I)-restricted CD8(+) T-cell responses play a pivotal role in anti-human immunodeficiency virus (HIV) immunity and the control of viremia. The rhesus macaque is an important animal model for HIV-related research. Among the MHC I alleles of the rhesus macaque, Mamu-A 02 is prevalent, presenting in ≥20% of macaques. In this study, we determined the crystal structure of Mamu-A 02, the second structure-determined MHC I from the rhesus macaque after Mamu-A 01. The peptide presentation characteristics of Mamu-A 02 are exhibited in complex structures with two typical Mamu-A 02-restricted CD8(+) T-cell epitopes, YY9 (Nef159 to -167; YTSGPGIRY) and GY9 (Gag71 to -79; GSENLKSLY), derived from simian immunodeficiency virus (SIV). These two peptides utilize similar primary anchor residues (Ser or Thr) at position 2 and Tyr at position 9. However, the central region of YY9 is different from that of GY9, a difference that may correlate with the immunogenic variance of these peptides. Further analysis indicated that the distinct conformations of these two peptides are modulated by four flexible residues in the Mamu-A 02 peptide-binding groove. The rare combination of these four residues in Mamu-A 02 leads to a variant presentation for peptides with different residues in their central regions. Additionally, in the two structures of the Mamu-A 02 complex, we compared the binding of rhesus and human β(2) microglobulin (β(2)m) to Mamu-A 02. We found that the peptide presentation of Mamu-A 02 is not affected by the interspecies interaction with human β(2)m. Our work broadens the understanding of CD8(+) T-cell-specific immunity against SIV in the rhesus macaque.
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Insights into the structure of the LC13 TCR/HLA-B8-EBV peptide complex with molecular dynamics simulations. Cell Biochem Biophys 2011; 60:283-95. [DOI: 10.1007/s12013-011-9151-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Jia X, McLaren PJ, Ripke S, Brumme CJ, Pulit SL, Telenti A, Carrington M, Kadie CM, Carlson JM, Heckerman D, de Bakker PI, Pereyra F, de Bakker PI, Graham RR, Plenge RM, Deeks SG, Walker BD, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Carrington M, Gao X, Qi Y, Yuki Y, Pereyra F, Piechocka-Trocha A, Cutrell E, Rosenberg R, Moss KL, Lemay P, O’Leary J, Schaefer T, Verma P, Toth I, Block B, Baker B, Rothchild A, Lian J, Proudfoot J, Alvino DML, Vine S, Addo MM, Allen TM, Altfeld M, Henn MR, Le Gall S, Streeck H, Walker BD, Haas DW, Kuritzkes DR, Robbins GK, Shafer RW, Gulick RM, Shikuma CM, Haubrich R, Riddler S, Sax PE, Daar ES, Ribaudo HJ, Agan B, Agarwal S, Ahern RL, Allen BL, Altidor S, Altschuler EL, Ambardar S, Anastos K, Anderson B, Anderson V, Andrady U, Antoniskis D, Bangsberg D, Barbaro D, Barrie W, Bartczak J, Barton S, Basden P, Basgoz N, Bazner S, Bellos NC, Benson AM, Berger J, Bernard NF, Bernard AM, Birch C, Bodner SJ, Bolan RK, Boudreaux ET, Bradley M, Braun JF, Brndjar JE, Brown SJ, Brown K, Brown ST, Burack J, Bush LM, Cafaro V, Campbell O, Campbell J, Carlson RH, Carmichael JK, Casey KK, Cavacuiti C, Celestin G, Chambers ST, Chez N, Chirch LM, Cimoch PJ, Cohen D, Cohn LE, Conway B, Cooper DA, Cornelson B, Cox DT, Cristofano MV, Cuchural G, Czartoski JL, Dahman JM, Daly JS, Davis BT, Davis K, Davod SM, Deeks SG, DeJesus E, Dietz CA, Dunham E, Dunn ME, Ellerin TB, Eron JJ, Fangman JJ, Farel CE, Ferlazzo H, Fidler S, Fleenor-Ford A, Frankel R, Freedberg KA, French NK, Fuchs JD, Fuller JD, Gaberman J, Gallant JE, Gandhi RT, Garcia E, Garmon D, Gathe JC, Gaultier CR, Gebre W, Gilman FD, Gilson I, Goepfert PA, Gottlieb MS, Goulston C, Groger RK, Gurley TD, Haber S, Hardwicke R, Hardy WD, Harrigan PR, Hawkins TN, Heath S, Hecht FM, Henry WK, Hladek M, Hoffman RP, Horton JM, Hsu RK, Huhn GD, Hunt P, Hupert MJ, Illeman ML, Jaeger H, Jellinger RM, John M, Johnson JA, Johnson KL, Johnson H, Johnson K, Joly J, Jordan WC, Kauffman CA, Khanlou H, Killian RK, Kim AY, Kim DD, Kinder CA, Kirchner JT, Kogelman L, Kojic EM, Korthuis PT, Kurisu W, Kwon DS, LaMar M, Lampiris H, Lanzafame M, Lederman MM, Lee DM, Lee JM, Lee MJ, Lee ET, Lemoine J, Levy JA, Llibre JM, Liguori MA, Little SJ, Liu AY, Lopez AJ, Loutfy MR, Loy D, Mohammed DY, Man A, Mansour MK, Marconi VC, Markowitz M, Marques R, Martin JN, Martin HL, Mayer KH, McElrath MJ, McGhee TA, McGovern BH, McGowan K, McIntyre D, Mcleod GX, Menezes P, Mesa G, Metroka CE, Meyer-Olson D, Miller AO, Montgomery K, Mounzer KC, Nagami EH, Nagin I, Nahass RG, Nelson MO, Nielsen C, Norene DL, O’Connor DH, Ojikutu BO, Okulicz J, Oladehin OO, Oldfield EC, Olender SA, Ostrowski M, Owen WF, Pae E, Parsonnet J, Pavlatos AM, Perlmutter AM, Pierce MN, Pincus JM, Pisani L, Price LJ, Proia L, Prokesch RC, Pujet HC, Ramgopal M, Rathod A, Rausch M, Ravishankar J, Rhame FS, Richards CS, Richman DD, Robbins GK, Rodes B, Rodriguez M, Rose RC, Rosenberg ES, Rosenthal D, Ross PE, Rubin DS, Rumbaugh E, Saenz L, Salvaggio MR, Sanchez WC, Sanjana VM, Santiago S, Schmidt W, Schuitemaker H, Sestak PM, Shalit P, Shay W, Shirvani VN, Silebi VI, Sizemore JM, Skolnik PR, Sokol-Anderson M, Sosman JM, Stabile P, Stapleton JT, Starrett S, Stein F, Stellbrink HJ, Sterman FL, Stone VE, Stone DR, Tambussi G, Taplitz RA, Tedaldi EM, Telenti A, Theisen W, Torres R, Tosiello L, Tremblay C, Tribble MA, Trinh PD, Tsao A, Ueda P, Vaccaro A, Valadas E, Vanig TJ, Vecino I, Vega VM, Veikley W, Wade BH, Walworth C, Wanidworanun C, Ward DJ, Warner DA, Weber RD, Webster D, Weis S, Wheeler DA, White DJ, Wilkins E, Winston A, Wlodaver CG, Wout AV, Wright DP, Yang OO, Yurdin DL, Zabukovic BW, Zachary KC, Zeeman B, Zhao M. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 2010; 330:1551-7. [PMID: 21051598 PMCID: PMC3235490 DOI: 10.1126/science.1195271] [Citation(s) in RCA: 913] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. We identified >300 genome-wide significant single-nucleotide polymorphisms (SNPs) within the MHC and none elsewhere. Specific amino acids in the HLA-B peptide binding groove, as well as an independent HLA-C effect, explain the SNP associations and reconcile both protective and risk HLA alleles. These results implicate the nature of the HLA-viral peptide interaction as the major factor modulating durable control of HIV infection.
