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Moody MA, Pedroza-Pacheco I, Vandergrift NA, Chui C, Lloyd KE, Parks R, Soderberg KA, Ogbe AT, Cohen MS, Liao HX, Gao F, McMichael AJ, Montefiori DC, Verkoczy L, Kelsoe G, Huang J, Shea PR, Connors M, Borrow P, Haynes BF. Immune perturbations in HIV-1-infected individuals who make broadly neutralizing antibodies. Sci Immunol 2016; 1:aag0851. [PMID: 28783677 DOI: 10.1126/sciimmunol.aag0851] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 06/05/2016] [Indexed: 12/16/2022]
Abstract
Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. bnAbs occur in some HIV-1-infected individuals and frequently have characteristics of autoantibodies. We have studied cohorts of HIV-1-infected individuals who made bnAbs and compared them with those who did not do so, and determined immune traits associated with the ability to produce bnAbs. HIV-1-infected individuals with bnAbs had a higher frequency of blood autoantibodies, a lower frequency of regulatory CD4+ T cells, a higher frequency of circulating memory T follicular helper CD4+ cells, and a higher T regulatory cell level of programmed cell death-1 expression compared with HIV-1-infected individuals without bnAbs. Thus, induction of HIV-1 bnAbs may require vaccination regimens that transiently mimic immunologic perturbations in HIV-1-infected individuals.
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Affiliation(s)
- M Anthony Moody
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. .,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Nathan A Vandergrift
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cecilia Chui
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Krissey E Lloyd
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kelly A Soderberg
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ane T Ogbe
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Myron S Cohen
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hua-Xin Liao
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Feng Gao
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laurent Verkoczy
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Garnett Kelsoe
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jinghe Huang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK.
| | - Barton F Haynes
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. .,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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2
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Santra S, Tomaras GD, Warrier R, Nicely NI, Liao HX, Pollara J, Liu P, Alam SM, Zhang R, Cocklin SL, Shen X, Duffy R, Xia SM, Schutte RJ, Pemble IV CW, Dennison SM, Li H, Chao A, Vidnovic K, Evans A, Klein K, Kumar A, Robinson J, Landucci G, Forthal DN, Montefiori DC, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Robb ML, Michael NL, Kim JH, Soderberg KA, Giorgi EE, Blair L, Korber BT, Moog C, Shattock RJ, Letvin NL, Schmitz JE, Moody MA, Gao F, Ferrari G, Shaw GM, Haynes BF. Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques. PLoS Pathog 2015; 11:e1005042. [PMID: 26237403 PMCID: PMC4523205 DOI: 10.1371/journal.ppat.1005042] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/23/2015] [Indexed: 11/19/2022] Open
Abstract
HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4+ T cells. Although broadly neutralizing antibodies (bnAbs) are the type of HIV-1 antibodies that are most likely protective, they are not induced with current vaccine candidates. In contrast, antibodies that do not neutralize primary HIV-1 strains in the TZM-bl infection assay are readily induced by current vaccine candidates and have also been implicated as secondary correlates of decreased HIV-1 risk in the RV144 vaccine efficacy trial. Here, we have studied the capacity of anti-Env monoclonal antibodies (mAbs) against either the immunodominant region of gp41 (7B2 IgG1), the first constant region of gp120 (A32 IgG1), or the third variable loop (V3) of gp120 (CH22 IgG1) to modulate in vivo rectal mucosal transmission of a high-dose simian-human immunodeficiency virus (SHIV-BaL) in rhesus macaques. 7B2 IgG1 or A32 IgG1, each containing mutations to enhance Fc function, was administered passively to rhesus macaques but afforded no protection against productive clinical infection while the positive control antibody CH22 IgG1 prevented infection in 4 of 6 animals. Enumeration of transmitted/founder (T/F) viruses revealed that passive infusion of each of the three antibodies significantly reduced the number of T/F genomes. Thus, some antibodies that bind HIV-1 Env but fail to neutralize virus in traditional neutralization assays may limit the number of T/F viruses involved in transmission without leading to enhancement of viral infection. For one of these mAbs, gp41 mAb 7B2, we provide the first co-crystal structure in complex with a common cyclical loop motif demonstrated to be critical for infection by other retroviruses.
