51
|
Pae J, Jacobsen JT, Victora GD. Imaging the different timescales of germinal center selection. Immunol Rev 2021; 306:234-243. [PMID: 34825386 DOI: 10.1111/imr.13039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/06/2021] [Indexed: 12/16/2022]
Abstract
Germinal centers (GCs) are the site of antibody affinity maturation, a fundamental immunological process that increases the potency of antibodies and thereby their ability to protect against infection. GC biology is highly dynamic in both time and space, making it ideally suited for intravital imaging. Using multiphoton laser scanning microscopy (MPLSM), the field has gained insight into the molecular, cellular, and structural changes and movements that coordinate affinity maturation in real time in their native environment. On the other hand, several limitations of MPLSM have had to be overcome to allow full appreciation of GC events taking place across different timescales. Here, we review the technical advances afforded by intravital imaging and their contributions to our understanding of GC biology.
Collapse
Affiliation(s)
- Juhee Pae
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, USA
| |
Collapse
|
52
|
Escolano A, Gristick HB, Gautam R, DeLaitsch AT, Abernathy ME, Yang Z, Wang H, Hoffmann MAG, Nishimura Y, Wang Z, Koranda N, Kakutani LM, Gao H, Gnanapragasam PNP, Raina H, Gazumyan A, Cipolla M, Oliveira TY, Ramos V, Irvine DJ, Silva M, West AP, Keeffe JR, Barnes CO, Seaman MS, Nussenzweig MC, Martin MA, Bjorkman PJ. Sequential immunization of macaques elicits heterologous neutralizing antibodies targeting the V3-glycan patch of HIV-1 Env. Sci Transl Med 2021; 13:eabk1533. [PMID: 34818054 DOI: 10.1126/scitranslmed.abk1533] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew T DeLaitsch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Morgan E Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Haoqing Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Magnus A G Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Henna Raina
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Darrell J Irvine
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Murillo Silva
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Malcolm A Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
53
|
Williams WB, Wiehe K, Saunders KO, Haynes BF. Strategies for induction of HIV-1 envelope-reactive broadly neutralizing antibodies. J Int AIDS Soc 2021; 24 Suppl 7:e25831. [PMID: 34806332 PMCID: PMC8606870 DOI: 10.1002/jia2.25831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/23/2021] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION A primary focus of HIV-1 vaccine development is the activation of B cell receptors for naïve or precursor broadly neutralizing antibodies (bnAbs), followed by expansion and maturation of bnAb B cell lineage intermediates leading to highly affinity-matured bnAbs. HIV-1 envelope (Env) encodes epitopes for bnAbs of different specificities. Design of immunogens to induce bnAb precursors of different specificities and mature them into bnAb status is a goal for HIV-1 vaccine development. We review vaccine strategies for bnAb lineages development and highlight the immunological barriers that these strategies must overcome to generate bnAbs. METHODS We provide perspectives based on published research articles and reviews. DISCUSSION The recent Antibody Mediated Protection (AMP) trial that tested the protective efficacy of one HIV-1 Env bnAb specificity demonstrated that relatively high levels of long-lasting serum titers of multiple specificities of bnAbs will be required for protection from HIV-1 transmission. Current vaccine efforts for induction of bnAb lineages are focused on immunogens designed to expand naïve HIV-1 bnAb precursor B cells following the recent success of vaccine-induction of bnAb precursor B cells in macaques and humans. BnAb precursor B cells serve as templates for priming-immunogen design. However, design of boosting immunogens for bnAb maturation requires knowledge of the optimal immunogen design and immunological environment for bnAb B cell lineage affinity maturation. BnAb lineages acquire rare genetic changes as mutations during B cell maturation. Moreover, the immunological environment that supports bnAb development during HIV-1 infection is perturbed with an altered B cell repertoire and dysfunctional immunoregulatory controls, suggesting that in normal settings, bnAb development will be disfavoured. Thus, strategies for vaccine induction of bnAbs must circumvent immunological barriers for bnAb development that normally constrain bnAb B cell affinity maturation. CONCLUSIONS A fully protective HIV-1 vaccine needs to induce durable high titers of bnAbs that can be generated by a sequential set of Env immunogens for expansion and maturation of bnAb B cell lineages in a permitted immunological environment. Moreover, multiple specificities of bnAbs will be required to be sufficiently broad to prevent the escape of HIV-1 strains during transmission.
Collapse
Affiliation(s)
- Wilton B. Williams
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin Wiehe
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin O. Saunders
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Barton F. Haynes
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
| |
Collapse
|
54
|
Griffith SA, McCoy LE. To bnAb or Not to bnAb: Defining Broadly Neutralising Antibodies Against HIV-1. Front Immunol 2021; 12:708227. [PMID: 34737737 PMCID: PMC8560739 DOI: 10.3389/fimmu.2021.708227] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Since their discovery, antibodies capable of broad neutralisation have been at the forefront of HIV-1 research and are of particular interest due to in vivo passive transfer studies demonstrating their potential to provide protection. Currently an exact definition of what is required for a monoclonal antibody to be classed as a broadly neutralising antibody (bnAb) has not yet been established. This has led to hundreds of antibodies with varying neutralisation breadth being studied and has given insight into antibody maturation pathways and epitopes targeted. However, even with this knowledge, immunisation studies and vaccination trials to date have had limited success in eliciting antibodies with neutralisation breadth. For this reason there is a growing need to identify factors specifically associated with bnAb development, yet to do this a set of criteria is necessary to distinguish bnAbs from non-bnAbs. This review aims to define what it means to be a HIV-1 bnAb by comparing neutralisation breadth, genetic features and epitopes of bnAbs, and in the process highlights the challenges of comparing the array of antibodies that have been isolated over the years.
Collapse
Affiliation(s)
- Sarah A Griffith
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Laura E McCoy
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| |
Collapse
|
55
|
Cottrell CA, Manne K, Kong R, Wang S, Zhou T, Chuang GY, Edwards RJ, Henderson R, Janowska K, Kopp M, Lin BC, Louder MK, Olia AS, Rawi R, Shen CH, Taft JD, Torres JL, Wu NR, Zhang B, Doria-Rose NA, Cohen MS, Haynes BF, Shapiro L, Ward AB, Acharya P, Mascola JR, Kwong PD. Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies. Cell Rep 2021; 37:109922. [PMID: 34731616 PMCID: PMC9058982 DOI: 10.1016/j.celrep.2021.109922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.
Collapse
Affiliation(s)
- Christopher A Cottrell
- IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kartik Manne
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert J Edwards
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Rory Henderson
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Katarzyna Janowska
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Megan Kopp
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin D Taft
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan L Torres
- IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nelson R Wu
- IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myron S Cohen
- Departments of Medicine, Epidemiology, and Microbiology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Barton F Haynes
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, Consortium for HIV/AIDS Vaccine Development (CHAVD), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Priyamvada Acharya
- Duke University Human Vaccine Institute, Departments of Medicine and Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery at Duke University, Durham, NC 27710, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
56
|
Mielke D, Bandawe G, Zheng J, Jones J, Abrahams MR, Bekker V, Ochsenbauer C, Garrett N, Abdool Karim S, Moore PL, Morris L, Montefiori D, Anthony C, Ferrari G, Williamson C. ADCC-mediating non-neutralizing antibodies can exert immune pressure in early HIV-1 infection. PLoS Pathog 2021; 17:e1010046. [PMID: 34788337 PMCID: PMC8598021 DOI: 10.1371/journal.ppat.1010046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022] Open
Abstract
Despite antibody-dependent cellular cytotoxicity (ADCC) responses being implicated in protection from HIV-1 infection, there is limited evidence that they control virus replication. The high mutability of HIV-1 enables the virus to rapidly adapt, and thus evidence of viral escape is a very sensitive approach to demonstrate the importance of this response. To enable us to deconvolute ADCC escape from neutralizing antibody (nAb) escape, we identified individuals soon after infection with detectable ADCC responses, but no nAb responses. We evaluated the kinetics of ADCC and nAb responses, and viral escape, in five recently HIV-1-infected individuals. In one individual we detected viruses that escaped from ADCC responses but were sensitive to nAbs. In the remaining four participants, we did not find evidence of viral evolution exclusively associated with ADCC-mediating non-neutralizing Abs (nnAbs). However, in all individuals escape from nAbs was rapid, occurred at very low titers, and in three of five cases we found evidence of viral escape before detectable nAb responses. These data show that ADCC-mediating nnAbs can drive immune escape in early infection, but that nAbs were far more effective. This suggests that if ADCC responses have a protective role, their impact is limited after systemic virus dissemination.
Collapse
Affiliation(s)
- Dieter Mielke
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
- Institute of Infectious Diseases and Molecular Medicine and Division of Medical Virology, University of Cape Town, Cape Town, South Africa
| | - Gama Bandawe
- Institute of Infectious Diseases and Molecular Medicine and Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Malawi University of Science and Technology, Thyolo, Malawi
| | - Jie Zheng
- University of Alabama at Birmingham, Department of Medicine, Birmingham, Alabama, United States of America
| | - Jennifer Jones
- University of Alabama at Birmingham, Department of Medicine, Birmingham, Alabama, United States of America
| | - Melissa-Rose Abrahams
- Institute of Infectious Diseases and Molecular Medicine and Division of Medical Virology, University of Cape Town, Cape Town, South Africa
| | - Valerie Bekker
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Christina Ochsenbauer
- University of Alabama at Birmingham, Department of Medicine, Birmingham, Alabama, United States of America
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu Natal, Durban, South Africa
| | - Salim 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, New York, United States of America
| | - Penny L. Moore
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa
- University of Witswaterstrand, Johannesburg, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa
- University of Witswaterstrand, Johannesburg, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
| | - David Montefiori
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Colin Anthony
- Institute of Infectious Diseases and Molecular Medicine and Division of Medical Virology, University of Cape Town, Cape Town, South Africa
| | - Guido Ferrari
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine and Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
| |
Collapse
|
57
|
Petersen BM, Ulmer SA, Rhodes ER, Gutierrez-Gonzalez MF, Dekosky BJ, Sprenger KG, Whitehead TA. Regulatory Approved Monoclonal Antibodies Contain Framework Mutations Predicted From Human Antibody Repertoires. Front Immunol 2021; 12:728694. [PMID: 34646268 PMCID: PMC8503325 DOI: 10.3389/fimmu.2021.728694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/03/2021] [Indexed: 11/13/2022] Open
Abstract
Monoclonal antibodies (mAbs) are an important class of therapeutics used to treat cancer, inflammation, and infectious diseases. Identifying highly developable mAb sequences in silico could greatly reduce the time and cost required for therapeutic mAb development. Here, we present position-specific scoring matrices (PSSMs) for antibody framework mutations developed using baseline human antibody repertoire sequences. Our analysis shows that human antibody repertoire-based PSSMs are consistent across individuals and demonstrate high correlations between related germlines. We show that mutations in existing therapeutic antibodies can be accurately predicted solely from baseline human antibody sequence data. We find that mAbs developed using humanized mice had more human-like FR mutations than mAbs originally developed by hybridoma technology. A quantitative assessment of entire framework regions of therapeutic antibodies revealed that there may be potential for improving the properties of existing therapeutic antibodies by incorporating additional mutations of high frequency in baseline human antibody repertoires. In addition, high frequency mutations in baseline human antibody repertoires were predicted in silico to reduce immunogenicity in therapeutic mAbs due to the removal of T cell epitopes. Several therapeutic mAbs were identified to have common, universally high-scoring framework mutations, and molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Our results suggest that baseline human antibody repertoires may be useful as predictive tools to guide mAb development in the future.