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Affiliation(s)
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaoming Jia
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA
| | - Paul J. McLaren
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Xiaoming Jia
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA
| | - Paul J. McLaren
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephan Ripke
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Center for Human Genetic Research, MGH, Harvard Medical School, Boston, MA, USA
| | - Chanson J. Brumme
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Sara L. Pulit
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | | | | | | | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | | | - Robert M. Plenge
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven G. Deeks
- University of California San Francisco, San Francisco, CA, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | | | | | | | - Leela Davies
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amy Camargo
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | - Supriya Gupta
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Noël P. Burtt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Namrata Gupta
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Yuko Yuki
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Emily Cutrell
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Rachel Rosenberg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Kristin L. Moss
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Paul Lemay
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jessica O’Leary
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Todd Schaefer
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Pranshu Verma
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Ildiko Toth
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Brian Block
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Brett Baker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Alissa Rothchild
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jeffrey Lian
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jacqueline Proudfoot
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Donna Marie L. Alvino
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Seanna Vine
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Marylyn M. Addo
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Todd M. Allen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Marcus Altfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Sylvie Le Gall
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Hendrik Streeck
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - David W. Haas
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel R. Kuritzkes
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Roy M. Gulick
- Weill Medical College of Cornell University, New York, NY, USA
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | | | | | - Paul E. Sax
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric S. Daar
- University of California Los Angeles, Los Angeles, CA, USA
| | - Heather J. Ribaudo
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | | | - Brian Agan
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | | | | | | | - Kathryn Anastos
- Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ben Anderson
- St. Leonards Medical Centre, St. Leonards, Australia
| | | | | | | | - David Bangsberg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- MGH, Harvard Medical School, Boston, MA, USA
| | - Daniel Barbaro
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | | | | | - Simon Barton
- Chelsea and Westminster Hospital, St. Stephen’s Centre, London, UK
| | | | | | - Suzane Bazner
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | | | - Nicole F. Bernard
- Research Institute, McGill University Health Centre, Montreal General Hospital, Montreal, Canada
| | | | - Christopher Birch
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | - Emilie T. Boudreaux
- Louisiana State University Health Sciences Center, University Medical Center East Clinic, Lafayatte, LA, USA
| | - Meg Bradley
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - James F. Braun
- Physicians’ Research Network, Callen-Lorde Community Health Center, New York, NY, USA
| | | | | | | | | | | | - Larry M. Bush
- University of Miami-Miller School of Medicine, Lake Worth, FL, USA
| | | | | | | | | | | | | | | | | | | | - Nancy Chez
- H.E.L.P./Project Samaritan, Bronx, NY, USA
| | - Lisa M. Chirch
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | - Lillian E. Cohn
- 9th Street Internal Medicine Associates, Philadelphia, PA, USA
| | - Brian Conway
- University of British Columbia, Vancouver, Canada
| | - David A. Cooper
- National Centre in HIV Epidemiology and Clinical Research, Sydney, Australia
| | | | - David T. Cox
- Metro Infectious Disease Consultants, Indianapolis, IN, USA
| | | | | | | | | | - Jennifer S. Daly
- University of Massachusetts Memorial Medical Center, Worcester, MA, USA
| | | | - Kristine Davis
- University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | | | - Steven G. Deeks
- University of California San Francisco, San Francisco, CA, USA
| | | | - Craig A. Dietz
- The Kansas City Free Health Clinic, Kansas City, MO, USA
| | - Eleanor Dunham
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | - Joseph J. Eron
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Claire E. Farel
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Helen Ferlazzo
- Visiting Nurse Association of Central New Jersey, Community Health Center, Asbury Park, NJ, USA
| | | | | | | | | | - Neel K. French
- Private Practice of Neel K. French, M.D., Chicago, IL, USA
| | | | | | | | - Joel E. Gallant
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Efrain Garcia
- Private Practice of Efrain Garcia, M.D., Miami, FL, USA
| | | | - Joseph C. Gathe
- Private Practice of Joseph C. Gathe Jr., M.D., Houston, TX, USA
| | | | | | | | - Ian Gilson
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | | | | | | | | | | | | | - W. David Hardy
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Sonya Heath
- University of Alabama, Birmingham, Birmingham, AL, USA
| | | | | | - Melissa Hladek
