1
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Koornneef A, Vanshylla K, Hardenberg G, Rutten L, Strokappe NM, Tolboom J, Vreugdenhil J, Boer KFD, Perkasa A, Blokland S, Burger JA, Huang WC, Lovell JF, van Manen D, Sanders RW, Zahn RC, Schuitemaker H, Langedijk JPM, Wegmann F. CoPoP liposomes displaying stabilized clade C HIV-1 Env elicit tier 2 multiclade neutralization in rabbits. Nat Commun 2024; 15:3128. [PMID: 38605096 PMCID: PMC11009251 DOI: 10.1038/s41467-024-47492-1] [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: 09/21/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
One of the strategies towards an effective HIV-1 vaccine is to elicit broadly neutralizing antibody responses that target the high HIV-1 Env diversity. Here, we present an HIV-1 vaccine candidate that consists of cobalt porphyrin-phospholipid (CoPoP) liposomes decorated with repaired and stabilized clade C HIV-1 Env trimers in a prefusion conformation. These particles exhibit high HIV-1 Env trimer decoration, serum stability and bind broadly neutralizing antibodies. Three sequential immunizations of female rabbits with CoPoP liposomes displaying a different clade C HIV-1 gp140 trimer at each dosing generate high HIV-1 Env-specific antibody responses. Additionally, serum neutralization is detectable against 18 of 20 multiclade tier 2 HIV-1 strains. Furthermore, the peak antibody titers induced by CoPoP liposomes can be recalled by subsequent heterologous immunization with Ad26-encoded membrane-bound stabilized Env antigens. Hence, a CoPoP liposome-based HIV-1 vaccine that can generate cross-clade neutralizing antibody immunity could potentially be a component of an efficacious HIV-1 vaccine.
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Affiliation(s)
| | | | | | - Lucy Rutten
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | | | | | | | | | | | - Sven Blokland
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Wei-Chiao Huang
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | - Jonathan F Lovell
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | | | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Roland C Zahn
- Janssen Vaccines & Prevention, Leiden, The Netherlands
| | | | - Johannes P M Langedijk
- Janssen Vaccines & Prevention, Leiden, The Netherlands.
- ForgeBio, Amsterdam, The Netherlands.
| | - Frank Wegmann
- Janssen Vaccines & Prevention, Leiden, The Netherlands.
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2
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Éliás S, Wrzodek C, Deane CM, Tissot AC, Klostermann S, Ros F. Prediction of polyspecificity from antibody sequence data by machine learning. FRONTIERS IN BIOINFORMATICS 2024; 3:1286883. [PMID: 38651055 PMCID: PMC11033685 DOI: 10.3389/fbinf.2023.1286883] [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: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 04/25/2024] Open
Abstract
Antibodies are generated with great diversity in nature resulting in a set of molecules, each optimized to bind a specific target. Taking advantage of their diversity and specificity, antibodies make up for a large part of recently developed biologic drugs. For therapeutic use antibodies need to fulfill several criteria to be safe and efficient. Polyspecific antibodies can bind structurally unrelated molecules in addition to their main target, which can lead to side effects and decreased efficacy in a therapeutic setting, for example via reduction of effective drug levels. Therefore, we created a neural-network-based model to predict polyspecificity of antibodies using the heavy chain variable region sequence as input. We devised a strategy for enriching antibodies from an immunization campaign either for antigen-specific or polyspecific binding properties, followed by generation of a large sequencing data set for training and cross-validation of the model. We identified important physico-chemical features influencing polyspecificity by investigating the behaviour of this model. This work is a machine-learning-based approach to polyspecificity prediction and, besides increasing our understanding of polyspecificity, it might contribute to therapeutic antibody development.
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Affiliation(s)
- Szabolcs Éliás
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Clemens Wrzodek
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Alain C. Tissot
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Stefan Klostermann
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Francesca Ros
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
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3
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Li W, Lin H, Huang Z, Xie S, Zhou Y, Gong R, Jiang Q, Xiang C, Huang J. DOTAD: A Database of Therapeutic Antibody Developability. Interdiscip Sci 2024:10.1007/s12539-024-00613-2. [PMID: 38530613 DOI: 10.1007/s12539-024-00613-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 03/28/2024]
Abstract
The development of therapeutic antibodies is an important aspect of new drug discovery pipelines. The assessment of an antibody's developability-its suitability for large-scale production and therapeutic use-is a particularly important step in this process. Given that experimental assays to assess antibody developability in large scale are expensive and time-consuming, computational methods have been a more efficient alternative. However, the antibody research community faces significant challenges due to the scarcity of readily accessible data on antibody developability, which is essential for training and validating computational models. To address this gap, DOTAD (Database Of Therapeutic Antibody Developability) has been built as the first database dedicated exclusively to the curation of therapeutic antibody developability information. DOTAD aggregates all available therapeutic antibody sequence data along with various developability metrics from the scientific literature, offering researchers a robust platform for data storage, retrieval, exploration, and downloading. In addition to serving as a comprehensive repository, DOTAD enhances its utility by integrating a web-based interface that features state-of-the-art tools for the assessment of antibody developability. This ensures that users not only have access to critical data but also have the convenience of analyzing and interpreting this information. The DOTAD database represents a valuable resource for the scientific community, facilitating the advancement of therapeutic antibody research. It is freely accessible at http://i.uestc.edu.cn/DOTAD/ , providing an open data platform that supports the continuous growth and evolution of computational methods in the field of antibody development.
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Affiliation(s)
- Wenzhen Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Hongyan Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Ziru Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Shiyang Xie
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yuwei Zhou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Rong Gong
- School of Computer Science and Technology, Aba Teachers University, Aba, 623002, China
| | - Qianhu Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - ChangCheng Xiang
- School of Computer Science and Technology, Aba Teachers University, Aba, 623002, China.
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China.
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, 611844, China.
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4
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Makowski EK, Wang T, Zupancic JM, Huang J, Wu L, Schardt JS, De Groot AS, Elkins SL, Martin WD, Tessier PM. Optimization of therapeutic antibodies for reduced self-association and non-specific binding via interpretable machine learning. Nat Biomed Eng 2024; 8:45-56. [PMID: 37666923 PMCID: PMC10842909 DOI: 10.1038/s41551-023-01074-6] [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: 10/21/2022] [Accepted: 06/29/2023] [Indexed: 09/06/2023]
Abstract
Antibody development, delivery, and efficacy are influenced by antibody-antigen affinity interactions, off-target interactions that reduce antibody bioavailability and pharmacokinetics, and repulsive self-interactions that increase the stability of concentrated antibody formulations and reduce their corresponding viscosity. Yet identifying antibody variants with optimal combinations of these three types of interactions is challenging. Here we show that interpretable machine-learning classifiers, leveraging antibody structural features descriptive of their variable regions and trained on experimental data for a panel of 80 clinical-stage monoclonal antibodies, can identify antibodies with optimal combinations of low off-target binding in a common physiological-solution condition and low self-association in a common antibody-formulation condition. For three clinical-stage antibodies with suboptimal combinations of off-target binding and self-association, the classifiers predicted variable-region mutations that optimized non-affinity interactions while maintaining high-affinity antibody-antigen interactions. Interpretable machine-learning models may facilitate the optimization of antibody candidates for therapeutic applications.
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Affiliation(s)
- Emily K Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tiexin Wang
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer M Zupancic
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jie Huang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Peter M Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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5
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Lecerf M, Lacombe RV, Dimitrov JD. Polyreactivity of antibodies from different B-cell subpopulations is determined by distinct sequence patterns of variable region. Front Immunol 2023; 14:1266668. [PMID: 38077343 PMCID: PMC10710144 DOI: 10.3389/fimmu.2023.1266668] [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: 07/25/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023] Open
Abstract
An antibody molecule that can bind to multiple distinct antigens is defined as polyreactive. In the present study, we performed statistical analyses to assess sequence correlates of polyreactivity of >600 antibodies cloned from different B-cell types of healthy humans. The data revealed several sequence patterns of variable regions of heavy and light immunoglobulin chains that determine polyreactivity. The most prominent identified patterns were increased number of basic amino acid residues, reduced frequency of acidic residues, increased number of aromatic and hydrophobic residues, and longer length of CDR L1. Importantly, our study revealed that antibodies isolated from different B-cell populations used distinct sequence patterns (or combinations of them) for polyreactive antigen binding. Furthermore, we combined the data from sequence analyses with molecular modeling of selected polyreactive antibodies and demonstrated that human antibodies can use multiple pathways for achieving antigen-binding promiscuity. These data reconcile some contradictions in the literature regarding the determinants of antibody polyreactivity. Moreover, our study demonstrates that the mechanism of polyreactivity of antibodies evolves during immune response and might be tailored to specific functional properties of different B-cell compartments. Finally, these data can be of use for efforts in the development and engineering of therapeutic antibodies.
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Affiliation(s)
| | | | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
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6
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Borowska MT, Boughter CT, Bunker JJ, Guthmiller JJ, Wilson PC, Roux B, Bendelac A, Adams EJ. Biochemical and biophysical characterization of natural polyreactivity in antibodies. Cell Rep 2023; 42:113190. [PMID: 37804505 PMCID: PMC10858392 DOI: 10.1016/j.celrep.2023.113190] [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: 05/05/2023] [Revised: 08/25/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023] Open
Abstract
To become specialized binders, antibodies undergo a process called affinity maturation to maximize their binding affinity. Despite this process, some antibodies retain low-affinity binding to diverse epitopes in a phenomenon called polyreactivity. Here we seek to understand the molecular basis of this polyreactivity in antibodies. Our results highlight that polyreactive antigen-binding fragments (Fabs) bind their targets with low affinities, comparable to T cell receptor recognition of autologous classical major histocompatibility complex. Extensive mutagenic studies find no singular amino acid residue or biochemical property responsible for polyreactive interaction, suggesting that polyreactive antibodies use multiple strategies for engagement. Finally, our crystal structures and all-atom molecular dynamics simulations of polyreactive Fabs show increased rigidity compared to their monoreactive relatives, forming a neutral and accessible platform for diverse antigens to bind. Together, these data support a cooperative strategy of rigid neutrality in establishing the polyreactive status of an antibody molecule.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Jeffrey J Bunker
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
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7
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Molinos-Albert LM, Baquero E, Bouvin-Pley M, Lorin V, Charre C, Planchais C, Dimitrov JD, Monceaux V, Vos M, Hocqueloux L, Berger JL, Seaman MS, Braibant M, Avettand-Fenoël V, Sáez-Cirión A, Mouquet H. Anti-V1/V3-glycan broadly HIV-1 neutralizing antibodies in a post-treatment controller. Cell Host Microbe 2023; 31:1275-1287.e8. [PMID: 37433296 DOI: 10.1016/j.chom.2023.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023]
Abstract
HIV-1 broadly neutralizing antibodies (bNAbs) can decrease viremia but are usually unable to counteract autologous viruses escaping the antibody pressure. Nonetheless, bNAbs may contribute to natural HIV-1 control in individuals off antiretroviral therapy (ART). Here, we describe a bNAb B cell lineage elicited in a post-treatment controller (PTC) that exhibits broad seroneutralization and show that a representative antibody from this lineage, EPTC112, targets a quaternary epitope in the glycan-V3 loop supersite of the HIV-1 envelope glycoprotein. The cryo-EM structure of EPTC112 complexed with soluble BG505 SOSIP.664 envelope trimers revealed interactions with N301- and N156-branched N-glycans and the 324GDIR327 V3 loop motif. Although the sole contemporaneous virus circulating in this PTC was resistant to EPTC112, it was potently neutralized by autologous plasma IgG antibodies. Our findings illuminate how cross-neutralizing antibodies can alter the HIV-1 infection course in PTCs and may control viremia off-ART, supporting their role in functional HIV-1 cure strategies.