Collapse
Affiliation(s)
- Brian M Petersen
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | - Sophia A Ulmer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | - Emily R Rhodes
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | | | - Brandon J Dekosky
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States.,Department of Chemical Engineering, University of Kansas, Lawrence, KS, United States
| | - Kayla G Sprenger
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, United States
| |
Collapse
|
58
|
Crooks ET, Almanza F, D’Addabbo A, Duggan E, Zhang J, Wagh K, Mou H, Allen JD, Thomas A, Osawa K, Korber BT, Tsybovsky Y, Cale E, Nolan J, Crispin M, Verkoczy LK, Binley JM. Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens. PLoS Pathog 2021; 17:e1009807. [PMID: 34679128 PMCID: PMC8565784 DOI: 10.1371/journal.ppat.1009807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/03/2021] [Accepted: 10/07/2021] [Indexed: 02/07/2023] Open
Abstract
HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets-the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity-and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30-40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts.
Collapse
Affiliation(s)
- Emma T. Crooks
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Francisco Almanza
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Alessio D’Addabbo
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Erika Duggan
- Scintillon Institute, San Diego, California, United States of America
- Cellarcus BioSciences, La Jolla, California, United States of America
| | - Jinsong Zhang
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Kshitij Wagh
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Huihui Mou
- Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Alyssa Thomas
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Keiko Osawa
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Bette T. Korber
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Yaroslav Tsybovsky
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
| | - Evan Cale
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John Nolan
- Scintillon Institute, San Diego, California, United States of America
- Cellarcus BioSciences, La Jolla, California, United States of America
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Laurent K. Verkoczy
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - James M. Binley
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| |
Collapse
|
59
|
Swanson O, Rhodes B, Wang A, Xia SM, Parks R, Chen H, Sanzone A, Cooper M, Louder MK, Lin BC, Doria-Rose NA, Bonsignori M, Saunders KO, Wiehe K, Haynes BF, Azoitei ML. Rapid selection of HIV envelopes that bind to neutralizing antibody B cell lineage members with functional improbable mutations. Cell Rep 2021; 36:109561. [PMID: 34407396 PMCID: PMC8493474 DOI: 10.1016/j.celrep.2021.109561] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/25/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
Abstract
Elicitation of broadly neutralizing antibodies (bnAbs) by an HIV vaccine will involve priming the immune system to activate antibody precursors, followed by boosting immunizations to select for antibodies with functional features required for neutralization breadth. The higher the number of acquired mutations necessary for function, the more convoluted are the antibody developmental pathways. HIV bnAbs acquire a large number of somatic mutations, but not all mutations are functionally important. In this study, we identify a minimal subset of mutations sufficient for the function of the naturally occurring V3-glycan bnAb DH270.6. Using antibody library screening, candidate envelope immunogens that interact with DH270.6-like antibodies containing this set of key mutations are identified and selected in vitro. Our results demonstrate that less complex B cell evolutionary pathways than those naturally observed exist for the induction of HIV bnAbs by vaccination, and they establish rational approaches to identify boosting candidate immunogens.
Collapse
Affiliation(s)
- Olivia Swanson
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA
| | - Brianna Rhodes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA
| | - Avivah Wang
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA
| | - Haiyan Chen
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA
| | - Aja Sanzone
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA
| | - Melissa Cooper
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA
| | - Mark K. Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Bob C. Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA,Department of Medicine, Duke University, Durham, NC 27610, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA,Department of Surgery, Duke University, Durham, NC 27610, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA,Department of Medicine, Duke University, Durham, NC 27610, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA,Department of Medicine, Duke University, Durham, NC 27610, USA,Department of Immunology, Duke University, Durham, NC 27610, USA
| | - Mihai L. Azoitei
- Duke Human Vaccine Institute, Duke University, Durham, NC 27610, USA,Department of Medicine, Duke University, Durham, NC 27610, USA,Lead contact,Correspondence:
| |
Collapse
|
60
|
Mu Z, Wiehe K, Saunders KO, Henderson R, Cain DW, Parks R, Martik D, Mansouri K, Edwards RJ, Newman A, Lu X, Xia SM, Bonsignori M, Montefiori D, Han Q, Venkatayogi S, Evangelous T, Wang Y, Rountree W, Tam Y, Barbosa C, Alam SM, Williams WB, Pardi N, Weissman D, Haynes BF. Ability of nucleoside-modified mRNA to encode HIV-1 envelope trimer nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.09.455714. [PMID: 34401876 PMCID: PMC8366792 DOI: 10.1101/2021.08.09.455714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The success of nucleoside-modified mRNAs in lipid nanoparticles (mRNA-LNP) as COVID-19 vaccines heralded a new era of vaccine development. For HIV-1, multivalent envelope (Env) trimer protein nanoparticles are superior immunogens compared to trimers alone for priming of broadly neutralizing antibody (bnAb) B cell lineages. The successful expression of complex multivalent nanoparticle immunogens with mRNAs has not been demonstrated. Here we show that mRNAs can encode antigenic Env trimers on ferritin nanoparticles that initiate bnAb precursor B cell expansion and induce serum autologous tier 2 neutralizing activity in bnAb precursor VH + VL knock-in mice. Next generation sequencing demonstrated acquisition of critical mutations, and monoclonal antibodies that neutralized heterologous HIV-1 isolates were isolated. Thus, mRNA-LNP can encode complex immunogens and are of use in design of germline-targeting and sequential boosting immunogens for HIV-1 vaccine development.
Collapse
Affiliation(s)
- Zekun Mu
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin O. Saunders
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Derek W. Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Diana Martik
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Current Address: Translational Immunobiology Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Qifeng Han
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tyler Evangelous
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wilton B. Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Norbert Pardi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Drew Weissman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barton F. Haynes
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
61
|
Sheng J, Wang S. Coevolutionary transitions emerging from flexible molecular recognition and eco-evolutionary feedback. iScience 2021; 24:102861. [PMID: 34401660 PMCID: PMC8353512 DOI: 10.1016/j.isci.2021.102861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/16/2021] [Accepted: 07/13/2021] [Indexed: 01/16/2023] Open
Abstract
Highly mutable viruses evolve to evade host immunity that exerts selective pressure and adapts to viral dynamics. Here, we provide a framework for identifying key determinants of the mode and fate of viral-immune coevolution by linking molecular recognition and eco-evolutionary dynamics. We find that conservation level and initial diversity of antigen jointly determine the timing and efficacy of narrow and broad antibody responses, which in turn control the transition between viral persistence, clearance, and rebound. In particular, clearance of structurally complex antigens relies on antibody evolution in a larger antigenic space than where selection directly acts; viral rebound manifests binding-mediated feedback between ecology and rapid evolution. Finally, immune compartmentalization can slow viral escape but also delay clearance. This work suggests that flexible molecular binding allows a plastic phenotype that exploits potentiating neutral variations outside direct contact, opening new and shorter paths toward highly adaptable states. A scale-crossing framework identifies key determinants of viral-immune coevolution Fast specific response influences slow broad response by shaping antigen dynamics Antibody footprint shift enables breadth acquisition and viral clearance Model explains divergent kinetics and outcomes of HCV infection in humans
Collapse
Affiliation(s)
- Jiming Sheng
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shenshen Wang
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
62
|
Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San JE, de Oliveira T, Gnanakaran S, Korber B. HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens. Cell Host Microbe 2021; 29:1093-1110. [PMID: 34242582 PMCID: PMC8173590 DOI: 10.1016/j.chom.2021.05.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Humanity is currently facing the challenge of two devastating pandemics caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, multi-base insertions and deletions, recombination, and variation in surface glycans all generate the variability that, guided by natural selection, enables both HIV-1's extraordinary diversity and SARS-CoV-2's slower pace of mutation accumulation. Even though SARS-CoV-2 diversity is more limited, recently emergent SARS-CoV-2 variants carry Spike mutations that have important phenotypic consequences in terms of both antibody resistance and enhanced infectivity. We review and compare how these mutational patterns manifest in these two distinct viruses to provide the variability that fuels their evolution by natural selection.
Collapse
Affiliation(s)
- Will Fischer
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA
| | - Elena E Giorgi
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA
| | - Srirupa Chakraborty
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Kien Nguyen
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Tanmoy Bhattacharya
- T-2: Nuclear and Particle Physics, Astrophysics and Cosmology, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545 USA
| | - James Theiler
- ISR-3: Space Data Science and Systems, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Pablo A Goloboff
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas - Fundación Miguel Lillo, S. M. de Tucumán, Miguel Lillo 251 4000, Argentina; Research Associate, American Museum of Natural History, New York 10024, USA
| | - Hyejin Yoon
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Werner Abfalterer
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Brian T Foley
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sandrasegaram Gnanakaran
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA; New Mexico Consortium, Los Alamos, New Mexico, 87545, USA.
| |
Collapse
|
63
|
Neutralizing Antibody Induction Associated with a Germline Immunoglobulin Gene Polymorphism in Neutralization-Resistant SIVsmE543-3 Infection. Viruses 2021; 13:v13061181. [PMID: 34205728 PMCID: PMC8235048 DOI: 10.3390/v13061181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Antibody responses are crucial for the control of virus infection. Understanding of the mechanism of antibody induction is important for the development of a vaccine eliciting effective anti-virus antibodies. Virus-specific B cell receptor (BCR)/antibody repertoires are different among individuals, but determinants for this difference remain largely unclear. We have recently reported that a germline BCR immunoglobulin (IgG) gene polymorphism (VH3.33_ET or VH3.33_VI) in rhesus macaques is the determinant for induction of potent B404-class anti-simian immunodeficiency virus (SIV) neutralizing antibodies in neutralization-sensitive SIVsmH635FC infection. In the present study, we examined whether neutralization-resistant SIVsmE543-3 infection can induce the anti-SIV neutralizing antibodies associated with the germline VH3.33 polymorphism. Anti-SIVsmE543-3 neutralizing antibodies were induced in all the macaques possessing the VH3.33_ET allele, but not in those without VH3.33_ET, in the chronic phase of SIVsmE543-3 infection. Next generation sequencing analysis of BCR VH genes found B404-class antibody sequences only in those with VH3.33_ET. These results indicate that anti-SIVsmE543-3 neutralizing antibody induction associated with the germline BCR IgG gene polymorphism can be triggered by infection with neutralization-resistant SIVsmE543-3. This animal model would be useful for the elucidation of the mechanism of potent antibody induction against neutralization-resistant viruses.