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Affiliation(s)
- Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (SS); (GDT); (BFH)
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (SS); (GDT); (BFH)
| | - Ranjit Warrier
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nathan I. Nicely
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Justin Pollara
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Pinghuang Liu
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Sarah L. Cocklin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Ryan Duffy
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Robert J. Schutte
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Charles W. Pemble IV
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - S. Moses Dennison
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Hui Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew Chao
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kora Vidnovic
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Abbey Evans
- Department of Medicine, St Mary’s Campus, Imperial College London, London, United Kingdom
| | - Katja Klein
- Department of Medicine, St Mary’s Campus, Imperial College London, London, United Kingdom
| | - Amit Kumar
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - James Robinson
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Gary Landucci
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, Irvine, California, United States of America
| | - Donald N. Forthal
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, Irvine, California, United States of America
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | | | - Sorachai Nitayaphan
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | | | | | - Merlin L. Robb
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Nelson L. Michael
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jerome H. Kim
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Kelly A. Soderberg
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Elena E. Giorgi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Lily Blair
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bette T. Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christiane Moog
- U1109, INSERM University of Strasbourg, Strasbourg, Alsace, France
| | - Robin J. Shattock
- Department of Medicine, St Mary’s Campus, Imperial College London, London, United Kingdom
| | - Norman L. Letvin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joern E. Schmitz
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - M. A. Moody
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
| | - George M. Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (SS); (GDT); (BFH)
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3
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Zolla-Pazner S, deCamp A, Gilbert PB, Williams C, Yates NL, Williams WT, Howington R, Fong Y, Morris DE, Soderberg KA, Irene C, Reichman C, Pinter A, Parks R, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Nitayaphan S, Andrews C, O’Connell RJ, Yang ZY, Nabel GJ, Kim JH, Michael NL, Montefiori DC, Liao HX, Haynes BF, Tomaras GD. Vaccine-induced IgG antibodies to V1V2 regions of multiple HIV-1 subtypes correlate with decreased risk of HIV-1 infection. PLoS One 2014; 9:e87572. [PMID: 24504509 PMCID: PMC3913641 DOI: 10.1371/journal.pone.0087572] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/16/2013] [Indexed: 11/18/2022] Open
Abstract
UNLABELLED In the RV144 HIV-1 vaccine efficacy trial, IgG antibody (Ab) binding levels to variable regions 1 and 2 (V1V2) of the HIV-1 envelope glycoprotein gp120 were an inverse correlate of risk of HIV-1 infection. To determine if V1V2-specific Abs cross-react with V1V2 from different HIV-1 subtypes, if the nature of the V1V2 antigen used to asses cross-reactivity influenced infection risk, and to identify immune assays for upcoming HIV-1 vaccine efficacy trials, new V1V2-scaffold antigens were designed and tested. Protein scaffold antigens carrying the V1V2 regions from HIV-1 subtypes A, B, C, D or CRF01_AE were assayed in pilot studies, and six were selected to assess cross-reactive Abs in the plasma from the original RV144 case-control cohort (41 infected vaccinees, 205 frequency-matched uninfected vaccinees, and 40 placebo recipients) using ELISA and a binding Ab multiplex assay. IgG levels to these antigens were assessed as correlates of risk in vaccine recipients using weighted logistic regression models. Levels of Abs reactive with subtype A, B, C and CRF01_AE V1V2-scaffold antigens were all significant inverse correlates of risk (p-values of 0.0008-0.05; estimated odds ratios of 0.53-0.68 per 1 standard deviation increase). Thus, levels of vaccine-induced IgG Abs recognizing V1V2 regions from multiple HIV-1 subtypes, and presented on different scaffolds, constitute inverse correlates of risk for HIV-1 infection in the RV144 vaccine trial. The V1V2 antigens provide a link between RV144 and upcoming HIV-1 vaccine trials, and identify reagents and methods for evaluating V1V2 Abs as possible correlates of protection against HIV-1 infection. TRIAL REGISTRATION ClinicalTrials.gov NCT00223080.
