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Caniels TG, Medina-Ramìrez M, Zhang S, Kratochvil S, Xian Y, Koo JH, Derking R, Samsel J, van Schooten J, Pecetta S, Lamperti E, Yuan M, Carrasco MR, Del Moral Sánchez I, Allen JD, Bouhuijs JH, Yasmeen A, Ketas TJ, Snitselaar JL, Bijl TPL, Martin IC, Torres JL, Cupo A, Shirreff L, Rogers K, Mason RD, Roederer M, Greene KM, Gao H, Silva CM, Baken IJL, Tian M, Alt FW, Pulendran B, Seaman MS, Crispin M, van Gils MJ, Montefiori DC, McDermott AB, Villinger FJ, Koup RA, Moore JP, Klasse PJ, Ozorowski G, Batista FD, Wilson IA, Ward AB, Sanders RW. Germline-targeting HIV vaccination induces neutralizing antibodies to the CD4 binding site. Sci Immunol 2024; 9:eadk9550. [PMID: 39213338 DOI: 10.1126/sciimmunol.adk9550] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 04/09/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
Eliciting potent and broadly neutralizing antibodies (bnAbs) is a major goal in HIV-1 vaccine development. Here, we describe how germline-targeting immunogen BG505 SOSIP germline trimer 1.1 (GT1.1), generated through structure-based design, engages a diverse range of VRC01-class bnAb precursors. A single immunization with GT1.1 expands CD4 binding site (CD4bs)-specific VRC01-class B cells in knock-in mice and drives VRC01-class maturation. In nonhuman primates (NHPs), GT1.1 primes CD4bs-specific neutralizing serum responses. Selected monoclonal antibodies (mAbs) isolated from GT1.1-immunized NHPs neutralize fully glycosylated BG505 virus. Two mAbs, 12C11 and 21N13, neutralize subsets of diverse heterologous neutralization-resistant viruses. High-resolution structures revealed that 21N13 targets the same conserved residues in the CD4bs as VRC01-class and CH235-class bnAbs despite its low sequence similarity (~40%), whereas mAb 12C11 binds predominantly through its heavy chain complementarity-determining region 3. These preclinical data underpin the ongoing evaluation of GT1.1 in a phase 1 clinical trial in healthy volunteers.
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Affiliation(s)
- Tom G Caniels
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Max Medina-Ramìrez
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Shiyu Zhang
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Sven Kratochvil
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Yuejiao Xian
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Ja-Hyun Koo
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Ronald Derking
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Jakob Samsel
- Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, USA
- Institute for Biomedical Sciences, George Washington University, Washington, DC, USA
| | - Jelle van Schooten
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Simone Pecetta
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Edward Lamperti
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - María Ríos Carrasco
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Iván Del Moral Sánchez
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Joey H Bouhuijs
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Jonne L Snitselaar
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Tom P L Bijl
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Isabel Cuella Martin
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Lisa Shirreff
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Kenneth Rogers
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | | | - Mario Roederer
- Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, USA
| | | | - Hongmei Gao
- Duke University Medical Center, Durham, NC, USA
| | - Catarina Mendes Silva
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Isabel J L Baken
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | - Ming Tian
- Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Marit J van Gils
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
| | | | | | - François J Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Richard A Koup
- Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Facundo D Batista
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
- Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Rogier W Sanders
- Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
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2
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Zhang P, Gorman J, Tsybovsky Y, Lu M, Liu Q, Gopan V, Singh M, Lin Y, Miao H, Seo Y, Kwon A, Olia AS, Chuang GY, Geng H, Lai YT, Zhou T, Mascola JR, Mothes W, Kwong PD, Lusso P. Design of soluble HIV-1 envelope trimers free of covalent gp120-gp41 bonds with prevalent native-like conformation. Cell Rep 2024; 43:114518. [PMID: 39028623 DOI: 10.1016/j.celrep.2024.114518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/21/2024] Open
Abstract
Soluble HIV-1 envelope (Env) trimers may serve as effective vaccine immunogens. The widely utilized SOSIP trimers have been paramount for structural studies, but the disulfide bond they feature between gp120 and gp41 constrains intersubunit mobility and may alter antigenicity. Here, we report an alternative strategy to generate stabilized soluble Env trimers free of covalent gp120-gp41 bonds. Stabilization was achieved by introducing an intrasubunit disulfide bond between the inner and outer domains of gp120, defined as interdomain lock (IDL). Correctly folded IDL trimers displaying a native-like antigenic profile were produced for HIV-1 Envs of different clades. Importantly, the IDL design abrogated CD4 binding while not affecting recognition by potent neutralizing antibodies to the CD4-binding site. By cryoelectron microscopy, IDL trimers were shown to adopt a closed prefusion configuration, while single-molecule fluorescence resonance energy transfer documented a high prevalence of native-like conformation. Thus, IDL trimers may be promising candidates as vaccine immunogens.
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Affiliation(s)
- Peng Zhang
- Laboratory of Immunoregulation, 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; Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Qingbo Liu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Vinay Gopan
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mamta Singh
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yin Lin
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huiyi Miao
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuna Seo
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alice Kwon
- Laboratory of Immunoregulation, 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
| | - 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
| | - Yen-Ting Lai
- 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
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; ModeX Therapeutics, 20 Riverside Road, Weston, MA 02493, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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4
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Shimagaki KS, Lynch RM, Barton JP. Parallel HIV-1 evolutionary dynamics in humans and rhesus macaques who develop broadly neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603090. [PMID: 39071321 PMCID: PMC11275900 DOI: 10.1101/2024.07.12.603090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Human immunodeficiency virus (HIV)-1 exhibits remarkable genetic diversity. For this reason, an effective HIV-1 vaccine must elicit antibodies that can neutralize many variants of the virus. While broadly neutralizing antibodies (bnAbs) have been isolated from HIV-1 infected individuals, a general understanding of the virus-antibody coevolutionary processes that lead to their development remains incomplete. We performed a quantitative study of HIV-1 evolution in two individuals who developed bnAbs. We observed strong selection early in infection for mutations affecting HIV-1 envelope glycosylation and escape from autologous strain-specific antibodies, followed by weaker selection for bnAb resistance later in infection. To confirm our findings, we analyzed data from rhesus macaques infected with viruses derived from the same two individuals. We inferred remarkably similar fitness effects of HIV-1 mutations in humans and macaques. Moreover, we observed a striking pattern of rapid HIV-1 evolution, consistent in both humans and macaques, that precedes the development of bnAbs. Our work highlights strong parallels between infection in rhesus macaques and humans, and it reveals a quantitative evolutionary signature of bnAb development.
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Affiliation(s)
- Kai S. Shimagaki
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, USA
- Department of Physics and Astronomy, University of Pittsburgh, USA
| | - Rebecca M. Lynch
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, USA
| | - John P. Barton
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, USA
- Department of Physics and Astronomy, University of Pittsburgh, USA
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5
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Gai Y, Gao N, Mou Z, Yang C, Wang L, Ji W, Gu T, Yu B, Wang C, Yu X, Gao F. Recapitulation of HIV-1 Neutralization Breadth in Plasma by the Combination of Two Broadly Neutralizing Antibodies from Different Lineages in the Same SHIV-Infected Rhesus Macaque. Int J Mol Sci 2024; 25:7200. [PMID: 39000308 PMCID: PMC11240982 DOI: 10.3390/ijms25137200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/18/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Viral infection generally induces polyclonal neutralizing antibody responses. However, how many lineages of antibody responses can fully represent the neutralization activities in sera has not been well studied. Using the newly designed stable HIV-1 Env trimer as hook, we isolated two distinct broadly neutralizing antibodies (bnAbs) from Chinese rhesus macaques infected with SHIV1157ipd3N4 for 5 years. One lineage of neutralizing antibodies (JT15 and JT16) targeted the V2-apex in the Env trimers, similar to the J038 lineage bnAbs identified in our previous study. The other lineage neutralizing antibody (JT18) targeted the V3 crown region in the Env, which strongly competed with human 447-52D. Each lineage antibody neutralized a different set of viruses. Interestingly, when the two neutralizing antibodies from different lineages isolated from the same macaque were combined, the mixture had a neutralization breath very similar to that from the cognate sera. Our study demonstrated that a minimum of two different neutralizing antibodies can fully recapitulate the serum neutralization breadth. This observation can have important implications in AIDS vaccine design.
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Affiliation(s)
- Yanxin Gai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Nan Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zhaoyang Mou
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Chumeng Yang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Libian Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wanshan Ji
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Tiejun Gu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
- Institute of Molecular and Medical Virology, School of Medicine, Jinan University, Guangzhou 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control, Jinan University, Ministry of Education, Guangzhou 510632, China
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6
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Giorgi EE, Li H, Hora B, Shaw GM, Wagh K, Williams WB. Viral Envelope Evolution in Simian-HIV-Infected Neonate and Adult-Dam Pairs of Rhesus Macaques. Viruses 2024; 16:1014. [PMID: 39066177 PMCID: PMC11281369 DOI: 10.3390/v16071014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/15/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
We recently demonstrated that Simian-HIV (SHIV)-infected neonate rhesus macaques (RMs) generated heterologous HIV-1 neutralizing antibodies (NAbs) with broadly-NAb (bNAb) characteristics at a higher frequency compared with their corresponding dam. Here, we characterized genetic diversity in Env sequences from four neonate or adult/dam RM pairs: in two pairs, neonate and dam RMs made heterologous HIV-1 NAbs; in one pair, neither the neonate nor the dam made heterologous HIV-1 NAbs; and in another pair, only the neonate made heterologous HIV-1 NAbs. Phylogenetic and sequence diversity analyses of longitudinal Envs revealed that a higher genetic diversity, within the host and away from the infecting SHIV strain, was correlated with heterologous HIV-1 NAb development. We identified 22 Env variable sites, of which 9 were associated with heterologous HIV-1 NAb development; 3/9 sites had mutations previously linked to HIV-1 Env bNAb development. These data suggested that viral diversity drives heterologous HIV-1 NAb development, and the faster accumulation of viral diversity in neonate RMs may be a potential mechanism underlying bNAb induction in pediatric populations. Moreover, these data may inform candidate Env immunogens to guide precursor B cells to bNAb status via vaccination by the Env-based selection of bNAb lineage members with the appropriate mutations associated with neutralization breadth.