Collapse
|
64
|
Andreano E, Paciello I, Bardelli M, Tavarini S, Sammicheli C, Frigimelica E, Guidotti S, Torricelli G, Biancucci M, D’Oro U, Chandramouli S, Bottomley MJ, Rappuoli R, Finco O, Buricchi F. The respiratory syncytial virus (RSV) prefusion F-protein functional antibody repertoire in adult healthy donors. EMBO Mol Med 2021; 13:e14035. [PMID: 33998144 PMCID: PMC8185550 DOI: 10.15252/emmm.202114035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of death from lower respiratory tract infection in infants and children, and is responsible for considerable morbidity and mortality in older adults. Vaccines for pregnant women and elderly which are in phase III clinical studies target people with pre-existing natural immunity against RSV. To investigate the background immunity which will be impacted by vaccination, we single cell-sorted human memory B cells and dissected functional and genetic features of neutralizing antibodies (nAbs) induced by natural infection. Most nAbs recognized both the prefusion and postfusion conformations of the RSV F-protein (cross-binders) while a smaller fraction bound exclusively to the prefusion conformation. Cross-binder nAbs used a wide array of gene rearrangements, while preF-binder nAbs derived mostly from the expansion of B-cell clonotypes from the IGHV1 germline. This latter class of nAbs recognizes an epitope located between Site Ø, Site II, and Site V on the F-protein, identifying an important site of pathogen vulnerability.
Collapse
Affiliation(s)
- Emanuele Andreano
- Department of Life SciencesUniversity of SienaSienaItaly
- GSK VaccinesSienaItaly
- Present address:
Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | - Ida Paciello
- GSK VaccinesSienaItaly
- Present address:
Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | | | | | | | | | | | | | | | | | - Sumana Chandramouli
- GSK VaccinesRockvilleMDUSA
- Present address:
Moderna Therapeutics IncCambridgeMAUSA
| | | | - Rino Rappuoli
- GSK VaccinesSienaItaly
- Faculty of MedicineImperial CollegeLondonUK
- Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | | | | |
Collapse
|
65
|
Cai F, Chen WH, Wu W, Jones JA, Choe M, Gohain N, Shen X, LaBranche C, Eaton A, Sutherland L, Lee EM, Hernandez GE, Wu NR, Scearce R, Seaman MS, Moody MA, Santra S, Wiehe K, Tomaras GD, Wagh K, Korber B, Bonsignori M, Montefiori DC, Haynes BF, de Val N, Joyce MG, Saunders KO. Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates. PLoS Pathog 2021; 17:e1009624. [PMID: 34086838 PMCID: PMC8216552 DOI: 10.1371/journal.ppat.1009624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/21/2021] [Accepted: 05/07/2021] [Indexed: 11/19/2022] Open
Abstract
A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.
Collapse
Affiliation(s)
- Fangping Cai
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland, United States of America
| | - Julia A. Jones
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Misook Choe
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Neelakshi Gohain
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Amanda Eaton
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Laura Sutherland
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Esther M. Lee
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Giovanna E. Hernandez
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nelson R. Wu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Richard Scearce
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland, United States of America
| | - M. Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| |
Collapse
|
66
|
Chuang GY, Shen CH, Cheung CSF, Gorman J, Creanga A, Joyce MG, Leung K, Rawi R, Wang L, Yang ES, Yang Y, Zhang B, Zhang Y, Kanekiyo M, Zhou T, DeKosky BJ, Graham BS, Mascola JR, Kwong PD. Sequence-Signature Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies That Neutralize Diverse Influenza A Viruses. Front Immunol 2021; 12:662909. [PMID: 34135892 PMCID: PMC8201785 DOI: 10.3389/fimmu.2021.662909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Sequence signatures of multidonor broadly neutralizing influenza antibodies can be used to quantify the prevalence of B cells with virus-neutralizing potential to accelerate development of broadly protective vaccine strategies. Antibodies of the same class share similar recognition modes and developmental pathways, and several antibody classes have been identified that neutralize diverse group 1- and group 2-influenza A viruses and have been observed in multiple human donors. One such multidonor antibody class, the HV6-1-derived class, targets the stem region of hemagglutinin with extraordinary neutralization breadth. Here, we use an iterative process to combine informatics, biochemical, and structural analyses to delineate an improved sequence signature for HV6-1-class antibodies. Based on sequence and structure analyses of known HV6-1 class antibodies, we derived a more inclusive signature (version 1), which we used to search for matching B-cell transcripts from published next-generation sequencing datasets of influenza vaccination studies. We expressed selected antibodies, evaluated their function, and identified amino acid-level requirements from which to refine the sequence signature (version 2). The cryo-electron microscopy structure for one of the signature-identified antibodies in complex with hemagglutinin confirmed motif recognition to be similar to known HV6-1-class members, MEDI8852 and 56.a.09, despite differences in recognition-loop length. Threading indicated the refined signature to have increased accuracy, and signature-identified heavy chains, when paired with the light chain of MEDI8852, showed neutralization comparable to the most potent members of the class. Incorporating sequences of additional class members thus enables an improved sequence signature for HV6-1-class antibodies, which can identify class members with increased accuracy.
Collapse
Affiliation(s)
- Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry and Department of Chemical Engineering, University of Kansas, Lawrence, KS, United States
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
67
|
Felber BK, Lu Z, Hu X, Valentin A, Rosati M, Remmel CAL, Weiner JA, Carpenter MC, Faircloth K, Stanfield-Oakley S, Williams WB, Shen X, Tomaras GD, LaBranche CC, Montefiori D, Trinh HV, Rao M, Alam MS, Vandergrift NA, Saunders KO, Wang Y, Rountree W, Das J, Alter G, Reed SG, Aye PP, Schiro F, Pahar B, Dufour JP, Veazey RS, Marx PA, Venzon DJ, Shaw GM, Ferrari G, Ackerman ME, Haynes BF, Pavlakis GN. Co-immunization of DNA and Protein in the Same Anatomical Sites Induces Superior Protective Immune Responses against SHIV Challenge. Cell Rep 2021; 31:107624. [PMID: 32402293 DOI: 10.1016/j.celrep.2020.107624] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/10/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
We compare immunogenicity and protective efficacy of an HIV vaccine comprised of env and gag DNA and Env (Envelope) proteins by co-administration of the vaccine components in the same muscles or by separate administration of DNA + protein in contralateral sites in female rhesus macaques. The 6-valent vaccine includes gp145 Env DNAs, representing six sequentially isolated Envs from the HIV-infected individual CH505, and matching GLA-SE-adjuvanted gp120 Env proteins. Interestingly, only macaques in the co-administration vaccine group are protected against SHIV CH505 acquisition after repeated low-dose intravaginal challenge and show 67% risk reduction per exposure. Macaques in the co-administration group develop higher Env-specific humoral and cellular immune responses. Non-neutralizing Env antibodies, ADCC, and antibodies binding to FcγRIIIa are associated with decreased transmission risk. These data suggest that simultaneous recognition, processing, and presentation of DNA + Env protein in the same draining lymph nodes play a critical role in the development of protective immunity.
Collapse
Affiliation(s)
- Barbara K Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - Zhongyan Lu
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Xintao Hu
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Antonio Valentin
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Margherita Rosati
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | | | - Joshua A Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | | | - Katelyn Faircloth
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Sherry Stanfield-Oakley
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Hung V Trinh
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Munir S Alam
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | | | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Steven G Reed
- Infectious Disease Research Institute, Seattle, WA 98102, USA
| | - Pyone P Aye
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Faith Schiro
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Bapi Pahar
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Jason P Dufour
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Ronald S Veazey
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Preston A Marx
- Tulane National Primate Research Center, and Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - David J Venzon
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | | | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| | - George N Pavlakis
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| |
Collapse
|
68
|
Song G, He WT, Callaghan S, Anzanello F, Huang D, Ricketts J, Torres JL, Beutler N, Peng L, Vargas S, Cassell J, Parren M, Yang L, Ignacio C, Smith DM, Voss JE, Nemazee D, Ward AB, Rogers T, Burton DR, Andrabi R. Cross-reactive serum and memory B-cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection. Nat Commun 2021; 12:2938. [PMID: 34011939 PMCID: PMC8134462 DOI: 10.1038/s41467-021-23074-3] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 04/08/2021] [Indexed: 01/09/2023] Open
Abstract
Pre-existing immunity to seasonal endemic coronaviruses could have profound consequences for antibody responses to SARS-CoV-2, induced from natural infection or vaccination. A first step to establish whether pre-existing responses can impact SARS-CoV-2 infection is to understand the nature and extent of cross-reactivity in humans to coronaviruses. Here we compare serum antibody and memory B cell responses to coronavirus spike proteins from pre-pandemic and SARS-CoV-2 convalescent donors using binding and functional assays. We show weak evidence of pre-existing SARS-CoV-2 cross-reactive serum antibodies in pre-pandemic donors. However, we find evidence of pre-existing cross-reactive memory B cells that are activated during SARS-CoV-2 infection. Monoclonal antibodies show varying degrees of cross-reactivity with betacoronaviruses, including SARS-CoV-1 and endemic coronaviruses. We identify one cross-reactive neutralizing antibody specific to the S2 subunit of the S protein. Our results suggest that pre-existing immunity to endemic coronaviruses should be considered in evaluating antibody responses to SARS-CoV-2.
Collapse
Affiliation(s)
- Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - James Ricketts
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sirena Vargas
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jon Cassell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linlin Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Caroline Ignacio
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Davey M Smith
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA.
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
69
|
Wang Y, Wu C, Yu J, Lin S, Liu T, Zan L, Li N, Hong P, Wang X, Jia Z, Li J, Wang Y, Zhang M, Yuan X, Li C, Xu W, Zheng W, Wang X, Liao HX. Structural basis of tetanus toxin neutralization by native human monoclonal antibodies. Cell Rep 2021; 35:109070. [PMID: 33951441 DOI: 10.1016/j.celrep.2021.109070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/31/2021] [Accepted: 04/09/2021] [Indexed: 01/19/2023] Open
Abstract
Four potent native human monoclonal antibodies (mAbs) targeting distinct epitopes on tetanus toxin (TeNT) are isolated with neutralization potency ranging from approximately 17 mg to 6 mg each that are equivalent to 250 IU of human anti-TeNT immunoglobulin. TT0170 binds fragment B, and TT0069 and TT0155 bind fragment AB. mAb TT0067 binds fragment C and blocks the binding of TeNT to gangliosides. The co-crystal structure of TT0067 with fragment C of TeNT at a 2.0-Å resolution demonstrates that mAb TT0067 directly occupies the W pocket of one of the receptor binding sites on TeNT, resulting in blocking the binding of TeNT to ganglioside on the surface of host cells. This study reveals at the atomic level the mechanism of action by the TeNT neutralizing antibody. The key neutralization epitope on the fragment C of TeNT identified in our work provides the critical information for the development of fragment C of TeNT as a better and safer tetanus vaccine.