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Affiliation(s)
- Luis M Molinos-Albert
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris 75015, France
| | - Eduard Baquero
- NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Université Paris Cité, Institut Pasteur, Paris 75015, France
| | | | - Valérie Lorin
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris 75015, France
| | - Caroline Charre
- Université Cité, Faculté de Médecine, Paris 75014, France; INSERM U1016, CNRS UMR8104, Institut Cochin, Paris 75014, France; AP-HP, Service de Virologie, Hôpital Cochin, Paris 75014, France
| | - Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris 75015, France
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris 75006, France
| | - Valérie Monceaux
- Viral Reservoirs and Immune control Unit, Institut Pasteur, Université Paris Cité, Paris 75015, France; HIV, Inflammation and Persistence Unit, Institut Pasteur, Université Paris Cité, Paris 75015, France
| | - Matthijn Vos
- NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Université Paris Cité, Institut Pasteur, Paris 75015, France
| | - Laurent Hocqueloux
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire d'Orléans La Source, Orléans 45067, France
| | - Jean-Luc Berger
- Department of Internal Medicine, Clinical Immunology and Infectious Diseases, Reims University Hospital, Reims 51100, France
| | | | | | - Véronique Avettand-Fenoël
- Université Cité, Faculté de Médecine, Paris 75014, France; INSERM U1016, CNRS UMR8104, Institut Cochin, Paris 75014, France; AP-HP, Service de Virologie, Hôpital Cochin, Paris 75014, France
| | - Asier Sáez-Cirión
- Viral Reservoirs and Immune control Unit, Institut Pasteur, Université Paris Cité, Paris 75015, France; HIV, Inflammation and Persistence Unit, Institut Pasteur, Université Paris Cité, Paris 75015, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris 75015, France.
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8
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Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
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Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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9
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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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10
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Huhtinen O, Salbo R, Lamminmäki U, Prince S. Selection of biophysically favorable antibody variants using a modified Flp-In CHO mammalian display platform. Front Bioeng Biotechnol 2023; 11:1170081. [PMID: 37229492 PMCID: PMC10203562 DOI: 10.3389/fbioe.2023.1170081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
Mammalian display enables the selection of biophysically favorable antibodies from a large IgG antibody library displayed on the plasma membrane of mammalian cells. We constructed and validated a novel mammalian display platform utilizing the commercially available Flp-In CHO cell line as a starting point. We introduced a single copy of a landing pad for Bxb1 integrase-driven recombinase-mediated cassette exchange into the FRT site of the Flp-In CHO line to facilitate the efficient single-copy integration of an antibody display cassette into the genome of the cell line. We then proceeded to demonstrate the ability of our platform to select biophysically favorable antibodies from a library of 1 × 106 displayed antibodies designed to improve the biophysical properties of bococizumab via randomization of problematic hydrophobic surface residues of the antibody. Enrichment of bococizumab variants via fluorescence-activated cell sorting selections was followed by next generation sequencing and thorough characterization of biophysical properties of 10 bococizumab variants that subsequently allowed attribution of the mutations to the biophysical properties of the antibody variants. The mammalian displayed variants exhibited reduced aggregation propensity and polyreactivity, while critically retaining its target binding thereby demonstrating the utility of this valuable tool.
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Affiliation(s)
- Olli Huhtinen
- Protein and Antibody Engineering, Orion Corporation, Turku, Finland
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Rune Salbo
- Protein and Antibody Engineering, Orion Corporation, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Stuart Prince
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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11
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Wilson A, Manuzak JA, Liang H, Leda AR, Klatt N, Lynch RM. Probiotic Therapy During Vaccination Alters Antibody Response to Simian-Human Immunodeficiency Virus Infection But Not to Commensals. AIDS Res Hum Retroviruses 2023; 39:222-231. [PMID: 36517984 PMCID: PMC10171943 DOI: 10.1089/aid.2022.0123] [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: 12/23/2022] Open
Abstract
The induction of robust circulating antibody titers is a key goal of HIV-1 vaccination. Probiotic supplementation is an established strategy to enhance microbiota and boost antibody responses to vaccines. A recent study tested whether oral probiotics could enhance vaccine-specific mucosal immunity by testing vaccination with and without supplementation in a Rhesus macaque Simian-Human Immunodeficiency Virus challenge model. Although supplementation was not associated with protection, the effects of probiotics on immunity after infection were not examined. To address this question, we measured antibody titers to HIV Env and commensal bacteria in plasma from the vaccination/supplementation time points as well as after Simian-Human Immunodeficiency Virus (SHIV) acquisition. We found that a trend toward lower HIV Env-specific titers in the animals given probiotics plus vaccine became greater after SHIV infection. Significantly lower Immunoglobulin (Ig) A titers were observed in animals vaccinated and supplemented compared with vaccine alone due to a delay in antibody kinetics at week 2 postinfection. We observed no difference, however, in titers to commensal bacteria during probiotic supplementation or after SHIV infection. These results suggest that probiotic supplementation may be a strategy for reducing IgA-specific HIV antibodies in the plasma, a correlate associated with increased HIV infection in the RV144 clinical trial.
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Affiliation(s)
- Andrew Wilson
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia, USA
| | - Jennifer A. Manuzak
- Division of Immunology, Tulane National Primate Research Center, Covington, Louisiana, USA
| | - Hua Liang
- Department of Statistics, George Washington University, Washington, District of Columbia, USA
| | - Ana R. Leda
- Department of Microbiology and Immunology, Scripps Biomedical Research, University of Florida, Jupiter, Florida, USA
| | - Nichole Klatt
- Department of Surgery, Division of Surgical Outcomes and Precision Medicine Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rebecca M. Lynch
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, District of Columbia, USA
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12
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Ávila-Nieto C, Pedreño-López N, Mitjà O, Clotet B, Blanco J, Carrillo J. Syphilis vaccine: challenges, controversies and opportunities. Front Immunol 2023; 14:1126170. [PMID: 37090699 PMCID: PMC10118025 DOI: 10.3389/fimmu.2023.1126170] [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: 12/17/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Syphilis is a sexually or vertically (mother to fetus) transmitted disease caused by the infection of Treponema pallidum subspecie pallidum (TPA). The incidence of syphilis has increased over the past years despite the fact that this bacterium is an obligate human pathogen, the infection route is well known, and the disease can be successfully treated with penicillin. As complementary measures to preventive campaigns and early treatment of infected individuals, development of a syphilis vaccine may be crucial for controlling disease spread and/or severity, particularly in countries where the effectiveness of the aforementioned measures is limited. In the last century, several vaccine prototypes have been tested in preclinical studies, mainly in rabbits. While none of them provided protection against infection, some prototypes prevented bacteria from disseminating to distal organs, attenuated lesion development, and accelerated their healing. In spite of these promising results, there is still some controversy regarding the identification of vaccine candidates and the characteristics of a syphilis-protective immune response. In this review, we describe what is known about TPA immune response, and the main mechanisms used by this pathogen to evade it. Moreover, we emphasize the importance of integrating this knowledge, in conjunction with the characterization of outer membrane proteins (OMPs), to expedite the development of a syphilis vaccine that can protect against TPA infection.
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Affiliation(s)
- Carlos Ávila-Nieto
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Autonomous University of Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | | | - Oriol Mitjà
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Department, Germans Trias i Pujol Hospital, Badalona, Spain
- Fight Infections Foundation, Germans Trias i Pujol Hospital, Badalona, Catalonia, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Catalonia, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Fight Infections Foundation, Germans Trias i Pujol Hospital, Badalona, Catalonia, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Catalonia, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- CIBERINFEC, Instituto de Salut Carlos III (ISCIII), Madrid, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Catalonia, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- CIBERINFEC, Instituto de Salut Carlos III (ISCIII), Madrid, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- CIBERINFEC, Instituto de Salut Carlos III (ISCIII), Madrid, Spain
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13
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Scheid JF, Eraslan B, Hudak A, Brown EM, Sergio D, Delorey TM, Phillips D, Lefkovith A, Jess AT, Duck LW, Elson CO, Vlamakis H, Plichta DR, Deguine J, Ananthakrishnan AN, Graham DB, Regev A, Xavier RJ. Remodeling of colon plasma cell repertoire within ulcerative colitis patients. J Exp Med 2023; 220:e20220538. [PMID: 36752797 PMCID: PMC9949229 DOI: 10.1084/jem.20220538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 10/03/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
Plasma cells (PCs) constitute a significant fraction of colonic mucosal cells and contribute to inflammatory infiltrates in ulcerative colitis (UC). While gut PCs secrete bacteria-targeting IgA antibodies, their role in UC pathogenesis is unknown. We performed single-cell V(D)J- and RNA-seq on sorted B cells from the colon of healthy individuals and patients with UC. A large fraction of B cell clones is shared between different colon regions, but inflammation in UC broadly disrupts this landscape, causing transcriptomic changes characterized by an increase in the unfolded protein response (UPR) and antigen presentation genes, clonal expansion, and isotype skewing from IgA1 and IgA2 to IgG1. We also directly expressed and assessed the specificity of 152 mAbs from expanded PC clones. These mAbs show low polyreactivity and autoreactivity and instead target both shared bacterial antigens and specific bacterial strains. Altogether, our results characterize the microbiome-specific colon PC response and how its disruption might contribute to inflammation in UC.