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Affiliation(s)
| | - Hui Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.L.); (G.M.S.)
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA;
| | - George M. Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.L.); (G.M.S.)
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87544, 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
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
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7
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Roark RS, Habib R, Gorman J, Li H, Connell AJ, Bonsignori M, Guo Y, Hogarty MP, Olia AS, Sowers K, Zhang B, Bibollet-Ruche F, Callaghan S, Carey JW, Cerutti G, Harris DR, He W, Lewis E, Liu T, Mason RD, Park Y, Rando JM, Singh A, Wolff J, Lei QP, Louder MK, Doria-Rose NA, Andrabi R, Saunders KO, Seaman MS, Haynes BF, Kulp DW, Mascola JR, Roederer M, Sheng Z, Hahn BH, Shaw GM, Kwong PD, Shapiro L. HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598384. [PMID: 38903070 PMCID: PMC11188099 DOI: 10.1101/2024.06.11.598384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Broadly neutralizing antibodies targeting the V2 apex of the HIV-1 envelope trimer are among the most common specificities elicited in HIV-1-infected humans and simian-human immunodeficiency virus (SHIV)-infected macaques. To gain insight into the prevalent induction of these antibodies, we isolated and characterized 11 V2 apex-directed neutralizing antibody lineages from SHIV-infected rhesus macaques. Remarkably, all SHIV-induced V2 apex lineages were derived from reading frame two of the rhesus DH3-15*01 gene. Cryo-EM structures of envelope trimers in complex with antibodies from nine rhesus lineages revealed modes of recognition that mimicked three canonical human V2 apex-recognition modes. Notably, amino acids encoded by DH3-15*01 played divergent structural roles, inserting into a hole at the trimer apex, H-bonding to an exposed strand, or forming part of a loop scaffold. Overall, we identify a DH3-15*01-signature for rhesus V2 apex broadly neutralizing antibodies and show that highly selected genetic elements can play multiple roles in antigen recognition. Highlights Isolated 11 V2 apex-targeted HIV-neutralizing lineages from 10 SHIV-infected Indian-origin rhesus macaquesCryo-EM structures of Fab-Env complexes for nine rhesus lineages reveal modes of recognition that mimic three modes of human V2 apex antibody recognitionAll SHIV-elicited V2 apex lineages, including two others previously published, derive from the same DH3-15*01 gene utilizing reading frame twoThe DH3-15*01 gene in reading frame two provides a necessary, but not sufficient, signature for V2 apex-directed broadly neutralizing antibodiesStructural roles played by DH3-15*01-encoded amino acids differed substantially in different lineages, even for those with the same recognition modePropose that the anionic, aromatic, and extended character of DH3-15*01 in reading frame two provides a selective advantage for V2 apex recognition compared to B cells derived from other D genes in the naïve rhesus repertoireDemonstrate that highly selected genetic elements can play multiple roles in antigen recognition, providing a structural means to enhance recognition diversity.
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8
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Trkola A, Moore PL. Vaccinating people living with HIV: a fast track to preventive and therapeutic HIV vaccines. THE LANCET. INFECTIOUS DISEASES 2024; 24:e252-e255. [PMID: 37883985 DOI: 10.1016/s1473-3099(23)00481-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/18/2023] [Indexed: 10/28/2023]
Abstract
Globally, the number of new HIV infections remains unacceptably high, and urgent new approaches are needed to advance HIV vaccine science. However, the development of a preventive HIV vaccine has proven to be an intractable scientific challenge. Recent advances in HIV immunogen design have taken the field a step closer to triggering the rare precursors of broadly neutralising antibodies, which are widely assumed to be necessary for a vaccine. Nonetheless, these same studies and previous studies in people living with HIV have also highlighted the major hurdles that must be overcome to boost the cross-reactivity and potency of these responses to sufficient levels. Here, we describe an opportunity for fast-tracking the evaluation of candidate preventive and therapeutic vaccines by immunising people with HIV who are antiretroviral therapy suppressed. We argue that such studies, unlike traditional studies of vaccines in participants not infected with HIV, will be faster and more informative and will allow the vaccine field to bypass multiple hurdles. This approach will accelerate the process of defining the capacity of immunogens to trigger relevant antibodies, currently an extremely slow and expensive pathway, and provide a quick path to creating an HIV vaccine.
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Affiliation(s)
- Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
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9
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Evangelous TD, Berry M, Venkatayogi S, LeMaster C, Geanes ES, De Naeyer N, DeMarco T, Shen X, Li H, Hora B, Solomonis N, Misamore J, Lewis MG, Denny TN, Montefiori D, Shaw GM, Wiehe K, Bradley T, Williams WB. Host immunity associated with spontaneous suppression of viremia in therapy-naïve young rhesus macaques following neonatal SHIV infection. J Virol 2023; 97:e0109423. [PMID: 37874153 PMCID: PMC10688376 DOI: 10.1128/jvi.01094-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Despite the advent of highly active anti-retroviral therapy, people are still dying from HIV-related causes, many of whom are children, and a protective vaccine or cure is needed to end the HIV pandemic. Understanding the nature and activation states of immune cell subsets during infection will provide insights into the immunologic milieu associated with viremia suppression that can be harnessed via therapeutic strategies to achieve a functional cure, but these are understudied in pediatric subjects. We evaluated humoral and adaptive host immunity associated with suppression of viremia in rhesus macaques infected soon after birth with a pathogenic SHIV. The results from our study provide insights into the immune cell subsets and functions associated with viremia control in young macaques that may translate to pediatric subjects for the design of future anti-viral strategies in HIV-1-infected infants and children and contribute to an understudied area of HIV-1 pathogenesis in pediatric subjects.
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Affiliation(s)
- Tyler D. Evangelous
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Cas LeMaster
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Eric S. Geanes
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Nicole De Naeyer
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Todd DeMarco
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | | | | | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Todd Bradley
- Children’s Mercy Kansas City, Kansas City, Missouri, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, Missouri, USA
- Departments of Pediatrics and Pathology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Wilton B. Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Division of Surgical Sciences, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
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10
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Haynes BF, Wiehe K, Alam SM, Weissman D, Saunders KO. Progress with induction of HIV broadly neutralizing antibodies in the Duke Consortia for HIV/AIDS Vaccine Development. Curr Opin HIV AIDS 2023; 18:300-308. [PMID: 37751363 PMCID: PMC10552807 DOI: 10.1097/coh.0000000000000820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
PURPOSE OF REVIEW Design of an HIV vaccine that can induce broadly neutralizing antibodies (bnAbs) is a major goal. However, HIV bnAbs are not readily made by the immune system. Rather HIV bnAbs are disfavored by a number of virus and host factors. The purpose of the review is to discuss recent progress made in the design and use of immunogens capable of inducing HIV bnAbs in the Duke Consortia for HIV/AIDS Vaccine Development. RECENT FINDINGS New immunogens capable of binding with high affinity to unmutated common ancestors (UCAs) of bnAb B cell lineages have been designed and strategies for stabilization of HIV Env in its prefusion state are being developed. Success is starting to be translated from preclinical studies of UCA-targeting immunogens in animals, to success of initiating bnAb lineages in humans. SUMMARY Recent progress has been made in both immunogen design and in achieving bnAb B cell lineage induction in animal models and now in human clinical trials. With continued progress, a practical HIV/AIDS vaccine may be possible. However, host constraints on full bnAb maturation remain as potential roadblocks for full maturation of some types of bnAbs.
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Affiliation(s)
- Barton F. Haynes
- Duke Human Vaccine Institute, Departments of Medicine and Immunology
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - S. Munir Alam
- Duke Human Vaccine Institute, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Drew Weissman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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11
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Counts JA, Saunders KO. Guiding HIV-1 vaccine development with preclinical nonhuman primate research. Curr Opin HIV AIDS 2023; 18:315-322. [PMID: 37712825 PMCID: PMC10810179 DOI: 10.1097/coh.0000000000000819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
PURPOSE OF THE REVIEW Nonhuman primates (NHPs) are seen as the closest animal model to humans in terms of anatomy and immune system makeup. Here, we review how preclinical studies in this model system are teaching the field of HIV vaccinology the basic immunology that is needed to induce broadly neutralizing antibodies (bnAbs) with vaccination and elicit protective T cell responses. These lessons are being translated into clinical trials to advance towards protective active vaccination against HIV-1 infection. RECENT FINDINGS Preclinical vaccination studies in NHPs have shown that highly engineered HIV-1 immunogens can initiate bnAb precursors providing proof of concept for Phase I clinical trials. Additionally, NHP models of HIV-1 infection are elucidating the pathways for bnAb development while serving as systems to evaluate vaccine protection. Innovative immunization strategies have increased affinity maturation of HIV-1 antibodies in long-lived germinal centers. Preclinical studies in macaques have defined the protective level of neutralizing antibodies and have shown that T cell responses can synergize with antibody-mediated immunity to provide protection in the presence of lower neutralizing antibody titers. SUMMARY The NHP model provides vaccine regimens and desired antibody and T cell responses that serve as benchmarks for clinical trials, accelerating HIV vaccine design.