Collapse
Affiliation(s)
- Yueming Wang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Trinomab Biotech Co., Ltd, Zhuhai 519040, China
| | - Changwen Wu
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shujian Lin
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Liu
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Institute of Biomedicine, Jinan University, Guangzhou 510632, China
| | - Lipeng Zan
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Institute of Biomedicine, Jinan University, Guangzhou 510632, China
| | - Nan Li
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
| | - Po Hong
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
| | - Xiaoli Wang
- Trinomab Biotech Co., Ltd, Zhuhai 519040, China
| | | | - Jason Li
- Trinomab Biotech Co., Ltd, Zhuhai 519040, China
| | - Yao Wang
- Trinomab Biotech Co., Ltd, Zhuhai 519040, China
| | - Ming Zhang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaohui Yuan
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Trinomab Biotech Co., Ltd, Zhuhai 519040, China
| | - Chengming Li
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Trinomab Biotech Co., Ltd, Zhuhai 519040, China
| | - Wenwen Xu
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
| | | | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Hua-Xin Liao
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Trinomab Biotech Co., Ltd, Zhuhai 519040, China; Institute of Biomedicine, Jinan University, Guangzhou 510632, China.
| |
Collapse
|
70
|
Lin YR, Parks KR, Weidle C, Naidu AS, Khechaduri A, Riker AO, Takushi B, Chun JH, Borst AJ, Veesler D, Stuart A, Agrawal P, Gray M, Pancera M, Huang PS, Stamatatos L. HIV-1 VRC01 Germline-Targeting Immunogens Select Distinct Epitope-Specific B Cell Receptors. Immunity 2021; 53:840-851.e6. [PMID: 33053332 DOI: 10.1016/j.immuni.2020.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/12/2020] [Accepted: 09/10/2020] [Indexed: 01/23/2023]
Abstract
Activating precursor B cell receptors of HIV-1 broadly neutralizing antibodies requires specifically designed immunogens. Here, we compared the abilities of three such germline-targeting immunogens against the VRC01-class receptors to activate the targeted B cells in transgenic mice expressing the germline VH of the VRC01 antibody but diverse mouse light chains. Immunogen-specific VRC01-like B cells were isolated at different time points after immunization, their VH and VL genes were sequenced, and the corresponding antibodies characterized. VRC01 B cell sub-populations with distinct cross-reactivity properties were activated by each immunogen, and these differences correlated with distinct biophysical and biochemical features of the germline-targeting immunogens. Our study indicates that the design of effective immunogens to activate B cell receptors leading to protective HIV-1 antibodies will require a better understanding of how the biophysical properties of the epitope and its surrounding surface on the germline-targeting immunogen influence its interaction with the available receptor variants in vivo.
Collapse
Affiliation(s)
- Yu-Ru Lin
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - K Rachael Parks
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; University of Washington, Department of Global Health, Seattle, WA, USA
| | - Connor Weidle
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Anika S Naidu
- Stanford University, Department of Bioengineering, Stanford, CA, USA
| | - Arineh Khechaduri
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Andrew O Riker
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Brittany Takushi
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Jung-Ho Chun
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - Andrew J Borst
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - David Veesler
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - Andrew Stuart
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Parul Agrawal
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Matthew Gray
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA.
| | - Po-Ssu Huang
- Stanford University, Department of Bioengineering, Stanford, CA, USA.
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; University of Washington, Department of Global Health, Seattle, WA, USA.
| |
Collapse
|
71
|
Virus Evolution and Neutralization Sensitivity in an HIV-1 Subtype B' Infected Plasma Donor with Broadly Neutralizing Activity. Vaccines (Basel) 2021; 9:vaccines9040311. [PMID: 33805985 PMCID: PMC8064334 DOI: 10.3390/vaccines9040311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
We sought to analyze the evolutionary characteristics and neutralization sensitivity of viruses in a human immunodeficiency virus type 1 (HIV-1) subtype B′ infected plasma donor with broadly neutralizing activity, which may provide information for new broadly neutralizing antibodies (bNAbs) isolation and immunogen design. A total of 83 full-length envelope genes were obtained by single-genome amplification (SGA) from the patient’s plasma at three consecutive time points (2005, 2006, and 2008) spanning four years. In addition, 28 Env-pseudotyped viruses were constructed and their neutralization sensitivity to autologous plasma and several representative bNAbs were measured. Phylogenetic analysis showed that these env sequences formed two evolutionary clusters (Cluster I and II). Cluster I viruses vanished in 2006 and then appeared as recombinants two years later. In Cluster II viruses, the V1 length and N-glycosylation sites increased over the four years of the study period. Most viruses were sensitive to concurrent and subsequent autologous plasma, and to bNAbs, including 10E8, PGT121, VRC01, and 12A21, but all viruses were resistant to PGT135. Overall, 90% of Cluster I viruses were resistant to 2G12, while 94% of Cluster II viruses were sensitive to 2G12. We confirmed that HIV-1 continued to evolve even in the presence of bNAbs, and two virus clusters in this donor adopted different escape mechanisms under the same humoral immune pressure.
Collapse
|
72
|
Han Q, Bradley T, Williams WB, Cain DW, Montefiori DC, Saunders KO, Parks RJ, Edwards RW, Ferrari G, Mueller O, Shen X, Wiehe KJ, Reed S, Fox CB, Rountree W, Vandergrift NA, Wang Y, Sutherland LL, Santra S, Moody MA, Permar SR, Tomaras GD, Lewis MG, Van Rompay KKA, Haynes BF. Neonatal Rhesus Macaques Have Distinct Immune Cell Transcriptional Profiles following HIV Envelope Immunization. Cell Rep 2021; 30:1553-1569.e6. [PMID: 32023469 PMCID: PMC7243677 DOI: 10.1016/j.celrep.2019.12.091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/16/2019] [Accepted: 12/24/2019] [Indexed: 12/30/2022] Open
Abstract
HIV-1-infected infants develop broadly neutralizing antibodies (bnAbs) more rapidly than adults, suggesting differences in the neonatal versus adult responses to the HIV-1 envelope (Env). Here, trimeric forms of HIV-1 Env immunogens elicit increased gp120- and gp41-specific antibodies more rapidly in neonatal macaques than adult macaques. Transcriptome analyses of neonatal versus adult immune cells after Env vaccination reveal that neonatal macaques have higher levels of the apoptosis regulator BCL2 in T cells and lower levels of the immunosuppressive interleukin-10 (IL-10) receptor alpha (IL10RA) mRNA transcripts in T cells, B cells, natural killer (NK) cells, and monocytes. In addition, immunized neonatal macaques exhibit increased frequencies of activated blood T follicular helper-like (Tfh) cells compared to adults. Thus, neonatal macaques have transcriptome signatures of decreased immunosuppression and apoptosis compared with adult macaques, providing an immune landscape conducive to early-life immunization prior to sexual debut.
Collapse
Affiliation(s)
- Qifeng Han
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Robert J Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Regina W Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Olaf Mueller
- Center for Genomics of Microbial Systems, Duke University Medical Center, Durham, NC, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin J Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | | | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Nathan A Vandergrift
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sallie R Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
73
|
A Potent anti-Simian Immunodeficiency Virus Neutralizing Antibody Induction Associated with a Germline Immunoglobulin Gene Polymorphism in Rhesus Macaques. J Virol 2021; 95:JVI.02455-20. [PMID: 33441342 PMCID: PMC8092685 DOI: 10.1128/jvi.02455-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virus infection induces B cells with a wide variety of B cell receptor (BCR) repertoires. Patterns of induced BCR repertoires are different in individuals, while the underlying mechanism causing this difference remains largely unclear. In particular, the impact of germ line BCR immunoglobulin (Ig) gene polymorphism on B cell/antibody induction has not fully been determined. In the present study, we found a potent antibody induction associated with a germ line BCR Ig gene polymorphism. B404-class antibodies, which were previously reported as potent anti-simian immunodeficiency virus (SIV) neutralizing antibodies using the germ line VH3.33 gene-derived Ig heavy chain, were induced in five of 10 rhesus macaques after SIVsmH635FC infection. Investigation of VH3.33 genes in B404-class antibody inducers (n = 5) and non-inducers (n = 5) revealed association of B404-class antibody induction with a germ line VH3.33 polymorphism. Analysis of reconstructed antibodies indicated that the VH3.33 residue 38 is the determinant for B404-class antibody induction. B404-class antibodies were induced in all the macaques possessing the B404-associated VH3.33 allele, even under undetectable viremia. Our results show that a single nucleotide polymorphism in germ line VH genes could be a determinant for induction of potent antibodies against virus infection, implying that germ line VH-gene polymorphisms can be a factor restricting effective antibody induction or responsiveness to vaccination.IMPORTANCE Vaccines against a wide variety of infectious diseases have been developed mostly to induce antibodies targeting pathogens. However, small but significant percentage of people fail to mount potent antibody responses after vaccination, while the underlying mechanism of host failure in antibody induction remains largely unclear. In particular, the impact of germ line B cell receptor (BCR)/antibody immunoglobulin (Ig) gene polymorphism on B cell/antibody induction has not fully been determined. In the present study, we found a potent anti-simian immunodeficiency virus neutralizing antibody induction associated with a germ line BCR/antibody Ig gene polymorphism in rhesus macaques. Our results demonstrate that a single nucleotide polymorphism in germ line Ig genes could be a determinant for induction of potent antibodies against virus infection, implying that germ line BCR/antibody Ig gene polymorphisms can be a factor restricting effective antibody induction or responsiveness to vaccination.
Collapse
|
74
|
Wu F, Ourmanov I, Kirmaier A, Leviyang S, LaBranche C, Huang J, Whitted S, Matsuda K, Montefiori D, Hirsch VM. SIV infection duration largely determines broadening of neutralizing antibody response in macaques. J Clin Invest 2021; 130:5413-5424. [PMID: 32663192 DOI: 10.1172/jci139123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/01/2020] [Indexed: 01/23/2023] Open
Abstract
The development of broadly neutralizing antibodies (BNAbs) in HIV infection is a result of long-term coevolutionary interaction between viruses and antibodies. Understanding how this interaction promotes the increase of neutralization breadth during infection will improve the way in which AIDS vaccine strategies are designed. In this paper, we used SIV-infected rhesus macaques as a model to study the development of neutralization breadth by infecting rhesus macaques with longitudinal NAb escape variants and evaluating the kinetics of NAb response and viral evolution. We found that the infected macaques developed a stepwise NAb response against escape variants and increased neutralization breadth during the course of infection. Furthermore, the increase of neutralization breadth correlated with the duration of infection but was independent of properties of the inoculum, viral loads, or viral diversity during infection. These results imply that the duration of infection was the main factor driving the development of BNAbs. These data suggest the importance of novel immunization strategies to induce effective NAb response against HIV infection by mimicking long-term infection.
Collapse
Affiliation(s)
- Fan Wu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Ilnour Ourmanov
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Andrea Kirmaier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, USA
| | - Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, USA
| | - Celia LaBranche
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jinghe Huang
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Sonya Whitted
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Kenta Matsuda
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vanessa M Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| |
Collapse
|
75
|
Desikan R, Antia R, Dixit NM. Physical 'strength' of the multi-protein chain connecting immune cells: Does the weakest link limit antibody affinity maturation?: The weakest link in the multi-protein chain facilitating antigen acquisition by B cells in germinal centres limits antibody affinity maturation. Bioessays 2021; 43:e2000159. [PMID: 33448042 DOI: 10.1002/bies.202000159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022]
Abstract
The affinities of antibodies (Abs) for their target antigens (Ags) gradually increase in vivo following an infection or vaccination, but reach saturation at values well below those realisable in vitro. This 'affinity ceiling' could in many cases restrict our ability to fight infections and compromise vaccines. What determines the affinity ceiling has been an unresolved question for decades. Here, we argue that it arises from the strength of the chain of protein complexes that is pulled by B cells during the process of Ag acquisition. The affinity ceiling is determined by the strength of the weakest link in the chain. We identify the weakest link and show that the resulting affinity ceiling can explain the Ab affinities realized in vivo, providing a conceptual understanding of Ab affinity maturation. We explore plausible evolutionary underpinnings of the affinity ceiling, examine supporting evidence and alternative hypotheses and discuss implications for vaccination strategies.
