1
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Paciello I, Pierleoni G, Pantano E, Antonelli G, Pileri P, Maccari G, Cardamone D, Realini G, Perrone F, Neto MM, Pozzessere S, Fabbiani M, Panza F, Rancan I, Tumbarello M, Montagnani F, Medini D, Maes P, Temperton N, Simon-Loriere E, Schwartz O, Rappuoli R, Andreano E. Antigenic sin and multiple breakthrough infections drive converging evolution of COVID-19 neutralizing responses. Cell Rep 2024; 43:114645. [PMID: 39207904 DOI: 10.1016/j.celrep.2024.114645] [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: 04/29/2024] [Revised: 07/19/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Understanding the evolution of the B cell response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is fundamental to design the next generation of vaccines and therapeutics. We longitudinally analyze at the single-cell level almost 900 neutralizing human monoclonal antibodies (nAbs) isolated from vaccinated people and from individuals with hybrid and super hybrid immunity (SH), developed after three mRNA vaccine doses and two breakthrough infections. The most potent neutralization and Fc functions against highly mutated variants belong to the SH cohort. Repertoire analysis shows that the original Wuhan antigenic sin drives the convergent expansion of the same B cell germlines in vaccinated and SH cohorts. Only Omicron breakthrough infections expand previously unseen germ lines and generate broadly nAbs by restoring IGHV3-53/3-66 germ lines. Our analyses find that B cells initially expanded by the original antigenic sin continue to play a fundamental role in the evolution of the immune response toward an evolving virus.
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Affiliation(s)
- Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Giulio Pierleoni
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy; Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Elisa Pantano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy; Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Giada Antonelli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Piero Pileri
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Giuseppe Maccari
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Dario Cardamone
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Giulia Realini
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Federica Perrone
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy; Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Martin Mayora Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham Maritime, Kent, UK
| | - Simone Pozzessere
- Department of Cellular Therapies, Hematology, and Laboratory Medicine, University Hospital of Siena, Siena, Italy
| | - Massimiliano Fabbiani
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy; Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Panza
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy
| | - Ilaria Rancan
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy
| | - Mario Tumbarello
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy; Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Montagnani
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy; Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Duccio Medini
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Piet Maes
- KU Leuven, Rega Institute, Department of Microbiology, Immunology, and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham Maritime, Kent, UK
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France; National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; Vaccine Research Institute, Creteil, France
| | - Rino Rappuoli
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy; Fondazione Biotecnopolo di Siena, Siena, Italy
| | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy.
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2
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Kotaki R, Moriyama S, Oishi S, Onodera T, Adachi Y, Sasaki E, Ishino K, Morikawa M, Takei H, Takahashi H, Takano T, Nishiyama A, Yumoto K, Terahara K, Isogawa M, Matsumura T, Shinkai M, Takahashi Y. Repeated Omicron exposures redirect SARS-CoV-2-specific memory B cell evolution toward the latest variants. Sci Transl Med 2024; 16:eadp9927. [PMID: 39167666 DOI: 10.1126/scitranslmed.adp9927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024]
Abstract
Immunological imprinting by ancestral SARS-CoV-2 strains is thought to impede the robust induction of Omicron-specific humoral responses by Omicron-based booster vaccines. Here, we analyzed the specificity and neutralization activity of memory B (Bmem) cells after repeated BA.5 exposure in individuals previously imprinted by ancestral strain-based mRNA vaccines. After a second BA.5 exposure, Bmem cells with BA.5 spike protein-skewed reactivity were promptly elicited, correlating with preexisting antibody titers. Clonal lineage analysis identified BA.5-skewed Bmem cells that had redirected their specificity from the ancestral strain to BA.5 through somatic hypermutations. Moreover, Bmem cells with redirected BA.5 specificity exhibited accelerated development compared with de novo Bmem cells derived from naïve repertoires. This redirected BA.5 specificity demonstrated greater resilience to viral point mutation and adaptation to recent Omicron variants HK.3 and JN.1, months after the second BA.5 exposure, suggesting that existing Bmem cells elicited by older vaccines can redirect their specificity toward newly evolving variants.
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Affiliation(s)
- Ryutaro Kotaki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Shintaro Oishi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yu Adachi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Eita Sasaki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kota Ishino
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | | | | | | | - Tomohiro Takano
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Ayae Nishiyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kohei Yumoto
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kazutaka Terahara
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masanori Isogawa
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Takayuki Matsumura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | | | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Hokkaido 001-0021, Japan
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3
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Williams WB, Alam SM, Ofek G, Erdmann N, Montefiori DC, Seaman MS, Wagh K, Korber B, Edwards RJ, Mansouri K, Eaton A, Cain DW, Martin M, Hwang J, Arus-Altuz A, Lu X, Cai F, Jamieson N, Parks R, Barr M, Foulger A, Anasti K, Patel P, Sammour S, Parsons RJ, Huang X, Lindenberger J, Fetics S, Janowska K, Niyongabo A, Janus BM, Astavans A, Fox CB, Mohanty I, Evangelous T, Chen Y, Berry M, Kirshner H, Van Itallie E, Saunders KO, Wiehe K, Cohen KW, McElrath MJ, Corey L, Acharya P, Walsh SR, Baden LR, Haynes BF. Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans. Cell 2024; 187:2919-2934.e20. [PMID: 38761800 DOI: 10.1016/j.cell.2024.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/29/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
A critical roadblock to HIV vaccine development is the inability to induce B cell lineages of broadly neutralizing antibodies (bnAbs) in humans. In people living with HIV-1, bnAbs take years to develop. The HVTN 133 clinical trial studied a peptide/liposome immunogen targeting B cell lineages of HIV-1 envelope (Env) membrane-proximal external region (MPER) bnAbs (NCT03934541). Here, we report MPER peptide-liposome induction of polyclonal HIV-1 B cell lineages of mature bnAbs and their precursors, the most potent of which neutralized 15% of global tier 2 HIV-1 strains and 35% of clade B strains with lineage initiation after the second immunization. Neutralization was enhanced by vaccine selection of improbable mutations that increased antibody binding to gp41 and lipids. This study demonstrates proof of concept for rapid vaccine induction of human B cell lineages with heterologous neutralizing activity and selection of antibody improbable mutations and outlines a path for successful HIV-1 vaccine development.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunobiology, Duke School of Medicine, Durham, NC 27710, USA.
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA.
| | - Gilad Ofek
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke School of Medicine, Durham, NC 27710, USA
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Amanda Eaton
- Department of Surgery, Duke School of Medicine, Durham, NC 27710, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA
| | - Mitchell Martin
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - JongIn Hwang
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Aria Arus-Altuz
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Fangping Cai
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA
| | - Nolan Jamieson
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Parth Patel
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Salam Sammour
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Ruth J Parsons
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Xiao Huang
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Jared Lindenberger
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Susan Fetics
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Katarzyna Janowska
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Aurelie Niyongabo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Benjamin M Janus
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Anagh Astavans
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | | | - Ipsita Mohanty
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Tyler Evangelous
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Yue Chen
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Helene Kirshner
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA
| | | | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunobiology, Duke School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA
| | | | | | | | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke School of Medicine, Durham, NC 27710, USA; Department of Biochemistry, Duke School of Medicine, Durham, NC 27710, USA
| | - Stephen R Walsh
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Lindsey R Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunobiology, Duke School of Medicine, Durham, NC 27710, USA; Duke Global Health Institute, Duke School of Medicine, Durham, NC 27710, USA.
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4
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Wiehe K, Saunders KO, Stalls V, Cain DW, Venkatayogi S, Martin Beem JS, Berry M, Evangelous T, Henderson R, Hora B, Xia SM, Jiang C, Newman A, Bowman C, Lu X, Bryan ME, Bal J, Sanzone A, Chen H, Eaton A, Tomai MA, Fox CB, Tam YK, Barbosa C, Bonsignori M, Muramatsu H, Alam SM, Montefiori DC, Williams WB, Pardi N, Tian M, Weissman D, Alt FW, Acharya P, Haynes BF. Mutation-guided vaccine design: A process for developing boosting immunogens for HIV broadly neutralizing antibody induction. Cell Host Microbe 2024; 32:693-709.e7. [PMID: 38670093 DOI: 10.1016/j.chom.2024.04.006] [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: 04/28/2023] [Revised: 01/05/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
A major goal of HIV-1 vaccine development is the induction of broadly neutralizing antibodies (bnAbs). Although success has been achieved in initiating bnAb B cell lineages, design of boosting immunogens that select for bnAb B cell receptors with improbable mutations required for bnAb affinity maturation remains difficult. Here, we demonstrate a process for designing boosting immunogens for a V3-glycan bnAb B cell lineage. The immunogens induced affinity-matured antibodies by selecting for functional improbable mutations in bnAb precursor knockin mice. Moreover, we show similar success in prime and boosting with nucleoside-modified mRNA-encoded HIV-1 envelope trimer immunogens, with improved selection by mRNA immunogens of improbable mutations required for bnAb binding to key envelope glycans. These results demonstrate the ability of both protein and mRNA prime-boost immunogens for selection of rare B cell lineage intermediates with neutralizing breadth after bnAb precursor expansion, a key proof of concept and milestone toward development of an HIV-1 vaccine.
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Affiliation(s)
- Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Microbiology and Molecular Genetics, Duke University School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua S Martin Beem
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tyler Evangelous
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chuancang Jiang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cindy Bowman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mary E Bryan
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joena Bal
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Aja Sanzone
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Haiyan Chen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark A Tomai
- Corporate Research Materials Lab, 3M Company, St. Paul, MN 55144, USA
| | | | | | | | - Mattia Bonsignori
- Translational Immunobiology Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hiromi Muramatsu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Norbert Pardi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ming Tian
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Drew Weissman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick W Alt
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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5
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Feng F, Yuen R, Wang Y, Hua A, Kepler TB, Wetzler LM. Characterizing adjuvants' effects at murine immunoglobulin repertoire level. iScience 2024; 27:108749. [PMID: 38269092 PMCID: PMC10805652 DOI: 10.1016/j.isci.2023.108749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/29/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024] Open
Abstract
Generating large-scale, high-fidelity sequencing data is challenging and, furthermore, not much has been done to characterize adjuvants' effects at the repertoire level. Thus, we introduced an IgSeq pipeline that standardized library prep protocols and data analysis functions for accurate repertoire profiling. We then studied systemically effects of CpG and Alum on the Ig heavy chain repertoire using the ovalbumin (OVA) murine model. Ig repertoires of different tissues (spleen and bone marrow) and isotypes (IgG and IgM) were examined and compared in IGHV mutation, gene usage, CDR3 length, clonal diversity, and clonal selection. We found Ig repertoires of different compartments exhibited distinguishable profiles at the non-immunized steady state, and distinctions became more pronounced upon adjuvanted immunizations. Notably, Alum and CpG effects exhibited different tissue- and isotype-preferences. The former led to increased diversity of abundant clones in bone marrow, and the latter promoted the selection of IgG clones in both tissues.