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Affiliation(s)
- Susan Zolla-Pazner
- Department of Veterans Affairs New York Harbor Healthcare System, New York, New York, United States of America
- New York University School of Medicine, New York, New York, United States of America
- * E-mail:
| | - Allan deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Constance Williams
- New York University School of Medicine, New York, New York, United States of America
| | - Nicole L. Yates
- Duke University, Durham, North Carolina, United States of America
| | | | - Robert Howington
- Duke University, Durham, North Carolina, United States of America
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Daryl E. Morris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | | | - Carmela Irene
- Public Health Research Institute, University of Medicine and Dentistry, Newark, New Jersey, United States of America
| | - Charles Reichman
- Public Health Research Institute, University of Medicine and Dentistry, Newark, New Jersey, United States of America
| | - Abraham Pinter
- Public Health Research Institute, University of Medicine and Dentistry, Newark, New Jersey, United States of America
| | - Robert Parks
- Duke University, Durham, North Carolina, United States of America
| | | | | | | | | | - Charla Andrews
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Robert J. O’Connell
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Zhi-yong Yang
- Virology Laboratory, Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gary J. Nabel
- Virology Laboratory, Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jerome H. Kim
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Nelson L. Michael
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | | | - Hua-Xin Liao
- Duke University, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke University, Durham, North Carolina, United States of America
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4
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Apps R, Qi Y, Carlson JM, Chen H, Gao X, Thomas R, Yuki Y, Del Prete GQ, Goulder P, Brumme ZL, Brumme CJ, John M, Mallal S, Nelson G, Bosch R, Heckerman D, Stein JL, Soderberg KA, Moody MA, Denny TN, Zeng X, Fang J, Moffett A, Lifson JD, Goedert JJ, Buchbinder S, Kirk GD, Fellay J, McLaren P, Deeks SG, Pereyra F, Walker B, Michael NL, Weintrob A, Wolinsky S, Liao W, Carrington M. Influence of HLA-C expression level on HIV control. Science 2013; 340:87-91. [PMID: 23559252 PMCID: PMC3784322 DOI: 10.1126/science.1232685] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A variant upstream of human leukocyte antigen C (HLA-C) shows the most significant genome-wide effect on HIV control in European Americans and is also associated with the level of HLA-C expression. We characterized the differential cell surface expression levels of all common HLA-C allotypes and tested directly for effects of HLA-C expression on outcomes of HIV infection in 5243 individuals. Increasing HLA-C expression was associated with protection against multiple outcomes independently of individual HLA allelic effects in both African and European Americans, regardless of their distinct HLA-C frequencies and linkage relationships with HLA-B and HLA-A. Higher HLA-C expression was correlated with increased likelihood of cytotoxic T lymphocyte responses and frequency of viral escape mutation. In contrast, high HLA-C expression had a deleterious effect in Crohn's disease, suggesting a broader influence of HLA expression levels in human disease.