Collapse
Affiliation(s)
- Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| |
Collapse
|
76
|
Doepker LE, Danon S, Harkins E, Ralph DK, Yaffe Z, Garrett ME, Dhar A, Wagner C, Stumpf MM, Arenz D, Williams JA, Jaoko W, Mandaliya K, Lee KK, Matsen FA, Overbaugh JM. Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies. eLife 2021; 10:e63444. [PMID: 33427196 PMCID: PMC7884072 DOI: 10.7554/elife.63444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/08/2021] [Indexed: 11/27/2022] Open
Abstract
A prerequisite for the design of an HIV vaccine that elicits protective antibodies is understanding the developmental pathways that result in desirable antibody features. The development of antibodies that mediate antibody-dependent cellular cytotoxicity (ADCC) is particularly relevant because such antibodies have been associated with HIV protection in humans. We reconstructed the developmental pathways of six human HIV-specific ADCC antibodies using longitudinal antibody sequencing data. Most of the inferred naive antibodies did not mediate detectable ADCC. Gain of antigen binding and ADCC function typically required mutations in complementarity determining regions of one or both chains. Enhancement of ADCC potency often required additional mutations in framework regions. Antigen binding affinity and ADCC activity were correlated, but affinity alone was not sufficient to predict ADCC potency. Thus, elicitation of broadly active ADCC antibodies may require mutations that enable high-affinity antigen recognition along with mutations that optimize factors contributing to functional ADCC activity.
Collapse
Affiliation(s)
- Laura E Doepker
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Sonja Danon
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Elias Harkins
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Duncan K Ralph
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Zak Yaffe
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Medical Scientist Training Program, University of Washington School of MedicineSeattleUnited States
| | - Meghan E Garrett
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Amrit Dhar
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Statistics, University of WashingtonSeattleUnited States
| | - Cassia Wagner
- Medical Scientist Training Program, University of Washington School of MedicineSeattleUnited States
| | - Megan M Stumpf
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Dana Arenz
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - James A Williams
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Walter Jaoko
- Department of Medicinal Microbiology, University of NairobiNairobiKenya
| | - Kishor Mandaliya
- Coast Provincial General Hospital, Women’s Health ProjectMombasaKenya
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Julie M Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| |
Collapse
|
77
|
Abstract
T lymphocytes, the major effector cells in cellular immunity, produce cytokines in immune responses to mediate inflammation and regulate other types of immune cells. Work in the last three decades has revealed significant heterogeneity in CD4+ T cells, in terms of their cytokine expression, leading to the discoveries of T helper 1 (Th1), Th2, Th17, and T follicular helper (Tfh) cell subsets. These cells possess unique developmental and regulatory pathways and play distinct roles in immunity and immune-mediated pathologies. Other types of T cells, including regulatory T cells and γδ T cells, as well as innate lymphocytes, display similar features of subpopulations, which may play differential roles in immunity. Mechanisms exist to prevent cytokine production by T cells to maintain immune tolerance to self-antigens, some of which may also underscore immune exhaustion in the context of tumors. Understanding cytokine regulation and function has offered innovative treatment of many human diseases.
Collapse
Affiliation(s)
- Chen Dong
- Institute for Immunology, Tsinghua University, Beijing 100084, China.,Renji Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200127, China;
| |
Collapse
|
78
|
Roark RS, Li H, Williams WB, Chug H, Mason RD, Gorman J, Wang S, Lee FH, Rando J, Bonsignori M, Hwang KK, Saunders KO, Wiehe K, Moody MA, Hraber PT, Wagh K, Giorgi EE, Russell RM, Bibollet-Ruche F, Liu W, Connell J, Smith AG, DeVoto J, Murphy AI, Smith J, Ding W, Zhao C, Chohan N, Okumura M, Rosario C, Ding Y, Lindemuth E, Bauer AM, Bar KJ, Ambrozak D, Chao CW, Chuang GY, Geng H, Lin BC, Louder MK, Nguyen R, Zhang B, Lewis MG, Raymond DD, Doria-Rose NA, Schramm CA, Douek DC, Roederer M, Kepler TB, Kelsoe G, Mascola JR, Kwong PD, Korber BT, Harrison SC, Haynes BF, Hahn BH, Shaw GM. Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth. Science 2021; 371:eabd2638. [PMID: 33214287 PMCID: PMC8040783 DOI: 10.1126/science.abd2638] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022]
Abstract
Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution very similar to those in humans, including conserved immunogenetic, structural, and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions, and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2 apex mode of recognition like that of human broadly neutralizing antibodies (bNAbs) PGT145 and PCT64-35S. Another rhesus antibody bound the CD4 binding site by CD4 mimicry, mirroring human bNAbs 8ANC131, CH235, and VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design.
Collapse
Affiliation(s)
- Ryan S Roark
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hui Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hema Chug
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fang-Hua Lee
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juliette Rando
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kwan-Ki Hwang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Departments of Immunology and Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Departments of Pediatrics and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Peter T Hraber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ronnie M Russell
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jesse Connell
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew G Smith
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julia DeVoto
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander I Murphy
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica Smith
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenge Ding
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chengyan Zhao
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Neha Chohan
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maho Okumura
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christina Rosario
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yu Ding
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily Lindemuth
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anya M Bauer
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katharine J Bar
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Nguyen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Donald D Raymond
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Departments of Immunology and Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bette T Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Stephen C Harrison
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
79
|
Abstract
HIV is a virus that remains a major health concern and results in an infection that has no cure even after over 30 years since its discovery. As such, HIV vaccine discovery continues to be an area of intensive research. In this review, we summarize the most recent HIV vaccine efficacy trials, clinical trials initiated within the last 3 years, and discuss prominent improvements that have been made in prophylactic HIV vaccine designs.
Collapse
Affiliation(s)
- Jeong Hyun Lee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA.
| |
Collapse
|
80
|
Mogus AT, Liu L, Jia M, Ajayi DT, Xu K, Kong R, Huang J, Yu J, Kwong PD, Mascola JR, Ho DD, Tsuji M, Chackerian B. Virus-Like Particle Based Vaccines Elicit Neutralizing Antibodies against the HIV-1 Fusion Peptide. Vaccines (Basel) 2020; 8:vaccines8040765. [PMID: 33333740 PMCID: PMC7765226 DOI: 10.3390/vaccines8040765] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 01/01/2023] Open
Abstract
Broadly neutralizing antibodies (bnAbs) isolated from HIV-infected individuals delineate vulnerable sites on the HIV envelope glycoprotein that are potential vaccine targets. A linear epitope within the N-terminal region of the HIV-1 fusion peptide (FP8) is the primary target of VRC34.01, a bnAb that neutralizes ~50% of primary HIV isolates. FP8 has attracted attention as a potential HIV vaccine target because it is a simple linear epitope. Here, platform technologies based on RNA bacteriophage virus-like particles (VLPs) were used to develop multivalent vaccines targeting the FP8 epitope. Both recombinant MS2 VLPs displaying the FP8 peptide and Qβ VLPs displaying chemically conjugated FP8 peptide induced high titers of FP8-specific antibodies in mice. Moreover, a heterologous prime-boost-boost regimen employing the two FP8-VLP vaccines and native envelope trimer was the most effective approach for eliciting HIV-1 neutralizing antibodies. Given the potent immunogenicity of VLP-based vaccines, this vaccination strategy-inspired by bnAb-guided epitope mapping, VLP bioengineering, and prime-boost immunization approaches-may be a useful strategy for eliciting bnAb responses against HIV.
Collapse
Affiliation(s)
- Alemu Tekewe Mogus
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, USA; (A.T.M.); (D.T.A.)
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, New York, NY 10016, USA; (L.L.); (M.J.); (J.H.); (J.Y.); (D.D.H.)
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Manxue Jia
- Aaron Diamond AIDS Research Center, New York, NY 10016, USA; (L.L.); (M.J.); (J.H.); (J.Y.); (D.D.H.)
| | - Diane T. Ajayi
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, USA; (A.T.M.); (D.T.A.)
| | - Kai Xu
- Vaccine Research Center, NIAID, NIH, 40 Convent Drive, Bethesda, MD 20892, USA; (K.X.); (R.K.); (P.D.K.); (J.R.M.)
| | - Rui Kong
- Vaccine Research Center, NIAID, NIH, 40 Convent Drive, Bethesda, MD 20892, USA; (K.X.); (R.K.); (P.D.K.); (J.R.M.)
| | - Jing Huang
- Aaron Diamond AIDS Research Center, New York, NY 10016, USA; (L.L.); (M.J.); (J.H.); (J.Y.); (D.D.H.)
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, New York, NY 10016, USA; (L.L.); (M.J.); (J.H.); (J.Y.); (D.D.H.)
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter D. Kwong
- Vaccine Research Center, NIAID, NIH, 40 Convent Drive, Bethesda, MD 20892, USA; (K.X.); (R.K.); (P.D.K.); (J.R.M.)
| | - John R. Mascola
- Vaccine Research Center, NIAID, NIH, 40 Convent Drive, Bethesda, MD 20892, USA; (K.X.); (R.K.); (P.D.K.); (J.R.M.)
| | - David D. Ho
- Aaron Diamond AIDS Research Center, New York, NY 10016, USA; (L.L.); (M.J.); (J.H.); (J.Y.); (D.D.H.)
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Moriya Tsuji
- Aaron Diamond AIDS Research Center, New York, NY 10016, USA; (L.L.); (M.J.); (J.H.); (J.Y.); (D.D.H.)
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Correspondence: (M.T.); (B.C.); Tel.: +1-212-304-6165 (M.T.); +1-505-272-0269 (B.C.)
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, USA; (A.T.M.); (D.T.A.)
- Correspondence: (M.T.); (B.C.); Tel.: +1-212-304-6165 (M.T.); +1-505-272-0269 (B.C.)
| |
Collapse
|
81
|
Spisak N, Walczak AM, Mora T. Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data. Nucleic Acids Res 2020; 48:10702-10712. [PMID: 33035336 PMCID: PMC7641750 DOI: 10.1093/nar/gkaa825] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/07/2020] [Accepted: 09/18/2020] [Indexed: 01/23/2023] Open
Abstract
Somatic hypermutations of immunoglobulin (Ig) genes occurring during affinity maturation drive B-cell receptors’ ability to evolve strong binding to their antigenic targets. The landscape of these mutations is highly heterogeneous, with certain regions of the Ig gene being preferentially targeted. However, a rigorous quantification of this bias has been difficult because of phylogenetic correlations between sequences and the interference of selective forces. Here, we present an approach that corrects for these issues, and use it to learn a model of hypermutation preferences from a recently published large IgH repertoire dataset. The obtained model predicts mutation profiles accurately and in a reproducible way, including in the previously uncharacterized Complementarity Determining Region 3, revealing that both the sequence context of the mutation and its absolute position along the gene are important. In addition, we show that hypermutations occurring concomittantly along B-cell lineages tend to co-localize, suggesting a possible mechanism for accelerating affinity maturation.