- The Catholic University of America, School of Nursing, Washington, DC, USA
| | | | | | - Ricky K. Hsu
- New York University Medical Center, New York, NY, USA
| | | | - Peter Hunt
- University of California San Francisco, San Francisco, CA, USA
| | - Mark J. Hupert
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | | | - Hans Jaeger
- HIV Research and Clinical Care Centre, Munich, Germany
| | | | - Mina John
- Murdoch University, Murdoch, Australia
| | - Jennifer A. Johnson
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Heather Johnson
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | - Kay Johnson
- University of Cincinnati, Cincinnati, OH, USA
| | - Jennifer Joly
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Wayne Kurisu
- Sharp Rees Stealy Medical Center, San Diego, CA, USA
| | - Douglas S. Kwon
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Harry Lampiris
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - Jean M.L. Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Janice Lemoine
- Greater Lawrence Family Health Center, Lawrence, MA, USA
| | - Jay A. Levy
- University of California San Francisco, San Francisco, CA, USA
| | - Josep M. Llibre
- Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | | | | | - Anne Y. Liu
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Dawn Loy
- Infectious Disease Associates, Sarasota, FL, USA
| | | | - Alan Man
- Kaiser Permanente, Portland, OR, USA
| | | | | | - Martin Markowitz
- Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY, USA
| | - Rui Marques
- Deruico Doencas Infecciosas, Porto, Portugal
| | | | | | | | | | | | | | - Katherine McGowan
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dawn McIntyre
- Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Gavin X. Mcleod
- College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Prema Menezes
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Greg Mesa
- Highland Medical Associates, Hendersonville, NC, USA
| | | | - Dirk Meyer-Olson
- Medizinische Hochschule, Abteilung Klinische Immunologie, Hannover, Germany
| | | | | | | | - Ellen H. Nagami
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Iris Nagin
- Lower East Side Service Center, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Eunice Pae
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | - Moti Ramgopal
- Midway Immunology and Research Center, Fort Pierce, FL, USA
| | - Almas Rathod
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - J. Ravishankar
- State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | | | | | | | | | - Berta Rodes
- Fundacion para la Investigacion Biomedica del Hospital Carlos III, Madrid, Spain
| | | | | | | | | | - Polly E. Ross
- Western North Carolina Community Health Services, Asheville, NC, USA
| | - David S. Rubin
- New York Hospital Medical Center of Queens, Flushing, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Paul Stabile
- William F. Ryan Community Health Center, New York, NY, USA
| | | | | | - Francine Stein
- Visiting Nurse Association of Central New Jersey, Community Health Center, Asbury Park, NJ, USA
| | | | | | | | | | | | | | | | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - William Theisen
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Phuong D. Trinh
- Montgomery Infectious Disease Associates, Silver Spring, MD, USA
| | - Alice Tsao
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Peggy Ueda
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Emilia Valadas
- Hospital de Santa Maria, Faculdade de Medicina de Lisboa, Lisbon, Portugal
| | | | - Isabel Vecino
- University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | | | - Barbara H. Wade
- Infectious Diseases Associates of Northwest Florida, Pensacola, FL, USA
| | | | | | | | | | | | | | - Steve Weis
- University of North Texas Health Science Center, Fort Worth, TX, USA
| | - David A. Wheeler
- Clinical Alliance for Research and Education-Infectious Diseases, Annandale, VA, USA
| | - David J. White
- Hawthorn House, Birmingham Heartlands Hospital, Birmingham, UK
| | - Ed Wilkins
- North Manchester General Hospital, Manchester, UK
| | | | | | | | | | - Otto O. Yang
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | - Beth Zeeman
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Meng Zhao
- United Health Services Hospitals, Binghamton, NY, USA
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Bharadwaj M, Illing P, Kostenko L. Personalized medicine for HLA-associated drug-hypersensitivity reactions. Per Med 2010; 7:495-516. [DOI: 10.2217/pme.10.46] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple genetic and nongenetic factors can modify the action of a drug, resulting in varied responses to a particular drug across different individuals. Personalized medicine incorporates the comprehensive knowledge of these factors to facilitate the selection of optimal therapy, reduce adverse drug reactions, increase patient compliance and increase the efficiency of therapy. Pharmacogenomics, which integrates the knowledge of an individual’s genetic make-up for diagnostic decisions or therapeutic interventions is closely linked to personalized medicine, and is being increasingly used to prevent adverse drug reactions. There are various reports on genetic associations between particular HLA allotypes and drug hypersensitivities and the strongest associations reported thus far, are with the reverse transcriptase inhibitor, abacavir and HLA-B*5701, the gout prophylactic allopurinol and HLA-B*5801 and the antiepileptic carbamazepine and B*1502, providing a defined disease trigger and suggesting a general mechanism for these associations. Recognizing the strong HLA association, the US FDA has recommended genetic testing before starting abacavir and carbamazepine therapies. To incorporate HLA testing for other drug hypersensitivities and life-threatening reactions it is essential first to establish clear HLA associations, and second, to understand the immune-mechanism by which these drugs induce HLA-linked hypersensitivity. The latter will provide insight into the pathologic mechanisms of drug allergy allowing rational immunotherapy for these life-threatening reactions and the development of alternative drug therapies for hypersensitive patients.