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Affiliation(s)
- Feng Feng
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Rachel Yuen
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Yumei Wang
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Axin Hua
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Thomas B. Kepler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Mathematics and Statistics, Boston University, Boston, MA 02118, USA
| | - Lee M. Wetzler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
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6
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Saunders KO, Counts J, Thakur B, Stalls V, Edwards R, Manne K, Lu X, Mansouri K, Chen Y, Parks R, Barr M, Sutherland L, Bal J, Havill N, Chen H, Machiele E, Jamieson N, Hora B, Kopp M, Janowska K, Anasti K, Jiang C, Van Itallie E, Venkatayogi S, Eaton A, Henderson R, Barbosa C, Alam SM, Santra S, Weissman D, Moody MA, Cain DW, Tam YK, Lewis M, Williams WB, Wiehe K, Montefiori DC, Acharya P, Haynes BF. Vaccine induction of CD4-mimicking HIV-1 broadly neutralizing antibody precursors in macaques. Cell 2024; 187:79-94.e24. [PMID: 38181743 PMCID: PMC10860651 DOI: 10.1016/j.cell.2023.12.002] [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: 03/06/2023] [Revised: 09/08/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024]
Abstract
The CD4-binding site (CD4bs) is a conserved epitope on HIV-1 envelope (Env) that can be targeted by protective broadly neutralizing antibodies (bnAbs). HIV-1 vaccines have not elicited CD4bs bnAbs for many reasons, including the occlusion of CD4bs by glycans, expansion of appropriate naive B cells with immunogens, and selection of functional antibody mutations. Here, we demonstrate that immunization of macaques with a CD4bs-targeting immunogen elicits neutralizing bnAb precursors with structural and genetic features of CD4-mimicking bnAbs. Structures of the CD4bs nAb bound to HIV-1 Env demonstrated binding angles and heavy-chain interactions characteristic of all known human CD4-mimicking bnAbs. Macaque nAb were derived from variable and joining gene segments orthologous to the genes of human VH1-46-class bnAb. This vaccine study initiated in primates the B cells from which CD4bs bnAbs can derive, accomplishing the key first step in the development of an effective HIV-1 vaccine.
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Affiliation(s)
- Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - James Counts
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bhishem Thakur
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yue Chen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rob Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joena Bal
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas Havill
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA
| | - Haiyan Chen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Emily Machiele
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nolan Jamieson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Megan Kopp
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katarzyna Janowska
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chuancang Jiang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Elizabeth Van Itallie
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Drew Weissman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | - Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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7
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Hoehn KB, Kleinstein SH. B cell phylogenetics in the single cell era. Trends Immunol 2024; 45:62-74. [PMID: 38151443 PMCID: PMC10872299 DOI: 10.1016/j.it.2023.11.004] [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: 10/26/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/29/2023]
Abstract
The widespread availability of single-cell RNA sequencing (scRNA-seq) has led to the development of new methods for understanding immune responses. Single-cell transcriptome data can now be paired with B cell receptor (BCR) sequences. However, RNA from BCRs cannot be analyzed like most other genes because BCRs are genetically diverse within individuals. In humans, BCRs are shaped through recombination followed by mutation and selection for antigen binding. As these processes co-occur with cell division, B cells can be studied using phylogenetic trees representing the mutations within a clone. B cell trees can link experimental timepoints, tissues, or cellular subtypes. Here, we review the current state and potential of how B cell phylogenetics can be combined with single-cell data to understand immune responses.
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Affiliation(s)
- Kenneth B Hoehn
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
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8
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Henderson R, Anasti K, Manne K, Stalls V, Saunders C, Bililign Y, Williams A, Bubphamala P, Montani M, Kachhap S, Li J, Jaing C, Newman A, Cain D, Lu X, Venkatayogi S, Berry M, Wagh K, Korber B, Saunders KO, Tian M, Alt F, Wiehe K, Acharya P, Alam SM, Haynes BF. Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571700. [PMID: 38168268 PMCID: PMC10760096 DOI: 10.1101/2023.12.15.571700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Vaccine development targeting rapidly evolving pathogens such as HIV-1 requires induction of broadly neutralizing antibodies (bnAbs) with conserved paratopes and mutations, and, in some cases, the same Ig-heavy chains. The current trial-and-error search for immunogen modifications that improve selection for specific bnAb mutations is imprecise. To precisely engineer bnAb boosting immunogens, we used molecular dynamics simulations to examine encounter states that form when antibodies collide with the HIV-1 Envelope (Env). By mapping how bnAbs use encounter states to find their bound states, we identified Env mutations that were predicted to select for specific antibody mutations in two HIV-1 bnAb B cell lineages. The Env mutations encoded antibody affinity gains and selected for desired antibody mutations in vivo. These results demonstrate proof-of-concept that Env immunogens can be designed to directly select for specific antibody mutations at residue-level precision by vaccination, thus demonstrating the feasibility of sequential bnAb-inducing HIV-1 vaccine design.
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Affiliation(s)
- Rory Henderson
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Carrie Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Yishak Bililign
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashliegh Williams
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Pimthada Bubphamala
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Maya Montani
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Sangita Kachhap
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Jingjing Li
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Chuancang Jaing
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Derek Cain
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- The New Mexico Consortium, Los Alamos, NM, 87544 USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- The New Mexico Consortium, Los Alamos, NM, 87544 USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Ming Tian
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fred Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
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9
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Simmons HC, Watanabe A, Oguin III TH, Van Itallie ES, Wiehe KJ, Sempowski GD, Kuraoka M, Kelsoe G, McCarthy KR. A new class of antibodies that overcomes a steric barrier to cross-group neutralization of influenza viruses. PLoS Biol 2023; 21:e3002415. [PMID: 38127922 PMCID: PMC10734940 DOI: 10.1371/journal.pbio.3002415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/02/2023] [Indexed: 12/23/2023] Open
Abstract
Antibody titers that inhibit the influenza virus hemagglutinin (HA) from engaging its receptor are the accepted correlate of protection from infection. Many potent antibodies with broad, intra-subtype specificity bind HA at the receptor binding site (RBS). One barrier to broad H1-H3 cross-subtype neutralization is an insertion (133a) between positions 133 and 134 on the rim of the H1 HA RBS. We describe here a class of antibodies that overcomes this barrier. These genetically unrestricted antibodies are abundant in the human B cell memory compartment. Analysis of the affinities of selected members of this class for historical H1 and H3 isolates suggest that they were elicited by H3 exposure and broadened or diverted by later exposure(s) to H1 HA. RBS mutations in egg-adapted vaccine strains cause the new H1 specificity of these antibodies to depend on the egg adaptation. The results suggest that suitable immunogens might elicit 133a-independent, H1-H3 cross neutralization by RBS-directed antibodies.
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Affiliation(s)
- Holly C. Simmons
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Akiko Watanabe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
| | - Thomas H. Oguin III
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | | | - Kevin J. Wiehe
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Masayuki Kuraoka
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
| | - Garnett Kelsoe
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Kevin R. McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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10
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Mathews J, Van Itallie E, Wiehe K, Schmidler SC. Computing the inducibility of B cell lineages under a context-dependent model of affinity maturation: Applications to sequential vaccine design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562156. [PMID: 37905016 PMCID: PMC10614816 DOI: 10.1101/2023.10.13.562156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
A key challenge in B cell lineage-based vaccine design is understanding the inducibility of target neutralizing antibodies. We approach this problem through the use of detailed stochastic modeling of the somatic hypermutation process that occurs during affinity maturation. Under such a model, sequence mutation rates are context-dependent, rendering standard probability calculations for sequence evolution intractable. We develop an algorithmic approach to rapid, accurate approximation of key marginal sequence likelihoods required to inform modern sequential vaccine design strategies. These calculated probabilities are used to define an inducibility index for selecting among potential targets for immunogen design. We apply this approach to the problem of choosing targets for the design of boosting immunogens aimed at elicitation of the HIV broadly-neutralizing antibody DH270min11.
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Affiliation(s)
- Joseph Mathews
- Department of Statistical Science, Duke University, Durham, NC, USA
| | | | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Scott C. Schmidler
- Department of Statistical Science, Duke University, Durham, NC, USA
- Department of Computer Science, Duke University, Durham, NC, USA
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
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11
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Ronsard L, Yousif AS, Nait Mohamed FA, Feldman J, Okonkwo V, McCarthy C, Schnabel J, Caradonna T, Barnes RM, Rohrer D, Lonberg N, Schmidt A, Lingwood D. Engaging an HIV vaccine target through the acquisition of low B cell affinity. Nat Commun 2023; 14:5249. [PMID: 37640732 PMCID: PMC10462694 DOI: 10.1038/s41467-023-40918-2] [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: 12/07/2021] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Low affinity is common for germline B cell receptors (BCR) seeding development of broadly neutralizing antibodies (bnAbs) that engage hypervariable viruses, including HIV. Antibody affinity selection is also non-homogenizing, insuring the survival of low affinity B cell clones. To explore whether this provides a natural window for expanding human B cell lineages against conserved vaccine targets, we deploy transgenic mice mimicking human antibody diversity and somatic hypermutation (SHM) and immunize with simple monomeric HIV glycoprotein envelope immunogens. We report an immunization regimen that focuses B cell memory upon the conserved CD4 binding site (CD4bs) through both conventional affinity maturation and reproducible expansion of low affinity BCR clones with public patterns in SHM. In the latter instance, SHM facilitates target acquisition by decreasing binding strength. This suggests that permissive B cell selection enables the discovery of antibody epitopes, in this case an HIV bnAb site.
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Affiliation(s)
- Larance Ronsard
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Ashraf S Yousif
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Jared Feldman
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Vintus Okonkwo
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Caitlin McCarthy
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Julia Schnabel
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Timothy Caradonna
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Aaron Schmidt
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Lingwood
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA.
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12
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Aihara F, Wang Y, Belkina AC, Fearns R, Mizgerd JP, Feng F, Kepler TB. Diversity of B Cell Populations and Ig Repertoire in Human Lungs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:486-496. [PMID: 37314411 PMCID: PMC10352589 DOI: 10.4049/jimmunol.2200340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 05/25/2023] [Indexed: 06/15/2023]
Abstract
The human lung carries a unique microbiome adapted to the air-filled, mucous-lined environment, the presence of which requires an immune system capable of recognizing harmful populations while preventing reactions toward commensals. B cells in the lung play a key role in pulmonary immunity, generating Ag-specific Abs, as well as cytokine secretion for immune activation and regulation. In this study, we compared B cell subsets in human lungs versus circulating cells by analyzing patient-paired lung and blood samples. We found a significantly smaller pool of CD19+, CD20+ B cells in the lung relative to the blood. CD27+, IgD-, class-switched memory B cells (Bmems) composed a larger proportion of the pool of pulmonary B cells. The residency marker CD69 was also significantly higher in the lung. We also sequenced the Ig V region genes (IgVRGs) of class-switched Bmems that do, or do not, express CD69. We observed the IgVRGs of pulmonary Bmems to be as heavily mutated from the unmutated common ancestor as those in circulation. Furthermore, we found progenies within a quasi-clone can gain or lose CD69 expression, regardless of whether the parent clone expressed the residency marker. Overall, our results show that despite its vascularized nature, human lungs carry a unique proportion of B cell subsets. The IgVRGs of pulmonary Bmems are as diverse as those in blood, and progenies of Bmems retain the ability to gain or lose residency.