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Affiliation(s)
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Departments of Surgery, Immunology, and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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12
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Kumar MR, Fray EJ, Bender AM, Zitzmann C, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir. Proc Natl Acad Sci U S A 2023; 120:e2313209120. [PMID: 37844236 PMCID: PMC10614214 DOI: 10.1073/pnas.2313209120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy (ART) and precludes cure. Reservoir-targeting interventions are evaluated in ART-treated macaques infected with simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV). Efficacy is determined by reservoir measurements before and after the intervention. However, most proviruses persisting in the setting of ART are defective. In addition, intact HIV-1 and SIV genomes undergo complex, multiphasic decay observable when new infection events are blocked by ART. Intervention-induced elimination of latently infected cells must be distinguished from natural decay. Here, we address these issues for SHIV. We describe an intact proviral DNA assay that allows digital counting of SHIV genomes lacking common fatal defects. We show that intact SHIV genomes in circulating CD4+ T cells undergo biphasic decay during the first year of ART, with a rapid first phase (t1/2 = 30.1 d) and a slower second phase (t1/2 = 8.1 mo) that is still more rapid that the slow decay observed in people with HIV-1 on long-term ART (t1/2 = 3.7 y). In SHIV models, most interventions are tested during 2nd phase decay. Natural 2nd phase decay must be considered in evaluating interventions as most infected cells present at this time do not become part of the stable reservoir. In addition, for interventions tested during 2nd phase decay, a caveat is that the intervention may not be equally effective in people with HIV on long-term ART whose reservoirs are dominated by latently infected cells with a slower decay rate.
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Affiliation(s)
- Mithra R. Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Emily J. Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Alexandra M. Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | | | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA02215
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Baltimore, MD21205
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13
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He W, Ou T, Skamangas N, Bailey CC, Bronkema N, Guo Y, Yin Y, Kobzarenko V, Zhang X, Pan A, Liu X, Xu J, Zhang L, Allwardt AE, Mitra D, Quinlan B, Sanders RW, Choe H, Farzan M. Heavy-chain CDR3-engineered B cells facilitate in vivo evaluation of HIV-1 vaccine candidates. Immunity 2023; 56:2408-2424.e6. [PMID: 37531955 PMCID: PMC11092302 DOI: 10.1016/j.immuni.2023.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/04/2023]
Abstract
V2-glycan/apex broadly neutralizing antibodies (bnAbs) recognize a closed quaternary epitope of the HIV-1 envelope glycoprotein (Env). This closed structure is necessary to elicit apex antibodies and useful to guide the maturation of other bnAb classes. To compare antigens designed to maintain this conformation, we evaluated apex-specific responses in mice engrafted with a diverse repertoire of B cells expressing the HCDR3 of the apex bnAb VRC26.25. Engineered B cells affinity matured, guiding the improvement of VRC26.25 itself. We found that soluble Env (SOSIP) variants differed significantly in their ability to raise anti-apex responses. A transmembrane SOSIP (SOSIP-TM) delivered as an mRNA-lipid nanoparticle elicited more potent neutralizing responses than multimerized SOSIP proteins. Importantly, SOSIP-TM elicited neutralizing sera from B cells engineered with the predicted VRC26.25-HCDR3 progenitor, which also affinity matured. Our data show that HCDR3-edited B cells facilitate efficient in vivo comparisons of Env antigens and highlight the potential of an HCDR3-focused vaccine approach.
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Affiliation(s)
- Wenhui He
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Tianling Ou
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Nickolas Skamangas
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Charles C Bailey
- The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Naomi Bronkema
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA
| | - Yan Guo
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Yiming Yin
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Valerie Kobzarenko
- Department of Computer Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Xia Zhang
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Andi Pan
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA
| | - Xin Liu
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jinge Xu
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Lizhou Zhang
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Ava E Allwardt
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Debasis Mitra
- Department of Computer Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Brian Quinlan
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Hyeryun Choe
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Farzan
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA 02115, USA; The Center for Integrated Solutions to Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Skaggs Graduate School, Scripps Research, La Jolla, CA 92037, USA.
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14
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Mopuri R, Welbourn S, Charles T, Ralli-Jain P, Rosales D, Burton S, Aftab A, Karunakaran K, Pellegrini K, Kilembe W, Karita E, Gnanakaran S, Upadhyay AA, Bosinger SE, Derdeyn CA. High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope. PLoS Pathog 2023; 19:e1011717. [PMID: 37878666 PMCID: PMC10627474 DOI: 10.1371/journal.ppat.1011717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/06/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023] Open
Abstract
A protective HIV-1 vaccine has been hampered by a limited understanding of how B cells acquire neutralizing activity. Our previous vaccines expressing two different HIV-1 envelopes elicited robust antigen specific serum IgG titers in 20 rhesus macaques; yet serum from only two animals neutralized the autologous virus. Here, we used high throughput immunoglobulin receptor and single cell RNA sequencing to characterize the overall expansion, recall, and maturation of antigen specific B cells longitudinally over 90 weeks. Diversification and expansion of many B cell clonotypes occurred broadly in the absence of serum neutralization. However, in one animal that developed neutralization, two neutralizing B cell clonotypes arose from the same immunoglobulin germline and were tracked longitudinally. Early antibody variants with high identity to germline neutralized the autologous virus while later variants acquired somatic hypermutation and increased neutralization potency. The early engagement of precursors capable of neutralization with little to no SHM followed by prolonged affinity maturation allowed the two neutralizing lineages to successfully persist despite many other antigen specific B cells. The findings provide new insight into B cells responding to HIV-1 envelope during heterologous prime and boost immunization in rhesus macaques and the development of selected autologous neutralizing antibody lineages.
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Affiliation(s)
- Rohini Mopuri
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Sarah Welbourn
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Tysheena Charles
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Pooja Ralli-Jain
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - David Rosales
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Samantha Burton
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Areeb Aftab
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Kirti Karunakaran
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Kathryn Pellegrini
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | | | - Sandrasegaram Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Amit A. Upadhyay
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Cynthia A. Derdeyn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Infectious Diseases and Translational Medicine Unit, Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
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15
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Tong T, D’Addabbo A, Xu J, Chawla H, Nguyen A, Ochoa P, Crispin M, Binley JM. Impact of stabilizing mutations on the antigenic profile and glycosylation of membrane-expressed HIV-1 envelope glycoprotein. PLoS Pathog 2023; 19:e1011452. [PMID: 37549185 PMCID: PMC10434953 DOI: 10.1371/journal.ppat.1011452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/17/2023] [Accepted: 07/16/2023] [Indexed: 08/09/2023] Open
Abstract
Recent HIV-1 vaccine development has centered on "near native" soluble envelope glycoprotein (Env) trimers that are artificially stabilized laterally (between protomers) and apically (between gp120 and gp41). These mutations have been leveraged for use in membrane-expressed Env mRNA vaccines, although their effects in this context are unclear. To address this question, we used virus-like particle (VLP) produced in 293T cells. Uncleaved (UNC) trimers were laterally unstable upon gentle lysis from membranes. However, gp120/gp41 processing improved lateral stability. Due to inefficient gp120/gp41 processing, UNC is incorporated into VLPs. A linker between gp120 and gp41 neither improved trimer stability nor its antigenic profile. An artificially introduced enterokinase cleavage site allowed post-expression gp120/gp41 processing, concomitantly increasing trimer stability. Gp41 N-helix mutations I559P and NT1-5 imparted lateral trimer stability, but also reduced gp120/gp41 processing and/or impacted V2 apex and interface NAb binding. I559P consistently reduced recognition by HIV+ human plasmas, further supporting antigenic differences. Mutations in the gp120 bridging sheet failed to stabilize membrane trimers in a pre-fusion conformation, and also reduced gp120/gp41 processing and exposed non-neutralizing epitopes. Reduced glycan maturation and increased sequon skipping were common side effects of these mutations. In some cases, this may be due to increased rigidity which limits access to glycan processing enzymes. In contrast, viral gp120 did not show glycan skipping. A second, minor species of high mannose gp160 was unaffected by any mutations and instead bypasses normal folding and glycan maturation. Including the full gp41 cytoplasmic tail led to markedly reduced gp120/gp41 processing and greatly increased the proportion of high mannose gp160. Remarkably, monoclonal antibodies were unable to bind to this high mannose gp160 in native protein gels. Overall, our findings suggest caution in leveraging stabilizing mutations in nucleic acid-based immunogens to ensure they impart valuable membrane trimer phenotypes for vaccine use.
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Affiliation(s)
- Tommy Tong
- 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
| | - Jiamin Xu
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Himanshi Chawla
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Albert Nguyen
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Paola Ochoa
- San Diego Biomedical Research Institute, San Diego, California, United States of America
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - James M. Binley
- San Diego Biomedical Research Institute, San Diego, California, United States of America
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16
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Bauer A, Lindemuth E, Marino FE, Krause R, Joy J, Docken SS, Mallick S, McCormick K, Holt C, Georgiev I, Felber B, Keele BF, Veazey R, Davenport MP, Li H, Shaw GM, Bar KJ. Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques. PLoS Pathog 2023; 19:e1011059. [PMID: 37399208 PMCID: PMC10348547 DOI: 10.1371/journal.ppat.1011059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 07/14/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Transmitted/founder (TF) simian-human immunodeficiency viruses (SHIVs) express HIV-1 envelopes modified at position 375 to efficiently infect rhesus macaques while preserving authentic HIV-1 Env biology. SHIV.C.CH505 is an extensively characterized virus encoding the TF HIV-1 Env CH505 mutated at position 375 shown to recapitulate key features of HIV-1 immunobiology, including CCR5-tropism, a tier 2 neutralization profile, reproducible early viral kinetics, and authentic immune responses. SHIV.C.CH505 is used frequently in nonhuman primate studies of HIV, but viral loads after months of infection are variable and typically lower than those in people living with HIV. We hypothesized that additional mutations besides Δ375 might further enhance virus fitness without compromising essential components of CH505 Env biology. From sequence analysis of SHIV.C.CH505-infected macaques across multiple experiments, we identified a signature of envelope mutations associated with higher viremia. We then used short-term in vivo mutational selection and competition to identify a minimally adapted SHIV.C.CH505 with just five amino acid changes that substantially improve virus replication fitness in macaques. Next, we validated the performance of the adapted SHIV in vitro and in vivo and identified the mechanistic contributions of selected mutations. In vitro, the adapted SHIV shows improved virus entry, enhanced replication on primary rhesus cells, and preserved neutralization profiles. In vivo, the minimally adapted virus rapidly outcompetes the parental SHIV with an estimated growth advantage of 0.14 days-1 and persists through suppressive antiretroviral therapy to rebound at treatment interruption. Here, we report the successful generation of a well-characterized, minimally adapted virus, termed SHIV.C.CH505.v2, with enhanced replication fitness and preserved native Env properties that can serve as a new reagent for NHP studies of HIV-1 transmission, pathogenesis, and cure.