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Affiliation(s)
- Johannes F. Scheid
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Basak Eraslan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew Hudak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric M. Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dallis Sergio
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Alison T. Jess
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lennard W. Duck
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Charles O. Elson
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Ashwin N. Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel B. Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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14
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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: 80] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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15
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de Carvalho RVH, Ersching J, Barbulescu A, Hobbs A, Castro TBR, Mesin L, Jacobsen JT, Phillips BK, Hoffmann HH, Parsa R, Canesso MCC, Nowosad CR, Feng A, Leist SR, Baric RS, Yang E, Utz PJ, Victora GD. Clonal replacement sustains long-lived germinal centers primed by respiratory viruses. Cell 2023; 186:131-146.e13. [PMID: 36565697 PMCID: PMC9870066 DOI: 10.1016/j.cell.2022.11.031] [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: 04/13/2022] [Revised: 09/12/2022] [Accepted: 11/28/2022] [Indexed: 12/25/2022]
Abstract
Germinal centers (GCs) form in secondary lymphoid organs in response to infection and immunization and are the source of affinity-matured B cells. The duration of GC reactions spans a wide range, and long-lasting GCs (LLGCs) are potentially a source of highly mutated B cells. We show that rather than consisting of continuously evolving B cell clones, LLGCs elicited by influenza virus or SARS-CoV-2 infection in mice are sustained by progressive replacement of founder clones by naive-derived invader B cells that do not detectably bind viral antigens. Rare founder clones that resist replacement for long periods are enriched in clones with heavily mutated immunoglobulins, including some with very high affinity for antigen, that can be recalled by boosting. Our findings reveal underappreciated aspects of the biology of LLGCs generated by respiratory virus infection and identify clonal replacement as a potential constraint on the development of highly mutated antibodies within these structures.
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Affiliation(s)
| | - Jonatan Ersching
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Alexandru Barbulescu
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Alvaro Hobbs
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Tiago B R Castro
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA; Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Brooke K Phillips
- Rutgers Robert Wood Johnson Medical School and Princeton University MD/PhD Program, Piscataway, NJ, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Roham Parsa
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Maria Cecilia C Canesso
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA; Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Carla R Nowosad
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA; Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily Yang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - P J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
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16
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Jain T, Boland T, Vásquez M. Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches. MAbs 2023; 15:2200540. [PMID: 37072706 PMCID: PMC10114995 DOI: 10.1080/19420862.2023.2200540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
With the growing significance of antibodies as a therapeutic class, identifying developability risks early during development is of paramount importance. Several high-throughput in vitro assays and in silico approaches have been proposed to de-risk antibodies during early stages of the discovery process. In this review, we have compiled and collectively analyzed published experimental assessments and computational metrics for clinical antibodies. We show that flags assigned based on in vitro measurements of polyspecificity and hydrophobicity are more predictive of clinical progression than their in silico counterparts. Additionally, we assessed the performance of published models for developability predictions on molecules not used during model training. We find that generalization to data outside of those used for training remains a challenge for models. Finally, we highlight the challenges of reproducibility in computed metrics arising from differences in homology modeling, in vitro assessments relying on complex reagents, as well as curation of experimental data often used to assess the utility of high-throughput approaches. We end with a recommendation to enable assay reproducibility by inclusion of controls with disclosed sequences, as well as sharing of structural models to enable the critical assessment and improvement of in silico predictions.
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Affiliation(s)
| | - Todd Boland
- Computational Biology, Adimab LLC, Lebanon, NH, USA
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17
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Fernández-Quintero ML, Ljungars A, Waibl F, Greiff V, Andersen JT, Gjølberg TT, Jenkins TP, Voldborg BG, Grav LM, Kumar S, Georges G, Kettenberger H, Liedl KR, Tessier PM, McCafferty J, Laustsen AH. Assessing developability early in the discovery process for novel biologics. MAbs 2023; 15:2171248. [PMID: 36823021 PMCID: PMC9980699 DOI: 10.1080/19420862.2023.2171248] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/18/2023] [Indexed: 02/25/2023] Open
Abstract
Beyond potency, a good developability profile is a key attribute of a biological drug. Selecting and screening for such attributes early in the drug development process can save resources and avoid costly late-stage failures. Here, we review some of the most important developability properties that can be assessed early on for biologics. These include the influence of the source of the biologic, its biophysical and pharmacokinetic properties, and how well it can be expressed recombinantly. We furthermore present in silico, in vitro, and in vivo methods and techniques that can be exploited at different stages of the discovery process to identify molecules with liabilities and thereby facilitate the selection of the most optimal drug leads. Finally, we reflect on the most relevant developability parameters for injectable versus orally delivered biologics and provide an outlook toward what general trends are expected to rise in the development of biologics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, University of Oslo, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine and Department of Pharmacology, University of Oslo, Oslo, Norway
| | | | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjørn Gunnar Voldborg
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lise Marie Grav
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Peter M. Tessier
- Department of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - John McCafferty
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Maxion Therapeutics, Babraham Research Campus, Cambridge, UK
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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18
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Harvey EP, Shin JE, Skiba MA, Nemeth GR, Hurley JD, Wellner A, Shaw AY, Miranda VG, Min JK, Liu CC, Marks DS, Kruse AC. An in silico method to assess antibody fragment polyreactivity. Nat Commun 2022; 13:7554. [PMID: 36477674 PMCID: PMC9729196 DOI: 10.1038/s41467-022-35276-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Antibodies are essential biological research tools and important therapeutic agents, but some exhibit non-specific binding to off-target proteins and other biomolecules. Such polyreactive antibodies compromise screening pipelines, lead to incorrect and irreproducible experimental results, and are generally intractable for clinical development. Here, we design a set of experiments using a diverse naïve synthetic camelid antibody fragment (nanobody) library to enable machine learning models to accurately assess polyreactivity from protein sequence (AUC > 0.8). Moreover, our models provide quantitative scoring metrics that predict the effect of amino acid substitutions on polyreactivity. We experimentally test our models' performance on three independent nanobody scaffolds, where over 90% of predicted substitutions successfully reduced polyreactivity. Importantly, the models allow us to diminish the polyreactivity of an angiotensin II type I receptor antagonist nanobody, without compromising its functional properties. We provide a companion web-server that offers a straightforward means of predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.
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Affiliation(s)
- Edward P Harvey
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jung-Eun Shin
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Genevieve R Nemeth
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph D Hurley
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Alon Wellner
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, 92692, USA
| | - Ada Y Shaw
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Victor G Miranda
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph K Min
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Chang C Liu
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, 92692, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
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19
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Jaiswal D, Verma S, Nair DT, Salunke DM. Antibody multispecificity: A necessary evil? Mol Immunol 2022; 152:153-161. [DOI: 10.1016/j.molimm.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
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20
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Li X, Liao D, Li Z, Li J, Diaz M, Verkoczy L, Gao F. Autoreactivity and broad neutralization of antibodies against HIV-1 are governed by distinct mutations: Implications for vaccine design strategies. Front Immunol 2022; 13:977630. [PMID: 36479128 PMCID: PMC9720396 DOI: 10.3389/fimmu.2022.977630] [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: 06/24/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Many of the best HIV-1 broadly neutralizing antibodies (bnAbs) known have poly-/autoreactive features that disfavor normal B cell development and maturation, posing a major hurdle in developing an effective HIV-1 vaccine. Key to resolving this problem is to understand if, and to what extent, neutralization breadth-conferring mutations acquired by bnAbs contribute to their autoreactivity. Here, we back-mutated all known changes made by a prototype CD4 binding site-directed bnAb lineage, CH103-106, during its later maturation steps. Strikingly, of 29 mutations examined, only four were crucial for increased autoreactivity, with minimal or no impact on neutralization. Furthermore, three of these residues were clustered in the heavy chain complementarity-determining region 2 (HCDR2). Our results demonstrate that broad neutralization activity and autoreactivity in the CH103-106 bnAb lineage can be governed by a few, distinct mutations during maturation. This provides strong rationale for developing immunogens that favor bnAb lineages bearing "neutralization-only" mutations into current HIV-1 vaccine designs.
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Affiliation(s)
- Xiaojun Li
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Dongmei Liao
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Zhengyang Li
- School of Life Sciences, Fudan University, Shanghai, China
| | - Jixi Li
- School of Life Sciences, Fudan University, Shanghai, China
| | - Marilyn Diaz
- Applied Biomedical Science Institute, San Diego, CA, United States
| | - Laurent Verkoczy
- Applied Biomedical Science Institute, San Diego, CA, United States
| | - Feng Gao
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
- Institute of Molecular and Medical Virology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdongg, China
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21
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Young C, Lau AWY, Burnett DL. B cells in the balance: Offsetting self-reactivity avoidance with protection against foreign. Front Immunol 2022; 13:951385. [PMID: 35967439 PMCID: PMC9364820 DOI: 10.3389/fimmu.2022.951385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies are theoretically limitless in their diversity and specificity to foreign antigens; however they are constrained by the need to avoid binding to self. Germinal centers (GC) allow diversification and maturation of the antibody response towards the foreign antigen. While self-tolerance mechanisms controlling self-reactivity during B cell maturation are well recognized, the mechanisms by which GCs balance self-tolerance and foreign binding especially in the face of cross-reactivity between self and foreign, remain much less well defined. In this review we explore the extent to which GC self-tolerance restricts affinity maturation. We present studies suggesting that the outcome is situationally dependent, affected by affinity and avidity to self-antigen, and the extent to which self-binding and foreign-binding are interdependent. While auto-reactive GC B cells can mutate away from self while maturing towards the foreign antigen, if no mutational trajectories allow for self-reactive redemption, self-tolerance prevails and GC responses to the foreign pathogen are restricted, except when self-tolerance checkpoints are relaxed. Finally, we consider whether polyreactivity is subject to the same level of restriction in GC responses, especially if polyreactivity is linked to an increase in foreign protection, as occurs in certain broadly neutralizing antibodies. Overall, the outcomes for GC B cells that bind self-antigen can range from redemption, transient relaxation in self-tolerance or restriction of the antibody response to the foreign pathogen.