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Affiliation(s)
- Fumiaki Aihara
- Department of Microbiology, Boston University, Boston, MA
| | - Yumei Wang
- Department of Microbiology, Boston University, Boston, MA
| | | | - Rachel Fearns
- Department of Microbiology, Boston University, Boston, MA
| | | | - Feng Feng
- Department of Microbiology, Boston University, Boston, MA
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13
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Martin Beem J, Venkatayogi S, Haynes BF, Wiehe K. ARMADiLLO: a web server for analyzing antibody mutation probabilities. Nucleic Acids Res 2023; 51:W51-W56. [PMID: 37260077 PMCID: PMC10320107 DOI: 10.1093/nar/gkad398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Antibodies are generated by B cells that evolve receptor specificity to pathogens through rounds of mutation and selection in a process called affinity maturation. Somatic hypermutation is mediated by an enzyme with DNA sequence context-dependent targeting and substitution resulting in variable probabilities of amino acid substitutions during affinity maturation. We have previously developed a program called Antigen Receptor Mutation Analyzer for the Detection of Low Likelihood Occurrences (ARMADiLLO) that performs simulations of the somatic hypermutation process to estimate the probabilities of observed antibody mutations. Here we describe the ARMADiLLO web server (https://armadillo.dhvi.duke.edu), an easy-to-use web interface that analyzes input antibody sequences and displays the probability estimates for all possible amino acid changes over the full length of an antibody sequence. The probability of antibody mutations can be used by immunologists studying B cell ontogenies and by vaccine designers that are pursuing strategies to elicit broadly neutralizing antibodies which are enriched with developmentally rate-limiting improbable mutations. The ARMADiLLO web server also contains precomputed results reporting the probability of amino acid substitutions in all human V gene segments and in a collection of HIV broadly neutralizing antibodies.
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Affiliation(s)
- Joshua S Martin Beem
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC27710, USA
- Department of Immunology, Duke University Medical Center; Durham, NC27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC27710, USA
- Department of Medicine, Duke University Medical Center; Durham, NC27710, USA
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14
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Onodera T, Sax N, Sato T, Adachi Y, Kotaki R, Inoue T, Shinnakasu R, Nakagawa T, Fukushi S, Terooatea T, Yoshikawa M, Tonouchi K, Nagakura T, Moriyama S, Matsumura T, Isogawa M, Terahara K, Takano T, Sun L, Nishiyama A, Omoto S, Shinkai M, Kurosaki T, Yamashita K, Takahashi Y. CD62L expression marks SARS-CoV-2 memory B cell subset with preference for neutralizing epitopes. SCIENCE ADVANCES 2023; 9:eadf0661. [PMID: 37315144 DOI: 10.1126/sciadv.adf0661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 05/09/2023] [Indexed: 06/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2-neutralizing antibodies primarily target the spike receptor binding domain (RBD). However, B cell antigen receptors (BCRs) on RBD-binding memory B (Bmem) cells have variation in the neutralizing activities. Here, by combining single Bmem cell profiling with antibody functional assessment, we dissected the phenotype of Bmem cell harboring the potently neutralizing antibodies in coronavirus disease 2019 (COVID-19)-convalescent individuals. The neutralizing subset was marked by an elevated CD62L expression and characterized by distinct epitope preference and usage of convergent VH (variable region of immunoglobulin heavy chain) genes, accounting for the neutralizing activities. Concordantly, the correlation was observed between neutralizing antibody titers in blood and CD62L+ subset, despite the equivalent RBD binding of CD62L+ and CD62L- subset. Furthermore, the kinetics of CD62L+ subset differed between the patients who recovered from different COVID-19 severities. Our Bmem cell profiling reveals the unique phenotype of Bmem cell subset that harbors potently neutralizing BCRs, advancing our understanding of humoral protection.
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Affiliation(s)
- Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Yu Adachi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryutaro Kotaki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takeshi Inoue
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Ryo Shinnakasu
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | | | - Shuetsu Fukushi
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Keisuke Tonouchi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Takaki Nagakura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
- Laboratory of Viral Infection, Ōmura Satoshi Memorial Institute Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Matsumura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masanori Isogawa
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazutaka Terahara
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomohiro Takano
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Lin Sun
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ayae Nishiyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Osaka, Japan
| | | | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
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15
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Henderson R, Zhou Y, Stalls V, Wiehe K, Saunders KO, Wagh K, Anasti K, Barr M, Parks R, Alam SM, Korber B, Haynes BF, Bartesaghi A, Acharya P. Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage. Nat Commun 2023; 14:2782. [PMID: 37188681 PMCID: PMC10184639 DOI: 10.1038/s41467-023-38108-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affinity maturation and reveal solutions for these that will inform immunogen design aimed at eliciting a broadly neutralizing immune response by vaccination.
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Affiliation(s)
- Rory Henderson
- Department of Medicine and Immunology, Duke University School of Medicine, Durham, NC, USA.
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin Wiehe
- Department of Medicine and Immunology, Duke University School of Medicine, Durham, NC, USA
- 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
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - S Munir Alam
- Department of Medicine and Immunology, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Barton F Haynes
- Department of Medicine and Immunology, Duke University School of Medicine, Durham, NC, USA.
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC, USA.
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
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16
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Pelissier A, Luo S, Stratigopoulou M, Guikema JEJ, Rodríguez Martínez M. Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires. Front Immunol 2023; 14:1123968. [PMID: 37138881 PMCID: PMC10150052 DOI: 10.3389/fimmu.2023.1123968] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
The adaptive immune system has the extraordinary ability to produce a broad range of immunoglobulins that can bind a wide variety of antigens. During adaptive immune responses, activated B cells duplicate and undergo somatic hypermutation in their B-cell receptor (BCR) genes, resulting in clonal families of diversified B cells that can be related back to a common ancestor. Advances in high-throughput sequencing technologies have enabled the high-throughput characterization of B-cell repertoires, however, the accurate identification of clonally related BCR sequences remains a major challenge. In this study, we compare three different clone identification methods on both simulated and experimental data, and investigate their impact on the characterization of B-cell diversity. We observe that different methods lead to different clonal definitions, which affects the quantification of clonal diversity in repertoire data. Our analyses show that direct comparisons between clonal clusterings and clonal diversity of different repertoires should be avoided if different clone identification methods were used to define the clones. Despite this variability, the diversity indices inferred from the repertoires' clonal characterization across samples show similar patterns of variation regardless of the clonal identification method used. We find the Shannon entropy to be the most robust in terms of the variability of diversity rank across samples. Our analysis also suggests that the traditional germline gene alignment-based method for clonal identification remains the most accurate when the complete information about the sequence is known, but that alignment-free methods may be preferred for shorter sequencing read lengths. We make our implementation freely available as a Python library cdiversity.
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Affiliation(s)
- Aurelien Pelissier
- IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Siyuan Luo
- IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Maria Stratigopoulou
- Department of Pathology, Amsterdam University Medical Centers, location AMC, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, Netherlands
| | - Jeroen E. J. Guikema
- Department of Pathology, Amsterdam University Medical Centers, location AMC, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, Netherlands
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17
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Andreano E, Paciello I, Pierleoni G, Maccari G, Antonelli G, Abbiento V, Pileri P, Benincasa L, Giglioli G, Piccini G, De Santi C, Sala C, Medini D, Montomoli E, Maes P, Rappuoli R. mRNA vaccines and hybrid immunity use different B cell germlines against Omicron BA.4 and BA.5. Nat Commun 2023; 14:1734. [PMID: 36977711 PMCID: PMC10044118 DOI: 10.1038/s41467-023-37422-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Severe acute respiratory syndrome 2 Omicron BA.4 and BA.5 are characterized by high transmissibility and ability to escape natural and vaccine induced immunity. Here we test the neutralizing activity of 482 human monoclonal antibodies isolated from people who received two or three mRNA vaccine doses or from people vaccinated after infection. The BA.4 and BA.5 variants are neutralized only by approximately 15% of antibodies. Remarkably, the antibodies isolated after three vaccine doses target mainly the receptor binding domain Class 1/2, while antibodies isolated after infection recognize mostly the receptor binding domain Class 3 epitope region and the N-terminal domain. Different B cell germlines are used by the analyzed cohorts. The observation that mRNA vaccination and hybrid immunity elicit a different immunity against the same antigen is intriguing and its understanding may help to design the next generation of therapeutics and vaccines against coronavirus disease 2019.
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Affiliation(s)
- Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | | | - Giuseppe Maccari
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Giada Antonelli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Valentina Abbiento
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Piero Pileri
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | | | | | | | - Concetta De Santi
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Claudia Sala
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Duccio Medini
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Emanuele Montomoli
- VisMederi Research S.r.l., Siena, Italy
- VisMederi S.r.l, Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Piet Maes
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Rino Rappuoli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
- Fondazione Biotecnopolo di Siena, Siena, Italy.
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18
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Abdollahi N, Jeusset L, de Septenville A, Davi F, Bernardes JS. Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances. BMC Bioinformatics 2023; 24:70. [PMID: 36849917 PMCID: PMC9972711 DOI: 10.1186/s12859-022-05112-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/13/2022] [Indexed: 03/01/2023] Open
Abstract
B cell receptor (BCR) genes exposed to an antigen undergo somatic hypermutations and Darwinian antigen selection, generating a large BCR-antibody diversity. This process, known as B cell affinity maturation, increases antibody affinity, forming a specific B cell lineage that includes the unmutated ancestor and mutated variants. In a B cell lineage, cells with a higher antigen affinity will undergo clonal expansion, while those with a lower affinity will not proliferate and probably be eliminated. Therefore, cellular (genotype) abundance provides a valuable perspective on the ongoing evolutionary process. Phylogenetic tree inference is often used to reconstruct B cell lineage trees and represents the evolutionary dynamic of BCR affinity maturation. However, such methods should process B-cell population data derived from experimental sampling that might contain different cellular abundances. There are a few phylogenetic methods for tracing the evolutionary events occurring in B cell lineages; best-performing solutions are time-demanding and restricted to analysing a reduced number of sequences, while time-efficient methods do not consider cellular abundances. We propose ClonalTree, a low-complexity and accurate approach to construct B-cell lineage trees that incorporates genotype abundances into minimum spanning tree (MST) algorithms. Using both simulated and experimental data, we demonstrate that ClonalTree outperforms MST-based algorithms and achieves a comparable performance to a method that explores tree-generating space exhaustively. Furthermore, ClonalTree has a lower running time, being more convenient for building B-cell lineage trees from high-throughput BCR sequencing data, mainly in biomedical applications, where a lower computational time is appreciable. It is hundreds to thousands of times faster than exhaustive approaches, enabling the analysis of a large set of sequences within minutes or seconds and without loss of accuracy. The source code is freely available at github.com/julibinho/ClonalTree.