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Affiliation(s)
- Anya Bauer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Emily Lindemuth
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Francesco Elia Marino
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ryan Krause
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jaimy Joy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Suvadip Mallick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kevin McCormick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Clinton Holt
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ivelin Georgiev
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Barbara Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Ronald Veazey
- Department of Pathology and Laboratory Medicine, Tulane School of Medicine, New Orleans, Louisiana, United States of America
| | | | - Hui Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George M. Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katharine J. Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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17
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Zhang X, Zhou Z. The Mechanism of bnAb Production and Its Application in Mutable Virus Broad-Spectrum Vaccines: Inspiration from HIV-1 Broad Neutralization Research. Vaccines (Basel) 2023; 11:1143. [PMID: 37514959 PMCID: PMC10384589 DOI: 10.3390/vaccines11071143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Elite controllers among HIV-1-infected individuals have demonstrated a stronger ability to control the viral load in their bodies. Scientists have isolated antibodies with strong neutralizing ability from these individuals, which can neutralize HIV-1 variations; these are known as broadly neutralizing antibodies. The nucleic acid of some viruses will constantly mutate during replication (such as SARS-CoV-2), which will reduce the protective ability of the corresponding vaccines. The immune escape caused by this mutation is the most severe challenge faced by humans in the battle against the virus. Therefore, developing broad-spectrum vaccines that can induce broadly neutralizing antibodies against various viruses and their mutated strains is the best way to combat virus mutations. Exploring the mechanism by which the human immune system produces broadly neutralizing antibodies and its induction strategies is crucial in the design process of broad-spectrum vaccines.
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Affiliation(s)
- Xinyu Zhang
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- College of Life Science, Jilin University, Changchun 130012, China
| | - Zehua Zhou
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
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18
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Hora B, Li H, Shen X, Martin M, Chen Y, Berry M, Evangelous T, Macintyre AN, Arus-Altuz A, Wang S, Singh A, Zhao C, De Naeyer N, DeMarco T, Kuykendall C, Gurley T, Saunders KO, Denny T, Moody MA, Misamore J, Lewis MG, Wiehe K, Cain DW, Montefiori DC, Shaw GM, Williams WB. Neonatal SHIV infection in rhesus macaques elicited heterologous HIV-1-neutralizing antibodies. Cell Rep 2023; 42:112255. [PMID: 36924501 PMCID: PMC10117998 DOI: 10.1016/j.celrep.2023.112255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/21/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Infants and children infected with human immunodeficiency virus (HIV)-1 have been shown to develop neutralizing antibodies (nAbs) against heterologous HIV-1 strains, characteristic of broadly nAbs (bnAbs). Thus, having a neonatal model for the induction of heterologous HIV-1 nAbs may provide insights into the mechanisms of neonatal bnAb development. Here, we describe a neonatal model for heterologous HIV-1 nAb induction in pathogenic simian-HIV (SHIV)-infected rhesus macaques (RMs). Viral envelope (env) evolution showed mutations at multiple sites, including nAb epitopes. All 13 RMs generated plasma autologous HIV-1 nAbs. However, 8/13 (62%) RMs generated heterologous HIV-1 nAbs with increasing potency over time, albeit with limited breadth, and mapped to multiple nAb epitopes, suggestive of a polyclonal response. Moreover, plasma heterologous HIV-1 nAb development was associated with antigen-specific, lymph-node-derived germinal center activity. We define a neonatal model for heterologous HIV-1 nAb induction that may inform future pediatric HIV-1 vaccines for bnAb induction in infants and children.
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Affiliation(s)
- Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hui Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mitchell Martin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yue Chen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Madison Berry
- 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
| | - Andrew N Macintyre
- 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
| | - Aria Arus-Altuz
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ajay Singh
- 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
| | - Nicole De Naeyer
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Todd DeMarco
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cindy Kuykendall
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thaddeus Gurley
- 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; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas Denny
- 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; Department of Pediatrics, 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
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C 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
| | - George M Shaw
- 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 Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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19
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Haynes BF, Wiehe K, Borrow P, Saunders KO, Korber B, Wagh K, McMichael AJ, Kelsoe G, Hahn BH, Alt F, Shaw GM. Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies. Nat Rev Immunol 2023; 23:142-158. [PMID: 35962033 PMCID: PMC9372928 DOI: 10.1038/s41577-022-00753-w] [Citation(s) in RCA: 113] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
After nearly four decades of research, a safe and effective HIV-1 vaccine remains elusive. There are many reasons why the development of a potent and durable HIV-1 vaccine is challenging, including the extraordinary genetic diversity of HIV-1 and its complex mechanisms of immune evasion. HIV-1 envelope glycoproteins are poorly recognized by the immune system, which means that potent broadly neutralizing antibodies (bnAbs) are only infrequently induced in the setting of HIV-1 infection or through vaccination. Thus, the biology of HIV-1-host interactions necessitates novel strategies for vaccine development to be designed to activate and expand rare bnAb-producing B cell lineages and to select for the acquisition of critical improbable bnAb mutations. Here we discuss strategies for the induction of potent and broad HIV-1 bnAbs and outline the steps that may be necessary for ultimate success.
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Affiliation(s)
- Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Kshitij Wagh
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Immunology, Duke University of School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederick Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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20
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Bibollet-Ruche F, Russell RM, Ding W, Liu W, Li Y, Wagh K, Wrapp D, Habib R, Skelly AN, Roark RS, Sherrill-Mix S, Wang S, Rando J, Lindemuth E, Cruickshank K, Park Y, Baum R, Carey JW, Connell AJ, Li H, Giorgi EE, Song GS, Ding S, Finzi A, Newman A, Hernandez GE, Machiele E, Cain DW, Mansouri K, Lewis MG, Montefiori DC, Wiehe KJ, Alam SM, Teng IT, Kwong PD, Andrabi R, Verkoczy L, Burton DR, Korber BT, Saunders KO, Haynes BF, Edwards RJ, Shaw GM, Hahn BH. A Germline-Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex Directed Cross-Neutralizing Antibodies. mBio 2023; 14:e0337022. [PMID: 36629414 PMCID: PMC9973348 DOI: 10.1128/mbio.03370-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
HIV-1 and its SIV precursors share a broadly neutralizing antibody (bNAb) epitope in variable loop 2 (V2) at the envelope glycoprotein (Env) trimer apex. Here, we tested the immunogenicity of germ line-targeting versions of a chimpanzee SIV (SIVcpz) Env in human V2-apex bNAb heavy-chain precursor-expressing knock-in mice and as chimeric simian-chimpanzee immunodeficiency viruses (SCIVs) in rhesus macaques (RMs). Trimer immunization of knock-in mice induced V2-directed NAbs, indicating activation of V2-apex bNAb precursor-expressing mouse B cells. SCIV infection of RMs elicited high-titer viremia, potent autologous tier 2 neutralizing antibodies, and rapid sequence escape in the canonical V2-apex epitope. Six of seven animals also developed low-titer heterologous plasma breadth that mapped to the V2-apex. Antibody cloning from two of these animals identified multiple expanded lineages with long heavy chain third complementarity determining regions that cross-neutralized as many as 7 of 19 primary HIV-1 strains, but with low potency. Negative stain electron microscopy (NSEM) of members of the two most cross-reactive lineages confirmed V2 targeting but identified an angle of approach distinct from prototypical V2-apex bNAbs, with antibody binding either requiring or inducing an occluded-open trimer. Probing with conformation-sensitive, nonneutralizing antibodies revealed that SCIV-expressed, but not wild-type SIVcpz Envs, as well as a subset of primary HIV-1 Envs, preferentially adopted a more open trimeric state. These results reveal the existence of a cryptic V2 epitope that is exposed in occluded-open SIVcpz and HIV-1 Env trimers and elicits cross-neutralizing responses of limited breadth and potency. IMPORTANCE An effective HIV-1 vaccination strategy will need to stimulate rare precursor B cells of multiple bNAb lineages and affinity mature them along desired pathways. Here, we searched for V2-apex germ line-targeting Envs among a large set of diverse primate lentiviruses and identified minimally modified versions of one chimpanzee SIV Env that bound several human V2-apex bNAb precursors and stimulated one of these in a V2-apex bNAb precursor-expressing knock-in mouse. We also generated chimeric simian-chimpanzee immunodeficiency viruses and showed that they elicit low-titer V2-directed heterologous plasma breadth in six of seven infected rhesus macaques. Characterization of this antibody response identified a new class of weakly cross-reactive neutralizing antibodies that target the V2-apex, but only in occluded-open Env trimers. The existence of this cryptic epitope, which in some Env backgrounds is immunodominant, needs to be considered in immunogen design.