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Affiliation(s)
- Richard Apps
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | | | - Haoyan Chen
- Department of Dermatology, University of California, San Francisco, CA 94115, USA
- Department of Gastroenterology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Diseases, Shanghai 200001, China
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Rasmi Thomas
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yuko Yuki
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Greg Q. Del Prete
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Philip Goulder
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
- Department of Paediatrics, Oxford University, Oxford OX1 3SY, UK
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada V6Z 1Y6
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada V6Z 1Y6
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, 6150
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, 6150
| | - George Nelson
- Basic Research Program, Center for Cancer Research Genetics Core, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ronald Bosch
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA 02115, USA
| | - David Heckerman
- Microsoft Research, eScience Group, Los Angeles, CA 90024, USA
| | - Judy L. Stein
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | | | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Xue Zeng
- Department of Dermatology, University of California, San Francisco, CA 94115, USA
- Department of Dermatology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Jingyuan Fang
- Department of Gastroenterology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Diseases, Shanghai 200001, China
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, CB2 1QP, UK
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - James J. Goedert
- Infectious and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Susan Buchbinder
- San Francisco Department of Public Health, Bridge HIV, San Francisco, CA 94102, USA
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jacques Fellay
- Institute of Microbiology, University Hospital Lausanne and School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Paul McLaren
- Institute of Microbiology, University Hospital Lausanne and School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, CA 94105, USA
| | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Bruce Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Amy Weintrob
- Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD, 20817, USA
| | - Steven Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, CA 94115, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Science Applications International Corporation (SAIC)-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA 02114, USA
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5
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Haynes BF, Gilbert PB, McElrath MJ, Zolla-Pazner S, Tomaras GD, Alam SM, Evans DT, Montefiori DC, Karnasuta C, Sutthent R, Liao HX, DeVico AL, Lewis GK, Williams C, Pinter A, Fong Y, Janes H, DeCamp A, Huang Y, Rao M, Billings E, Karasavvas N, Robb ML, Ngauy V, de Souza MS, Paris R, Ferrari G, Bailer RT, Soderberg KA, Andrews C, Berman PW, Frahm N, De Rosa SC, Alpert MD, Yates NL, Shen X, Koup RA, Pitisuttithum P, Kaewkungwal J, Nitayaphan S, Rerks-Ngarm S, Michael NL, Kim JH. Immune-correlates analysis of an HIV-1 vaccine efficacy trial. N Engl J Med 2012; 366:1275-86. [PMID: 22475592 PMCID: PMC3371689 DOI: 10.1056/nejmoa1113425] [Citation(s) in RCA: 1493] [Impact Index Per Article: 124.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND In the RV144 trial, the estimated efficacy of a vaccine regimen against human immunodeficiency virus type 1 (HIV-1) was 31.2%. We performed a case-control analysis to identify antibody and cellular immune correlates of infection risk. METHODS In pilot studies conducted with RV144 blood samples, 17 antibody or cellular assays met prespecified criteria, of which 6 were chosen for primary analysis to determine the roles of T-cell, IgG antibody, and IgA antibody responses in the modulation of infection risk. Assays were performed on samples from 41 vaccinees who became infected and 205 uninfected vaccinees, obtained 2 weeks after final immunization, to evaluate whether immune-response variables predicted HIV-1 infection through 42 months of follow-up. RESULTS Of six primary variables, two correlated significantly with infection risk: the binding of IgG antibodies to variable regions 1 and 2 (V1V2) of HIV-1 envelope proteins (Env) correlated inversely with the rate of HIV-1 infection (estimated odds ratio, 0.57 per 1-SD increase; P=0.02; q=0.08), and the binding of plasma IgA antibodies to Env correlated directly with the rate of infection (estimated odds ratio, 1.54 per 1-SD increase; P=0.03; q=0.08). Neither low levels of V1V2 antibodies nor high levels of Env-specific IgA antibodies were associated with higher rates of infection than were found in the placebo group. Secondary analyses suggested that Env-specific IgA antibodies may mitigate the effects of potentially protective antibodies. CONCLUSIONS This immune-correlates study generated the hypotheses that V1V2 antibodies may have contributed to protection against HIV-1 infection, whereas high levels of Env-specific IgA antibodies may have mitigated the effects of protective antibodies. Vaccines that are designed to induce higher levels of V1V2 antibodies and lower levels of Env-specific IgA antibodies than are induced by the RV144 vaccine may have improved efficacy against HIV-1 infection.
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Affiliation(s)
- Barton F Haynes
- Duke University Human Vaccine Institute and the Center for HIV/AIDS Vaccine Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Ban YEA, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog 2011; 7:e1002209. [PMID: 21980282 PMCID: PMC3182927 DOI: 10.1371/journal.ppat.1002209] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 06/26/2011] [Indexed: 12/15/2022] Open
Abstract
Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413-415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.