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Affiliation(s)
- Clara Young
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
- *Correspondence: Clara Young, ; Deborah L. Burnett,
| | - Angelica W. Y. Lau
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
| | - Deborah L. Burnett
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
- *Correspondence: Clara Young, ; Deborah L. Burnett,
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22
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Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis. Sci Rep 2022; 12:11876. [PMID: 35831338 PMCID: PMC9279471 DOI: 10.1038/s41598-022-15293-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/22/2022] [Indexed: 11/15/2022] Open
Abstract
B cells play a significant role in established Rheumatoid Arthritis (RA). However, it is unclear to what extent differentiated B cells are present in joint tissue already at the onset of disease. Here, we studied synovial biopsies (n = 8) captured from untreated patients at time of diagnosis. 3414 index-sorted B cells underwent RNA sequencing and paired tissue pieces were subjected to spatial transcriptomics (n = 4). We performed extensive bioinformatics analyses to dissect the local B cell composition. Select plasma cell immunoglobulin sequences were expressed as monoclonal antibodies and tested by ELISA. Memory and plasma cells were found irrespective of autoantibody status of the patients. Double negative memory B cells were prominent, but did not display a distinct transcriptional profile. The tissue architecture implicate both local B cell maturation via T cell help and plasma cell survival niches with a strong CXCL12–CXCR4 axis. The immunoglobulin sequence analyses revealed clonality between the memory B and plasma cell pools further supporting local maturation. One of the plasma cell-derived antibodies displayed citrulline autoreactivity, demonstrating local autoreactive plasma cell differentiation in joint biopsies captured from untreated early RA. Hence, plasma cell niches are not a consequence of chronic inflammation, but are already present at the time of diagnosis.
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23
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Oostindie SC, Lazar GA, Schuurman J, Parren PWHI. Avidity in antibody effector functions and biotherapeutic drug design. Nat Rev Drug Discov 2022; 21:715-735. [PMID: 35790857 PMCID: PMC9255845 DOI: 10.1038/s41573-022-00501-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 12/16/2022]
Abstract
Antibodies are the cardinal effector molecules of the immune system and are being leveraged with enormous success as biotherapeutic drugs. A key part of the adaptive immune response is the production of an epitope-diverse, polyclonal antibody mixture that is capable of neutralizing invading pathogens or disease-causing molecules through binding interference and by mediating humoral and cellular effector functions. Avidity - the accumulated binding strength derived from the affinities of multiple individual non-covalent interactions - is fundamental to virtually all aspects of antibody biology, including antibody-antigen binding, clonal selection and effector functions. The manipulation of antibody avidity has since emerged as an important design principle for enhancing or engineering novel properties in antibody biotherapeutics. In this Review, we describe the multiple levels of avidity interactions that trigger the overall efficacy and control of functional responses in both natural antibody biology and their therapeutic applications. Within this framework, we comprehensively review therapeutic antibody mechanisms of action, with particular emphasis on engineered optimizations and platforms. Overall, we describe how affinity and avidity tuning of engineered antibody formats are enabling a new wave of differentiated antibody drugs with tailored properties and novel functions, promising improved treatment options for a wide variety of diseases.
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Affiliation(s)
- Simone C Oostindie
- Genmab, Utrecht, Netherlands.,Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Greg A Lazar
- Department of Antibody Engineering, Genentech, San Francisco, CA, USA
| | | | - Paul W H I Parren
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands. .,Sparring Bioconsult, Odijk, Netherlands. .,Lava Therapeutics, Utrecht, Netherlands.
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24
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Nguyen K, Alsaati N, Le Coz C, Romberg N. Genetic obstacles to developing and tolerizing human B cells. WIREs Mech Dis 2022; 14:e1554. [DOI: 10.1002/wsbm.1554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Kim Nguyen
- Division of Immunology and Allergy Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Nouf Alsaati
- Division of Immunology and Allergy Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Carole Le Coz
- Division of Immunology and Allergy Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Neil Romberg
- Division of Immunology and Allergy Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Department of Pediatrics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
- Institute for Immunology University of Pennsylvania Philadelphia Pennsylvania USA
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25
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Gupta P, Makowski EK, Kumar S, Zhang Y, Scheer JM, Tessier PM. Antibodies with Weakly Basic Isoelectric Points Minimize Trade-offs between Formulation and Physiological Colloidal Properties. Mol Pharm 2022; 19:775-787. [PMID: 35108018 PMCID: PMC9350878 DOI: 10.1021/acs.molpharmaceut.1c00373] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The widespread interest in antibody therapeutics has led to much focus on identifying antibody candidates with favorable developability properties. In particular, there is broad interest in identifying antibody candidates with highly repulsive self-interactions in standard formulations (e.g., low ionic strength buffers at pH 5-6) for high solubility and low viscosity. Likewise, there is also broad interest in identifying antibody candidates with low levels of non-specific interactions in physiological solution conditions (PBS, pH 7.4) to promote favorable pharmacokinetic properties. To what extent antibodies that possess both highly repulsive self-interactions in standard formulations and weak non-specific interactions in physiological solution conditions can be systematically identified remains unclear and is a potential impediment to successful therapeutic drug development. Here, we evaluate these two properties for 42 IgG1 variants based on the variable fragments (Fvs) from four clinical-stage antibodies and complementarity-determining regions from 10 clinical-stage antibodies. Interestingly, we find that antibodies with the strongest repulsive self-interactions in a standard formulation (pH 6 and 10 mM histidine) display the strongest non-specific interactions in physiological solution conditions. Conversely, antibodies with the weakest non-specific interactions under physiological conditions display the least repulsive self-interactions in standard formulations. This behavior can be largely explained by the antibody isoelectric point, as highly basic antibodies that are highly positively charged under standard formulation conditions (pH 5-6) promote repulsive self-interactions that mediate high colloidal stability but also mediate strong non-specific interactions with negatively charged biomolecules at physiological pH and vice versa for antibodies with negatively charged Fv regions. Therefore, IgG1s with weakly basic isoelectric points between 8 and 8.5 and Fv isoelectric points between 7.5 and 9 typically display the best combinations of strong repulsive self-interactions and weak non-specific interactions. We expect that these findings will improve the identification and engineering of antibody candidates with drug-like biophysical properties.
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Affiliation(s)
- Priyanka Gupta
- Biochemistry and Biophysics Department, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Emily K Makowski
- Department of Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sandeep Kumar
- Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Yulei Zhang
- Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Justin M Scheer
- Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States.,Janssen R&D, South San Francisco, California 94080, United States
| | - Peter M Tessier
- Biochemistry and Biophysics Department, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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26
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Lorin V, Fernández I, Masse-Ranson G, Bouvin-Pley M, Molinos-Albert LM, Planchais C, Hieu T, Péhau-Arnaudet G, Hrebík D, Girelli-Zubani G, Fiquet O, Guivel-Benhassine F, Sanders RW, Walker BD, Schwartz O, Scheid JF, Dimitrov JD, Plevka P, Braibant M, Seaman MS, Bontems F, Di Santo JP, Rey FA, Mouquet H. Epitope convergence of broadly HIV-1 neutralizing IgA and IgG antibody lineages in a viremic controller. J Exp Med 2022; 219:213042. [PMID: 35230385 PMCID: PMC8932546 DOI: 10.1084/jem.20212045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a viremic controller, two of which comprised only IgG+ or IgA+ blood memory B cells; the third combined both IgG and IgA clonal variants. 7-269 bNAb in the IgA-only lineage displayed the highest neutralizing capacity despite limited somatic mutation, and delayed viral rebound in humanized mice. bNAbs in all three lineages targeted the N332 glycan supersite. The 2.8-Å resolution cryo-EM structure of 7-269-BG505 SOSIP.664 complex showed a similar pose as 2G12, on an epitope mainly composed of sugar residues comprising the N332 and N295 glycans. Binding and cryo-EM structural analyses showed that antibodies from the two other lineages interact mostly with glycans N332 and N386. Hence, multiple B cell lineages of IgG and IgA bNAbs focused on a unique HIV-1 site of vulnerability can codevelop in HIV-1 viremic controllers.
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Affiliation(s)
- Valérie Lorin
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Ignacio Fernández
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre national de la recherche scientifique URA3015, Paris, France
| | - Guillemette Masse-Ranson
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Mélanie Bouvin-Pley
- Université de Tours, Institut national de la santé et de la recherche médicale U1259, Tours, France
| | - Luis M Molinos-Albert
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Thierry Hieu
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Gérard Péhau-Arnaudet
- Imagopole, Plate-Forme de Microscopie Ultrastructurale and UMR 3528, Institut Pasteur, Paris, France
| | - Dominik Hrebík
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Giulia Girelli-Zubani
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Oriane Fiquet
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Florence Guivel-Benhassine
- Centre national de la recherche scientifique URA3015, Paris, France.,Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA.,Partners AIDS Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Olivier Schwartz
- Centre national de la recherche scientifique URA3015, Paris, France.,Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Johannes F Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, Institut national de la santé et de la recherche médicale, Sorbonne Université, Université de Paris, Paris, France
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martine Braibant
- Université de Tours, Institut national de la santé et de la recherche médicale U1259, Tours, France
| | | | - François Bontems
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Institut de Chimie des Substances Naturelles, Centre national de la recherche scientifique, Université Paris Saclay, Gif-sur-Yvette, France
| | - James P Di Santo
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Félix A Rey
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre national de la recherche scientifique URA3015, Paris, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
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27
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Timofeeva A, Sedykh S, Nevinsky G. Post-Immune Antibodies in HIV-1 Infection in the Context of Vaccine Development: A Variety of Biological Functions and Catalytic Activities. Vaccines (Basel) 2022; 10:vaccines10030384. [PMID: 35335016 PMCID: PMC8955465 DOI: 10.3390/vaccines10030384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
Unlike many other viruses, HIV-1 is highly variable. The structure of the viral envelope changes as the infection progresses and is one of the biggest obstacles in developing an HIV-1 vaccine. HIV-1 infection can cause the production of various natural autoantibodies, including catalytic antibodies hydrolyzing DNA, myelin basic protein, histones, HIV-integrase, HIV-reverse transcriptase, β-casein, serum albumin, and some other natural substrates. Currently, there are various directions for the development of HIV-1 vaccines: stimulation of the immune response on the mucous membranes; induction of cytotoxic T cells, which lyse infected cells and hold back HIV-infection; immunization with recombinant Env proteins or vectors encoding Env; mRNA-based vaccines and some others. However, despite many attempts to develop an HIV-1 vaccine, none have been successful. Here we review the entire spectrum of antibodies found in HIV-infected patients, including neutralizing antibodies specific to various viral epitopes, as well as antibodies formed against various autoantigens, catalytic antibodies against autoantigens, and some viral proteins. We consider various promising targets for developing a vaccine that will not produce unwanted antibodies in vaccinated patients. In addition, we review common problems in the development of a vaccine against HIV-1.
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Affiliation(s)
- Anna Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (S.S.); (G.N.)