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Affiliation(s)
- Mandvi Bharadwaj
- Department of Microbiology & Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Patricia Illing
- Department of Microbiology & Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lyudmila Kostenko
- Department of Microbiology & Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia
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Zhang L, Li W, Song L, Chen L. A towards-multidimensional screening approach to predict candidate genes of rheumatoid arthritis based on SNP, structural and functional annotations. BMC Med Genomics 2010; 3:38. [PMID: 20727150 PMCID: PMC2939610 DOI: 10.1186/1755-8794-3-38] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 08/20/2010] [Indexed: 11/20/2022] Open
Abstract
Background According to the Genetic Analysis Workshops (GAW), hundreds of thousands of SNPs have been tested for association with rheumatoid arthritis. Traditional genome-wide association studies (GWAS) have been developed to identify susceptibility genes using a "most significant SNPs/genes" model. However, many minor- or modest-risk genes are likely to be missed after adjustment of multiple testing. This screening process uses a strict selection of statistical thresholds that aim to identify susceptibility genes based only on statistical model, without considering multi-dimensional biological similarities in sequence arrangement, crystal structure, or functional categories/biological pathways between candidate and known disease genes. Methods Multidimensional screening approaches combined with traditional statistical genetics methods can consider multiple biological backgrounds of genetic mutation, structural, and functional annotations. Here we introduce a newly developed multidimensional screening approach for rheumatoid arthritis candidate genes that considers all SNPs with nominal evidence of Bayesian association (BFLn > 0), and structural and functional similarities of corresponding genes or proteins. Results Our multidimensional screening approach extracted all risk genes (BFLn > 0) by odd ratios of hypothesis H1 to H0, and determined whether a particular group of genes shared underlying biological similarities with known disease genes. Using this method, we found 6614 risk SNPs in our Bayesian screen result set. Finally, we identified 146 likely causal genes for rheumatoid arthritis, including CD4, FGFR1, and KDR, which have been reported as high risk factors by recent studies. We must denote that 790 (96.1%) of genes identified by GWAS could not easily be classified into related functional categories or biological processes associated with the disease, while our candidate genes shared underlying biological similarities (e.g. were in the same pathway or GO term) and contributed to disease etiology, but where common variations in each of these genes make modest contributions to disease risk. We also found 6141 risk SNPs that were too minor to be detected by conventional approaches, and associations between 58 candidate genes and rheumatoid arthritis were verified by literature retrieved from the NCBI PubMed module. Conclusions Our proposed approach to the analysis of GAW16 data for rheumatoid arthritis was based on an underlying biological similarities-based method applied to candidate and known disease genes. Application of our method could identify likely causal candidate disease genes of rheumatoid arthritis, and could yield biological insights that not detected when focusing only on genes that give the strongest evidence by multiple testing. We hope that our proposed method complements the "most significant SNPs/genes" model, and provides additional insights into the pathogenesis of rheumatoid arthritis and other diseases, when searching datasets for hundreds of genetic variances.
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Affiliation(s)
- Liangcai Zhang
- Department of Biophysics, College of Bioinformatics Science and Technology; Harbin Medical University, Harbin, Hei Longjiang Province, China
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37
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Motozono C, Mwimanzi P, Ueno T. Dynamic interplay between viral adaptation and immune recognition during HIV-1 infection. Protein Cell 2010; 1:514-9. [PMID: 21204005 DOI: 10.1007/s13238-010-0068-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 05/28/2010] [Indexed: 01/08/2023] Open
Abstract
Untreated human immunodeficiency virus (HIV) infections usually lead to death from AIDS, although the rate of the disease progression varies widely among individuals. The cytotoxic T lymphocyte (CTL) response, which is restricted by highly polymorphic MHC class I alleles, plays a central role in controlling HIV replication. It is now recognized that the antiviral efficacy of CTLs at the single cell level is dependent on their antigen specificity and is important in determining the quality of host response to viruses so that the individual will remain asymptomatic. However, because of the extreme mutational plasticity of HIV, HIV-specific CTL responses are continuously and dynamically changing. In order to rationally design an effective vaccine, the questions as to what constitutes an effective antiviral CTL response and what characterizes a potent antigenic peptide to induce such responses are becoming highlighted as needing to be answered.