Collapse
Affiliation(s)
- Natanael Spisak
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, 24 rue Lhomond, 75005 Paris, France
| | | | | |
Collapse
|
82
|
Blasi M, Negri D, Saunders KO, Baker EJ, Stadtler H, LaBranche C, Mildenberg B, Morton G, Ciarla A, Shen X, Wang Y, Rountree W, Balakumaran B, Santra S, Haynes BF, Moody AM, Cara A, Klotman ME. Immunogenicity, safety, and efficacy of sequential immunizations with an SIV-based IDLV expressing CH505 Envs. NPJ Vaccines 2020; 5:107. [PMID: 33298954 PMCID: PMC7674457 DOI: 10.1038/s41541-020-00252-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/30/2020] [Indexed: 12/20/2022] Open
Abstract
A preventative HIV-1 vaccine is an essential intervention needed to halt the HIV-1 pandemic. Neutralizing antibodies protect against HIV-1 infection in animal models, and thus an approach toward a protective HIV-1 vaccine is to induce broadly cross-reactive neutralizing antibodies (bnAbs). One strategy to achieve this goal is to define envelope (Env) evolution that drives bnAb development in infection and to recreate those events by vaccination. In this study, we report the immunogenicity, safety, and efficacy in rhesus macaques of an SIV-based integrase defective lentiviral vector (IDLV) expressing sequential gp140 Env immunogens derived from the CH505 HIV-1-infected individual who made the CH103 and CH235 bnAb lineages. Immunization with IDLV expressing sequential CH505 Envs induced higher magnitude and more durable binding and neutralizing antibody responses compared to protein or DNA +/− protein immunizations using the same sequential envelopes. Compared to monkeys immunized with a vector expressing Envs alone, those immunized with the combination of IDLV expressing Env and CH505 Env protein demonstrated improved durability of antibody responses at six months after the last immunization as well as lower peak viremia and better virus control following autologous SHIV-CH505 challenge. There was no evidence of vector mobilization or recombination in the immunized and challenged monkeys. Although the tested vaccines failed to induce bnAbs and to mediate significant protection following SHIV-challenge, our results show that IDLV proved safe and successful at inducing higher titer and more durable immune responses compared to other vaccine platforms.
Collapse
Affiliation(s)
- Maria Blasi
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA. .,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
| | - Donatella Negri
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Erich J Baker
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Harvard Law School, Cambridge, MA, USA
| | - Hannah Stadtler
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Celia LaBranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | | | - Andrew Ciarla
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xiaoying Shen
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Bala Balakumaran
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Anthony M Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Andrea Cara
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.,National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Mary E Klotman
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA. .,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
83
|
Ralph DK, Matsen FA. Using B cell receptor lineage structures to predict affinity. PLoS Comput Biol 2020; 16:e1008391. [PMID: 33175831 PMCID: PMC7682889 DOI: 10.1371/journal.pcbi.1008391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/23/2020] [Accepted: 08/30/2020] [Indexed: 11/18/2022] Open
Abstract
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such antibodies in patients that have recovered. There exist effective experimental methods of accomplishing this, such as cell sorting and baiting; however they are time consuming and expensive. Next generation sequencing of B cell receptor (BCR) repertoires offers an additional source of sequences that could be tapped if we had a reliable method of selecting those coding for the best antibodies. In this paper we introduce a method that uses evolutionary information from the family of related sequences that share a naive ancestor to predict the affinity of each resulting antibody for its antigen. When combined with information on the identity of the antigen, this method should provide a source of effective new antibodies. We also introduce a method for a related task: given an antibody of interest and its inferred ancestral lineage, which branches in the tree are likely to harbor key affinity-increasing mutations? We evaluate the performance of these methods on a wide variety of simulated samples, as well as two real data samples. These methods are implemented as part of continuing development of the partis BCR inference package, available at https://github.com/psathyrella/partis. Comments Please post comments or questions on this paper as new issues at https://git.io/Jvxkn.
Collapse
Affiliation(s)
- Duncan K. Ralph
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | |
Collapse
|
84
|
Wang Z, Barnes CO, Gautam R, Cetrulo Lorenzi JC, Mayer CT, Oliveira TY, Ramos V, Cipolla M, Gordon KM, Gristick HB, West AP, Nishimura Y, Raina H, Seaman MS, Gazumyan A, Martin M, Bjorkman PJ, Nussenzweig MC, Escolano A. A broadly neutralizing macaque monoclonal antibody against the HIV-1 V3-Glycan patch. eLife 2020; 9:e61991. [PMID: 33084569 PMCID: PMC7577740 DOI: 10.7554/elife.61991] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
A small fraction of HIV-1- infected humans develop broadly neutralizing antibodies (bNAbs) against HIV-1 that protect macaques from simian immunodeficiency HIV chimeric virus (SHIV). Similarly, a small number of macaques infected with SHIVs develop broadly neutralizing serologic activity, but less is known about the nature of simian antibodies. Here, we report on a monoclonal antibody, Ab1485, isolated from a macaque infected with SHIVAD8 that developed broadly neutralizing serologic activity targeting the V3-glycan region of HIV-1 Env. Ab1485 neutralizes 38.1% of HIV-1 isolates in a 42-pseudovirus panel with a geometric mean IC50 of 0.055 µg/mLl and SHIVAD8 with an IC50 of 0.028 µg/mLl. Ab1485 binds the V3-glycan epitope in a glycan-dependent manner. A 3.5 Å cryo-electron microscopy structure of Ab1485 in complex with a native-like SOSIP Env trimer showed conserved contacts with the N332gp120 glycan and gp120 GDIR peptide motif, but in a distinct Env-binding orientation relative to human V3/N332gp120 glycan-targeting bNAbs. Intravenous infusion of Ab1485 protected macaques from a high dose challenge with SHIVAD8. We conclude that macaques can develop bNAbs against the V3-glycan patch that resemble human V3-glycan bNAbs.
Collapse
Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | | | - Christian T Mayer
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Kristie M Gordon
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Henna Raina
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical CenterBostonUnited States
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Malcolm Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute. The Rockefeller UniversityNew YorkUnited States
| | - Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| |
Collapse
|
85
|
Kräutler NJ, Yermanos A, Pedrioli A, Welten SPM, Lorgé D, Greczmiel U, Bartsch I, Scheuermann J, Kiefer JD, Eyer K, Menzel U, Greiff V, Neri D, Stadler T, Reddy ST, Oxenius A. Quantitative and Qualitative Analysis of Humoral Immunity Reveals Continued and Personalized Evolution in Chronic Viral Infection. Cell Rep 2020; 30:997-1012.e6. [PMID: 31995768 DOI: 10.1016/j.celrep.2019.12.088] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/20/2019] [Accepted: 12/23/2019] [Indexed: 12/31/2022] Open
Abstract
Control of established chronic lymphocytic choriomeningitis virus (LCMV) infection requires the production of neutralizing antibodies, but it remains unknown how the ensemble of antibodies evolves during ongoing infection. Here, we analyze the evolution of antibody responses during acute or chronic LCMV infection, combining quantitative functional assays and time-resolved antibody repertoire sequencing. We establish that antibody responses initially converge in both infection types on a functional and repertoire level, but diverge later during chronic infection, showing increased clonal diversity, the appearance of mouse-specific persistent clones, and distinct phylogenetic signatures. Chronic infection is characterized by a longer-lasting germinal center reaction and a continuous differentiation of plasma cells, resulting in the emergence of higher-affinity plasma cells exhibiting increased antibody secretion rates. Taken together, our findings reveal the emergence of a personalized antibody response in chronic infection and support the concept that maintaining B cell diversity throughout chronic LCMV infection correlates with the development of infection-resolving antibodies.
Collapse
Affiliation(s)
- Nike Julia Kräutler
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Alexander Yermanos
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland; Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Alessandro Pedrioli
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Suzanne P M Welten
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Dominique Lorgé
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Ute Greczmiel
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Ilka Bartsch
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Institute for Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jonathan D Kiefer
- Institute for Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Klaus Eyer
- Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
| | - Ulrike Menzel
- Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Victor Greiff
- Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Immunology, University of Oslo, Sognsvannsveien 20 Rikshospitalet, 0372 Oslo, Norway
| | - Dario Neri
- Institute for Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Tanja Stadler
- Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| |
Collapse
|
86
|
Antigenicity and Immunogenicity of HIV-1 Envelope Trimers Complexed to a Small-Molecule Viral Entry Inhibitor. J Virol 2020; 94:JVI.00958-20. [PMID: 32817216 DOI: 10.1128/jvi.00958-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Small-molecule viral entry inhibitors, such as BMS-626529 (BMS-529), allosterically block CD4 binding to HIV-1 envelope (Env) and inhibit CD4-induced structural changes in Env trimers. Here, we show that the binding of BMS-529 to clade C soluble chimeric gp140 SOSIP (ch.SOSIP) and membrane-bound trimers with intact transmembrane domain (gp150) prevented trimer conformational transitions and enhanced their immunogenicity. When complexed to BMS-529, ch.SOSIP trimers retained their binding to broadly neutralizing antibodies (bNAbs) and to their unmutated common ancestor (UCA) antibodies, while exposure of CD4-induced (CD4i) non-bNAb epitopes was inhibited. BMS-529-complexed gp150 trimers in detergent micelles, which were isolated from CHO cells, bound to bNAbs, including UCA and intermediates of the CD4 binding site (bs) CH103 bNAb lineage, and showed limited exposure of CD4i epitopes and a glycosylation pattern with a preponderance of high-mannose glycans. In rabbits, BMS-529-complexed V3 glycan-targeting ch.SOSIP immunogen induced in the majority of immunized animals higher neutralization titers against both autologous and select high mannose-bearing heterologous tier 2 pseudoviruses than those immunized with the noncomplexed ch.SOSIP. In rhesus macaques, BMS-529 complexed to CD4 bs-targeting ch.SOSIP immunogen induced stronger neutralization against tier 2 pseudoviruses bearing high-mannose glycans than noncomplexed ch.SOSIP trimer immunogen. When immunized with gp150 complexed to BMS-529, rhesus macaques showed neutralization against tier 2 pseudoviruses with targeted glycan deletion and high-mannose glycan enrichment. These results demonstrated that stabilization of Env trimer conformation with BMS-529 improved the immunogenicity of select chimeric SOSIP trimers and elicited tier 2 neutralizing antibodies of higher potency than noncomplexed trimers.IMPORTANCE Soluble forms of HIV-1 envelope trimers exhibit conformational heterogeneity and undergo CD4-induced (CD4i) exposure of epitopes of non-neutralizing antibodies that can potentially hinder induction of broad neutralizing antibody responses. These limitations have been mitigated through recent structure-guided approaches and include trimer-stabilizing mutations that resist trimer conformational transition and exposure of CD4i epitopes. The use of small-molecule viral inhibitors that allosterically block CD4 binding represents an alternative strategy for stabilizing Env trimer in the pre-CD4-triggered state of both soluble and membrane-bound trimers. In this study, we report that the viral entry inhibitor BMS-626529 restricts trimer conformational transition and improves the immunogenicity of select Env trimer immunogens.