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Affiliation(s)
- Nika Abdollahi
- grid.462844.80000 0001 2308 1657UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne University, Paris, France ,grid.121334.60000 0001 2097 0141IMGT®, The International ImMunoGeneTics Information System, CNRS, Institute of Human Genetics, Montpellier University, Montpellier, France
| | - Lucile Jeusset
- grid.462844.80000 0001 2308 1657UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne University, Paris, France ,grid.462844.80000 0001 2308 1657AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris, France
| | - Anne de Septenville
- grid.462844.80000 0001 2308 1657AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris, France
| | - Frederic Davi
- grid.462844.80000 0001 2308 1657AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris, France
| | - Juliana Silva Bernardes
- UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne University, Paris, France.
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19
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Kuraoka M, Aschner CB, Windsor IW, Mahant AM, Garforth SJ, Kong SL, Achkar JM, Almo SC, Kelsoe G, Herold BC. A non-neutralizing glycoprotein B monoclonal antibody protects against herpes simplex virus disease in mice. J Clin Invest 2023; 133:161968. [PMID: 36454639 PMCID: PMC9888390 DOI: 10.1172/jci161968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
There is an unmet need for monoclonal antibodies (mAbs) for prevention or as adjunctive treatment of herpes simplex virus (HSV) disease. Most vaccine and mAb efforts focus on neutralizing antibodies, but for HSV this strategy has proven ineffective. Preclinical studies with a candidate HSV vaccine strain, ΔgD-2, demonstrated that non-neutralizing antibodies that activate Fcγ receptors (FcγRs) to mediate antibody-dependent cellular cytotoxicity (ADCC) provide active and passive protection against HSV-1 and HSV-2. We hypothesized that this vaccine provides a tool to identify and characterize protective mAbs. We isolated HSV-specific mAbs from germinal center and memory B cells and bone marrow plasmacytes of ΔgD-2-vaccinated mice and evaluated these mAbs for binding, neutralizing, and FcγR-activating activity and for protective efficacy in mice. The most potent protective mAb, BMPC-23, was not neutralizing but activated murine FcγRIV, a biomarker of ADCC. The cryo-electron microscopic structure of the Fab-glycoprotein B (gB) assembly identified domain IV of gB as the epitope. A single dose of BMPC-23 administered 24 hours before or after viral challenge provided significant protection when configured as mouse IgG2c and protected mice expressing human FcγRIII when engineered as a human IgG1. These results highlight the importance of FcR-activating antibodies in protecting against HSV.
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Affiliation(s)
- Masayuki Kuraoka
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Clare Burn Aschner
- Department of Microbiology-Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Ian W. Windsor
- Department of Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Aakash Mahant Mahant
- Department of Microbiology-Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Susan Luozheng Kong
- Department of Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jacqueline M. Achkar
- Department of Microbiology-Immunology, Albert Einstein College of Medicine, New York, New York, USA.,Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Garnett Kelsoe
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Surgery and,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Betsy C. Herold
- Department of Microbiology-Immunology, Albert Einstein College of Medicine, New York, New York, USA.,Department of Pediatrics Albert Einstein College of Medicine, New York, New York, USA
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20
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Dacon C, Peng L, Lin TH, Tucker C, Lee CCD, Cong Y, Wang L, Purser L, Cooper AJR, Williams JK, Pyo CW, Yuan M, Kosik I, Hu Z, Zhao M, Mohan D, Peterson M, Skinner J, Dixit S, Kollins E, Huzella L, Perry D, Byrum R, Lembirik S, Murphy M, Zhang Y, Yang ES, Chen M, Leung K, Weinberg RS, Pegu A, Geraghty DE, Davidson E, Doranz BJ, Douagi I, Moir S, Yewdell JW, Schmaljohn C, Crompton PD, Mascola JR, Holbrook MR, Nemazee D, Wilson IA, Tan J. Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses. Cell Host Microbe 2023; 31:97-111.e12. [PMID: 36347257 PMCID: PMC9639329 DOI: 10.1016/j.chom.2022.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/04/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.
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Affiliation(s)
- Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrew J R Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Divya Mohan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Saurabh Dixit
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin Kollins
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Louis Huzella
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Donna Perry
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Russell Byrum
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sanae Lembirik
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rona S Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- B Cell Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
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21
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Andreano E, Paciello I, Pierleoni G, Piccini G, Abbiento V, Antonelli G, Pileri P, Manganaro N, Pantano E, Maccari G, Marchese S, Donnici L, Benincasa L, Giglioli G, Leonardi M, De Santi C, Fabbiani M, Rancan I, Tumbarello M, Montagnani F, Sala C, Medini D, De Francesco R, Montomoli E, Rappuoli R. B cell analyses after SARS-CoV-2 mRNA third vaccination reveals a hybrid immunity like antibody response. Nat Commun 2023; 14:53. [PMID: 36599850 DOI: 10.1038/s41467-022-35781-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
The continuous evolution of SARS-CoV-2 generated highly mutated variants able to escape natural and vaccine-induced primary immunity. The administration of a third mRNA vaccine dose induces a secondary response with increased protection. Here we investigate the longitudinal evolution of the neutralizing antibody response in four donors after three mRNA doses at single-cell level. We sorted 4100 spike protein specific memory B cells identifying 350 neutralizing antibodies. The third dose increases the antibody neutralization potency and breadth against all SARS-CoV-2 variants as observed with hybrid immunity. However, the B cell repertoire generating this response is different. The increases of neutralizing antibody responses is largely due to the expansion of B cell germlines poorly represented after two doses, and the reduction of germlines predominant after primary immunization. Our data show that different immunization regimens induce specific molecular signatures which should be considered while designing new vaccines and immunization strategies.
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Affiliation(s)
- Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | | | | | - Valentina Abbiento
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Giada Antonelli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Piero Pileri
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Noemi Manganaro
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Elisa Pantano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Giuseppe Maccari
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Silvia Marchese
- Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, Milan, Italy
| | - Lorena Donnici
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | | | | | | | - Concetta De Santi
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Massimiliano Fabbiani
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy
| | - Ilaria Rancan
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy
| | - Mario Tumbarello
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Montagnani
- Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Claudia Sala
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Duccio Medini
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Raffaele De Francesco
- Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, Milan, Italy
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Emanuele Montomoli
- VisMederi Research S.r.l., Siena, Italy
- VisMederi S.r.l, Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy.
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
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22
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Luo S, Jing C, Ye AY, Kratochvil S, Cottrell CA, Koo JH, Chapdelaine Williams A, Francisco LV, Batra H, Lamperti E, Kalyuzhniy O, Zhang Y, Barbieri A, Manis JP, Haynes BF, Schief WR, Batista FD, Tian M, Alt FW. Humanized V(D)J-rearranging and TdT-expressing mouse vaccine models with physiological HIV-1 broadly neutralizing antibody precursors. Proc Natl Acad Sci U S A 2023; 120:e2217883120. [PMID: 36574685 PMCID: PMC9910454 DOI: 10.1073/pnas.2217883120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 12/28/2022] Open
Abstract
Antibody heavy chain (HC) and light chain (LC) variable region exons are assembled by V(D)J recombination. V(D)J junctional regions encode complementarity-determining-region 3 (CDR3), an antigen-contact region immensely diversified through nontemplated nucleotide additions ("N-regions") by terminal deoxynucleotidyl transferase (TdT). HIV-1 vaccine strategies seek to elicit human HIV-1 broadly neutralizing antibodies (bnAbs), such as the potent CD4-binding site VRC01-class bnAbs. Mice with primary B cells that express receptors (BCRs) representing bnAb precursors are used as vaccination models. VRC01-class bnAbs uniformly use human HC VH1-2 and commonly use human LCs Vκ3-20 or Vκ1-33 associated with an exceptionally short 5-amino-acid (5-aa) CDR3. Prior VRC01-class models had nonphysiological precursor levels and/or limited precursor diversity. Here, we describe VRC01-class rearranging mice that generate more physiological primary VRC01-class BCR repertoires via rearrangement of VH1-2, as well as Vκ1-33 and/or Vκ3-20 in association with diverse CDR3s. Human-like TdT expression in mouse precursor B cells increased LC CDR3 length and diversity and also promoted the generation of shorter LC CDR3s via N-region suppression of dominant microhomology-mediated Vκ-to-Jκ joins. Priming immunization with eOD-GT8 60mer, which strongly engages VRC01 precursors, induced robust VRC01-class germinal center B cell responses. Vκ3-20-based responses were enhanced by N-region addition, which generates Vκ3-20-to-Jκ junctional sequence combinations that encode VRC01-class 5-aa CDR3s with a critical E residue. VRC01-class-rearranging models should facilitate further evaluation of VRC01-class prime and boost immunogens. These new VRC01-class mouse models establish a prototype for the generation of vaccine-testing mouse models for other HIV-1 bnAb lineages that employ different HC or LC Vs.
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Affiliation(s)
- Sai Luo
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Changbin Jing
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Adam Yongxin Ye
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Sven Kratochvil
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
| | - Christopher A. Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA92037
| | - Ja-Hyun Koo
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
| | - Aimee Chapdelaine Williams
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Lucas Vieira Francisco
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Himanshu Batra
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Edward Lamperti
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA92037
| | - Yuxiang Zhang
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Alessandro Barbieri
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA02115
| | - John P. Manis
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA02115
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC27710
- Department of Medicine, Duke University School of Medicine, Durham, NC27710
- Department of Immunology, Duke University School of Medicine, Durham, NC27710
| | - William R. Schief
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA92037
| | - Facundo D. Batista
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Immunology, Harvard Medical School, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
| | - Ming Tian
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Frederick W. Alt
- HHMI, Boston Children's Hospital, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Genetics, Harvard Medical School, Boston, MA02115
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23
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Singh T, Hwang KK, Miller AS, Jones RL, Lopez CA, Dulson SJ, Giuberti C, Gladden MA, Miller I, Webster HS, Eudailey JA, Luo K, Von Holle T, Edwards RJ, Valencia S, Burgomaster KE, Zhang S, Mangold JF, Tu JJ, Dennis M, Alam SM, Premkumar L, Dietze R, Pierson TC, Eong Ooi E, Lazear HM, Kuhn RJ, Permar SR, Bonsignori M. A Zika virus-specific IgM elicited in pregnancy exhibits ultrapotent neutralization. Cell 2022; 185:4826-4840.e17. [PMID: 36402135 PMCID: PMC9742325 DOI: 10.1016/j.cell.2022.10.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/23/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022]
Abstract
Congenital Zika virus (ZIKV) infection results in neurodevelopmental deficits in up to 14% of infants born to ZIKV-infected mothers. Neutralizing antibodies are a critical component of protective immunity. Here, we demonstrate that plasma IgM contributes to ZIKV immunity in pregnancy, mediating neutralization up to 3 months post-symptoms. From a ZIKV-infected pregnant woman, we isolated a pentameric ZIKV-specific IgM (DH1017.IgM) that exhibited ultrapotent ZIKV neutralization dependent on the IgM isotype. DH1017.IgM targets an envelope dimer epitope within domain II. The epitope arrangement on the virion is compatible with concurrent engagement of all ten antigen-binding sites of DH1017.IgM, a solution not available to IgG. DH1017.IgM protected mice against viremia upon lethal ZIKV challenge more efficiently than when expressed as an IgG. Our findings identify a role for antibodies of the IgM isotype in protection against ZIKV and posit DH1017.IgM as a safe and effective candidate immunotherapeutic, particularly during pregnancy.