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Affiliation(s)
- Frederic Bibollet-Ruche
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronnie M. Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wenge Ding
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Daniel Wrapp
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rumi Habib
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ashwin N. Skelly
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ryan S. Roark
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Juliette Rando
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emily Lindemuth
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kendra Cruickshank
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Younghoon Park
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rachel Baum
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John W. Carey
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew Jesse Connell
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elena E. Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Ge S. Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Giovanna E. Hernandez
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Emily Machiele
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Derek W. Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - David C. Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Kevin J. Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Laurent Verkoczy
- San Diego Biomedical Research Institute, San Diego, California, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Ragon Institute of MGH, Harvard and MIT, Cambridge, Massachusetts, USA
| | - Bette T. Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - George M. Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H. Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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21
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Kumar S, Singh S, Luthra K. An Overview of Human Anti-HIV-1 Neutralizing Antibodies against Diverse Epitopes of HIV-1. ACS OMEGA 2023; 8:7252-7261. [PMID: 36873012 PMCID: PMC9979333 DOI: 10.1021/acsomega.2c07933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/06/2023] [Indexed: 06/01/2023]
Abstract
In this Review, we have addressed some recent developments in the discovery and applications of anti-human immunodeficiency virus type- 1 (HIV-1) broadly neutralizing antibodies (bnAbs) isolated from infected adults and children. The recent developments in human antibody isolation technologies have led to the discovery of several highly potent anti-HIV-1 bnAbs. Herein, we have discussed the characteristics of recently identified bnAbs directed at distinct epitopes of HIV-1, in addition to the existing antibodies, from adults and children and have shed light on the benefits of multispecific HIV-1 bnAbs and their role in the design of polyvalent vaccines.
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22
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Samsel J, Boswell KL, Watkins T, Ambrozak DR, Mason R, Yamamoto T, Ko S, Yang Y, Zhou T, Doria-Rose NA, Foulds KE, Roederer M, Mascola JR, Kwong PD, Gama L, Koup RA. Rhesus macaque Bcl-6/Bcl-xL B cell immortalization: Discovery of HIV-1 neutralizing antibodies from lymph node. J Immunol Methods 2023; 516:113445. [PMID: 36848985 DOI: 10.1016/j.jim.2023.113445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Many HIV-1 vaccines are designed to elicit neutralizing antibodies, and pre-clinical testing is often carried out in rhesus macaques (RMs). We have therefore adapted a method of B cell immortalization for use with RM B cells. In this system, RM B cells are activated with CD40 ligand and RM IL-21 before transduction with a retroviral vector encoding Bcl-6, Bcl-xL, and green fluorescent protein. Importantly, RM B cells from lymph nodes are more effectively immortalized by this method than B cells from PBMC, a difference not seen in humans. We suggest the discrepancy between these two tissues is due to increased expression of CD40 on RM lymph node B cells. Immortalized RM B cells expand long-term, undergo minimal somatic hypermutation, express surface B cell receptor, and secrete antibodies into culture. This allows for the identification of cells based on antigen specificity and/or functional assays. Here, we show the characterization of this system and its application for the isolation of HIV-1 neutralizing antibodies from a SHIV.CH505-infected animal, both with and without antigen probe. Taken together, we show that Bcl-6/xL immortalization is a valuable and flexible tool for antibody discovery in RMs, but with important distinctions from application of the system in human cells.
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Affiliation(s)
- Jakob Samsel
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America; Institute for Biomedical Sciences, George Washington University, Washington, D.C., United States of America.
| | - Kristin L Boswell
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | - Timothy Watkins
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | - David R Ambrozak
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | - Rosemarie Mason
- ImmunoTechnology Section, VRC; Humoral Immunology Section, VRC
| | - Takuya Yamamoto
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | | | | | | | | | | | | | | | | | - Lucio Gama
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center (VRC), NIAID, NIH, Bethesda, MD, United States of America
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23
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Wrapp D, Mu Z, Thakur B, Janowska K, Ajayi O, Barr M, Parks R, Mansouri K, Edwards RJ, Hahn BH, Acharya P, Saunders KO, Haynes BF. Structure-Based Stabilization of SOSIP Env Enhances Recombinant Ectodomain Durability and Yield. J Virol 2023; 97:e0167322. [PMID: 36633409 PMCID: PMC9888283 DOI: 10.1128/jvi.01673-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/09/2022] [Indexed: 01/13/2023] Open
Abstract
The envelope glycoprotein (Env) is the main focus of human immunodeficiency virus type 1 (HIV-1) vaccine development due to its critical role in viral entry. Despite advances in protein engineering, many Env proteins remain recalcitrant to recombinant expression due to their inherent metastability, making biochemical and immunological experiments impractical or impossible. Here, we report a novel proline stabilization strategy to facilitate the production of prefusion Env trimers. This approach, termed "2P," works synergistically with previously described SOSIP mutations and dramatically increases the yield of recombinantly expressed Env ectodomains without altering the antigenic or conformational properties of near-native Env. We determined that the 2P mutations function by enhancing the durability of the prefusion conformation and that this stabilization strategy is broadly applicable to evolutionarily and antigenically diverse Env constructs. These findings provide a new Env stabilization platform to facilitate biochemical research and expand the number of Env variants that can be developed as future HIV-1 vaccine candidates. IMPORTANCE Recent estimates have placed the number of new human immunodeficiency virus type 1 (HIV-1) infections at approximately 1.5 million per year, emphasizing the ongoing and urgent need for an effective vaccine. The envelope (Env) glycoprotein is the main focus of HIV-1 vaccine development, but, due to its inherent metastability, many Env variants are difficult to recombinantly express in the relatively large quantities that are required for biochemical studies and animal trials. Here, we describe a novel structure-based stabilization strategy that works synergistically with previously described SOSIP mutations to increase the yield of prefusion HIV-1 Env.
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Affiliation(s)
- Daniel Wrapp
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Zekun Mu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Bhishem Thakur
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Katarzyna Janowska
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Oluwatobi Ajayi
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Beatrice H. Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Department of Microbiology and Molecular Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
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24
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Hägglöf T, Cipolla M, Loewe M, Chen ST, Mesin L, Hartweger H, ElTanbouly MA, Cho A, Gazumyan A, Ramos V, Stamatatos L, Oliveira TY, Nussenzweig MC, Viant C. Continuous germinal center invasion contributes to the diversity of the immune response. Cell 2023; 186:147-161.e15. [PMID: 36565698 PMCID: PMC9825658 DOI: 10.1016/j.cell.2022.11.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/12/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
Abstract
Antibody responses are characterized by increasing affinity and diversity over time. Affinity maturation occurs in germinal centers by a mechanism that involves repeated cycles of somatic mutation and selection. How antibody responses diversify while also undergoing affinity maturation is not as well understood. Here, we examined germinal center (GC) dynamics by tracking B cell entry, division, somatic mutation, and specificity. Our experiments show that naive B cells continuously enter GCs where they compete for T cell help and undergo clonal expansion. Consistent with late entry, invaders carry fewer mutations but can contribute up to 30% or more of the cells in late-stage germinal centers. Notably, cells entering the germinal center at later stages of the reaction diversify the immune response by expressing receptors that show low affinity to the immunogen. Paradoxically, the affinity threshold for late GC entry is lowered in the presence of high-affinity antibodies.
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Affiliation(s)
- Thomas Hägglöf
- 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
| | - Maximilian Loewe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Spencer T Chen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY 10065, USA
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Mohamed A ElTanbouly
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- 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
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute (HHMI), The Rockefeller University, New York, NY 10065, USA.
| | - Charlotte Viant
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.
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25
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Saunders KO, Edwards RJ, Tilahun K, Manne K, Lu X, Cain DW, Wiehe K, Williams WB, Mansouri K, Hernandez GE, Sutherland L, Scearce R, Parks R, Barr M, DeMarco T, Eater CM, Eaton A, Morton G, Mildenberg B, Wang Y, Rountree RW, Tomai MA, Fox CB, Moody MA, Alam SM, Santra S, Lewis MG, Denny TN, Shaw GM, Montefiori DC, Acharya P, Haynes BF. Stabilized HIV-1 envelope immunization induces neutralizing antibodies to the CD4bs and protects macaques against mucosal infection. Sci Transl Med 2022; 14:eabo5598. [PMID: 36070369 PMCID: PMC10034035 DOI: 10.1126/scitranslmed.abo5598] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A successful HIV-1 vaccine will require induction of a polyclonal neutralizing antibody (nAb) response, yet vaccine-mediated induction of such a response in primates remains a challenge. We found that a stabilized HIV-1 CH505 envelope (Env) trimer formulated with a Toll-like receptor 7/8 agonist induced potent HIV-1 polyclonal nAbs that correlated with protection from homologous simian-human immunodeficiency virus (SHIV) infection. The serum dilution that neutralized 50% of virus replication (ID50 titer) required to protect 90% of macaques was 1:364 against the challenge virus grown in primary rhesus CD4+ T cells. Structural analyses of vaccine-induced nAbs demonstrated targeting of the Env CD4 binding site or the N156 glycan and the third variable loop base. Autologous nAb specificities similar to those elicited in macaques by vaccination were isolated from the human living with HIV from which the CH505 Env immunogen was derived. CH505 viral isolates were isolated that mutated the V1 to escape both the infection-induced and vaccine-induced antibodies. These results define the specificities of a vaccine-induced nAb response and the protective titers of HIV-1 vaccine-induced nAbs required to protect nonhuman primates from low-dose mucosal challenge by SHIVs bearing a primary transmitted/founder Env.