Collapse
|
87
|
Tuyishime M, Garrido C, Jha S, Moeser M, Mielke D, LaBranche C, Montefiori D, Haynes BF, Joseph S, Margolis DM, Ferrari G. Improved killing of HIV-infected cells using three neutralizing and non-neutralizing antibodies. J Clin Invest 2020; 130:5157-5170. [PMID: 32584790 PMCID: PMC7524508 DOI: 10.1172/jci135557] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/24/2020] [Indexed: 02/06/2023] Open
Abstract
The correlation of HIV-specific antibody-dependent cellular cytotoxicity (ADCC) responses with protection from and delayed progression of HIV-1 infection provides a rationale to leverage ADCC-mediating antibodies for treatment purposes. We evaluated ADCC mediated by different combinations of 2 to 6 neutralizing and non-neutralizing anti-HIV-1 Envelope (Env) mAbs, using concentrations ≤ 1 μg/mL, to identify combinations effective at targeting latent reservoir HIV-1 viruses from 10 individuals. We found that within 2 hours, combinations of 3 mAbs mediated more than 30% killing of HIV-infected primary CD4+ T cells in the presence of autologous NK cells, with the combination of A32 (C1C2), DH511.2K3 (MPER), and PGT121 (V3) mAbs being the most effective. Increasing the incubation of target and effector cells in the presence of mAb combinations from 2 to 24 hours resulted in increased specific killing of infected cells, even with neutralization-resistant viruses. The same combination eliminated reactivated latently HIV-1-infected cells in an ex vivo quantitative viral outgrowth assay. Therefore, administration of a combination of 3 mAbs should be considered in planning in vivo studies seeking to eliminate persistently HIV-1-infected cells.
Collapse
Affiliation(s)
- Marina Tuyishime
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Shalini Jha
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Matt Moeser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dieter Mielke
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine and
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Sarah Joseph
- UNC HIV Cure Center and
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology and
| | - David M. Margolis
- UNC HIV Cure Center and
- Department of Microbiology and Immunology and
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| |
Collapse
|
88
|
Song G, He WT, Callaghan S, Anzanello F, Huang D, Ricketts J, Torres JL, Beutler N, Peng L, Vargas S, Cassell J, Parren M, Yang L, Ignacio C, Smith DM, Voss JE, Nemazee D, Ward AB, Rogers T, Burton DR, Andrabi R. Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.22.308965. [PMID: 32995770 PMCID: PMC7523096 DOI: 10.1101/2020.09.22.308965] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pre-existing immune responses to seasonal endemic coronaviruses could have profound consequences for antibody responses to SARS-CoV-2, either induced in natural infection or through vaccination. Such consequences are well established in the influenza and flavivirus fields. A first step to establish whether pre-existing responses can impact SARS-CoV-2 infection is to understand the nature and extent of cross-reactivity in humans to coronaviruses. We compared serum antibody and memory B cell responses to coronavirus spike (S) proteins from pre-pandemic and SARS-CoV-2 convalescent donors using a series of binding and functional assays. We found weak evidence of pre-existing SARS-CoV-2 cross-reactive serum antibodies in pre-pandemic donors. However, we found stronger evidence of pre-existing cross-reactive memory B cells that were activated on SARS-CoV-2 infection. Monoclonal antibodies (mAbs) isolated from the donors showed varying degrees of cross-reactivity with betacoronaviruses, including SARS and endemic coronaviruses. None of the cross-reactive mAbs were neutralizing except for one that targeted the S2 subunit of the S protein. The results suggest that pre-existing immunity to endemic coronaviruses should be considered in evaluating antibody responses to SARS-CoV-2.
Collapse
Affiliation(s)
- Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- These authors contributed equally to this work
| | - Wan-ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- These authors contributed equally to this work
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James Ricketts
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sirena Vargas
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jon Cassell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linlin Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Caroline Ignacio
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davey M. Smith
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - James E. Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
89
|
Kumar S, Ju B, Shapero B, Lin X, Ren L, Zhang L, Li D, Zhou Z, Feng Y, Sou C, Mann CJ, Hao Y, Sarkar A, Hou J, Nunnally C, Hong K, Wang S, Ge X, Su B, Landais E, Sok D, Zwick MB, He L, Zhu J, Wilson IA, Shao Y. A V H1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite. SCIENCE ADVANCES 2020; 6:eabb1328. [PMID: 32938661 PMCID: PMC7494343 DOI: 10.1126/sciadv.abb1328] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/31/2020] [Indexed: 05/03/2023]
Abstract
An oligomannose patch around the V3 base of HIV-1 envelope glycoprotein (Env) is recognized by multiple classes of broadly neutralizing antibodies (bNAbs). Here, we investigated the bNAb response to the V3 glycan supersite in an HIV-1-infected Chinese donor by Env-specific single B cell sorting, structural and functional studies, and longitudinal analysis of antibody and virus repertoires. Monoclonal antibodies 438-B11 and 438-D5 were isolated that potently neutralize HIV-1 with moderate breadth, are encoded by the VH1-69 germline gene, and have a disulfide-linked long HCDR3 loop. Crystal structures of Env-bound and unbound antibodies revealed heavy chain-mediated recognition of the glycan supersite with a unique angle of approach and a critical role of the intra-HCDR3 disulfide. The mechanism of viral escape was examined via single-genome amplification/sequencing and glycan mutations around the N332 supersite. Our findings further emphasize the V3 glycan supersite as a prominent target for Env-based vaccine design.
Collapse
Affiliation(s)
- Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bin Ju
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
| | - Benjamin Shapero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Li Ren
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Lei Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Zehua Zhou
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colin J Mann
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yanling Hao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiali Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Christian Nunnally
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kunxue Hong
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Shuo Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Xiangyang Ge
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui Province 230601, China
| | - Elise Landais
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Devin Sok
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Michael B Zwick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China.
- School of Medicine, Nankai University, Nankai District, Tianjin 300071, China
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
| |
Collapse
|
90
|
Optimizing immunization protocols to elicit broadly neutralizing antibodies. Proc Natl Acad Sci U S A 2020; 117:20077-20087. [PMID: 32747563 DOI: 10.1073/pnas.1919329117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural infections and vaccination with a pathogen typically stimulate the production of potent antibodies specific for the pathogen through a Darwinian evolutionary process known as affinity maturation. Such antibodies provide protection against reinfection by the same strain of a pathogen. A highly mutable virus, like HIV or influenza, evades recognition by these strain-specific antibodies via the emergence of new mutant strains. A vaccine that elicits antibodies that can bind to many diverse strains of the virus-known as broadly neutralizing antibodies (bnAbs)-could protect against highly mutable pathogens. Despite much work, the mechanisms by which bnAbs emerge remain uncertain. Using a computational model of affinity maturation, we studied a wide variety of vaccination strategies. Our results suggest that an effective strategy to maximize bnAb evolution is through a sequential immunization protocol, wherein each new immunization optimally increases the pressure on the immune system to target conserved antigenic sites, thus conferring breadth. We describe the mechanisms underlying why sequentially driving the immune system increasingly further from steady state, in an optimal fashion, is effective. The optimal protocol allows many evolving B cells to become bnAbs via diverse evolutionary paths.
Collapse
|
91
|
Abstract
In this issue of Cell Host & Microbe, Jia et al. used a vesicular stomatitis virus-based probe to isolate B cells expressing broadly neutralizing HIV-1 antibodies. Besides identifying neutralizing epitopes, this study highlights potential protection afforded by IgA arising from either direct IgM-to-IgA or sequential IgM-to-IgG-to-IgA class switching.
Collapse
Affiliation(s)
- Giuliana Magri
- Program in Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona Biomedical Research Park, Av. Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Andrea Cerutti
- Program in Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona Biomedical Research Park, Av. Dr. Aiguader 88, 08003 Barcelona, Spain; The Immunology Institute, Department of Medicine, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 100129, USA; Catalan Institute for Research and Advanced Studies (ICREA), Barcelona Biomedical Research Park, Av. Dr. Aiguader 88, 08003 Barcelona, Spain.
| |
Collapse
|
92
|
Abstract
PURPOSE OF REVIEW Exploring the molecular details of the coevolution of HIV-1 Envelope with broadly neutralizing antibodies (bNAbs) in infected individuals over time provides insights for vaccine design. Since mid-2017, the number of individuals described in such publications has nearly tripled. New publications have extended such studies to new epitopes on Env and provided more detail on previously known sites. RECENT FINDINGS Studies of two donors - one of them an infant, the other with three lineages targeting the same site - has deepened our understanding of V3-glycan-directed lineages. A V2-apex-directed lineage showed remarkable similarity to a lineage from a previously described donor, revealing general principles for this class of bNAbs. Understanding development of CD4 binding site antibodies has been enriched by the study of a VRC01-class lineage. Finally, the membrane-proximal external region is a new addition to the set of epitopes studied in this manner, with early development events explored in a study of three lineages from a single donor. SUMMARY These studies provide templates for immunogen design to elicit bNAbs against a widened set of epitopes, generating new directions in the quest for an HIV vaccine.
Collapse
|
93
|
Targeting broadly neutralizing antibody precursors: a naïve approach to vaccine design. Curr Opin HIV AIDS 2020; 14:294-301. [PMID: 30946041 DOI: 10.1097/coh.0000000000000548] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW It is believed that broadly neutralizing antibodies (bNAbs) will be an important component of an effective HIV-1 vaccine. Several immunogens have been designed that can target specific precursor B cells as a first step in a vaccine strategy to elicit bNAbs. RECENT FINDINGS Germline-targeting immunogens have been developed that specifically engage precursors of reproducible classes of anti-HIV antibodies, such as VRC01-class and apex-directed bNAbs. However, these precursors represent only a small portion of the immune repertoire and any antigen will inherently present off-target epitopes to the immune system that may confound bNAb development. Novel animal models are being utilized to understand the competitive fitness of bNAb precursors in the context of immunization with germline-targeting immunogens. In parallel, immunogen design efforts are being pursued to favor the development of bNAb responses over off-target responses following immunization. New studies of bNAb precursor interactions with glycosylated Env variants can inform prime-boost regimens geared towards accelerating bNAb development. SUMMARY Germline-targeting immunogens hold promise as a first step in eliciting a bNAb response through vaccination. A better understating of how efficiently germline-targeting immunogens can specifically target rare bNAb precursors is emerging. In addition, a more comprehensive structure-based understanding of critical barriers to bNAb elicitation, as well as commonalities between bNAb classes can further inform vaccine design.
Collapse
|
94
|
Sachdeva V, Husain K, Sheng J, Wang S, Murugan A. Tuning environmental timescales to evolve and maintain generalists. Proc Natl Acad Sci U S A 2020; 117:12693-12699. [PMID: 32457160 PMCID: PMC7293598 DOI: 10.1073/pnas.1914586117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Natural environments can present diverse challenges, but some genotypes remain fit across many environments. Such "generalists" can be hard to evolve, outcompeted by specialists fitter in any particular environment. Here, inspired by the search for broadly neutralizing antibodies during B cell affinity maturation, we demonstrate that environmental changes on an intermediate timescale can reliably evolve generalists, even when faster or slower environmental changes are unable to do so. We find that changing environments on timescales comparable with evolutionary transients in a population enhance the rate of evolving generalists from specialists, without enhancing the reverse process. The yield of generalists is further increased in more complex dynamic environments, such as a "chirp" of increasing frequency. Our work offers design principles for how nonequilibrium fitness "seascapes" can dynamically funnel populations to genotypes unobtainable in static environments.
