1
|
Prigent J, Jarossay A, Planchais C, Eden C, Dufloo J, Kök A, Lorin V, Vratskikh O, Couderc T, Bruel T, Schwartz O, Seaman MS, Ohlenschläger O, Dimitrov JD, Mouquet H. Conformational Plasticity in Broadly Neutralizing HIV-1 Antibodies Triggers Polyreactivity. Cell Rep 2019; 23:2568-2581. [PMID: 29847789 PMCID: PMC5990490 DOI: 10.1016/j.celrep.2018.04.101] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 12/18/2022] Open
Abstract
Human high-affinity antibodies to pathogens often recognize unrelated ligands. The molecular origin and the role of this polyreactivity are largely unknown. Here, we report that HIV-1 broadly neutralizing antibodies (bNAbs) are frequently polyreactive, cross-reacting with non-HIV-1 molecules, including self-antigens. Mutating bNAb genes to increase HIV-1 binding and neutralization also results in de novo polyreactivity. Unliganded paratopes of polyreactive bNAbs with improved HIV-1 neutralization exhibit a conformational flexibility, which contributes to enhanced affinity of bNAbs to various HIV-1 envelope glycoproteins and non-HIV antigens. Binding adaptation of polyreactive bNAbs to the divergent ligands mainly involves hydrophophic interactions. Plasticity of bNAbs' paratopes may, therefore, facilitate accommodating divergent viral variants, but it simultaneously triggers promiscuous binding to non-HIV-1 antigens. Thus, a certain level of polyreactivity can be a mark of adaptable antibodies displaying optimal pathogens' recognition.
Collapse
Affiliation(s)
- Julie Prigent
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Annaëlle Jarossay
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France; INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France; Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France
| | - Cyril Planchais
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Caroline Eden
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jérémy Dufloo
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris 75015, France; CNRS URA3015, Paris 75015, France
| | - Ayrin Kök
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Valérie Lorin
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Oxana Vratskikh
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Thérèse Couderc
- Biology of Infection Unit, INSERM U1117, Department of Cell Biology and Infection, Institut Pasteur, Paris 75015, France
| | - Timothée Bruel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris 75015, France; CNRS URA3015, Paris 75015, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris 75015, France; CNRS URA3015, Paris 75015, France
| | | | | | - Jordan D Dimitrov
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France; INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France; Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France.
| | - Hugo Mouquet
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France.
| |
Collapse
|
2
|
Abstract
The benefits of combination antiretroviral therapy (cART) for HIV replication and transmission control have led to its universal recommendation. Many people living with HIV are, however, still undiagnosed or diagnosed late, especially in sub-Saharan Africa, where the HIV disease burden is highest. Further expansion in HIV treatment options, incorporating women-centred approaches, is essential to make individualised care a reality. With a longer life expectancy than before, people living with HIV are at an increased risk of developing non-AIDS comorbidities, such as cardiovascular diseases and cancers. Antiretroviral strategies are evolving towards a decrease in drug burden, and some two-drug combinations have proven efficacy for maintenance therapy. Investigational immune checkpoint inhibitors and broadly neutralising antibodies with effector functions have energised the HIV cure research field as the search for an effective vaccine continues. In this Seminar, we review advances and challenges relating to the goal of an AIDS-free world.
Collapse
Affiliation(s)
- Jade Ghosn
- Inserm UMR-S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - Babafemi Taiwo
- Division of Infectious Diseases and Center for Global Health, Northwestern University, Chicago, Illinois, USA
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brigitte Autran
- Inserm UMR-S 1135, Centre de Recherches en Immunologie et Maladies Infectieus, CIMI-Paris, Université Pierre et Marie Curie, Paris, France
| | - Christine Katlama
- Inserm UMR-S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France; Paris-Sorbonne University, Paris, France; Assistance Publique-Hôpitaux de Paris, Department of Infectious Diseases, Hôpital Pitié Salpêtrière, Paris, France.
| |
Collapse
|
3
|
Abstract
Glycosylation is an important post-translational modification that is required for structural and stability purposes and functional roles such as signalling, attachment and shielding. Many human pathogens such as bacteria display an array of carbohydrates on their surface that are non-self to the host; others such as viruses highjack the host-cell machinery and present self-carbohydrates sometimes arranged in a non-self more immunogenic manner. In combination with carrier proteins, these glycan structures can be highly immunogenic. During natural infection, glycan-binding antibodies are often elicited that correlate with long-lasting protection. A great amount of research has been invested in carbohydrate vaccine design to elicit such an immune response, which has led to the development of vaccines against the bacterial pathogens Haemophilus influenzae type b, Streptococcus pneumonia and Neisseria meningitidis. Other vaccines, e.g. against HIV-1, are still in development, but promising progress has been made with the isolation of broadly neutralizing glycan-binding antibodies and the engineering of stable trimeric envelope glycoproteins. Carbohydrate vaccines against other pathogens such as viruses (Dengue, Hepatitis C), parasites (Plasmodium) and fungi (Candida) are at different stages of development. This chapter will discuss the challenges in inducing cross-reactive carbohydrate-targeting antibodies and progress towards carbohydrate vaccines.