- Correspondence: ; Tel.: +7-91-32-027-154
| | - Sergey Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (S.S.); (G.N.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Georgy Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (S.S.); (G.N.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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28
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Ferrara F, Erasmus MF, D'Angelo S, Leal-Lopes C, Teixeira AA, Choudhary A, Honnen W, Calianese D, Huang D, Peng L, Voss JE, Nemazee D, Burton DR, Pinter A, Bradbury ARM. A pandemic-enabled comparison of discovery platforms demonstrates a naïve antibody library can match the best immune-sourced antibodies. Nat Commun 2022; 13:462. [PMID: 35075126 PMCID: PMC8786865 DOI: 10.1038/s41467-021-27799-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
As a result of the SARS-CoV-2 pandemic numerous scientific groups have generated antibodies against a single target: the CoV-2 spike antigen. This has provided an unprecedented opportunity to compare the efficacy of different methods and the specificities and qualities of the antibodies generated by those methods. Generally, the most potent neutralizing antibodies have been generated from convalescent patients and immunized animals, with non-immune phage libraries usually yielding significantly less potent antibodies. Here, we show that it is possible to generate ultra-potent (IC50 < 2 ng/ml) human neutralizing antibodies directly from a unique semisynthetic naïve antibody library format with affinities, developability properties and neutralization activities comparable to the best from hyperimmune sources. This demonstrates that appropriately designed and constructed naïve antibody libraries can effectively compete with immunization to directly provide therapeutic antibodies against a viral pathogen, without the need for immune sources or downstream optimization. The most potent neutralizing antibodies are typically generated from convalescent patients and immunized animals. Here, the authors show it is possible to generate highly potent human neutralizing antibodies against the SARS-CoV-2 spike protein directly from a semisynthetic naïve antibody library.
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Affiliation(s)
| | | | | | - Camila Leal-Lopes
- Bioscience Division, New Mexico Consortium, Los Alamos, NM, 87544, USA
| | - André A Teixeira
- Bioscience Division, New Mexico Consortium, Los Alamos, NM, 87544, USA
| | - Alok Choudhary
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - William Honnen
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - David Calianese
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - Deli Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Linghan Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Abraham Pinter
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
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29
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Makowski EK, Schardt JS, Tessier PM. Improving antibody drug development using bionanotechnology. Curr Opin Biotechnol 2021; 74:137-145. [PMID: 34890875 DOI: 10.1016/j.copbio.2021.10.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/31/2021] [Indexed: 12/20/2022]
Abstract
Monoclonal antibodies are being used to treat a remarkable breadth of human disorders. Nevertheless, there are several key challenges at the earliest stages of antibody drug development that need to be addressed using simple and widely accessible methods, especially related to generating antibodies against membrane proteins and identifying antibody candidates with drug-like biophysical properties (high solubility and low viscosity). Here we highlight key bionanotechnologies for preparing functional and stable membrane proteins in diverse types of lipoparticles that are being used to improve antibody discovery and engineering efforts. We also highlight key bionanotechnologies for high-throughput and ultra-dilute screening of antibody biophysical properties during antibody discovery and optimization that are being used for identifying antibodies with superior combinations of in vitro (formulation) and in vivo (half-life) properties.
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Affiliation(s)
- Emily K Makowski
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Departmant of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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30
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Burnett DL, Jackson KJL, Langley DB, Aggrawal A, Stella AO, Johansen MD, Balachandran H, Lenthall H, Rouet R, Walker G, Saunders BM, Singh M, Li H, Henry JY, Jackson J, Stewart AG, Witthauer F, Spence MA, Hansbro NG, Jackson C, Schofield P, Milthorpe C, Martinello M, Schulz SR, Roth E, Kelleher A, Emery S, Britton WJ, Rawlinson WD, Karl R, Schäfer S, Winkler TH, Brink R, Bull RA, Hansbro PM, Jäck HM, Turville S, Christ D, Goodnow CC. Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability. Immunity 2021; 54:2908-2921.e6. [PMID: 34788600 PMCID: PMC8554075 DOI: 10.1016/j.immuni.2021.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/24/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022]
Abstract
Viral mutations are an emerging concern in reducing SARS-CoV-2 vaccination efficacy. Second-generation vaccines will need to elicit neutralizing antibodies against sites that are evolutionarily conserved across the sarbecovirus subgenus. Here, we immunized mice containing a human antibody repertoire with diverse sarbecovirus receptor-binding domains (RBDs) to identify antibodies targeting conserved sites of vulnerability. Antibodies with broad reactivity against diverse clade B RBDs targeting the conserved class 4 epitope, with recurring IGHV/IGKV pairs, were readily elicited but were non-neutralizing. However, rare class 4 antibodies binding this conserved RBD supersite showed potent neutralization of SARS-CoV-2 and all variants of concern. Structural analysis revealed that the neutralizing ability of cross-reactive antibodies was reserved only for those with an elongated CDRH3 that extends the antiparallel beta-sheet RBD core and orients the antibody light chain to obstruct ACE2-RBD interactions. These results identify a structurally defined pathway for vaccine strategies eliciting escape-resistant SARS-CoV-2 neutralizing antibodies.
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Affiliation(s)
- Deborah L Burnett
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia.
| | | | - David B Langley
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | | | | | - Matt D Johansen
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | | | - Helen Lenthall
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Gregory Walker
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Bernadette M Saunders
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Hui Li
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Jake Y Henry
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Alastair G Stewart
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Franka Witthauer
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Nicole G Hansbro
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Claire Milthorpe
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | | | - Sebastian R Schulz
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Edith Roth
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | | | - Sean Emery
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - William D Rawlinson
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, SEALS Randwick, Sydney, NSW 2031, Australia
| | - Rudolfo Karl
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Simon Schäfer
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Thomas H Winkler
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Robert Brink
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Rowena A Bull
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Philip M Hansbro
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Hans-Martin Jäck
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stuart Turville
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW 2052, Australia
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31
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Perera Molligoda Arachchige AS. NK cell-based therapies for HIV infection: Investigating current advances and future possibilities. J Leukoc Biol 2021; 111:921-931. [PMID: 34668588 DOI: 10.1002/jlb.5ru0821-412rr] [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: 11/08/2022] Open
Abstract
NK cells are well-known for their antiviral functions. Also, their role in HIV has been well established, with rapid responses elicited during early HIV infection. Most immune cells including CD4+ T cells, monocytes, Mϕs, and dendritic cells are readily infected by HIV. Recent evidence from multiple studies has suggested that similar to these cells, in chronic conditions like HIV, NK cells also undergo functional exhaustion with impaired cytotoxicity, altered cytokine production, and impaired ADCC. NK-based immunotherapy aims to successfully restore, boost, and modify their activity as has been already demonstrated in the field of cancer immunotherapy. The utilization of NK cell-based strategies for the eradication of HIV from the body provides many advantages over classical ART. The literature search consisted of manually selecting the most relevant studies from databases including PubMed, Embase, Google Scholar, and ClinicalTrial.gov. Some of the treatments currently under consideration are CAR-NK cell therapy, facilitating ADCC, TLR agonists, bNAbs, and BiKEs/TriKEs, blocking inhibitory NK receptors during infection, IL-15 and IL-15 superagonists (eg: ALT-803), and so on. This review aims to discuss the NK cell-based therapies currently under experimentation against HIV infection and finally highlight the challenges associated with NK cell-based immunotherapies.
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Miersch S, Li Z, Saberianfar R, Ustav M, Brett Case J, Blazer L, Chen C, Ye W, Pavlenco A, Gorelik M, Garcia Perez J, Subramania S, Singh S, Ploder L, Ganaie S, Chen RE, Leung DW, Pandolfi PP, Novelli G, Matusali G, Colavita F, Capobianchi MR, Jain S, Gupta JB, Amarasinghe GK, Diamond MS, Rini J, Sidhu SS. Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations. J Mol Biol 2021; 433:167177. [PMID: 34329642 PMCID: PMC8316672 DOI: 10.1016/j.jmb.2021.167177] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/17/2021] [Accepted: 07/21/2021] [Indexed: 12/16/2022]
Abstract
Neutralizing antibodies (nAbs) hold promise as therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic bivalent and tetravalent nAbs against SARS-CoV-2. The best nAb targets the host receptor binding site of the viral S-protein and tetravalent versions block entry with a potency exceeding bivalent nAbs by an order of magnitude. Structural studies show that both the bivalent and tetravalent nAbs can make multivalent interactions with a single S-protein trimer, consistent with the avidity and potency of these molecules. Significantly, we show that the tetravalent nAbs show increased tolerance to potential virus escape mutants and an emerging variant of concern. Bivalent and tetravalent nAbs can be produced at large-scale and are as stable and specific as approved antibody drugs. Our results provide a general framework for enhancing antiviral therapies against COVID-19 and related viral threats, and our strategy can be applied to virtually any antibody drug.
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Affiliation(s)
- Shane Miersch
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | | | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Levi Blazer
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Chao Chen
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Wei Ye
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | | | - Maryna Gorelik
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | | | | | - Serena Singh
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Lynda Ploder
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Safder Ganaie
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pier Paolo Pandolfi
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, USA; Department of Molecular Biotechnologies & Health Sciences, Molecular Biotechnology Center, University of Turin, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Giulia Matusali
- Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Francesca Colavita
- Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Maria R Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | | | - J B Gupta
- Virna Therapeutics, West Roxbury, MA, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - James Rini
- Department of Molecular Genetics, University of Toronto, Toronto, Canada; Department of Biochemistry, University of Toronto, Toronto, Canada.
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Canada.
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Sobia P, Archary D. Preventive HIV Vaccines-Leveraging on Lessons from the Past to Pave the Way Forward. Vaccines (Basel) 2021; 9:vaccines9091001. [PMID: 34579238 PMCID: PMC8472969 DOI: 10.3390/vaccines9091001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Almost four decades on, since the 1980’s, with hundreds of HIV vaccine candidates tested in both non-human primates and humans, and several HIV vaccines trials later, an efficacious HIV vaccine continues to evade us. The enormous worldwide genetic diversity of HIV, combined with HIV’s inherent recombination and high mutation rates, has hampered the development of an effective vaccine. Despite the advent of antiretrovirals as pre-exposure prophylaxis and preventative treatment, which have shown to be effective, HIV infections continue to proliferate, highlighting the great need for a vaccine. Here, we provide a brief history for the HIV vaccine field, with the most recent disappointments and advancements. We also provide an update on current passive immunity trials, testing proof of the concept of the most clinically advanced broadly neutralizing monoclonal antibodies for HIV prevention. Finally, we include mucosal immunity, the importance of vaccine-elicited immune responses and the challenges thereof in the most vulnerable environment–the female genital tract and the rectal surfaces of the gastrointestinal tract for heterosexual and men who have sex with men transmissions, respectively.