Collapse
Affiliation(s)
- Vedant Sachdeva
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60627
| | - Kabir Husain
- Department of Physics, The University of Chicago, Chicago, IL 60627
| | - Jiming Sheng
- Department of Physics and Astronomy, The University of California, Los Angeles, CA 90095
| | - Shenshen Wang
- Department of Physics and Astronomy, The University of California, Los Angeles, CA 90095
| | - Arvind Murugan
- Department of Physics, The University of Chicago, Chicago, IL 60627;
| |
Collapse
|
95
|
The Conformational States of the HIV-1 Envelope Glycoproteins. Trends Microbiol 2020; 28:655-667. [PMID: 32418859 DOI: 10.1016/j.tim.2020.03.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022]
Abstract
During HIV-1 entry into target cells, binding of the virus to host receptors, CD4 and CCR5/CXCR4, triggers serial conformational changes in the envelope glycoprotein (Env) trimer that result in the fusion of the viral and cell membranes. Recent discoveries have refined our knowledge of Env conformational states, allowing characterization of the targets of small-molecule HIV-1 entry inhibitors and neutralizing antibodies, and identifying a novel off-pathway conformation (State 2A). Here, we provide an overview of the current understanding of these conformational states, focusing on (i) the events during HIV-1 entry; (ii) conformational preferences of HIV-1 Env ligands; (iii) evasion of the host antibody response; and (iv) potential implications for therapy and prevention of HIV-1 infection.
Collapse
|
96
|
Abstract
Development of improved approaches for HIV-1 prevention will likely be required for a durable end to the global AIDS pandemic. Recent advances in preclinical studies and early phase clinical trials offer renewed promise for immunologic strategies for blocking acquisition of HIV-1 infection. Clinical trials are currently underway to evaluate the efficacy of two vaccine candidates and a broadly neutralizing antibody (bNAb) to prevent HIV-1 infection in humans. However, the vast diversity of HIV-1 is a major challenge for both active and passive immunization. Here we review current immunologic strategies for HIV-1 prevention, with a focus on current and next-generation vaccines and bNAbs.
Collapse
Affiliation(s)
- Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA;
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- New Mexico Consortium, Los Alamos, New Mexico 87545, USA
| | - Bette Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- New Mexico Consortium, Los Alamos, New Mexico 87545, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA;
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
| |
Collapse
|
97
|
Ndlovu B, Gounder K, Muema D, Raju N, Hermanus T, Mthethwa Q, Robertson K, Walker BD, Georgiev IS, Morris L, Moore PL, Ndung'u T. Envelope characteristics in individuals who developed neutralizing antibodies targeting different epitopes in HIV-1 subtype C infection. Virology 2020; 546:1-12. [PMID: 32275203 DOI: 10.1016/j.virol.2020.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 11/29/2022]
Abstract
Broadly neutralizing antibodies (bNAbs) may constitute an essential component of a protective vaccine against HIV-1, yet no immunogen has been able to elicit them. To characterize the development of bNAbs in HIV-1 subtype C infected individuals, a panel of 18 Env-pseudotyped viruses was used to screen 18 study participants. The specificity of plasma neutralization was mapped against Env mutants and MPER chimeras. Envelope (env) gene sequence evolution was characterized by single genome amplification and sequencing. Three out of eighteen individuals developed broad plasma neutralizing activity (>60% breadth). Two of the three participants may target epitopes comprising glycans at position 276 of the D loop in the CD4 binding site and 332 glycan supersite, respectively. Deletion of these glycans was associated with neutralization resistance. Our study describes the kinetics of the development of plasma neutralizing activity and identified amino acid residue changes suggestive of immune pressure on putative epitopes. The study enhances our understanding of how neutralization breadth develops in the course of HIV-1 subtype C infection.
Collapse
Affiliation(s)
- Bongiwe Ndlovu
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Kamini Gounder
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa.
| | - Daniel Muema
- Africa Health Research Institute, Durban, South Africa.
| | - Nagarajan Raju
- Vanderbilt Vaccine Center and Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Tandile Hermanus
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
| | - Qiniso Mthethwa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Kim Robertson
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Bruce D Walker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center and Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; University of the Witwatersrand, Johannesburg, South Africa.
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; University of the Witwatersrand, Johannesburg, South Africa.
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Max Planck Institute for Infection Biology, Berlin, Germany; Division of Infection and Immunity, University College London, UK.
| |
Collapse
|
98
|
Liao H, Li S, Yu Y, Yue Y, Su K, Zheng Q, Jiang N, Zhang Z. Characteristics of Plasmablast Repertoire in Chronically HIV-Infected Individuals for Immunoglobulin H and L Chain Profiled by Single-Cell Analysis. Front Immunol 2020; 10:3163. [PMID: 32117215 PMCID: PMC7026028 DOI: 10.3389/fimmu.2019.03163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/31/2019] [Indexed: 02/05/2023] Open
Abstract
Characterization of the diversified immunoglobulin (Ig) repertoire may provide insight into pathways that shape an efficient antibody (Ab) repertoire for immune response against human immunodeficiency virus (HIV) infection. This study aimed to profile characteristics of the plasmablast repertoire during chronic HIV infection. Ig variable regions of plasmablasts from both chronically HIV-infected donors (HIVDs) previously treated with antiretroviral therapy (ART) and healthy donors (HDs) were amplified by single-cell PCR to establish the basis for further repertoire analysis. We compared the plasmablast repertoires expressed in multiple chronically HIVDs after ART treatment cessation and HDs. We also examined the non-productive repertoire to identify the indication of the immediate products of the rearrangement machinery without an impact of selection during HIV infection. We found multiple differences between the productive repertoires of HIVD and HD subjects, including biased usages of VH3-49, VH1-2, VH3-33, VH3-74, and VH5-51 in VH and D1-7, D1-14, D1-20, and D5-5/18 in D segments in the HIVD group, as well as shorter and preferential glycine usages in CDRH3 regions. Gene selections were also detected in light chains. Notably, differences between productive rearrangements of HIVDs and HDs outnumbered those between productive and non-productive rearrangements within HIVDs. HIV infection may exert a dominant impact on the development of the plasmablast repertoire. The impact of selection is of limited significance in shaping the plasmablast repertoire. Overall, the data indicate that the environment in which the plasmablasts live can affect the distribution of the VH and VL genes in the repertoire and the amino acid compositions of the expressed Abs.
Collapse
Affiliation(s)
- Hongyan Liao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Song Li
- Department of Chemotherapy, Cancer Center, Qilu Hospital of Shandong University, Jinan, China
| | - Yangsheng Yu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Yinshi Yue
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Kaihong Su
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States.,Eppley Research Institute, University of Nebraska Medical Center, Omaha, NE, United States
| | - Qin Zheng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Nenggang Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Zhixin Zhang
- State Key Laboratory of Biotherapy, Ministry of Education Key Laboratory of Birth Defects, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
99
|
Phad GE, Pushparaj P, Tran K, Dubrovskaya V, Àdori M, Martinez-Murillo P, Vázquez Bernat N, Singh S, Dionne G, O’Dell S, Bhullar K, Narang S, Sorini C, Villablanca EJ, Sundling C, Murrell B, Mascola JR, Shapiro L, Pancera M, Martin M, Corcoran M, Wyatt RT, Karlsson Hedestam GB. Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. J Exp Med 2020; 217:e20191155. [PMID: 31704807 PMCID: PMC7041718 DOI: 10.1084/jem.20191155] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022] Open
Abstract
Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from ∼1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages.
Collapse
Affiliation(s)
- Ganesh E. Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karen Tran
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Viktoriya Dubrovskaya
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paola Martinez-Murillo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Suruchi Singh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Gilman Dionne
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Komal Bhullar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sanjana Narang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Chiara Sorini
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Eduardo J. Villablanca
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Christopher Sundling
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Benjamin Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Marcel Martin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Richard T. Wyatt
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | | |
Collapse
|
100
|
Gao N, Gai Y, Meng L, Wang C, Zhang X, Wang W, Qin C, Yu X, Gao F. Development of Antibodies with Broad Neutralization Specificities against HIV-1 after Long Term SHIV Infection in Macaques. Viruses 2020; 12:v12020163. [PMID: 32023860 PMCID: PMC7077270 DOI: 10.3390/v12020163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 01/13/2023] Open
Abstract
Non-human primates (NHP) are the only animal model suitable to evaluate the protection efficacy of HIV-1 vaccines. It is important to understand how and when neutralizing antibodies (nAbs) with specificities similar to those of human broadly neutralizing antibodies (bnAbs) develop in NHPs. To address these questions, we determined plasma neutralization specificities in two macaques which developed neutralization breadth after long-term simian/human immunodeficiency virus (SHIV) infection and identified neutralization escape mutations by analyzing the env sequences from longitudinal plasma samples. Neutralization activities targeting V2, CD4bs, V3 and gp120-gp41 interface only became detectable in week 350 plasma from macaques G1015R and G1020R using 25710 env mutants. When mapped with CAP45 env mutants, only V2 specificity was detected at week 217 and persisted until week 350 in G1015R. Neutralization escape mutations were found in CD4bs and V2 regions. However, all of them were different from those resistant mutations identified for human bnAbs. These results show that nAbs with specificities similar to human bnAbs are only detectable after long-term SHIV infection and that neutralization escape mutations in macaques are different from those found in HIV-1-infected individuals. These findings can have important implications in the best utilization of the NHP model to evaluate HIV-1 vaccines.
Collapse
Affiliation(s)
- Nan Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (N.G.); (Y.G.); (L.M.); (C.W.); (X.Z.)
| | - Yanxin Gai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (N.G.); (Y.G.); (L.M.); (C.W.); (X.Z.)
| | - Lina Meng
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (N.G.); (Y.G.); (L.M.); (C.W.); (X.Z.)
| | - Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (N.G.); (Y.G.); (L.M.); (C.W.); (X.Z.)
| | - Xin Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (N.G.); (Y.G.); (L.M.); (C.W.); (X.Z.)
| | - Wei Wang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China; (W.W.)
- Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Chuan Qin
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China; (W.W.)
- Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (N.G.); (Y.G.); (L.M.); (C.W.); (X.Z.)
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
- Correspondence: (X.Y.); (F.G.); Tel.: +86-431-8516-7826 (X.Y.); +1-919-668-6433 (F.G.); Fax: +86-431-8516-7674 (X.Y.); +1-919-681-8992 (F.G.)
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (N.G.); (Y.G.); (L.M.); (C.W.); (X.Z.)
- Departments of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Correspondence: (X.Y.); (F.G.); Tel.: +86-431-8516-7826 (X.Y.); +1-919-668-6433 (F.G.); Fax: +86-431-8516-7674 (X.Y.); +1-919-681-8992 (F.G.)
| |
Collapse
|