Collapse
|
4
|
Rouers A, Jeger-Madiot R, Moris A, Graff-Dubois S. [Follicular helper T cells and HIV - United for better and worse]. Med Sci (Paris) 2017; 33:878-886. [PMID: 28994384 DOI: 10.1051/medsci/20173310020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Follicular helper T cells (Tfh) have been discovered in lymph nodes and, since then, are the focus of very intensive research to understand their origin, differentiation and functions. Tfh interact with B cells in the secondary lymphoid organs leading to B cell differentiation and maturation. Tfh are particularly studied in pathological contexts such as autoimmune diseases and infection by the human immunodeficiency virus (HIV). In the context of HIV infection, broadly neutralizing antibodies have been identified in a few patients. The generation of these broadly neutralizing antibodies requires a long and complex maturation of B cells in the secondary lymphoid organs. Characterizing Tfh functions and the relation with the quality of antibodies in HIV infection might help in designing novel immunotherapies and vaccination strategies to induce broadly neutralizing antibodies.
Collapse
Affiliation(s)
- Angeline Rouers
- Sorbonne universités, UPMC Univ Paris 06, Inserm U1135, CNRS ERL 8255, Centre d'immunologie et des maladies infectieuses, CIMI-Paris, 91, boulevard de l'Hôpital, 75013 Paris, France
| | - Raphaël Jeger-Madiot
- Sorbonne universités, UPMC Univ Paris 06, Inserm U1135, CNRS ERL 8255, Centre d'immunologie et des maladies infectieuses, CIMI-Paris, 91, boulevard de l'Hôpital, 75013 Paris, France
| | - Arnaud Moris
- Sorbonne universités, UPMC Univ Paris 06, Inserm U1135, CNRS ERL 8255, Centre d'immunologie et des maladies infectieuses, CIMI-Paris, 91, boulevard de l'Hôpital, 75013 Paris, France
| | - Stéphanie Graff-Dubois
- Sorbonne universités, UPMC Univ Paris 06, Inserm U1135, CNRS ERL 8255, Centre d'immunologie et des maladies infectieuses, CIMI-Paris, 91, boulevard de l'Hôpital, 75013 Paris, France
| |
Collapse
|
5
|
Doria-Rose NA, Altae-Tran HR, Roark RS, Schmidt SD, Sutton MS, Louder MK, Chuang GY, Bailer RT, Cortez V, Kong R, McKee K, O’Dell S, Wang F, Abdool Karim SS, Binley JM, Connors M, Haynes BF, Martin MA, Montefiori DC, Morris L, Overbaugh J, Kwong PD, Mascola JR, Georgiev IS. Mapping Polyclonal HIV-1 Antibody Responses via Next-Generation Neutralization Fingerprinting. PLoS Pathog 2017; 13:e1006148. [PMID: 28052137 PMCID: PMC5241146 DOI: 10.1371/journal.ppat.1006148] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 01/17/2017] [Accepted: 12/22/2016] [Indexed: 11/27/2022] Open
Abstract
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially novel epitope specificities. At the individual donor level, the next-generation NFP algorithms particularly improved the ability to detect multiple epitope specificities in a sample, as confirmed both for computationally simulated polyclonal sera and for samples from HIV-infected donors. Specifically, the next-generation NFP algorithms detected multiple specificities in twice as many samples of simulated sera. Further, unlike the first-generation NFP, the new algorithms were able to detect both of the previously confirmed antibody specificities, VRC01-like and PG9-like, in donor CHAVI 0219. At the cohort level, analysis of ~150 broadly neutralizing HIV-infected donor samples suggested a potential connection between clade of infection and types of elicited epitope specificities. Most notably, while 10E8-like antibodies were observed in infections from different clades, an enrichment of such antibodies was predicted for clade B samples. Ultimately, such large-scale analyses of antibody responses to HIV-1 infection can help guide the design of epitope-specific vaccines that are tailored to take into account the prevalence of infecting clades within a specific geographic region. Overall, the next-generation NFP technology will be an important tool for the analysis of broadly neutralizing polyclonal antibody responses against HIV-1. HIV-1 remains a significant global health threat, with no effective vaccine against the virus currently available. Since traditional vaccine design efforts have had limited success, much effort in recent years has focused on gaining a better understanding of the ways select individuals are able to effectively neutralize the virus upon natural infection, and to utilize that knowledge for the design of optimized vaccine candidates. Primary emphasis has been placed on characterizing the antibody arm of the immune system, and specifically on antibodies capable of neutralizing the majority of circulating HIV-1 strains. Various experimental techniques can be applied to map the epitope targets of these antibodies, but more recently, the development of computational methods has provided an efficient and accurate alternative for understanding the complex antibody responses to HIV-1 in a given individual. Here, we present the next generation of this computational technology, and show that these new methods have significantly improved accuracy and confidence, and that they enable the interrogation of biologically important questions that can lead to new insights for the design of an effective vaccine against HIV-1.