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Affiliation(s)
- S. Gnanakaran
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Marcus Daniels
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Brandon F. Keele
- SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter T. Hraber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Lapedes
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tongye Shen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Molecular Biophysics and Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brian Gaschen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mohan Krishnamoorthy
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hui Li
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Julie M. Decker
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jesus F. Salazar-Gonzalez
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Shuyi Wang
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chunlai Jiang
- National Engineering Laboratory of AIDS Vaccine School of Life Science, Jilin University, Changchun, China
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Feng Gao
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey A. Anderson
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Li-Hua Ping
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Myron S. Cohen
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, an affiliate of the Rockefeller University, New York, New York, United States of America
| | - Paul A. Goepfert
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Saag
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joseph J. Eron
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Charles B. Hicks
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - William A. Blattner
- Institute of Human Virology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Georgia D. Tomaras
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Mohammed Asmal
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Norman L. Letvin
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Division of Viral Pathogenesis, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter B. Gilbert
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Allan C. DeCamp
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Craig A. Magaret
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Yih-En Andrew Ban
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Arzeda Corporation, Seattle, Washington, United States of America
| | - Ming Zhang
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America
| | - Kelly A. Soderberg
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Joseph G. Sodroski
- Dana-Farber Cancer Institute, Department of Cancer Immunology and AIDS, Boston, Massachusetts, United States of America
| | - Barton F. Haynes
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - George M. Shaw
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Bette Korber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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Soderberg KA, Payne GW, Sato A, Medzhitov R, Segal SS, Iwasaki A. Innate control of adaptive immunity via remodeling of lymph node feed arteriole. Proc Natl Acad Sci U S A 2005; 102:16315-20. [PMID: 16260739 PMCID: PMC1283434 DOI: 10.1073/pnas.0506190102] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The adaptive immune system relies on rare cognate lymphocytes to detect pathogen-derived antigens. Naïve lymphocytes recirculate through secondary lymphoid organs in search of cognate antigen. Here, we show that the naïve-lymphocyte recirculation pattern is controlled at the level of innate immune recognition, independent of antigen-specific stimulation. We demonstrate that inflammation-induced lymphocyte recruitment to the lymph node is mediated by the remodeling of the primary feed arteriole, and that its physiological role is to increase the efficiency of screening for rare antigen-specific lymphocytes. Our data reveal a mechanism of innate control of adaptive immunity: by increasing the pool of naïve lymphocytes for detection of foreign antigens via regulation of vascular input to the local lymph node.
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Affiliation(s)
- Kelly A Soderberg
- Section of Immunobiology, John B. Pierce Laboratory and Department of Cellular and Molecular Physiology, and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA
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Soderberg KA, Linehan MM, Ruddle NH, Iwasaki A. MAdCAM-1 expressing sacral lymph node in the lymphotoxin beta-deficient mouse provides a site for immune generation following vaginal herpes simplex virus-2 infection. J Immunol 2004; 173:1908-13. [PMID: 15265924 DOI: 10.4049/jimmunol.173.3.1908] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The members of the lymphotoxin (LT) family of molecules play a critical role in lymphoid organogenesis. Whereas LT alpha-deficient mice lack all lymph nodes and Peyer's patches, mice deficient in LT beta retain mesenteric lymph nodes and cervical lymph nodes, suggesting that an LT beta-independent pathway exists for the generation of mucosal lymph nodes. In this study, we describe the presence of a lymph node in LT beta-deficient mice responsible for draining the genital mucosa. In the majority of LT beta-deficient mice, a lymph node was found near the iliac artery, slightly misplaced from the site of the sacral lymph node in wild-type mice. The sacral lymph node of the LT beta-deficient mice, as well as that of the wild-type mice, expressed the mucosal addressin cell adhesion molecule-1 similar to the mesenteric lymph node. Following intravaginal infection with HSV type 2, activated dendritic cells capable of stimulating a Th1 response were found in this sacral lymph node. Furthermore, normal HSV-2-specific IgG responses were generated in the LT beta-deficient mice following intravaginal HSV-2 infection even in the absence of the spleen. Therefore, an LT beta-independent pathway exists for the development of a lymph node associated with the genital mucosa, and such a lymph node serves to generate potent immune responses against viral challenge.
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Affiliation(s)
- Kelly A Soderberg
- Department of Epidemiology and Public Health and Section of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
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