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Affiliation(s)
- Parveen Sobia
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4001, South Africa
- Correspondence: ; Tel.: +27-(0)-31-655-0540
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34
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Ding C, Patel D, Ma Y, Mann JFS, Wu J, Gao Y. Employing Broadly Neutralizing Antibodies as a Human Immunodeficiency Virus Prophylactic & Therapeutic Application. Front Immunol 2021; 12:697683. [PMID: 34354709 PMCID: PMC8329590 DOI: 10.3389/fimmu.2021.697683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/05/2021] [Indexed: 11/18/2022] Open
Abstract
Despite the discovery that the human immunodeficiency virus 1 (HIV-1) is the pathogen of acquired immunodeficiency syndrome (AIDS) in 1983, there is still no effective anti-HIV-1 vaccine. The major obstacle to the development of HIV-1 vaccine is the extreme diversity of viral genome sequences. Nonetheless, a number of broadly neutralizing antibodies (bNAbs) against HIV-1 have been made and identified in this area. Novel strategies based on using these bNAbs as an efficacious preventive and/or therapeutic intervention have been applied in clinical. In this review, we summarize the recent development of bNAbs and its application in HIV-1 acquisition prevention as well as discuss the innovative approaches being used to try to convey protection within individuals at risk and being treated for HIV-1 infection.
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Affiliation(s)
- Chengchao Ding
- The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Darshit Patel
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Yunjing Ma
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Jamie F S Mann
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Jianjun Wu
- Department of AIDS Research, Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Yong Gao
- The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.,Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
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35
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Souda S, Mwita JC, Cainelli F, Mannathoko NB, Anderson M, Moyo S. Seroprevalence and risk factors of hepatitis B, C and D virus infection amongst patients with features of hepatitis in a referral hospital in Botswana: A cross-sectional study. S Afr J Infect Dis 2021. [DOI: 10.4102/sajid.v36i1.275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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36
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Jennewein MF, MacCamy AJ, Akins NR, Feng J, Homad LJ, Hurlburt NK, Seydoux E, Wan YH, Stuart AB, Edara VV, Floyd K, Vanderheiden A, Mascola JR, Doria-Rose N, Wang L, Yang ES, Chu HY, Torres JL, Ozorowski G, Ward AB, Whaley RE, Cohen KW, Pancera M, McElrath MJ, Englund JA, Finzi A, Suthar MS, McGuire AT, Stamatatos L. Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects. Cell Rep 2021; 36:109353. [PMID: 34237283 PMCID: PMC8216847 DOI: 10.1016/j.celrep.2021.109353] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/21/2021] [Accepted: 06/15/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterize 198 antibodies isolated from four COVID-19+ subjects and identify 14 SARS-CoV-2 neutralizing antibodies. One targets the N-terminal domain (NTD), one recognizes an epitope in S2, and 11 bind the receptor-binding domain (RBD). Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency and antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. All four cross-neutralizing antibodies neutralize the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.
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Affiliation(s)
- Madeleine F Jennewein
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Anna J MacCamy
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Nicholas R Akins
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Junli Feng
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Leah J Homad
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Nicholas K Hurlburt
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Emilie Seydoux
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Andrew B Stuart
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Venkata Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30322, USA
| | - Katharine Floyd
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30322, USA
| | - Abigail Vanderheiden
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30322, USA
| | - John R Mascola
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Lingshu Wang
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Helen Y Chu
- University of Washington, Department of Medicine, Seattle, WA 98109, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rachael E Whaley
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Kristen W Cohen
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA; Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - M Juliana McElrath
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA; University of Washington, Department of Medicine, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98109, USA
| | - Janet A Englund
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA 98109, USA
| | | | - Mehul S Suthar
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30322, USA.
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98109, USA.
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37
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Scheid JF, Barnes CO, Eraslan B, Hudak A, Keeffe JR, Cosimi LA, Brown EM, Muecksch F, Weisblum Y, Zhang S, Delorey T, Woolley AE, Ghantous F, Park SM, Phillips D, Tusi B, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Rzasa K, Hatziioanno T, Durney MA, Gu X, Tada T, Landau NR, West AP, Rozenblatt-Rosen O, Seaman MS, Baden LR, Graham DB, Deguine J, Bieniasz PD, Regev A, Hung D, Bjorkman PJ, Xavier RJ. B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell 2021; 184:3205-3221.e24. [PMID: 34015271 PMCID: PMC8064835 DOI: 10.1016/j.cell.2021.04.032] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/26/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell sorting with single-cell VDJ and RNA sequencing (RNA-seq) and mAb structures to characterize B cell responses against SARS-CoV-2. We show that the SARS-CoV-2-specific B cell repertoire consists of transcriptionally distinct B cell populations with cells producing potently neutralizing antibodies (nAbs) localized in two clusters that resemble memory and activated B cells. Cryo-electron microscopy structures of selected nAbs from these two clusters complexed with SARS-CoV-2 spike trimers show recognition of various receptor-binding domain (RBD) epitopes. One of these mAbs, BG10-19, locks the spike trimer in a closed conformation to potently neutralize SARS-CoV-2, the recently arising mutants B.1.1.7 and B.1.351, and SARS-CoV and cross-reacts with heterologous RBDs. Together, our results characterize transcriptional differences among SARS-CoV-2-specific B cells and uncover cross-neutralizing Ab targets that will inform immunogen and therapeutic design against coronaviruses.
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MESH Headings
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/metabolism
- Antigen-Antibody Reactions
- B-Lymphocytes/cytology
- B-Lymphocytes/metabolism
- B-Lymphocytes/virology
- COVID-19/pathology
- COVID-19/virology
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Gene Expression Profiling
- Humans
- Immunoglobulin A/immunology
- Immunoglobulin Variable Region/chemistry
- Immunoglobulin Variable Region/genetics
- Protein Domains/immunology
- Protein Multimerization
- Protein Structure, Quaternary
- SARS-CoV-2/immunology
- SARS-CoV-2/isolation & purification
- SARS-CoV-2/metabolism
- Sequence Analysis, RNA
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Johannes F Scheid
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Basak Eraslan
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew Hudak
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lisa A Cosimi
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric M Brown
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Frauke Muecksch
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Shuting Zhang
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Toni Delorey
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ann E Woolley
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Fadi Ghantous
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Sung-Moo Park
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Devan Phillips
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Betsabeh Tusi
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Kara Rzasa
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Theodora Hatziioanno
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Michael A Durney
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Xiebin Gu
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Lindsey R Baden
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel B Graham
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jacques Deguine
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Paul D Bieniasz
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Deborah Hung
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ramnik J Xavier
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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38
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Starr CG, Makowski EK, Wu L, Berg B, Kingsbury JS, Gokarn YR, Tessier PM. Ultradilute Measurements of Self-Association for the Identification of Antibodies with Favorable High-Concentration Solution Properties. Mol Pharm 2021; 18:2744-2753. [PMID: 34105965 DOI: 10.1021/acs.molpharmaceut.1c00280] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is significant interest in formulating antibody therapeutics as concentrated liquid solutions, but early identification of developable antibodies with optimal manufacturability, stability, and delivery attributes remains challenging. Traditional methods of identifying developable mAbs with low self-association in common antibody formulations require relatively concentrated protein solutions (>1 mg/mL), and this single challenge has frustrated early-stage and large-scale identification of antibody candidates with drug-like colloidal properties. Here, we describe charge-stabilized self-interaction nanoparticle spectroscopy (CS-SINS), an affinity-capture nanoparticle assay that measures colloidal self-interactions at ultradilute antibody concentrations (0.01 mg/mL), and is predictive of antibody developability issues of high viscosity and opalescence that manifest at four orders of magnitude higher concentrations (>100 mg/mL). CS-SINS enables large-scale, high-throughput selection of developable antibodies during early discovery.
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Affiliation(s)
- Charles G Starr
- Biologics Development, Sanofi, Framingham, Massachusetts 01701, United States
| | | | | | | | | | - Yatin R Gokarn
- Biologics Development, Sanofi, Framingham, Massachusetts 01701, United States
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39
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Jacque E, Chottin C, Laubreton D, Nogre M, Ferret C, de Marcos S, Baptista L, Drajac C, Mondon P, De Romeuf C, Rameix-Welti MA, Eléouët JF, Chtourou S, Riffault S, Perret G, Descamps D. Hyper-Enriched Anti-RSV Immunoglobulins Nasally Administered: A Promising Approach for Respiratory Syncytial Virus Prophylaxis. Front Immunol 2021; 12:683902. [PMID: 34163482 PMCID: PMC8215542 DOI: 10.3389/fimmu.2021.683902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 11/23/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a public health concern that causes acute lower respiratory tract infection. So far, no vaccine candidate under development has reached the market and the only licensed product to prevent RSV infection in at-risk infants and young children is a monoclonal antibody (Synagis®). Polyclonal human anti-RSV hyper-immune immunoglobulins (Igs) have also been used but were superseded by Synagis® owing to their low titer and large infused volume. Here we report a new drug class of immunoglobulins, derived from human non hyper-immune plasma that was generated by an innovative bioprocess, called Ig cracking, combining expertises in plasma-derived products and affinity chromatography. By using the RSV fusion protein (F protein) as ligand, the Ig cracking process provided a purified and concentrated product, designated hyper-enriched anti-RSV IgG, composed of at least 15-20% target-specific-antibodies from normal plasma. These anti-RSV Ig displayed a strong in vitro neutralization effect on RSV replication. Moreover, we described a novel prophylactic strategy based on local nasal administration of this unique hyper-enriched anti-RSV IgG solution using a mouse model of infection with bioluminescent RSV. Our results demonstrated that very low doses of hyper-enriched anti-RSV IgG can be administered locally to ensure rapid and efficient inhibition of virus infection. Thus, the general hyper-enriched Ig concept appeared a promising approach and might provide solutions to prevent and treat other infectious diseases.
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Affiliation(s)
| | - Claire Chottin
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Daphné Laubreton
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Cécile Ferret
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | | | - Carole Drajac
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | | | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, U1173, Montigny-Le-Bretonneux, France.,AP-HP, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | | | | | - Sabine Riffault
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
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40
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Zhang Z, Jara CJ, Singh M, Xu H, Goodnow CC, Jackson KJ, Reed JH. Human transitional and IgM low mature naïve B cells preserve permissive B-cell receptors. Immunol Cell Biol 2021; 99:865-878. [PMID: 33988890 PMCID: PMC8453828 DOI: 10.1111/imcb.12478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 12/02/2022]
Abstract
The level of immunoglobulin M (IgM) displayed on the surface of peripheral blood B cells exhibits a broad dynamic range and has been associated with both development and selection. To determine whether IgM surface expression associates with distinct immunoglobulin heavy‐chain (IGH) repertoire properties, we performed deep IgM sequencing of peripheral blood transitional and mature naïve B cells in the upper and lower quartiles of surface IgM expression for 12 healthy donors. Mature naïve B cells within the lowest quartile for surface IgM expression displayed more diverse IGH features including increased complementarity‐determining region 3 length, IGHJ6 segment usage and aromatic amino acids compared with mature naïve B cells with high surface IgM. There were no differences between IGH repertoires for transitional B cells with high or low surface IgM. These findings suggest that a selection checkpoint during progression of transitional to mature naïve B cells reduces the breadth of the IGH repertoire among high surface IgM B cells but that diversity is preserved in B cells expressing low levels of surface IgM.