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Affiliation(s)
- Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
- Department of Microbiology and Molecular Genetics, Duke University Medical Center; Durham, NC 27710
- Department of Immunology, Duke University Medical Center; Durham, NC, 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Kedamawit Tilahun
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Derek W. Cain
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Wilton B. Williams
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
- Department of Immunology, Duke University Medical Center; Durham, NC, 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Giovanna E. Hernandez
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Laura Sutherland
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Richard Scearce
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Todd DeMarco
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Chloe M. Eater
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
| | | | | | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - R. Wes Rountree
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Mark A. Tomai
- 3M Corporate Research Materials Lab, 3M Company; St. Paul, MN, 55144, USA
| | | | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Pediatrics, Duke University Medical Center; Durham, NC, 27710, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center; Boston, MA, 02215, USA
| | | | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - George M. Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Immunology, Duke University Medical Center; Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
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26
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Broadly neutralizing antibodies against HIV-1 and concepts for application. Curr Opin Virol 2022; 54:101211. [DOI: 10.1016/j.coviro.2022.101211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Accepted: 02/27/2022] [Indexed: 12/21/2022]
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27
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Welbourn S, Chakraborty S, Yang JE, Gleinich AS, Gangadhara S, Khan S, Ferrebee C, Yagnik B, Burton S, Charles T, Smith SA, Williams D, Mopuri R, Upadhyay AA, Thompson J, Price MA, Wang S, Qin Z, Shen X, Williams LD, Eisel N, Peters T, Zhang L, Kilembe W, Karita E, Tomaras GD, Bosinger SE, Amara RR, Azadi P, Wright ER, Gnanakaran S, Derdeyn CA. A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequence. PLoS Pathog 2022; 18:e1010488. [PMID: 35503780 PMCID: PMC9106183 DOI: 10.1371/journal.ppat.1010488] [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: 01/14/2022] [Revised: 05/13/2022] [Accepted: 04/01/2022] [Indexed: 11/21/2022] Open
Abstract
Transmitted/founder (T/F) HIV-1 envelope proteins (Envs) from infected individuals that developed neutralization breadth are likely to possess inherent features desirable for vaccine immunogen design. To explore this premise, we conducted an immunization study in rhesus macaques (RM) using T/F Env sequences from two human subjects, one of whom developed potent and broad neutralizing antibodies (Z1800M) while the other developed little to no neutralizing antibody responses (R66M) during HIV-1 infection. Using a DNA/MVA/protein immunization protocol, 10 RM were immunized with each T/F Env. Within each T/F Env group, the protein boosts were administered as either monomeric gp120 or stabilized trimeric gp140 protein. All vaccination regimens elicited high titers of antigen-specific IgG, and two animals that received monomeric Z1800M Env gp120 developed autologous neutralizing activity. Using early Env escape variants isolated from subject Z1800M as guides, the serum neutralizing activity of the two immunized RM was found to be dependent on the gp120 V5 region. Interestingly, the exact same residues of V5 were also targeted by a neutralizing monoclonal antibody (nmAb) isolated from the subject Z1800M early in infection. Glycan profiling and computational modeling of the Z1800M Env gp120 immunogen provided further evidence that the V5 loop is exposed in this T/F Env and was a dominant feature that drove neutralizing antibody targeting during infection and immunization. An expanded B cell clonotype was isolated from one of the neutralization-positive RM and nmAbs corresponding to this group demonstrated V5-dependent neutralization similar to both the RM serum and the human Z1800M nmAb. The results demonstrate that neutralizing antibody responses elicited by the Z1800M T/F Env in RM converged with those in the HIV-1 infected human subject, illustrating the potential of using immunogens based on this or other T/F Envs with well-defined immunogenicity as a starting point to drive breadth.
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Affiliation(s)
- Sarah Welbourn
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics Group, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anne S. Gleinich
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Sailaja Gangadhara
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Salar Khan
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Courtney Ferrebee
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Bhrugu Yagnik
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha Burton
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Tysheena Charles
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - S. Abigail Smith
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Danielle Williams
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Rohini Mopuri
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Amit A. Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Justin Thompson
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Matt A. Price
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- International AIDS Vaccine Initiative, New York city, New York, United States of America
| | - Shiyu Wang
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Xiaoying Shen
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - LaTonya D. Williams
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Nathan Eisel
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Tiffany Peters
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Lu Zhang
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - William Kilembe
- Center for Family Health Research in Zambia (CFHRZ), Lusaka, Zambia
| | | | - Georgia D. Tomaras
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Steven E. Bosinger
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Rama R. Amara
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cynthia A. Derdeyn
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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28
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Zhang D, Liu Z, Wang W, Chen MX, Hou JL, Zhang Z, Ren WH, Ren L, Hao YL. Viral resistance to VRC01-like antibodies with mutations in loop D and V5 from an HIV-1 B′ subtype infected individual with broadly neutralization activity. Mol Immunol 2022; 145:50-58. [DOI: 10.1016/j.molimm.2022.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
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29
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Gao N, Gai Y, Meng L, Wang C, Wang W, Li X, Gu T, Louder MK, Doria‐Rose NA, Wiehe K, Nazzari AF, Olia AS, Gorman J, Rawi R, Wu W, Smith C, Khant H, de Val N, Yu B, Luo J, Niu H, Tsybovsky Y, Liao H, Kepler TB, Kwong PD, Mascola JR, Qin C, Zhou T, Yu X, Gao F. Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200063. [PMID: 35319830 PMCID: PMC9130890 DOI: 10.1002/advs.202200063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Understanding maturation pathways of broadly neutralizing antibodies (bnAbs) against HIV-1 can be highly informative for HIV-1 vaccine development. A lineage of J038 bnAbs is now obtained from a long-term SHIV-infected macaque. J038 neutralizes 54% of global circulating HIV-1 strains. Its binding induces a unique "up" conformation for one of the V2 loops in the trimeric envelope glycoprotein and is heavily dependent on glycan, which provides nearly half of the binding surface. Their unmutated common ancestor neutralizes the autologous virus. Continuous maturation enhances neutralization potency and breadth of J038 lineage antibodies via expanding antibody-Env contact areas surrounding the core region contacted by germline-encoded residues. Developmental details and recognition features of J038 lineage antibodies revealed here provide a new pathway for elicitation and maturation of V2-targeting bnAbs.
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Affiliation(s)
- Nan Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Yanxin Gai
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Lina Meng
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Wei Wang
- Institute of Laboratory Animal ScienceChinese Academy of Medical SciencesBeijing100021China
- Comparative Medicine CenterPeking Union Medical CollegeBeijing100021China
| | - Xiaojun Li
- Department of MedicineDuke University School of MedicineDurhamNC27710USA
| | - Tiejun Gu
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Mark K. Louder
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Nicole A. Doria‐Rose
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Kevin Wiehe
- Duke University Human Vaccine InstituteDuke University School of MedicineDurhamNC27710USA
| | - Alexandra F. Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Wenmin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Clayton Smith
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Htet Khant
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Natalia de Val
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Junhong Luo
- Institute of Molecular and Medical Virology, School of MedicineJinan UniversityGuangzhouGuangdong Province510632China
| | - Haitao Niu
- Institute of Molecular and Medical Virology, School of MedicineJinan UniversityGuangzhouGuangdong Province510632China
| | - Yaroslav Tsybovsky
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Huaxin Liao
- Institute of Molecular and Medical Virology, School of MedicineJinan UniversityGuangzhouGuangdong Province510632China
| | | | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Chuan Qin
- Institute of Laboratory Animal ScienceChinese Academy of Medical SciencesBeijing100021China
- Comparative Medicine CenterPeking Union Medical CollegeBeijing100021China
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
- Department of MedicineDuke University School of MedicineDurhamNC27710USA
- Institute of Molecular and Medical Virology, School of MedicineJinan UniversityGuangzhouGuangdong Province510632China
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30
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Zhang B, Tian J, Zhang Q, Xie Y, Wang K, Qiu S, Lu K, Liu Y. Comparing the Nucleocapsid Proteins of Human Coronaviruses: Structure, Immunoregulation, Vaccine, and Targeted Drug. Front Mol Biosci 2022; 9:761173. [PMID: 35573742 PMCID: PMC9099148 DOI: 10.3389/fmolb.2022.761173] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/28/2022] [Indexed: 01/08/2023] Open
Abstract
The seven pathogenic human coronaviruses (HCoVs) include HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1, which usually cause mild upper respiratory tract diseases, and SARS-CoV, MERS-CoV, and SARS-CoV-2, which cause a severe acute respiratory syndrome. The nucleocapsid (N) protein, as the dominant structural protein from coronaviruses that bind to the genomic RNA, participates in various vital activities after virus invasion and will probably become a promising target of antiviral drug design. Therefore, a comprehensive literature review of human coronavirus’ pathogenic mechanism and therapeutic strategies is necessary for the control of the pandemic. Here, we give a systematic summary of the structures, immunoregulation, and potential vaccines and targeted drugs of the HCoVs N protein. First, we provide a general introduction to the fundamental structures and molecular function of N protein. Next, we outline the N protein mediated immune regulation and pathogenesis mechanism. Finally, we comprehensively summarize the development of potential N protein-targeted drugs and candidate vaccines to treat coronavirus disease 2019 (COVID-19). We believe this review provides insight into the virulence and transmission of SARS-CoV-2 as well as support for further study on epidemic control of COVID-19.