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Affiliation(s)
- Tulika Singh
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA,Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Kwan-Ki Hwang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew S. Miller
- Department of Biological Sciences, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Rebecca L. Jones
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cesar A. Lopez
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarah J. Dulson
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Camila Giuberti
- Núcleo de Doenças Infecciosas—Universidade Federal do Espírito Santo, Vitoria, Espírito Santo 29075-910, Brazil
| | - Morgan A. Gladden
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Itzayana Miller
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA,Department of Pediatrics, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Helen S. Webster
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua A. Eudailey
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA,Department of Pediatrics, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Kan Luo
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tarra Von Holle
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sarah Valencia
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katherine E. Burgomaster
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Summer Zhang
- Duke-National University of Singapore Medical School, 169857, Singapore
| | - Jesse F. Mangold
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua J. Tu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maria Dennis
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Reynaldo Dietze
- Núcleo de Doenças Infecciosas—Universidade Federal do Espírito Santo, Vitoria, Espírito Santo 29075-910, Brazil,Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon 1349-008, Portugal
| | - Theodore C. Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Eng Eong Ooi
- Duke-National University of Singapore Medical School, 169857, Singapore
| | - Helen M. Lazear
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Sallie R. Permar
- Department of Pediatrics, Weill Cornell Medicine, New York City, NY 10065, USA,Senior author. These authors contributed equally,Correspondence: (S.R.P.), (M.B.)
| | - Mattia Bonsignori
- Translational Immunobiology Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep 2022; 41:111628. [PMID: 36351401 PMCID: PMC9883670 DOI: 10.1016/j.celrep.2022.111628] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
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Affiliation(s)
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Rachel Hecht
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Anne A Roffler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elisa Marchiori
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Thomas H Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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25
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Saunders KO, Edwards RJ, Tilahun K, Manne K, Lu X, Cain DW, Wiehe K, Williams WB, Mansouri K, Hernandez GE, Sutherland L, Scearce R, Parks R, Barr M, DeMarco T, Eater CM, Eaton A, Morton G, Mildenberg B, Wang Y, Rountree RW, Tomai MA, Fox CB, Moody MA, Alam SM, Santra S, Lewis MG, Denny TN, Shaw GM, Montefiori DC, Acharya P, Haynes BF. Stabilized HIV-1 envelope immunization induces neutralizing antibodies to the CD4bs and protects macaques against mucosal infection. Sci Transl Med 2022; 14:eabo5598. [PMID: 36070369 PMCID: PMC10034035 DOI: 10.1126/scitranslmed.abo5598] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A successful HIV-1 vaccine will require induction of a polyclonal neutralizing antibody (nAb) response, yet vaccine-mediated induction of such a response in primates remains a challenge. We found that a stabilized HIV-1 CH505 envelope (Env) trimer formulated with a Toll-like receptor 7/8 agonist induced potent HIV-1 polyclonal nAbs that correlated with protection from homologous simian-human immunodeficiency virus (SHIV) infection. The serum dilution that neutralized 50% of virus replication (ID50 titer) required to protect 90% of macaques was 1:364 against the challenge virus grown in primary rhesus CD4+ T cells. Structural analyses of vaccine-induced nAbs demonstrated targeting of the Env CD4 binding site or the N156 glycan and the third variable loop base. Autologous nAb specificities similar to those elicited in macaques by vaccination were isolated from the human living with HIV from which the CH505 Env immunogen was derived. CH505 viral isolates were isolated that mutated the V1 to escape both the infection-induced and vaccine-induced antibodies. These results define the specificities of a vaccine-induced nAb response and the protective titers of HIV-1 vaccine-induced nAbs required to protect nonhuman primates from low-dose mucosal challenge by SHIVs bearing a primary transmitted/founder Env.
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Affiliation(s)
- Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
- Department of Microbiology and Molecular Genetics, Duke University Medical Center; Durham, NC 27710
- Department of Immunology, Duke University Medical Center; Durham, NC, 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Kedamawit Tilahun
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Derek W. Cain
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Wilton B. Williams
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
- Department of Immunology, Duke University Medical Center; Durham, NC, 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Giovanna E. Hernandez
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Laura Sutherland
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Richard Scearce
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Todd DeMarco
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Chloe M. Eater
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
| | | | | | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - R. Wes Rountree
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Mark A. Tomai
- 3M Corporate Research Materials Lab, 3M Company; St. Paul, MN, 55144, USA
| | | | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Pediatrics, Duke University Medical Center; Durham, NC, 27710, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center; Boston, MA, 02215, USA
| | | | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
| | - George M. Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Surgery, Duke University Medical Center; Durham, NC 27710
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center; Durham, NC 27710
- Department of Immunology, Duke University Medical Center; Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center; Durham, NC, 27710, USA
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26
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Rotavirus VP4 Epitope of a Broadly Neutralizing Human Antibody Defined by Its Structure Bound with an Attenuated-Strain Virion. J Virol 2022; 96:e0062722. [PMID: 35924923 PMCID: PMC9400500 DOI: 10.1128/jvi.00627-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Rotavirus live-attenuated vaccines, both mono- and pentavalent, generate broadly heterotypic protection. B-cells isolated from adults encode neutralizing antibodies, some with affinity for VP5*, that afford broad protection in mice. We have mapped the epitope of one such antibody by determining the high-resolution cryo-EM structure of its antigen-binding fragment (Fab) bound to the virion of a candidate vaccine strain, CDC-9. The Fab contacts both the distal end of a VP5* β-barrel domain and the two VP8* lectin-like domains at the tip of a projecting spike. Its interactions with VP8* do not impinge on the likely receptor-binding site, suggesting that the mechanism of neutralization is at a step subsequent to initial attachment. We also examined structures of CDC-9 virions from two different stages of serial passaging. Nearly all the VP4 (cleaved to VP8*/VP5*) spikes on particles from the earlier passage (wild-type isolate) had transitioned from the "upright" conformation present on fully infectious virions to the "reversed" conformation that is probably the end state of membrane insertion, unable to mediate penetration, consistent with the very low in vitro infectivity of the wild-type isolate. About half the VP4 spikes were upright on particles from the later passage, which had recovered substantial in vitro infectivity but had acquired an attenuated phenotype in neonatal rats. A mutation in VP4 that occurred during passaging appears to stabilize the interface at the apex of the spike and could account for the greater stability of the upright spikes on the late-passage, attenuated isolate. IMPORTANCE Rotavirus live-attenuated vaccines generate broadly heterotypic protection, and B-cells isolated from adults encode antibodies that are broadly protective in mice. Determining the structural and mechanistic basis of broad protection can contribute to understanding the current limitations of vaccine efficacy in developing countries. The structure of an attenuated human rotavirus isolate (CDC-9) bound with the Fab fragment of a broadly heterotypic protective antibody shows that protection is probably due to inhibition of the conformational transition in the viral spike protein (VP4) critical for viral penetration, rather than to inhibition of receptor binding. A comparison of structures of CDC-9 virus particles at two stages of serial passaging supports a proposed mechanism for initial steps in rotavirus membrane penetration.
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27
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Andreano E, Paciello I, Marchese S, Donnici L, Pierleoni G, Piccini G, Manganaro N, Pantano E, Abbiento V, Pileri P, Benincasa L, Giglioli G, Leonardi M, Maes P, De Santi C, Sala C, Montomoli E, De Francesco R, Rappuoli R. Anatomy of Omicron BA.1 and BA.2 neutralizing antibodies in COVID-19 mRNA vaccinees. Nat Commun 2022; 13:3375. [PMID: 35697673 PMCID: PMC9189263 DOI: 10.1038/s41467-022-31115-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/05/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 vaccines, administered to billions of people worldwide, mitigate the effects of the COVID-19 pandemic, however little is known about the molecular basis of antibody cross-protection to emerging variants, such as Omicron BA.1, its sublineage BA.2, and other coronaviruses. To answer this question, 276 neutralizing monoclonal antibodies (nAbs), previously isolated from seronegative and seropositive donors vaccinated with BNT162b2 mRNA vaccine, were tested for neutralization against the Omicron BA.1 and BA.2 variants, and SARS-CoV-1 virus. Only 14.2, 19.9 and 4.0% of tested antibodies neutralize BA.1, BA.2, and SARS-CoV-1 respectively. These nAbs recognize mainly the SARS-CoV-2 receptor binding domain (RBD) and target Class 3 and Class 4 epitope regions on the SARS-CoV-2 spike protein. Interestingly, around 50% of BA.2 nAbs did not neutralize BA.1 and among these, several targeted the NTD. Cross-protective antibodies derive from a variety of germlines, the most frequents of which were the IGHV1-58;IGHJ3-1, IGHV2-5;IGHJ4-1 and IGHV1-69;IGHV4-1. Only 15.6, 20.3 and 7.8% of predominant gene-derived nAbs elicited against the original Wuhan virus cross-neutralize Omicron BA.1, BA.2 and SARS-CoV-1 respectively. Our data provide evidence, at molecular level, of the presence of cross-neutralizing antibodies induced by vaccination and map conserved epitopes on the S protein that can inform vaccine design.
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Affiliation(s)
- Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Silvia Marchese
- Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, Milan, Italy
| | - Lorena Donnici
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Giulio Pierleoni
- VisMederi S.r.l, Siena, Italy
- VisMederi Research S.r.l., Siena, Italy
| | | | - Noemi Manganaro
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Elisa Pantano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Valentina Abbiento
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Piero Pileri
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | | | | | | | - Piet Maes
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Concetta De Santi
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Claudia Sala
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Emanuele Montomoli
- VisMederi S.r.l, Siena, Italy
- VisMederi Research S.r.l., Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Raffaele De Francesco
- Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, Milan, Italy
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy.
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
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Abstract
High-throughput sequencing for B cell receptor (BCR) repertoire provides useful insights for the adaptive immune system. With the continuous development of the BCR-seq technology, many efforts have been made to develop methods for analyzing the ever-increasing BCR repertoire data. In this review, we comprehensively outline different BCR repertoire library preparation protocols and summarize three major steps of BCR-seq data analysis, i. e., V(D)J sequence annotation, clonal phylogenetic inference, and BCR repertoire profiling and mining. Different from other reviews in this field, we emphasize background intuition and the statistical principle of each method to help biologists better understand it. Finally, we discuss data mining problems for BCR-seq data and with a highlight on recently emerging multiple-sample analysis.