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Affiliation(s)
- Chihiro Motozono
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
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38
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Lacerda M, Scheffler K, Seoighe C. Epitope discovery with phylogenetic hidden Markov models. Mol Biol Evol 2010; 27:1212-20. [PMID: 20089717 PMCID: PMC2857806 DOI: 10.1093/molbev/msq008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Existing methods for the prediction of immunologically active T-cell epitopes are based on the amino acid sequence or structure of pathogen proteins. Additional information regarding the locations of epitopes may be acquired by considering the evolution of viruses in hosts with different immune backgrounds. In particular, immune-dependent evolutionary patterns at sites within or near T-cell epitopes can be used to enhance epitope identification. We have developed a mutation-selection model of T-cell epitope evolution that allows the human leukocyte antigen (HLA) genotype of the host to influence the evolutionary process. This is one of the first examples of the incorporation of environmental parameters into a phylogenetic model and has many other potential applications where the selection pressures exerted on an organism can be related directly to environmental factors. We combine this novel evolutionary model with a hidden Markov model to identify contiguous amino acid positions that appear to evolve under immune pressure in the presence of specific host immune alleles and that therefore represent potential epitopes. This phylogenetic hidden Markov model provides a rigorous probabilistic framework that can be combined with sequence or structural information to improve epitope prediction. As a demonstration, we apply the model to a data set of HIV-1 protein-coding sequences and host HLA genotypes.
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Affiliation(s)
- Miguel Lacerda
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
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39
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Huang J, Goedert JJ, Sundberg EJ, Cung TDH, Burke PS, Martin MP, Preiss L, Lifson J, Lichterfeld M, Carrington M, Yu XG. HLA-B*35-Px-mediated acceleration of HIV-1 infection by increased inhibitory immunoregulatory impulses. J Exp Med 2009; 206:2959-66. [PMID: 20008523 PMCID: PMC2806456 DOI: 10.1084/jem.20091386] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 11/12/2009] [Indexed: 01/29/2023] Open
Abstract
A subset of HLA-B*35 alleles, B*35-Px, are strongly associated with accelerated HIV-1 disease progression for reasons that are not understood. Interestingly, the alternative set of B*35 subtypes, B*35-PY, have no detectable impact on HIV-1 disease outcomes, even though they can present identical HIV-1 epitopes as B*35-Px molecules. Thus, the differential impact of these alleles on HIV-1 disease progression may be unrelated to interactions with HIV-1-specific CD8(+) T cells. Here, we show that the B*35-Px molecule B*3503 binds with greater affinity to immunoglobulin-like transcript 4 (ILT4), an inhibitory MHC class I receptor expressed on dendritic cells, than does the B*35-PY molecule B*3501, even though these two B*35 molecules differ by only one amino acid and present identical HIV-1 epitopes. The preferential recognition of B*3503 by ILT4 was associated with significantly stronger dendritic cell dysfunction in in vitro functional assays. Moreover, HIV-1-infected carriers of B*3503 had poor dendritic cell functional properties in ex vivo assessments when compared with carriers of the B*3501 allele. Differential interactions between HLA class I allele subtypes and immunoregulatory MHC class I receptors on dendritic cells thus provide a novel perspective for the understanding of MHC class I associations with HIV-1 disease progression and for the manipulation of host immunity against HIV-1.
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Affiliation(s)
- Jinghe Huang
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02129
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892
| | | | - Thai Duong Hong Cung
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02129
| | - Patrick S. Burke
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02129
| | - Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, and AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, MD 21702
| | - Liliana Preiss
- Research Triangle Institute International, Rockville, MD 20852
| | - Jeffrey Lifson
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, and AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, MD 21702
| | - Mathias Lichterfeld
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, and AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, MD 21702
| | - Xu G. Yu
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02129
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40
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Bowman C, Delrieu O. Immunogenetics of drug-induced skin blistering disorders. Part II: Synthesis. Pharmacogenomics 2009; 10:779-816. [DOI: 10.2217/pgs.09.23] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The overall immunopathogenesis relevant to a large series of disorders caused by a drug or its associated hyperimmune condition is discussed based upon examining the genetics of severe drug-induced bullous skin problems (sporadic idiosyncratic adverse events including Stevens–Johnson syndrome and Toxic epidermal necrolysis). New results from an exemplar study on shared precipitating and perpetuating inner causes with other related disease phenotypes including aphtous stomatitis, Behçets, erythema multiforme, Hashimoto’s thyroiditis, pemphigus, periodic fevers, Sweet’s syndrome and drug-induced multisystem hypersensitivity are presented. A call for a collaborative, wider demographic profiling and deeper immunotyping in suggested future work is made.