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Affiliation(s)
- Zhiguo Zhang
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Christopher J Jara
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Medical Sciences and Cellular Genomics Futures Institute, UNSW, Sydney, NSW, Australia
| | | | - Joanne H Reed
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
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41
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Jia W, Wang Z, Lu Z, Ding B, Li Z, Xu D. The discovery of lactoferrin dual aptamers through surface plasmon resonance imaging combined with a bioinformation analysis. Analyst 2021; 145:6298-6306. [PMID: 32940261 DOI: 10.1039/d0an01513j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An analytical method for screening aptamers for different recognition sites in lactoferrin (Lac) molecules has been developed based on Surface Plasmon Resonance imaging (SPRi), combined with the cluster classification calculation of a quasi-aptamer library strategy and molecular docking simulation analysis. Using the software simulation, a homology analysis was performed on the selected quasi-aptamer sequences, which could be divided into 8 different families. Based on the principle of biomolecular recognition, a label-free, high-throughput dual immune site screening method was established, in which the nucleic acid aptamers of recognizing ability for lactoferrin molecules were fixed onto the surface of the SPRi sensor chip and could bind to the lactoferrin molecules. Then, the aptamer candidates to be paired were introduced, and the recognition event of the second immune site was judged by observing the binding signal of SPRi. The paired SPRi signal was generated only when the site identified by the second nucleic acid molecule was different from the first immune site. Based on this principle, a pair of Lac nucleic acid aptamers (Lac-8 and Lac-25) was finally screened and confirmed using computerized simulation, and has been employed to assay Lac in milk by ELONA (Enzyme-Linked Oligonucleotide Assay).
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Affiliation(s)
- Wenchao Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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42
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de Mattos Barbosa MG, Liu H, Huynh D, Shelley G, Keller ET, Emmer BT, Sherman E, Ginsburg D, Kennedy AA, Tai AW, Wobus C, Mirabeli C, Lanigan TM, Samaniego M, Meng W, Rosenfeld AM, Prak ETL, Platt JL, Cascalho M. IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. JCI Insight 2021; 6:147386. [PMID: 33769311 PMCID: PMC8262290 DOI: 10.1172/jci.insight.147386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022] Open
Abstract
Abs that neutralize SARS-CoV-2 are thought to provide the most immediate and effective treatment for those severely afflicted by this virus. Because coronavirus potentially diversifies by mutation, broadly neutralizing Abs are especially sought. Here, we report a possibly novel approach to rapid generation of potent broadly neutralizing human anti-SARS-CoV-2 Abs. We isolated SARS-CoV-2 spike protein-specific memory B cells by panning from the blood of convalescent subjects after infection with SARS-CoV-2 and sequenced and expressed Ig genes from individual B cells as human mAbs. All of 43 human mAbs generated in this way neutralized SARS-CoV-2. Eighteen of the forty-three human mAbs exhibited half-maximal inhibitory concentrations (IC50) of 6.7 × 10-12 M to 6.7 × 10-15 M for spike-pseudotyped virus. Seven of the human mAbs also neutralized (with IC50 < 6.7 × 10-12 M) viruses pseudotyped with mutant spike proteins (including receptor-binding domain mutants and the S1 C-terminal D614G mutant). Neutralization of the Wuhan Hu-1 founder strain and of some variants decreased when coding sequences were reverted to germline, suggesting that potency of neutralization was acquired by somatic hypermutation and selection of B cells. These results indicate that infection with SARS-CoV-2 evokes high-affinity B cell responses, some products of which are broadly neutralizing and others highly strain specific. We also identify variants that would potentially resist immunity evoked by infection with the Wuhan Hu-1 founder strain or by vaccines developed with products of that strain, suggesting evolutionary courses that SARS-CoV-2 could take.
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Affiliation(s)
| | | | | | | | | | | | - Emily Sherman
- Department of Internal Medicine
- Life Sciences Institute
| | - David Ginsburg
- Department of Internal Medicine
- Life Sciences Institute
- Departments of Human Genetics and Pediatrics and Howard Hughes Medical Institute
| | | | | | | | | | - Thomas M. Lanigan
- Department of Internal Medicine
- Vector Core, Biomedical Research Core Facilities, University of Michigan, Ann Arbor, Michigan, USA
| | - Milagros Samaniego
- Department of Medicine, Henry Ford Health Systems, Detroit, Michigan, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aaron M. Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jeffrey L. Platt
- Department of Surgery
- Department of Microbiology and Immunology, and
| | - Marilia Cascalho
- Department of Surgery
- Department of Microbiology and Immunology, and
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43
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Lin YR, Parks KR, Weidle C, Naidu AS, Khechaduri A, Riker AO, Takushi B, Chun JH, Borst AJ, Veesler D, Stuart A, Agrawal P, Gray M, Pancera M, Huang PS, Stamatatos L. HIV-1 VRC01 Germline-Targeting Immunogens Select Distinct Epitope-Specific B Cell Receptors. Immunity 2021; 53:840-851.e6. [PMID: 33053332 DOI: 10.1016/j.immuni.2020.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/12/2020] [Accepted: 09/10/2020] [Indexed: 01/23/2023]
Abstract
Activating precursor B cell receptors of HIV-1 broadly neutralizing antibodies requires specifically designed immunogens. Here, we compared the abilities of three such germline-targeting immunogens against the VRC01-class receptors to activate the targeted B cells in transgenic mice expressing the germline VH of the VRC01 antibody but diverse mouse light chains. Immunogen-specific VRC01-like B cells were isolated at different time points after immunization, their VH and VL genes were sequenced, and the corresponding antibodies characterized. VRC01 B cell sub-populations with distinct cross-reactivity properties were activated by each immunogen, and these differences correlated with distinct biophysical and biochemical features of the germline-targeting immunogens. Our study indicates that the design of effective immunogens to activate B cell receptors leading to protective HIV-1 antibodies will require a better understanding of how the biophysical properties of the epitope and its surrounding surface on the germline-targeting immunogen influence its interaction with the available receptor variants in vivo.
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Affiliation(s)
- Yu-Ru Lin
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - K Rachael Parks
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; University of Washington, Department of Global Health, Seattle, WA, USA
| | - Connor Weidle
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Anika S Naidu
- Stanford University, Department of Bioengineering, Stanford, CA, USA
| | - Arineh Khechaduri
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Andrew O Riker
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Brittany Takushi
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Jung-Ho Chun
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - Andrew J Borst
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - David Veesler
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - Andrew Stuart
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Parul Agrawal
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Matthew Gray
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA.
| | - Po-Ssu Huang
- Stanford University, Department of Bioengineering, Stanford, CA, USA.
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA; University of Washington, Department of Global Health, Seattle, WA, USA.
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44
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Han Q, Bradley T, Williams WB, Cain DW, Montefiori DC, Saunders KO, Parks RJ, Edwards RW, Ferrari G, Mueller O, Shen X, Wiehe KJ, Reed S, Fox CB, Rountree W, Vandergrift NA, Wang Y, Sutherland LL, Santra S, Moody MA, Permar SR, Tomaras GD, Lewis MG, Van Rompay KKA, Haynes BF. Neonatal Rhesus Macaques Have Distinct Immune Cell Transcriptional Profiles following HIV Envelope Immunization. Cell Rep 2021; 30:1553-1569.e6. [PMID: 32023469 PMCID: PMC7243677 DOI: 10.1016/j.celrep.2019.12.091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/16/2019] [Accepted: 12/24/2019] [Indexed: 12/30/2022] Open
Abstract
HIV-1-infected infants develop broadly neutralizing antibodies (bnAbs) more rapidly than adults, suggesting differences in the neonatal versus adult responses to the HIV-1 envelope (Env). Here, trimeric forms of HIV-1 Env immunogens elicit increased gp120- and gp41-specific antibodies more rapidly in neonatal macaques than adult macaques. Transcriptome analyses of neonatal versus adult immune cells after Env vaccination reveal that neonatal macaques have higher levels of the apoptosis regulator BCL2 in T cells and lower levels of the immunosuppressive interleukin-10 (IL-10) receptor alpha (IL10RA) mRNA transcripts in T cells, B cells, natural killer (NK) cells, and monocytes. In addition, immunized neonatal macaques exhibit increased frequencies of activated blood T follicular helper-like (Tfh) cells compared to adults. Thus, neonatal macaques have transcriptome signatures of decreased immunosuppression and apoptosis compared with adult macaques, providing an immune landscape conducive to early-life immunization prior to sexual debut.
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Affiliation(s)
- Qifeng Han
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Robert J Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Regina W Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Olaf Mueller
- Center for Genomics of Microbial Systems, Duke University Medical Center, Durham, NC, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin J Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | | | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Nathan A Vandergrift
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sallie R Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
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45
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Madan B, Zhang B, Xu K, Chao CW, O'Dell S, Wolfe JR, Chuang GY, Fahad AS, Geng H, Kong R, Louder MK, Nguyen TD, Rawi R, Schön A, Sheng Z, Nimrania R, Wang Y, Zhou T, Lin BC, Doria-Rose NA, Shapiro L, Kwong PD, DeKosky BJ. Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody. Proc Natl Acad Sci U S A 2021; 118:e2011653118. [PMID: 33649208 PMCID: PMC7958426 DOI: 10.1073/pnas.2011653118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Vaccine-based elicitation of broadly neutralizing antibodies holds great promise for preventing HIV-1 transmission. However, the key biophysical markers of improved antibody recognition remain uncertain in the diverse landscape of potential antibody mutation pathways, and a more complete understanding of anti-HIV-1 fusion peptide (FP) antibody development will accelerate rational vaccine designs. Here we survey the mutational landscape of the vaccine-elicited anti-FP antibody, vFP16.02, to determine the genetic, structural, and functional features associated with antibody improvement or fitness. Using site-saturation mutagenesis and yeast display functional screening, we found that 1% of possible single mutations improved HIV-1 envelope trimer (Env) affinity, but generally comprised rare somatic hypermutations that may not arise frequently in vivo. We observed that many single mutations in the vFP16.02 Fab could enhance affinity >1,000-fold against soluble FP, although affinity improvements against the HIV-1 trimer were more measured and rare. The most potent variants enhanced affinity to both soluble FP and Env, had mutations concentrated in antibody framework regions, and achieved up to 37% neutralization breadth compared to 28% neutralization of the template antibody. Altered heavy- and light-chain interface angles and conformational dynamics, as well as reduced Fab thermal stability, were associated with improved HIV-1 neutralization breadth and potency. We also observed parallel sets of mutations that enhanced viral neutralization through similar structural mechanisms. These data provide a quantitative understanding of the mutational landscape for vaccine-elicited FP-directed broadly neutralizing antibody and demonstrate that numerous antigen-distal framework mutations can improve antibody function by enhancing affinity simultaneously toward HIV-1 Env and FP.