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Kuraoka M, Yeh CH, Bajic G, Kotaki R, Song S, Windsor I, Harrison SC, Kelsoe G. Recall of B cell memory depends on relative locations of prime and boost immunization. Sci Immunol 2022; 7:eabn5311. [PMID: 35522723 PMCID: PMC9169233 DOI: 10.1126/sciimmunol.abn5311] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Immunization or microbial infection can establish long-term B cell memory not only systemically but also locally. Evidence has suggested that local B cell memory contributes to early local plasmacytic responses after secondary challenge. However, it is unclear whether locality of immunization plays any role in memory B cell participation in recall germinal centers (GCs), which is essential for updating their B cell antigen receptors (BCRs). Using single B cell culture and fate mapping, we have characterized BCR repertoires in recall GCs after boost immunizations at sites local or distal to the priming. Local boosts with homologous antigen recruit the progeny of primary GC B cells to recall GCs more efficiently than do distal boosts. Recall GCs elicited by local boosts contain significantly more B cells with elevated levels of immunoglobulin (Ig) mutation and higher avidity BCRs. This local preference is unaffected by blocking CD40:CD154 interaction to terminate active, GC responses. Local boosts with heterologous antigens elicit secondary GCs with B cell populations enriched for cross-reactivity to the prime and boost antigens; in contrast, cross-reactive GC B cells are rare after distal boosts. Our results suggest that local B cell memory is retained in the form of memory B cells, GC B cells, and GC phenotype B cells that are independent of organized GC structures and that these persistent "primed B cells" contribute to recall GC responses at local sites. Our findings indicate the importance of locality in humoral immunity and inform serial vaccination strategies for evolving viruses.
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Affiliation(s)
| | - Chen-Hao Yeh
- Department of Immunology, Duke University, Durham, NC, USA
| | - Goran Bajic
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ryutaro Kotaki
- Department of Immunology, Duke University, Durham, NC, USA
| | - Shengli Song
- Department of Immunology, Duke University, Durham, NC, USA
| | - Ian Windsor
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
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30
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Gao N, Gai Y, Meng L, Wang C, Wang W, Li X, Gu T, Louder MK, Doria‐Rose NA, Wiehe K, Nazzari AF, Olia AS, Gorman J, Rawi R, Wu W, Smith C, Khant H, de Val N, Yu B, Luo J, Niu H, Tsybovsky Y, Liao H, Kepler TB, Kwong PD, Mascola JR, Qin C, Zhou T, Yu X, Gao F. Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200063. [PMID: 35319830 PMCID: PMC9130890 DOI: 10.1002/advs.202200063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Understanding maturation pathways of broadly neutralizing antibodies (bnAbs) against HIV-1 can be highly informative for HIV-1 vaccine development. A lineage of J038 bnAbs is now obtained from a long-term SHIV-infected macaque. J038 neutralizes 54% of global circulating HIV-1 strains. Its binding induces a unique "up" conformation for one of the V2 loops in the trimeric envelope glycoprotein and is heavily dependent on glycan, which provides nearly half of the binding surface. Their unmutated common ancestor neutralizes the autologous virus. Continuous maturation enhances neutralization potency and breadth of J038 lineage antibodies via expanding antibody-Env contact areas surrounding the core region contacted by germline-encoded residues. Developmental details and recognition features of J038 lineage antibodies revealed here provide a new pathway for elicitation and maturation of V2-targeting bnAbs.
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Affiliation(s)
- Nan Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Yanxin Gai
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Lina Meng
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Wei Wang
- Institute of Laboratory Animal ScienceChinese Academy of Medical SciencesBeijing100021China
- Comparative Medicine CenterPeking Union Medical CollegeBeijing100021China
| | - Xiaojun Li
- Department of MedicineDuke University School of MedicineDurhamNC27710USA
| | - Tiejun Gu
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Mark K. Louder
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Nicole A. Doria‐Rose
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Kevin Wiehe
- Duke University Human Vaccine InstituteDuke University School of MedicineDurhamNC27710USA
| | - Alexandra F. Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Wenmin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Clayton Smith
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Htet Khant
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Natalia de Val
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Junhong Luo
- Institute of Molecular and Medical Virology, School of MedicineJinan UniversityGuangzhouGuangdong Province510632China
| | - Haitao Niu
- Institute of Molecular and Medical Virology, School of MedicineJinan UniversityGuangzhouGuangdong Province510632China
| | - Yaroslav Tsybovsky
- Cancer Research Technology Program, Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research Inc.FrederickMD21701USA
| | - Huaxin Liao
- Institute of Molecular and Medical Virology, School of MedicineJinan UniversityGuangzhouGuangdong Province510632China
| | | | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Chuan Qin
- Institute of Laboratory Animal ScienceChinese Academy of Medical SciencesBeijing100021China
- Comparative Medicine CenterPeking Union Medical CollegeBeijing100021China
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life SciencesJilin UniversityChangchunJilin Province130012China
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life SciencesJilin UniversityChangchunJilin Province130012China
- Department of MedicineDuke University School of MedicineDurhamNC27710USA
- Institute of Molecular and Medical Virology, School of MedicineJinan UniversityGuangzhouGuangdong Province510632China
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31
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Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints. Proc Natl Acad Sci U S A 2022; 119:2113512119. [PMID: 35177475 PMCID: PMC8872716 DOI: 10.1073/pnas.2113512119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/15/2022] Open
Abstract
Humoral immunity relies on the mutation and selection of B cells to better recognize pathogens. This affinity maturation process produces cells with diverse recognition capabilities. Examining optimal immune strategies that maximize the long-term immune coverage at a minimal metabolic cost, we show when the immune system should mount a de novo response rather than rely on existing memory cells. Our theory recapitulates known modes of the B cell response, predicts the empirical form of the distribution of clone sizes, and rationalizes as a trade-off between metabolic and immune costs the antigenic imprinting effects that limit the efficacy of vaccines (original antigenic sin). Our predictions provide a framework to interpret experimental results that could be used to inform vaccination strategies. In order to target threatening pathogens, the adaptive immune system performs a continuous reorganization of its lymphocyte repertoire. Following an immune challenge, the B cell repertoire can evolve cells of increased specificity for the encountered strain. This process of affinity maturation generates a memory pool whose diversity and size remain difficult to predict. We assume that the immune system follows a strategy that maximizes the long-term immune coverage and minimizes the short-term metabolic costs associated with affinity maturation. This strategy is defined as an optimal decision process on a finite dimensional phenotypic space, where a preexisting population of cells is sequentially challenged with a neutrally evolving strain. We show that the low specificity and high diversity of memory B cells—a key experimental result—can be explained as a strategy to protect against pathogens that evolve fast enough to escape highly potent but narrow memory. This plasticity of the repertoire drives the emergence of distinct regimes for the size and diversity of the memory pool, depending on the density of de novo responding cells and on the mutation rate of the strain. The model predicts power-law distributions of clonotype sizes observed in data and rationalizes antigenic imprinting as a strategy to minimize metabolic costs while keeping good immune protection against future strains.
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32
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Berendam SJ, Morgan-Asiedu PK, Mangan RJ, Li SH, Heimsath H, Luo K, Curtis AD, Eudailey JA, Fox CB, Tomai MA, Phillips B, Itell HL, Kunz E, Hudgens M, Cronin K, Wiehe K, Alam SM, Van Rompay KKA, De Paris K, Permar SR, Moody MA, Fouda GG. Different adjuvanted pediatric HIV envelope vaccines induced distinct plasma antibody responses despite similar B cell receptor repertoires in infant rhesus macaques. PLoS One 2022; 16:e0256885. [PMID: 34972105 PMCID: PMC8719683 DOI: 10.1371/journal.pone.0256885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022] Open
Abstract
Different HIV vaccine regimens elicit distinct plasma antibody responses in both human and nonhuman primate models. Previous studies in human and non-human primate infants showed that adjuvants influenced the quality of plasma antibody responses induced by pediatric HIV envelope vaccine regimens. We recently reported that use of the 3M052-SE adjuvant and longer intervals between vaccinations are associated with higher magnitude of antibody responses in infant rhesus macaques. However, the impact of different adjuvants in HIV vaccine regimens on the developing infant B cell receptor (BCR) repertoire has not been studied. This study evaluated whether pediatric HIV envelope vaccine regimens with different adjuvants induced distinct antigen-specific memory B cell repertoires and whether specific immunoglobulin (Ig) immunogenetic characteristics are associated with higher magnitude of plasma antibody responses in vaccinated infant rhesus macaques. We utilized archived preclinical pediatric HIV vaccine studies PBMCs and tissue samples from 19 infant rhesus macaques immunized either with (i) HIV Env protein with a squalene adjuvant, (ii) MVA-HIV and Env protein co-administered using a 3-week interval, (iii) MVA-HIV prime/ protein boost with an extended 6-week interval between immunizations, or (iv) with HIV Env administered with 3M-052-SE adjuvant. Frequencies of vaccine-elicited HIV Env-specific memory B cells from PBMCs and tissues were similar across vaccination groups (frequency range of 0.06–1.72%). There was no association between vaccine-elicited antigen-specific memory B cell frequencies and plasma antibody titer or avidity. Moreover, the epitope specificity and Ig immunogenetic features of vaccine-elicited monoclonal antibodies did not differ between the different vaccine regimens. These data suggest that pediatric HIV envelope vaccine candidates with different adjuvants that previously induced higher magnitude and quality of plasma antibody responses in infant rhesus macaques were not driven by distinct antigen-specific memory BCR repertoires.
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Affiliation(s)
- Stella J. Berendam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Papa K. Morgan-Asiedu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Riley J. Mangan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Shuk Hang Li
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Holly Heimsath
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kan Luo
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Alan D. Curtis
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joshua A. Eudailey
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Weill Cornell College of Medicine, New York City, New York, United States of America
| | - Christopher B. Fox
- Infectious Disease Research Institute (IDRI), Seattle, Washington State, United States of America
- Department of Global Health, University of Washington, Seattle, Washington State, United States of America
| | - Mark A. Tomai
- 3M Center, 3 M Drug Delivery Systems, St. Paul, Minnesota, United States of America
| | - Bonnie Phillips
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hannah L. Itell
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Erika Kunz
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Koen K. A. Van Rompay
- California National Primate Research Center, University of California at Davis, Davis, California, United States of America
| | - Kristina De Paris
- Department of Microbiology and Immunology, Children’s Research Institute and Center for AIDS Research, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Weill Cornell College of Medicine, New York City, New York, United States of America
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Genevieve G. Fouda
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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33
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Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community. Methods Mol Biol 2022; 2453:317-343. [PMID: 35622334 PMCID: PMC9374196 DOI: 10.1007/978-1-0716-2115-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this method we illustrate how to amplify, sequence, and analyze antibody/immunoglobulin (IG) heavy-chain gene rearrangements from genomic DNA that is derived from bulk populations of cells by next-generation sequencing (NGS). We focus on human source material and illustrate how bulk gDNA-based sequencing can be used to examine clonal architecture and networks in different samples that are sequenced from the same individual. Although bulk gDNA-based sequencing can be performed on both IG heavy (IGH) or kappa/lambda light (IGK/IGL) chains, we focus here on IGH gene rearrangements because IG heavy chains are more diverse, tend to harbor higher levels of somatic hypermutations (SHM), and are more reliable for clone identification and tracking. We also provide a procedure, including code, and detailed instructions for processing and annotation of the NGS data. From these data we show how to identify expanded clones, visualize the overall clonal landscape, and track clonal lineages in different samples from the same individual. This method has a broad range of applications, including the identification and monitoring of expanded clones, the analysis of blood and tissue-based clonal networks, and the study of immune responses including clonal evolution.