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Affiliation(s)
- Clive Bowman
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AH, UK
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41
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Bell MJ, Burrows JM, Brennan R, Miles JJ, Tellam J, McCluskey J, Rossjohn J, Khanna R, Burrows SR. The peptide length specificity of some HLA class I alleles is very broad and includes peptides of up to 25 amino acids in length. Mol Immunol 2009; 46:1911-7. [PMID: 19157553 DOI: 10.1016/j.molimm.2008.12.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 12/05/2008] [Accepted: 12/07/2008] [Indexed: 11/24/2022]
Abstract
The major ligands presented by MHC class I molecules after natural antigen processing are peptides of eight to ten residues in length, and it is widely accepted that the binding preferences of MHC class I molecules play a dominant role in dictating this classic feature of antigen presentation. In this report, we have reassessed the peptide size specificity of class I human leukocyte antigens (HLAs). By lengthening previously defined T cell epitopes by central amino acid insertion, we demonstrate that the peptide length specificity of some common HLA class I alleles (HLA-B*3501, B*0702 and A*2402) is very broad, and includes peptides of up to 25 residues. These data suggest that the length limitation of naturally processed MHC class I-associated peptides is primarily controlled by peptide availability after antigen processing rather than the binding specificity of MHC class I molecules. Furthermore, the findings provide an explanation for recent reports highlighting that epitopes of >10 amino acids play a minor but significant role in virus-specific immune surveillance by CD8(+) T cells.
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Affiliation(s)
- Melissa J Bell
- Queensland Institute of Medical Research and Australian Centre for Vaccine Development, Herston, Brisbane, Australia
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42
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Tang J, Shao W, Yoo YJ, Brill I, Mulenga J, Allen S, Hunter E, Kaslow RA. Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples. THE JOURNAL OF IMMUNOLOGY 2008; 181:2626-35. [PMID: 18684953 DOI: 10.4049/jimmunol.181.4.2626] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Differences in immune control of HIV-1 infection are often attributable to the highly variable HLA class I molecules that present viral epitopes to CTL. In our immunogenetic analyses of 429 HIV-1 discordant Zambian couples (infected index partners paired with cohabiting seronegative partners), several HLA class I variants in index partners were associated with contrasting rates and incidence of HIV-1 transmission within a 12-year study period. In particular, A*3601 on the A*36-Cw*04-B*53 haplotype was the most unfavorable marker of HIV-1 transmission by index partners, while Cw*1801 (primarily on the A*30-Cw*18-B*57 haplotype) was the most favorable, irrespective of the direction of transmission (male to female or female to male) and other commonly recognized cofactors of infection, including age and GUI. The same HLA markers were further associated with contrasting viral load levels in index partners, but they had no clear impact on HIV-1 acquisition by the seronegative partners. Thus, HLA class I gene products not only mediate HIV-1 pathogenesis and evolution but also influence heterosexual HIV-1 transmission.
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Affiliation(s)
- Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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43
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Chessman D, Kostenko L, Lethborg T, Purcell AW, Williamson NA, Chen Z, Kjer-Nielsen L, Mifsud NA, Tait BD, Holdsworth R, Almeida CA, Nolan D, Macdonald WA, Archbold JK, Kellerher AD, Marriott D, Mallal S, Bharadwaj M, Rossjohn J, McCluskey J. Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity. Immunity 2008; 28:822-32. [PMID: 18549801 DOI: 10.1016/j.immuni.2008.04.020] [Citation(s) in RCA: 236] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 03/25/2008] [Accepted: 04/01/2008] [Indexed: 10/22/2022]
Abstract
The basis for strong immunogenetic associations between particular human leukocyte antigen (HLA) class I allotypes and inflammatory conditions like Behçet's disease (HLA-B51) and ankylosing spondylitis (HLA-B27) remain mysterious. Recently, however, even stronger HLA associations are reported in drug hypersensitivities to the reverse-transcriptase inhibitor abacavir (HLA-B57), the gout prophylactic allopurinol (HLA-B58), and the antiepileptic carbamazepine (HLA-B*1502), providing a defined disease trigger and suggesting a general mechanism for these associations. We show that systemic reactions to abacavir were driven by drug-specific activation of cytokine-producing, cytotoxic CD8+ T cells. Recognition of abacavir required the transporter associated with antigen presentation and tapasin, was fixation sensitive, and was uniquely restricted by HLA-B*5701 and not closely related HLA allotypes with polymorphisms in the antigen-binding cleft. Hence, the strong association of HLA-B*5701 with abacavir hypersensitivity reflects specificity through creation of a unique ligand as well as HLA-restricted antigen presentation, suggesting a basis for the strong HLA class I-association with certain inflammatory disorders.
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Affiliation(s)
- Diana Chessman
- Department of Microbiology & Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia
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44
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T-cell receptor bias and immunity. Curr Opin Immunol 2008; 20:119-25. [PMID: 18207719 DOI: 10.1016/j.coi.2007.12.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 11/02/2007] [Accepted: 12/06/2007] [Indexed: 12/24/2022]
Abstract
Despite the potentially vast T-cell repertoire, biased alphabeta T-cell receptor (TCR) usage has emerged as a common theme in immunity. Examples of TCR bias are observed in classical polymorphic major histocompatibility complex (MHC)-restricted immune responses as well as in T-cell responses to non-classical, monomorphic Ag-presenting molecules, such as CD1d. Recent data have implicated the structural landscape of these antigen-presenting molecules as one of the drivers of TCR bias. Here we review recent advances in the field, focussing on structural data pertaining to biased TCR usage, and discuss the implications for T-cell repertoire selection, MHC restriction and therapeutic development.