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Affiliation(s)
- Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Jacy R Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Thuy Duong Nguyen
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Arne Schön
- Department of Biology, John Hopkins University, Baltimore, MD 21218
| | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027
| | - Rajani Nimrania
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Yiran Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027
- Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045;
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66045
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46
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Miersch S, Li Z, Saberianfar R, Ustav M, Case JB, Blazer L, Chen C, Ye W, Pavlenco A, Gorelik M, Perez JG, Subramania S, Singh S, Ploder L, Ganaie S, Chen RE, Leung DW, Pandolfi PP, Novelli G, Matusali G, Colavita F, Capobianchi MR, Jain S, Gupta JB, Amarasinghe GK, Diamond MS, Rini J, Sidhu SS. Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33398270 DOI: 10.1101/2020.10.31.362848] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Neutralizing antibodies (nAbs) hold promise as effective therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic bivalent and tetravalent nAbs against SARS-CoV-2. The best nAb targets the host receptor binding site of the viral S-protein and its tetravalent versions can block entry with a potency that exceeds the bivalent nAbs by an order of magnitude. Structural studies show that both the bivalent and tetravalent nAbs can make multivalent interactions with a single S-protein trimer, observations consistent with the avidity and potency of these molecules. Significantly, we show that the tetravalent nAbs show much increased tolerance to potential virus escape mutants. Bivalent and tetravalent nAbs can be produced at large-scale and are as stable and specific as approved antibody drugs. Our results provide a general framework for developing potent antiviral therapies against COVID-19 and related viral threats, and our strategy can be readily applied to any antibody drug currently in development.
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47
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Guthmiller JJ, Lan LYL, Fernández-Quintero ML, Han J, Utset HA, Bitar DJ, Hamel NJ, Stovicek O, Li L, Tepora M, Henry C, Neu KE, Dugan HL, Borowska MT, Chen YQ, Liu STH, Stamper CT, Zheng NY, Huang M, Palm AKE, García-Sastre A, Nachbagauer R, Palese P, Coughlan L, Krammer F, Ward AB, Liedl KR, Wilson PC. Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses. Immunity 2020; 53:1230-1244.e5. [PMID: 33096040 PMCID: PMC7772752 DOI: 10.1016/j.immuni.2020.10.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/14/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022]
Abstract
Polyreactivity is the ability of a single antibody to bind to multiple molecularly distinct antigens and is a common feature of antibodies induced upon pathogen exposure. However, little is known about the role of polyreactivity during anti-influenza virus antibody responses. By analyzing more than 500 monoclonal antibodies (mAbs) derived from B cells induced by numerous influenza virus vaccines and infections, we found mAbs targeting conserved neutralizing influenza virus hemagglutinin epitopes were polyreactive. Polyreactive mAbs were preferentially induced by novel viral exposures due to their broad viral binding breadth. Polyreactivity augmented mAb viral binding strength by increasing antibody flexibility, allowing for adaption to imperfectly conserved epitopes. Lastly, we found affinity-matured polyreactive B cells were typically derived from germline polyreactive B cells that were preferentially selected to participate in B cell responses over time. Together, our data reveal that polyreactivity is a beneficial feature of antibodies targeting conserved epitopes.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Linda Yu-Ling Lan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry A Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Dalia J Bitar
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Natalie J Hamel
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Micah Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Carole Henry
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Karlynn E Neu
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yao-Qing Chen
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Sean T H Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Anna-Karin E Palm
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lynda Coughlan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Microbiology and Immunology and Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
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48
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The CH1α domain of mucosal gp41 IgA contributes to antibody specificity and antiviral functions in HIV-1 highly exposed Sero-Negative individuals. PLoS Pathog 2020; 16:e1009103. [PMID: 33315937 PMCID: PMC7802955 DOI: 10.1371/journal.ppat.1009103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/12/2021] [Accepted: 10/26/2020] [Indexed: 01/22/2023] Open
Abstract
The antibody molecule comprises a variable domain conferring antigen specificity and affinity distinct from the heavy chain constant (CH) domains dictating effector functions. We here interrogate this paradigm by evaluating the unique influence of the CH1α domain on epitope specificity and functions using two mucosal gp41-specific Fab-IgAs (FabA) derived from HIV-1 highly-exposed but persistently seronegative individuals (HESN). These HESN develop selectively affinity-matured HIV-1-specific mucosal IgA that target the gp41 viral envelope and might provide protection although by unclear mechanisms. Isotype-switching FabAs into Fab-IgGs (FabGs) results in a >10-fold loss in affinity for HIV-1 clade A, B, and C gp41, together with reduced neutralization of HIV-1 cross-clade. The FabA conformational epitopes map selectively on gp41 in 6-Helix bundle and pre-fusion conformations cross-clade, unlike FabGs. Finally, we designed in silico, a 12 amino-acid peptide recapitulating one FabA conformational epitope that inhibits the FabA binding to gp41 cross-clade and its neutralizing activity. Altogether, our results reveal that the CH1α domain shapes the antibody paratope through an allosteric effect, thereby strengthening the antibody specificity and functional activities. Further, they clarify the mechanisms by which these HESN IgAs might confer protection against HIV-1-sexual acquisition. The IgA-specific epitope we characterized by reverse vaccinology could help designing a mucosal HIV-1 vaccine.
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49
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Boughter CT, Borowska MT, Guthmiller JJ, Bendelac A, Wilson PC, Roux B, Adams EJ. Biochemical patterns of antibody polyreactivity revealed through a bioinformatics-based analysis of CDR loops. eLife 2020; 9:61393. [PMID: 33169668 PMCID: PMC7755423 DOI: 10.7554/elife.61393] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
Antibodies are critical components of adaptive immunity, binding with high affinity to pathogenic epitopes. Antibodies undergo rigorous selection to achieve this high affinity, yet some maintain an additional basal level of low affinity, broad reactivity to diverse epitopes, a phenomenon termed ‘polyreactivity’. While polyreactivity has been observed in antibodies isolated from various immunological niches, the biophysical properties that allow for promiscuity in a protein selected for high-affinity binding to a single target remain unclear. Using a database of over 1000 polyreactive and non-polyreactive antibody sequences, we created a bioinformatic pipeline to isolate key determinants of polyreactivity. These determinants, which include an increase in inter-loop crosstalk and a propensity for a neutral binding surface, are sufficient to generate a classifier able to identify polyreactive antibodies with over 75% accuracy. The framework from which this classifier was built is generalizable, and represents a powerful, automated pipeline for future immune repertoire analysis. To defend itself against bacteria and viruses, the body depends on a group of proteins known as antibodies. Each subset of antibodies undergoes a rigorous training regimen to ensure it recognizes a single epitope well – that is, one specific region on the surface of foreign, harmful organisms. Most antibodies stick extremely tightly to their one unique epitope, but some can also weakly bind to molecules that are vastly different from their main trained targets. This feature – known as polyreactivity – can in some cases help the immune system fight against multiple strains of viruses. On the other hand, when antibodies are designed in the laboratory to treat diseases, this characteristic can sometimes lead to the failure of pre-clinical trials. Yet it is currently unclear why some antibodies are polyreactive when others are not. To investigate this question, Boughter et al. compared over 1,000 polyreactive and non-polyreactive antibody sequences from a large database, revealing differences in the physical properties of the region of the antibodies that attaches to epitopes. Using these defining features, Boughter et al. went on to design a new piece of freely available, automated software that could predict which antibodies would be polyreactive more than 75% of the time. Such software could ultimately help to guide the design of antibody-based treatments, while bypassing the need for costly laboratory tests.
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Affiliation(s)
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, United States.,Department of Pathology, University of Chicago, Chicago, United States
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States.,Committee on Immunology, University of Chicago, Chicago, United States
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Committee on Immunology, University of Chicago, Chicago, United States
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50
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Nowosad CR, Mesin L, Castro TBR, Wichmann C, Donaldson GP, Araki T, Schiepers A, Lockhart AAK, Bilate AM, Mucida D, Victora GD. Tunable dynamics of B cell selection in gut germinal centres. Nature 2020; 588:321-326. [PMID: 33116306 PMCID: PMC7726069 DOI: 10.1038/s41586-020-2865-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023]
Abstract
Germinal centers (GCs), structures normally associated with B cell immunoglobulin (Ig) hypermutation and development of high-affinity antibodies upon infection or immunization, are present in gut-associated lymphoid organs of humans and mice under steady state. Gut-associated (ga)GCs can support antibody responses to enteric infections and immunization1. However, whether B cell selection and antibody affinity maturation can take place in face of the chronic and diverse antigenic stimulation characteristic of steady-state gaGCs is less clear2–8. Combining multicolor “Brainbow” fate-mapping and single-cell Ig sequencing, we find that 5–10% of gaGCs from specific pathogen-free (SPF) mice contained highly-dominant “winner” clones at steady state, despite rapid turnover of GC B cells. Monoclonal antibodies (mAbs) derived from these clones showed increased binding to commensal bacteria compared to their unmutated ancestors, consistent with antigen-driven selection and affinity maturation. Frequency of highly-selected gaGCs was markedly higher in germ-free (GF) than in SPF mice, and winner B cells in GF gaGCs were enriched in public IgH clonotypes found across multiple individuals, indicating strong B cell receptor (BCR)-driven selection in the absence of microbiota. Vertical colonization of GF mice with a defined microbial consortium (Oligo-MM12) did not eliminate GF-associated clonotypes, yet induced a concomitant commensal-specific, affinity-matured B cell response. Thus, positive selection can take place in steady-state gaGCs, at a rate that is tunable over a wide range by the presence and composition of the microbiota.
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Affiliation(s)
- Carla R Nowosad
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.,Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Tiago B R Castro
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.,Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Christopher Wichmann
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA.,Mucosal Immunology Group, Department of Pediatrics, University Medical Center Rostock, Rostock, Germany
| | - Gregory P Donaldson
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Tatsuya Araki
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Ariën Schiepers
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | | | - Angelina M Bilate
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA.
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
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