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34
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
- Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lmar Babrak
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Enkelejda Miho
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
- Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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35
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Hybrid immunity improves B cells and antibodies against SARS-CoV-2 variants. Nature 2021; 600:530-535. [PMID: 34670266 PMCID: PMC8674140 DOI: 10.1038/s41586-021-04117-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/08/2021] [Indexed: 12/23/2022]
Abstract
The emergence of SARS-CoV-2 variants is jeopardizing the effectiveness of current vaccines and limiting the application of monoclonal antibody-based therapy for COVID-19 (refs. 1,2). Here we analysed the memory B cells of five naive and five convalescent people vaccinated with the BNT162b2 mRNA vaccine to investigate the nature of the B cell and antibody response at the single-cell level. Almost 6,000 cells were sorted, over 3,000 cells produced monoclonal antibodies against the spike protein and more than 400 cells neutralized the original SARS-CoV-2 virus first identified in Wuhan, China. The B.1.351 (Beta) and B.1.1.248 (Gamma) variants escaped almost 70% of these antibodies, while a much smaller portion was impacted by the B.1.1.7 (Alpha) and B.1.617.2 (Delta) variants. The overall loss of neutralization was always significantly higher in the antibodies from naive people. In part, this was due to the IGHV2-5;IGHJ4-1 germline, which was found only in people who were convalescent and generated potent and broadly neutralizing antibodies. Our data suggest that people who are seropositive following infection or primary vaccination will produce antibodies with increased potency and breadth and will be able to better control emerging SARS-CoV-2 variants. Single-cell-level analysis of memory B cells and their response to vaccination against all SARS-CoV-2 variants of concern in individuals who either had or had not been previously exposed to the virus.
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36
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Andreano E, Paciello I, Bardelli M, Tavarini S, Sammicheli C, Frigimelica E, Guidotti S, Torricelli G, Biancucci M, D’Oro U, Chandramouli S, Bottomley MJ, Rappuoli R, Finco O, Buricchi F. The respiratory syncytial virus (RSV) prefusion F-protein functional antibody repertoire in adult healthy donors. EMBO Mol Med 2021; 13:e14035. [PMID: 33998144 PMCID: PMC8185550 DOI: 10.15252/emmm.202114035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of death from lower respiratory tract infection in infants and children, and is responsible for considerable morbidity and mortality in older adults. Vaccines for pregnant women and elderly which are in phase III clinical studies target people with pre-existing natural immunity against RSV. To investigate the background immunity which will be impacted by vaccination, we single cell-sorted human memory B cells and dissected functional and genetic features of neutralizing antibodies (nAbs) induced by natural infection. Most nAbs recognized both the prefusion and postfusion conformations of the RSV F-protein (cross-binders) while a smaller fraction bound exclusively to the prefusion conformation. Cross-binder nAbs used a wide array of gene rearrangements, while preF-binder nAbs derived mostly from the expansion of B-cell clonotypes from the IGHV1 germline. This latter class of nAbs recognizes an epitope located between Site Ø, Site II, and Site V on the F-protein, identifying an important site of pathogen vulnerability.
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Affiliation(s)
- Emanuele Andreano
- Department of Life SciencesUniversity of SienaSienaItaly
- GSK VaccinesSienaItaly
- Present address:
Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | - Ida Paciello
- GSK VaccinesSienaItaly
- Present address:
Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | | | | | | | | | | | | | | | | | - Sumana Chandramouli
- GSK VaccinesRockvilleMDUSA
- Present address:
Moderna Therapeutics IncCambridgeMAUSA
| | | | - Rino Rappuoli
- GSK VaccinesSienaItaly
- Faculty of MedicineImperial CollegeLondonUK
- Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
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37
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Cai F, Chen WH, Wu W, Jones JA, Choe M, Gohain N, Shen X, LaBranche C, Eaton A, Sutherland L, Lee EM, Hernandez GE, Wu NR, Scearce R, Seaman MS, Moody MA, Santra S, Wiehe K, Tomaras GD, Wagh K, Korber B, Bonsignori M, Montefiori DC, Haynes BF, de Val N, Joyce MG, Saunders KO. Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates. PLoS Pathog 2021; 17:e1009624. [PMID: 34086838 PMCID: PMC8216552 DOI: 10.1371/journal.ppat.1009624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/21/2021] [Accepted: 05/07/2021] [Indexed: 11/19/2022] Open
Abstract
A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.
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Affiliation(s)
- Fangping Cai
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland, United States of America
| | - Julia A. Jones
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Misook Choe
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Neelakshi Gohain
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Amanda Eaton
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Laura Sutherland
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Esther M. Lee
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Giovanna E. Hernandez
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nelson R. Wu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Richard Scearce
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland, United States of America
| | - M. Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
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38
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Abstract
Novel animal influenza viruses emerge, initiate pandemics, and become endemic seasonal variants that have evolved to escape from prevalent herd immunity. These processes often outpace vaccine-elicited protection. Focusing immune responses on conserved epitopes may impart durable immunity. We describe a focused, protective antibody response, abundant in memory and serum repertoires, to a conserved region at the influenza virus hemagglutinin (HA) head interface. Structures of 11 examples, 8 reported here, from seven human donors demonstrate the convergence of responses on a single epitope. The 11 are genetically diverse, with one class having a common, IGκV1-39, light chain. All of the antibodies bind HAs from multiple serotypes. The lack of apparent genetic restriction and potential for elicitation by more than one serotype may explain their abundance. We define the head interface as a major target of broadly protective antibodies with the potential to influence the outcomes of influenza virus infection. IMPORTANCE The rapid appearance of mutations in circulating human influenza viruses and selection for escape from herd immunity require prediction of likely variants for an annual updating of influenza vaccines. The identification of human antibodies that recognize conserved surfaces on the influenza virus hemagglutinin (HA) has prompted efforts to design immunogens that might selectively elicit such antibodies. The recent discovery of a widely prevalent antibody response to the conserved interface between two HA "heads" (the globular, receptor-binding domains at the apex of the spike-like trimer) has added a new target for these efforts. We report structures of eight such antibodies, bound with HA heads, and compare them with each other and with three others previously described. Although genetically diverse, they all converge on a common binding site. The analysis here can guide immunogen design for preclinical trials.
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39
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Williams WB, Meyerhoff RR, Edwards RJ, Li H, Manne K, Nicely NI, Henderson R, Zhou Y, Janowska K, Mansouri K, Gobeil S, Evangelous T, Hora B, Berry M, Abuahmad AY, Sprenz J, Deyton M, Stalls V, Kopp M, Hsu AL, Borgnia MJ, Stewart-Jones GBE, Lee MS, Bronkema N, Moody MA, Wiehe K, Bradley T, Alam SM, Parks RJ, Foulger A, Oguin T, Sempowski GD, Bonsignori M, LaBranche CC, Montefiori DC, Seaman M, Santra S, Perfect J, Francica JR, Lynn GM, Aussedat B, Walkowicz WE, Laga R, Kelsoe G, Saunders KO, Fera D, Kwong PD, Seder RA, Bartesaghi A, Shaw GM, Acharya P, Haynes BF. Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell 2021; 184:2955-2972.e25. [PMID: 34019795 PMCID: PMC8135257 DOI: 10.1016/j.cell.2021.04.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/22/2021] [Accepted: 04/23/2021] [Indexed: 01/03/2023]
Abstract
Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA.
| | - R Ryan Meyerhoff
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - R J Edwards
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | | | | | | | | | - Bhavna Hora
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | | | | | | | | | - Megan Kopp
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | | | - Matthew S Lee
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Naomi Bronkema
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | | | - Thomas Oguin
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Michael Seaman
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - John Perfect
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - Geoffrey M Lynn
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Avidea Technologies, Inc., Baltimore, MD, USA
| | | | | | - Richard Laga
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27705, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA.
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40
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Pollara J, Tay MZ, Edwards RW, Goodman D, Crowley AR, Edwards RJ, Easterhoff D, Conley HE, Hoxie T, Gurley T, Jones C, Machiele E, Tuyishime M, Donahue E, Jha S, Spreng RL, Hope TJ, Wiehe K, He MM, Moody MA, Saunders KO, Ackerman ME, Ferrari G, Tomaras GD. Functional Homology for Antibody-Dependent Phagocytosis Across Humans and Rhesus Macaques. Front Immunol 2021; 12:678511. [PMID: 34093580 PMCID: PMC8174565 DOI: 10.3389/fimmu.2021.678511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Analyses of human clinical HIV-1 vaccine trials and preclinical vaccine studies performed in rhesus macaque (RM) models have identified associations between non-neutralizing Fc Receptor (FcR)-dependent antibody effector functions and reduced risk of infection. Specifically, antibody-dependent phagocytosis (ADP) has emerged as a common correlate of reduced infection risk in multiple RM studies and the human HVTN505 trial. This recurrent finding suggests that antibody responses with the capability to mediate ADP are most likely a desirable component of vaccine responses aimed at protecting against HIV-1 acquisition. As use of RM models is essential for development of the next generation of candidate HIV-1 vaccines, there is a need to determine how effectively ADP activity observed in RMs translates to activity in humans. In this study we compared ADP activity of human and RM monocytes and polymorphonuclear leukocytes (PMN) to bridge this gap in knowledge. We observed considerable variability in the magnitude of monocyte and PMN ADP activity across individual humans and RM that was not dependent on FcR alleles, and only modestly impacted by cell-surface levels of FcRs. Importantly, we found that for both human and RM phagocytes, ADP activity of antibodies targeting the CD4 binding site was greatest when mediated by human IgG3, followed by RM and human IgG1. These results demonstrate that there is functional homology between antibody and FcRs from these two species for ADP. We also used novel RM IgG1 monoclonal antibodies engineered with elongated hinge regions to show that hinge elongation augments RM ADP activity. The RM IgGs with engineered hinge regions can achieve ADP activity comparable to that observed with human IgG3. These novel modified antibodies will have utility in passive immunization studies aimed at defining the role of IgG3 and ADP in protection from virus challenge or control of disease in RM models. Our results contribute to a better translation of human and macaque antibody and FcR biology, and may help to improve testing accuracy and evaluations of future active and passive prevention strategies.