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45
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An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the Pumwani Sex Worker Cohort. J Virol 2007; 82:1980-92. [PMID: 18057233 DOI: 10.1128/jvi.02742-06] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is able to evade the host cytotoxic T-lymphocyte (CTL) response through a variety of escape avenues. Epitopes that are presented to CTLs are first processed in the presenting cell in several steps, including proteasomal cleavage, transport to the endoplasmic reticulum, binding by the HLA molecule, and finally presentation to the T-cell receptor. An understanding of the potential of the virus to escape CTL responses can aid in designing an effective vaccine. To investigate such a potential, we analyzed HIV-1 gag from 468 HIV-1-positive Kenyan women by using several bioinformatic approaches that allowed the identification of positively selected amino acids in the HIV-1 gag region and study of the effects that these mutations could have on the various stages of antigen processing. Correlations between positively selected residues and mean CD4 counts also allowed study of the effect of mutation on HIV disease progression. A number of mutations that could create or destroy proteasomal cleavage sites or reduce binding affinity of the transport antigen processing protein, effectively hindering epitope presentation, were identified. Many mutations correlated with the presence of specific HLA alleles and with lower or higher CD4 counts. For instance, the mutation V190I in subtype A1-infected individuals is associated with HLA-B*5802 (P = 4.73 x 10(-4)), a rapid-progression allele according to other studies, and also to a decreased mean CD4 count (P = 0.019). Thus, V190I is a possible HLA escape mutant. This method classifies many positively selected mutations across the entire gag region according to their potential for immune escape and their effect on disease progression.
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46
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Burrows JM, Bell MJ, Brennan R, Miles JJ, Khanna R, Burrows SR. Preferential binding of unusually long peptides to MHC class I and its influence on the selection of target peptides for T cell recognition. Mol Immunol 2007; 45:1818-24. [PMID: 17981331 DOI: 10.1016/j.molimm.2007.09.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 09/24/2007] [Accepted: 09/27/2007] [Indexed: 10/22/2022]
Abstract
A classic feature of antigen presentation for CD8+ T cell recognition is that MHC class I molecules generally present peptides of 8-10 amino acids in length. However, recent studies have demonstrated that peptides of >10 residues play a significant role in immune surveillance by T cells restricted by some HLA class I alleles. In the present study, we describe several examples of unusually long viral peptides of 11 or 12 residues, recognized by CTLs in the context of HLA-B35. Interestingly, all these immunogenic peptides completely encompass shorter canonical length sequences that conform to the HLA-B35 binding motif, but which fail to stimulate detectable T cell responses. The mechanism for this phenomenon appears to involve the preferential binding to HLA-B35 of the atypically long CD8+ T cell target peptides over the overlapping canonical length sequences. These data suggest that the peptide length specificity of some HLA class I alleles is broad, allowing peptides of >10 residues to sometimes dominate over canonical length class I ligands as targets for T cell recognition.
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Affiliation(s)
- Jacqueline M Burrows
- Queensland Institute of Medical Research and Australian Centre for Vaccine Development, 300 Herston Road, Herston 4029, Brisbane, Australia
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47
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Thananchai H, Gillespie G, Martin MP, Bashirova A, Yawata N, Yawata M, Easterbrook P, McVicar DW, Maenaka K, Parham P, Carrington M, Dong T, Rowland-Jones S. Cutting Edge: Allele-specific and peptide-dependent interactions between KIR3DL1 and HLA-A and HLA-B. THE JOURNAL OF IMMUNOLOGY 2007; 178:33-7. [PMID: 17182537 DOI: 10.4049/jimmunol.178.1.33] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although it is clear that KIR3DL1 recognizes Bw4(+) HLA-B, the role of Bw4(+) HLA-A allotypes as KIR3DL1 ligands is controversial. We therefore examined the binding of tetrameric HLA-A and -B complexes, including HLA*2402, a common Bw4(+) HLA-A allotype, to KIR3DL1*001, *005, *007, and *1502 allotypes. Only Bw4(+) tetramers bound KIR3DL1. Three of four HLA-A*2402 tetramers bound one or more KIR3DL1 allotypes and all four KIR3DL1 allotypes bound to one or more HLA-A*2402 tetramers, but with different binding specificities. Only KIR3DL1*005 bound both HLA-A*2402 and HLA-B*5703 tetramers. HLA-A*2402-expressing target cells were resistant to lysis by NK cells expressing KIR3DL1*001 or *005. This study shows that HLA-A*2402 is a ligand for KIR3DL1 and demonstrates how the binding of KIR3DL1 to Bw4(+) ligands depends upon the bound peptide as well as HLA and KIR3DL1 polymorphism.