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Affiliation(s)
- Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
| | - Junjie Tian
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Qintao Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Yan Xie
- School of Public Health, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Shuyi Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Keyu Lu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
| | - Yang Liu
- School of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
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31
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Kaduk M, Corcoran M, Karlsson Hedestam GB. Addressing IGHV Gene Structural Diversity Enhances Immunoglobulin Repertoire Analysis: Lessons From Rhesus Macaque. Front Immunol 2022; 13:818440. [PMID: 35419009 PMCID: PMC8995469 DOI: 10.3389/fimmu.2022.818440] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
The accurate germline gene assignment and assessment of somatic hypermutation in antibodies induced by immunization or infection are important in immunological studies. Here, we illustrate issues specific to the construction of comprehensive immunoglobulin (IG) germline gene reference databases for outbred animal species using rhesus macaques, a frequently used non-human primate model, as a model test case. We demonstrate that the genotypic variation found in macaque germline inference studies is reflected in similar levels of gene diversity in genomic assemblies. We show that the high frequency of IG heavy chain V (IGHV) region structural and gene copy number variation between subjects means that individual animals lack genes that are present in other animals. Therefore, gene databases compiled from a single or too few animals will inevitably result in inaccurate gene assignment and erroneous SHM level assessment for those genes it lacks. We demonstrate this by assigning a test macaque IgG library to the KIMDB, a database compiled of germline IGHV sequences from 27 rhesus macaques, and, alternatively, to the IMGT rhesus macaque database, based on IGHV genes inferred primarily from the genomic sequence of the rheMac10 reference assembly, supplemented with 10 genes from the Mmul_051212 assembly. We found that the use of a gene-restricted database led to overestimations of SHM by up to 5% due to misassignments. The principles described in the current study provide a model for the creation of comprehensive immunoglobulin reference databases from outbred species to ensure accurate gene assignment, lineage tracing and SHM calculations.
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Affiliation(s)
- Mateusz Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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IMGT® Biocuration and Analysis of the Rhesus Monkey IG Loci. Vaccines (Basel) 2022; 10:vaccines10030394. [PMID: 35335026 PMCID: PMC8950363 DOI: 10.3390/vaccines10030394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 11/29/2022] Open
Abstract
The adaptive immune system, along with the innate immune system, are the two main biological processes that protect an organism from pathogens. The adaptive immune system is characterized by the specificity and extreme diversity of its antigen receptors. These antigen receptors are the immunoglobulins (IG) or antibodies of the B cells and the T cell receptors (TR) of the T cells. The IG are proteins that have a dual role in immunity: they recognize antigens and trigger elimination mechanisms, to rid the body of foreign cells. The synthesis of the immunoglobulin heavy and light chains requires gene rearrangements at the DNA level in the IGH, IGK, and IGL loci. The rhesus monkey (Macaca mulatta) is one of the most widely used nonhuman primate species in biomedical research. In this manuscript, we provide a thorough analysis of the three IG loci of the Mmul_10 assembly of rhesus monkey, integrating IMGT previously existing data. Detailed characterization of IG genes includes their localization and position in the loci, the determination of the allele functionality, and the description of the regulatory elements of their promoters as well as the sequences of the conventional recombination signals (RS). This complete annotation of the genomic IG loci of Mmul_10 assembly and the highly detailed IG gene characterization could be used as a model, in additional rhesus monkey assemblies, for the analysis of the IG allelic polymorphism and structural variation, which have been described in rhesus monkeys.
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Chernyshev M, Kaduk M, Corcoran M, Karlsson Hedestam GB. VDJ Gene Usage in IgM Repertoires of Rhesus and Cynomolgus Macaques. Front Immunol 2022; 12:815680. [PMID: 35087534 PMCID: PMC8786739 DOI: 10.3389/fimmu.2021.815680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022] Open
Abstract
Macaques are frequently used to evaluate candidate vaccines and to study infection-induced antibody responses, requiring an improved understanding of their naïve immunoglobulin (IG) repertoires. Baseline gene usage frequencies contextualize studies of antigen-specific immune responses, providing information about how easily one may stimulate a response with a particular VDJ recombination. Studies of human IgM repertoires have shown that IG VDJ gene frequencies vary several orders of magnitude between the most and least utilized genes in a manner that is consistent across many individuals but to date similar analyses are lacking for macaque IgM repertoires. Here, we quantified VDJ gene usage levels in unmutated IgM repertoires of 45 macaques, belonging to two species and four commonly used subgroups: Indian and Chinese origin rhesus macaques and Indonesian and Mauritian origin cynomolgus macaques. We show that VDJ gene frequencies differed greatly between the most and least used genes, with similar overall patterns observed in macaque subgroups and individuals. However, there were also clear differences affecting the use of specific V, D and J genes. Furthermore, in contrast to humans, macaques of both species utilized IGHV4 family genes to a much higher extent and showed evidence of evolutionary expansion of genes of this family. Finally, we used the results to inform the analysis of a broadly neutralizing HIV-1 antibody elicited in SHIV-infected rhesus macaques, RHA1.V2.01, which binds the apex of the Env trimer in a manner that mimics the binding mode of PGT145. We discuss the likelihood that similar antibodies could be elicited in different macaque subgroups.
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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].
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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
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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.
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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
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36
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Derking R, Sanders RW. Structure-guided envelope trimer design in HIV-1 vaccine development: a narrative review. J Int AIDS Soc 2021; 24 Suppl 7:e25797. [PMID: 34806305 PMCID: PMC8606863 DOI: 10.1002/jia2.25797] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The development of a human immunodeficiency virus 1 (HIV-1) vaccine remains a formidable challenge. An effective vaccine likely requires the induction of broadly neutralizing antibodies (bNAbs), which likely involves the use of native-like HIV-1 envelope (Env) trimers at some or all stages of vaccination. Development of such trimers has been very difficult, but much progress has been made in the past decade, starting with the BG505 SOSIP trimer, elucidation of its atomic structure and implementing subsequent design iterations. This progress facilitated understanding the weaknesses of the Env trimer, fuelled structure-guided HIV-1 vaccine design and assisted in the development of new vaccine designs. This review summarizes the relevant literature focusing on studies using structural biology to reveal and define HIV-1 Env sites of vulnerability; to improve Env trimers, by creating more stable versions; understanding antibody responses in preclinical vaccination studies at the atomic level; understanding the glycan shield; and to improve "on-target" antibody responses versus "off-target" responses. METHODS The authors conducted a narrative review of recently published articles that made a major contribution to HIV-1 structural biology and vaccine design efforts between the years 2000 and 2021. DISCUSSION The field of structural biology is evolving at an unprecedented pace, where cryo-electron microscopy (cryo-EM) and X-ray crystallography provide complementary information. Resolving protein structures is necessary for defining which Env surfaces are accessible for the immune system and can be targeted by neutralizing antibodies. Recently developed techniques, such as electron microscopy-based polyclonal epitope mapping (EMPEM) are revolutionizing the way we are analysing immune responses and shed light on the immunodominant targets on new vaccine immunogens. Such information accelerates iterative vaccine design; for example, by reducing undesirable off-target responses, while improving immunogens to drive the more desirable on-target responses. CONCLUSIONS Resolving high-resolution structures of the HIV-1 Env trimer was instrumental in understanding and improving recombinant HIV-1 Env trimers that mimic the structure of viral HIV-1 Env spikes. Newly emerging techniques in structural biology are aiding vaccine design efforts and improving immunogens. The role of structural biology in HIV-1 vaccine design has indeed become very prominent and is unlikely to diminish any time soon.
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Affiliation(s)
- Ronald Derking
- Department of Medical MicrobiologyAmsterdam Infection & Immunity InstituteAmsterdam UMC, AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Rogier W. Sanders
- Department of Medical MicrobiologyAmsterdam Infection & Immunity InstituteAmsterdam UMC, AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Microbiology and ImmunologyWeill Medical College of Cornell UniversityNew YorkNew YorkUSA
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Kealy L, Good-Jacobson KL. Advances in understanding the formation and fate of B-cell memory in response to immunization or infection. OXFORD OPEN IMMUNOLOGY 2021; 2:iqab018. [PMID: 36845573 PMCID: PMC8499879 DOI: 10.1093/oxfimm/iqab018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/06/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023] Open
Abstract
Immunological memory has the potential to provide lifelong protection against recurrent infections. As such, it has been crucial to the success of vaccines. Yet, the recent pandemic has illuminated key gaps in our knowledge related to the factors influencing effective memory formation and the inability to predict the longevity of immune protection. In recent decades, researchers have acquired a number of novel and powerful tools with which to study the factors underpinning humoral memory. These tools have been used to study the B-cell fate decisions that occur within the germinal centre (GC), a site where responding B cells undergo affinity maturation and are one of the major routes for memory B cell and high-affinity long-lived plasma cell formation. The advent of single-cell sequencing technology has provided an enhanced resolution for studying fate decisions within the GC and cutting-edge techniques have enabled researchers to model this reaction with more accuracy both in vitro and in silico. Moreover, modern approaches to studying memory B cells have allowed us to gain a better appreciation for the heterogeneity and adaptability of this vital class of B cells. Together, these studies have facilitated important breakthroughs in our understanding of how these systems operate to ensure a successful immune response. In this review, we describe recent advances in the field of GC and memory B-cell biology in order to provide insight into how humoral memory is formed, as well as the potential for generating lasting immunity to novel pathogens such as severe acute respiratory syndrome coronavirus 2.
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Affiliation(s)
- Liam Kealy
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia,Correspondence address. Department of Biochemistry and Molecular Biology, Monash University, Ground floor reception, 23 Innovation Walk (Bldg 77), Clayton, Victoria 3800 Australia. Tel: (+613) 990-29510; E-mail: ; Twitter: @KimLJacobson
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38
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Parker Miller E, Finkelstein MT, Erdman MC, Seth PC, Fera D. A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target. Viruses 2021; 13:v13091774. [PMID: 34578355 PMCID: PMC8472920 DOI: 10.3390/v13091774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/29/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Antibodies that can neutralize diverse HIV-1 strains develop in ~10–20% of HIV-1 infected individuals, and their elicitation is a goal of vaccine design. Such antibodies can also serve as therapeutics for those who have already been infected with the virus. Structural characterizations of broadly reactive antibodies in complex with the HIV-1 spike indicate that there are a limited number of sites of vulnerability on the spike. Analysis of their structures can help reveal commonalities that would be useful in vaccine design and provide insights on combinations of antibodies that can be used to minimize the incidence of viral resistance mutations. In this review, we give an update on recent structures determined of the spike in complex with broadly neutralizing antibodies in the context of all epitopes on the HIV-1 spike identified to date.