Collapse
Affiliation(s)
- Nicole A. Doria-Rose
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Han R. Altae-Tran
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Ryan S. Roark
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Stephen D. Schmidt
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Matthew S. Sutton
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Mark K. Louder
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Robert T. Bailer
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Valerie Cortez
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, United States of America
| | - Rui Kong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Krisha McKee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Sijy O’Dell
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Felicia Wang
- Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, United States of America
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Department of Epidemiology, Columbia University, New York, NY, United States of America
| | - James M. Binley
- San Diego Biomedical Research Institute, San Diego, CA, United States of America
| | - Mark Connors
- HIV-Specific Immunity Section, National Institutes of Health, Bethesda, MD, United States of America
| | - Barton F. Haynes
- Duke University Human Vaccine Institute, Durham, NC, United States of America
- Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC, United States of America
- Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC, United States of America
| | - Malcolm A. Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - David C. Montefiori
- Duke University Human Vaccine Institute, Durham, NC, United States of America
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States of America
| | - Lynn Morris
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- University of the Witwatersrand, Johannesburg, South Africa
- Center for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Ivelin S. Georgiev
- Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
- Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States of America
- * E-mail:
| |
Collapse
|
6
|
Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens. Proc Natl Acad Sci U S A 2016; 113:E7039-E7048. [PMID: 27791170 DOI: 10.1073/pnas.1614940113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Strategies to elicit Abs that can neutralize diverse strains of a highly mutable pathogen are likely to result in a potent vaccine. Broadly neutralizing Abs (bnAbs) against HIV have been isolated from patients, proving that the human immune system can evolve them. Using computer simulations and theory, we study immunization with diverse mixtures of variant antigens (Ags). Our results show that particular choices for the number of variant Ags and the mutational distances separating them maximize the probability of inducing bnAbs. The variant Ags represent potentially conflicting selection forces that can frustrate the Darwinian evolutionary process of affinity maturation. An intermediate level of frustration maximizes the chance of evolving bnAbs. A simple model makes vivid the origin of this principle of optimal frustration. Our results, combined with past studies, suggest that an appropriately chosen permutation of immunization with an optimally designed mixture (using the principles that we describe) and sequential immunization with variant Ags that are separated by relatively large mutational distances may best promote the evolution of bnAbs.
Collapse
|
7
|
Native Conformation and Canonical Disulfide Bond Formation Are Interlinked Properties of HIV-1 Env Glycoproteins. J Virol 2015; 90:2884-94. [PMID: 26719247 DOI: 10.1128/jvi.01953-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/21/2015] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED We investigated whether there is any association between a native-like conformation and the presence of only the canonical (i.e., native) disulfide bonds in the gp120 subunits of a soluble recombinant human immunodeficiency virus type 1 (HIV-1) envelope (Env) glycoprotein. We used a mass spectrometry (MS)-based method to map the disulfide bonds present in nonnative uncleaved gp140 proteins and native-like SOSIP.664 trimers based on the BG505 env gene. Our results show that uncleaved gp140 proteins were not homogeneous, in that substantial subpopulations (20 to 80%) contained aberrant disulfide bonds. In contrast, the gp120 subunits of the native-like SOSIP.664 trimer almost exclusively retained the canonical disulfide bond pattern. We also observed that the purification method could influence the proportion of an Env protein population that contained aberrant disulfide bonds. We infer that gp140 proteins may always contain a variable but substantial proportion of aberrant disulfide bonds but that the impact of this problem can be minimized via design and/or purification strategies that yield native-like trimers. The same factors may also be relevant to the production and purification of monomeric gp120 proteins that are free of aberrant disulfide bonds. IMPORTANCE It is widely thought that a successful HIV-1 vaccine will include a recombinant form of the Env protein, a trimer located on the virion surface. To increase yield and simplify purification, Env proteins are often made in truncated, soluble forms. A consequence, however, can be the loss of the native conformation concomitant with the virion-associated trimer. Moreover, some soluble recombinant Env proteins contain aberrant disulfide bonds that are not expected to be present in the native trimer. To assess whether these observations are linked, to determine the extent of disulfide bond scrambling, and to understand why scrambling occurs, we determined the disulfide bond profiles of two soluble Env proteins with different designs that are being assessed as vaccine candidates. We found that uncleaved gp140 forms heterogeneous mixtures in which aberrant disulfide bonds abound. In contrast, BG505 SOSIP.664 trimers are more homogeneous, native-like entities that contain predominantly the native disulfide bond profile.
Collapse
|