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Affiliation(s)
- Hathairat Thananchai
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
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48
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Yu XG, Lichterfeld M, Chetty S, Williams KL, Mui SK, Miura T, Frahm N, Feeney ME, Tang Y, Pereyra F, Labute MX, Pfafferott K, Leslie A, Crawford H, Allgaier R, Hildebrand W, Kaslow R, Brander C, Allen TM, Rosenberg ES, Kiepiela P, Vajpayee M, Goepfert PA, Altfeld M, Goulder PJR, Walker BD. Mutually exclusive T-cell receptor induction and differential susceptibility to human immunodeficiency virus type 1 mutational escape associated with a two-amino-acid difference between HLA class I subtypes. J Virol 2007; 81:1619-31. [PMID: 17121793 PMCID: PMC1797559 DOI: 10.1128/jvi.01580-06] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 11/15/2006] [Indexed: 11/20/2022] Open
Abstract
The relative contributions of HLA alleles and T-cell receptors (TCRs) to the prevention of mutational viral escape are unclear. Here, we examined human immunodeficiency virus type 1 (HIV-1)-specific CD8(+) T-cell responses restricted by two closely related HLA class I alleles, B*5701 and B*5703, that differ by two amino acids but are both associated with a dominant response to the same HIV-1 Gag epitope KF11 (KAFSPEVIPMF). When this epitope is presented by HLA-B*5701, it induces a TCR repertoire that is highly conserved among individuals, cross-recognizes viral epitope variants, and is rarely associated with mutational escape. In contrast, KF11 presented by HLA-B*5703 induces an entirely different, more heterogeneous TCR beta-chain repertoire that fails to recognize specific KF11 escape variants which frequently arise in clade C-infected HLA-B*5703(+) individuals. These data show the influence of HLA allele subtypes on TCR selection and indicate that extensive TCR diversity is not a prerequisite to prevention of allowable viral mutations.
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Affiliation(s)
- Xu G Yu
- Partners AIDS Research Center, Massachusetts General Hospital, 149 13th Street, Room 5212, Charlestown, MA 02129, USA
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49
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Miles JJ, Borg NA, Brennan RM, Tynan FE, Kjer-Nielsen L, Silins SL, Bell MJ, Burrows JM, McCluskey J, Rossjohn J, Burrows SR. TCR alpha genes direct MHC restriction in the potent human T cell response to a class I-bound viral epitope. THE JOURNAL OF IMMUNOLOGY 2007; 177:6804-14. [PMID: 17082594 DOI: 10.4049/jimmunol.177.10.6804] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The underlying generic properties of alphabeta TCRs that control MHC restriction remain largely unresolved. To investigate MHC restriction, we have examined the CTL response to a viral epitope that binds promiscuously to two human leukocyte Ags (HLAs) that differ by a single amino acid at position 156. Individuals expressing either HLA-B*3501 (156Leucine) or HLA-B*3508 (156Arginine) showed a potent CTL response to the 407HPVGEADYFEY417 epitope from EBV. Interestingly, the response was characterized by highly restricted TCR beta-chain usage in both HLA-B*3501+ and HLA-B*3508+ individuals; however, this conserved TRBV9+ beta-chain was associated with distinct TCR alpha-chains depending upon the HLA-B*35 allele expressed by the virus-exposed host. Functional assays confirmed that TCR alpha-chain usage determined the HLA restriction of the CTLs. Structural studies revealed significant differences in the mobility of the peptide when bound to HLA-B*3501 or HLA-B*3508. In HLA-B*3501, the bulged section of the peptide was disordered, whereas in HLA-B*3508 the bulged epitope adopted an ordered conformation. Collectively, these data demonstrate not only that mobile MHC-bound peptides can be highly immunogenic but can also stimulate an extremely biased TCR repertoire. In addition, TCR alpha-chain usage is shown to play a critical role in controlling MHC restriction between closely related allomorphs.
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MESH Headings
- Amino Acid Sequence
- Antigen Presentation/genetics
- Cell Line, Transformed
- Cells, Cultured
- Crystallography, X-Ray
- Cytotoxicity, Immunologic/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Epstein-Barr Virus Nuclear Antigens/immunology
- Epstein-Barr Virus Nuclear Antigens/metabolism
- HLA Antigens/genetics
- HLA Antigens/immunology
- HLA Antigens/metabolism
- HLA-B Antigens/metabolism
- HLA-B35 Antigen
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Humans
- Molecular Sequence Data
- Protein Binding/genetics
- Protein Binding/immunology
- Protein Subunits/biosynthesis
- Protein Subunits/genetics
- Protein Subunits/physiology
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/physiology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- T-Lymphocytes, Cytotoxic/virology
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Affiliation(s)
- John J Miles
- Cellular Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
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50
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Blicher T, Kastrup JS, Pedersen LØ, Buus S, Gajhede M. Structure of HLA-A*1101 in complex with a hepatitis B peptide homologue. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1179-84. [PMID: 17142892 PMCID: PMC2225367 DOI: 10.1107/s1744309106044228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 10/23/2006] [Indexed: 01/18/2023]
Abstract
A high-resolution structure of the human MHC-I molecule HLA-A*1101 is presented in which it forms a complex with a sequence homologue of a peptide that occurs naturally in hepatitis B virus DNA polymerase. The sequence of the bound peptide is AIMPARFYPK, while that of the corresponding natural peptide is LIMPARFYPK. The peptide does not make efficient use of the middle E pocket for binding, which leads to a rather superficial and exposed binding mode for the central peptide residues. Despite this, the peptide binds with high affinity (IC50 of 31 nM).
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Affiliation(s)
- Thomas Blicher
- Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark
- Department of Medical Microbiology and Immunology, The Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars Østergaard Pedersen
- Department of Medical Microbiology and Immunology, The Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Søren Buus
- Department of Medical Microbiology and Immunology, The Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Michael Gajhede
- Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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