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39
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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.
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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
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van Schooten J, van Haaren MM, Li H, McCoy LE, Havenar-Daughton C, Cottrell CA, Burger JA, van der Woude P, Helgers LC, Tomris I, Labranche CC, Montefiori DC, Ward AB, Burton DR, Moore JP, Sanders RW, Crotty S, Shaw GM, van Gils MJ. Antibody responses induced by SHIV infection are more focused than those induced by soluble native HIV-1 envelope trimers in non-human primates. PLoS Pathog 2021; 17:e1009736. [PMID: 34432859 PMCID: PMC8423243 DOI: 10.1371/journal.ppat.1009736] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/07/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
The development of an effective human immunodeficiency virus (HIV-1) vaccine is a high global health priority. Soluble native-like HIV-1 envelope glycoprotein trimers (Env), including those based on the SOSIP design, have shown promise as vaccine candidates by inducing neutralizing antibody responses against the autologous virus in animal models. However, to overcome HIV-1's extreme diversity a vaccine needs to induce broadly neutralizing antibodies (bNAbs). Such bNAbs can protect non-human primates (NHPs) and humans from infection. The prototypic BG505 SOSIP.664 immunogen is based on the BG505 env sequence isolated from an HIV-1-infected infant from Kenya who developed a bNAb response. Studying bNAb development during natural HIV-1 infection can inform vaccine design, however, it is unclear to what extent vaccine-induced antibody responses to Env are comparable to those induced by natural infection. Here, we compared Env antibody responses in BG505 SOSIP-immunized NHPs with those in BG505 SHIV-infected NHPs, by analyzing monoclonal antibodies (mAbs). We observed three major differences between BG505 SOSIP immunization and BG505 SHIV infection. First, SHIV infection resulted in more clonal expansion and less antibody diversity compared to SOSIP immunization, likely because of higher and/or prolonged antigenic stimulation and increased antigen diversity during infection. Second, while we retrieved comparatively fewer neutralizing mAbs (NAbs) from SOSIP-immunized animals, these NAbs targeted more diverse epitopes compared to NAbs from SHIV-infected animals. However, none of the NAbs, either elicited by vaccination or infection, showed any breadth. Finally, SOSIP immunization elicited antibodies against the base of the trimer, while infection did not, consistent with the base being placed onto the virus membrane in the latter setting. Together these data provide new insights into the antibody response against BG505 Env during infection and immunization and limitations that need to be overcome to induce better responses after vaccination.
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Affiliation(s)
- Jelle van Schooten
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marlies M. van Haaren
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Laura E. McCoy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Judith A. Burger
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Patricia van der Woude
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Leanne C. Helgers
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ilhan Tomris
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Celia C. Labranche
- Laboratory for AIDS Vaccine Research and Development, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Laboratory for AIDS Vaccine Research and Development, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative—Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, California, United States of America
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative—Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, California, United States of America
- Center for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - George M. Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, The Netherlands
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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.
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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.
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42
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Williams WB, Meyerhoff RR, Edwards RJ, Li H, Manne K, Nicely NI, Henderson R, Zhou Y, Janowska K, Mansouri K, Gobeil S, Evangelous T, Hora B, Berry M, Abuahmad AY, Sprenz J, Deyton M, Stalls V, Kopp M, Hsu AL, Borgnia MJ, Stewart-Jones GBE, Lee MS, Bronkema N, Moody MA, Wiehe K, Bradley T, Alam SM, Parks RJ, Foulger A, Oguin T, Sempowski GD, Bonsignori M, LaBranche CC, Montefiori DC, Seaman M, Santra S, Perfect J, Francica JR, Lynn GM, Aussedat B, Walkowicz WE, Laga R, Kelsoe G, Saunders KO, Fera D, Kwong PD, Seder RA, Bartesaghi A, Shaw GM, Acharya P, Haynes BF. Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell 2021; 184:2955-2972.e25. [PMID: 34019795 PMCID: PMC8135257 DOI: 10.1016/j.cell.2021.04.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/22/2021] [Accepted: 04/23/2021] [Indexed: 01/03/2023]
Abstract
Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA.
| | - R Ryan Meyerhoff
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - R J Edwards
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | | | | | | | | | - Bhavna Hora
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | | | | | | | | | - Megan Kopp
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | | | - Matthew S Lee
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Naomi Bronkema
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | | | - Thomas Oguin
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Michael Seaman
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - John Perfect
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - Geoffrey M Lynn
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Avidea Technologies, Inc., Baltimore, MD, USA
| | | | | | - Richard Laga
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27705, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA.
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43
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Li H, Wang S, Lee FH, Roark RS, Murphy AI, Smith J, Zhao C, Rando J, Chohan N, Ding Y, Kim E, Lindemuth E, Bar KJ, Pandrea I, Apetrei C, Keele BF, Lifson JD, Lewis MG, Denny TN, Haynes BF, Hahn BH, Shaw GM. New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure. J Virol 2021; 95:JVI.00071-21. [PMID: 33658341 PMCID: PMC8139694 DOI: 10.1128/jvi.00071-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
Previously, we showed that substitution of HIV-1 Env residue 375-Ser by bulky aromatic residues enhances binding to rhesus CD4 and enables primary HIV-1 Envs to support efficient replication as simian-human immunodeficiency virus (SHIV) chimeras in rhesus macaques (RMs). Here, we test this design strategy more broadly by constructing SHIVs containing ten primary Envs corresponding to HIV-1 subtypes A, B, C, AE and AG. All ten SHIVs bearing wildtype Env375 residues replicated efficiently in human CD4+ T cells, but only one replicated efficiently in primary rhesus cells. This was a subtype AE SHIV that naturally contained His at Env375. Replacement of wildtype Env375 residues by Trp, Tyr, Phe or His in the other nine SHIVs led to efficient replication in rhesus CD4+ T cells in vitro and in vivo Nine SHIVs containing optimized Env375 alleles were grown large-scale in primary rhesus CD4+ T cells to serve as challenge stocks in preclinical prevention trials. These virus stocks were genetically homogeneous, native-like in Env antigenicity and tier-2 neutralization sensitivity, and transmissible by rectal, vaginal, penile, oral or intravenous routes. To facilitate future SHIV constructions, we engineered a simplified second-generation design scheme and validated it in RMs. Overall, our findings demonstrate that SHIVs bearing primary Envs with bulky aromatic substitutions at Env375 consistently replicate in RMs, recapitulating many features of HIV-1 infection in humans. Such SHIVs are efficiently transmitted by mucosal routes common to HIV-1 infection and can be used to test vaccine efficacy in preclinical monkey trials.ImportanceSHIV infection of Indian rhesus macaques is an important animal model for studying HIV-1 transmission, prevention, immunopathogenesis and cure. Such research is timely, given recent progress with active and passive immunization and novel approaches to HIV-1 cure. Given the multifaceted roles of HIV-1 Env in cell tropism and virus entry, and as a target for neutralizing and non-neutralizing antibodies, Envs selected for SHIV construction are of paramount importance. Until recently, it has been impossible to strategically design SHIVs bearing clinically relevant Envs that replicate consistently in monkeys. This changed with the discovery that bulky aromatic substitutions at residue Env375 confer enhanced affinity to rhesus CD4. Here, we show that 10 new SHIVs bearing primary HIV-1 Envs with residue 375 substitutions replicated efficiently in RMs and could be transmitted efficiently across rectal, vaginal, penile and oral mucosa. These findings suggest an expanded role for SHIVs as a model of HIV-1 infection.
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Affiliation(s)
- Hui Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shuyi Wang
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fang-Hua Lee
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ryan S Roark
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alex I Murphy
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jessica Smith
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chengyan Zhao
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Juliette Rando
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Neha Chohan
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yu Ding
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eunlim Kim
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emily Lindemuth
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katharine J Bar
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ivona Pandrea
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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44
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Landais E, Sok D. Nature or nurture: Factors that influence bnAb development. Cell Host Microbe 2021; 29:540-542. [PMID: 33857415 DOI: 10.1016/j.chom.2021.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The stochastic development of broadly neutralizing antibodies (bnAbs) to HIV-1 is influenced by complex viral and host interactions. In this issue of Cell Host & Microbe, Townsley et al. reveal that early B cell and virus interactions during acute infection are predictive for developing bnAb responses later in infection.
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Affiliation(s)
- Elise Landais
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI, New York, NY 10004, USA; Department of Immunology and Microbiology, 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.
| | - Devin Sok
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI, New York, NY 10004, USA; Department of Immunology and Microbiology, 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.
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45
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Mu Z, Haynes BF, Cain DW. HIV mRNA Vaccines-Progress and Future Paths. Vaccines (Basel) 2021; 9:134. [PMID: 33562203 PMCID: PMC7915550 DOI: 10.3390/vaccines9020134] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
The SARS-CoV-2 pandemic introduced the world to a new type of vaccine based on mRNA encapsulated in lipid nanoparticles (LNPs). Instead of delivering antigenic proteins directly, an mRNA-based vaccine relies on the host's cells to manufacture protein immunogens which, in turn, are targets for antibody and cytotoxic T cell responses. mRNA-based vaccines have been the subject of research for over three decades as a platform to protect against or treat a variety of cancers, amyloidosis and infectious diseases. In this review, we discuss mRNA-based approaches for the generation of prophylactic and therapeutic vaccines to HIV. We examine the special immunological hurdles for a vaccine to elicit broadly neutralizing antibodies and effective T cell responses to HIV. Lastly, we outline an mRNA-based HIV vaccination strategy based on the immunobiology of broadly neutralizing antibody development.
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Affiliation(s)
- Zekun Mu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; (Z.M.); (B.F.H.)
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; (Z.M.); (B.F.H.)
- Department of Immunology, 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; (Z.M.); (B.F.H.)
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