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Affiliation(s)
- Justin Pollara
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States.,Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Matthew Zirui Tay
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - R Whitney Edwards
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Derrick Goodman
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Andrew R Crowley
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
| | - Robert J Edwards
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - David Easterhoff
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Haleigh E Conley
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Taylor Hoxie
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Thaddeus Gurley
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Caroline Jones
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Emily Machiele
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Marina Tuyishime
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Elizabeth Donahue
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Shalini Jha
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Rachel L Spreng
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Thomas J Hope
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kevin Wiehe
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Max M He
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - M Anthony Moody
- Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Kevin O Saunders
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States.,Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | | | - Guido Ferrari
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States.,Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Georgia D Tomaras
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States.,Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
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41
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Rossignol ED, Dugast AS, Compere H, Cottrell CA, Copps J, Lin S, Cizmeci D, Seaman MS, Ackerman ME, Ward AB, Alter G, Julg B. Mining HIV controllers for broad and functional antibodies to recognize and eliminate HIV-infected cells. Cell Rep 2021; 35:109167. [PMID: 34038720 PMCID: PMC8196545 DOI: 10.1016/j.celrep.2021.109167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/27/2021] [Accepted: 05/01/2021] [Indexed: 12/11/2022] Open
Abstract
HIV monoclonal antibodies for viral reservoir eradication strategies will likely need to recognize reactivated infected cells and potently drive Fc-mediated innate effector cell activity. We systematically characterize a library of 185 HIV-envelope-specific antibodies derived from 15 spontaneous HIV controllers (HCs) that selectively exhibit robust serum Fc functionality and compared them to broadly neutralizing antibodies (bNAbs) in clinical development. Within the 10 antibodies with the broadest cell-recognition capability, seven originated from HCs and three were bNAbs. V3-loop-targeting antibodies are enriched among the top cell binders, suggesting the V3-loop may be selectively exposed and accessible on the cell surface. Fc functionality is more variable across antibodies, which is likely influenced by distinct binding topology and corresponding Fc accessibility, highlighting not only the importance of target-cell recognition but also the need to optimize for Fc-mediated elimination. Ultimately, our results demonstrate that this comprehensive selection process can identify monoclonal antibodies poised to eliminate infected cells. Rossignol et al. characterize 185 HIV-envelope-specific antibodies derived from spontaneous HIV controllers, downselecting antibodies based on their ability to broadly recognize infected cells and potently drive Fc-mediated innate effector cell activity. This comprehensive selection process can identify monoclonal antibodies poised to eliminate infected cells for viral reservoir eradication strategies.
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Affiliation(s)
- Evan D Rossignol
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Anne-Sophie Dugast
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Hacheming Compere
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shu Lin
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Deniz Cizmeci
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | | | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.
| | - Boris Julg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.
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42
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Lindenbaum O, Nouri N, Kluger Y, Kleinstein SH. Alignment free identification of clones in B cell receptor repertoires. Nucleic Acids Res 2021; 49:e21. [PMID: 33330933 PMCID: PMC7913774 DOI: 10.1093/nar/gkaa1160] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 11/22/2022] Open
Abstract
Following antigenic challenge, activated B cells rapidly expand and undergo somatic hypermutation, yielding groups of clonally related B cells with diversified immunoglobulin receptors. Inference of clonal relationships based on the receptor sequence is an essential step in many adaptive immune receptor repertoire sequencing studies. These relationships are typically identified by a multi-step process that involves: (i) grouping sequences based on shared V and J gene assignments, and junction lengths and (ii) clustering these sequences using a junction-based distance. However, this approach is sensitive to the initial gene assignments, which are error-prone, and fails to identify clonal relatives whose junction length has changed through accumulation of indels. Through defining a translation-invariant feature space in which we cluster the sequences, we develop an alignment free clonal identification method that does not require gene assignments and is not restricted to a fixed junction length. This alignment free approach has higher sensitivity compared to a typical junction-based distance method without loss of specificity and PPV. While the alignment free procedure identifies clones that are broadly consistent with the junction-based distance method, it also identifies clones with characteristics (multiple V or J gene assignments or junction lengths) that are not detectable with the junction-based distance method.
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Affiliation(s)
- Ofir Lindenbaum
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
| | - Nima Nouri
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.,Center for Medical Informatics, Yale University, New Haven, CT 06511, USA
| | - Yuval Kluger
- Program in Applied Mathematics, Yale University, New Haven, CT, USA.,Department of Pathology, Yale School of Medicine, New Haven, CT, USA.,Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.,Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
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43
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Krantsevich A, Tang C, MacCarthy T. Correlations in Somatic Hypermutation Between Sites in IGHV Genes Can Be Explained by Interactions Between AID and/or Polη Hotspots. Front Immunol 2021; 11:618409. [PMID: 33603748 PMCID: PMC7884765 DOI: 10.3389/fimmu.2020.618409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/18/2020] [Indexed: 12/27/2022] Open
Abstract
The somatic hypermutation (SHM) of Immunoglobulin (Ig) genes is a key process during antibody affinity maturation in B cells. The mutagenic enzyme activation induced deaminase (AID) is required for SHM and has a preference for WRC hotspots in DNA. Error-prone repair mechanisms acting downstream of AID introduce further mutations, including DNA polymerase eta (Polη), part of the non-canonical mismatch repair pathway (ncMMR), which preferentially generates mutations at WA hotspots. Previously proposed mechanistic models lead to a variety of predictions concerning interactions between hotspots, for example, how mutations in one hotspot will affect another hotspot. Using a large, high-quality, Ig repertoire sequencing dataset, we evaluated pairwise correlations between mutations site-by-site using an unbiased measure similar to mutual information which we termed “mutational association” (MA). Interactions are dominated by relatively strong correlations between nearby sites (short-range MAs), which can be almost entirely explained by interactions between overlapping hotspots for AID and/or Polη. We also found relatively weak dependencies between almost all sites throughout each gene (longer-range MAs), although these arise mostly as a statistical consequence of high pairwise mutation frequencies. The dominant short-range interactions are also highest within the most highly mutating IGHV sub-regions, such as the complementarity determining regions (CDRs), where there is a high hotspot density. Our results suggest that the hotspot preferences for AID and Polη have themselves evolved to allow for greater interactions between AID and/or Polη induced mutations.
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Affiliation(s)
- Artem Krantsevich
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States
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44
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The respiratory syncytial virus fusion protein-specific B cell receptor repertoire reshaped by post-fusion subunit vaccination. Vaccine 2020; 38:7916-7927. [PMID: 33131932 DOI: 10.1016/j.vaccine.2020.10.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 01/21/2023]
Abstract
Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory illness in children of less than 5 years of age which usually results in hospitalization or even in death. Vaccine development is hampered in consequence of a failed vaccine trial with fatalities in the 1960s. Even though research has been more focused on the RSV fusion protein in its pre-fusion conformation, maternal vaccination with post-fusion protein (post F) was considered as a promising vaccine strategy for passive immunization of babies, because post F preserves very potent neutralizing epitopes. We extensively analyzed post F-binding B cell receptor (BCR) repertoires of three vaccinees who received a post F-subunit vaccine in the context of a first-in-human, Phase 1, randomized, observer-blind, placebo-controlled clinical trial (ClinicalTrials.gov Identifier: NCT02298179). In order to compare the vaccine-induced BCR repertoires with BCR repertoires induced by natural infection, we also analyzed pre F- and post F-binding BCRs isolated from a healthy blood donor with relatively high F-binding memory B cell (MBC) frequencies. Analysis of the vaccine-induced repertoires revealed that preferentially VH4-encoded BCRs were expanded in response to vaccination. Estimation of antigen-driven selection further demonstrated that expanded BCRs accumulated positively selected replacement mutations which substantiated the hypothesis that post F-vaccination induces diversification of VH4-encoded BCRs in germinal centers. Comparison of the vaccine-induced BCR repertoires with clonally related pre and post F-binding BCRs of the healthy blood donor suggested that the vaccine expanded pre/post F cross-reactive MBCs. Interestingly, several vaccine-induced BCRs shared stereotypic VDJ gene junctions with known neutralizing Abs. Once expressed for functional characterization, the selected monoclonal Abs demonstrated the predicted neutralization activities in plaque reduction neutralization assays indicating that the post F-vaccine induced expansion of neutralizing BCRs.
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45
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Schneikart G, Tavarini S, Sammicheli C, Torricelli G, Guidotti S, D'Oro U, Finco O, Bardelli M. Dataset of antibody variable region sequence features inferred from a respiratory syncytial virus fusion protein-specific B cell receptor repertoire induced by natural infection of a healthy adult. Data Brief 2020; 33:106499. [PMID: 33225034 PMCID: PMC7666335 DOI: 10.1016/j.dib.2020.106499] [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: 10/22/2020] [Accepted: 10/30/2020] [Indexed: 11/17/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the primary cause for acute lower respiratory syndrome in children younger than 5 years. Research on B cell repertoires and antibodies binding the RSV fusion protein (RSV F) is of major interest in the development of potential vaccine candidates and therapies. B cell receptors (BCRs) which have higher affinities for a specific antigen are preferentially selected for B cell clonal expansion in germinal center reactions. Consequently, antigen-specific BCR repertoires share common features, as for instance preferential variable gene usage, variable region mutation levels or lengths of the heavy chain complementarity-determining region 3. Since RSV repeatedly infects every person throughout life, memory B cells (MBC) expressing RSV F-binding BCRs circulate in the blood of healthy adults. This dataset of BCR variable region sequence features was derived from single cell-sorted RSV F-directed MBCs of a healthy adult blood donor [1]. The dataset was produced with publicly available data analysis software programs and scripts, which facilitates integration or comparison with antibody sequence repertoire data of different individuals derived with the same or comparable data analysis approaches and tools.
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Affiliation(s)
- Gerald Schneikart
- GSK, Via Fiorentina 1, 53100 Siena, Italy
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | | | | | | | | | - Ugo D'Oro
- GSK, Via Fiorentina 1, 53100 Siena, Italy
| | | | - Monia Bardelli
- GSK, Via Fiorentina 1, 53100 Siena, Italy
- Corresponding author.
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46
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Dhar A, Ralph DK, Minin VN, Matsen FA. A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis. PLoS Comput Biol 2020; 16:e1008030. [PMID: 32804924 PMCID: PMC7451993 DOI: 10.1371/journal.pcbi.1008030] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 08/27/2020] [Accepted: 06/08/2020] [Indexed: 11/24/2022] Open
Abstract
The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling.
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MESH Headings
- Bayes Theorem
- Computational Biology
- Gene Rearrangement, B-Lymphocyte/genetics
- Humans
- Markov Chains
- Models, Genetic
- Phylogeny
- Receptors, Antigen, B-Cell/classification
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Sequence Analysis, DNA/methods
- Somatic Hypermutation, Immunoglobulin/genetics
- Vaccines
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Affiliation(s)
- Amrit Dhar
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Duncan K. Ralph
- Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Vladimir N. Minin
- Department of Statistics, University of California, Irvine, California, United States of America
| | - Frederick A. Matsen
- Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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47
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Antibody Feedback Limits the Expansion of B Cell Responses to Malaria Vaccination but Drives Diversification of the Humoral Response. Cell Host Microbe 2020; 28:572-585.e7. [PMID: 32697938 DOI: 10.1016/j.chom.2020.07.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/02/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022]
Abstract
Generating sufficient antibody to block infection is a key challenge for vaccines against malaria. Here, we show that antibody titers to a key target, the repeat region of the Plasmodium falciparum circumsporozoite protein (PfCSP), plateaued after two immunizations in a clinical trial of the radiation-attenuated sporozoite vaccine. To understand the mechanisms limiting vaccine responsiveness, we developed immunoglobulin (Ig)-knockin mice with elevated numbers of PfCSP-binding B cells. We determined that recall responses were inhibited by antibody feedback, potentially via epitope masking of the immunodominant PfCSP repeat region. Importantly, the amount of antibody that prevents boosting is below the amount of antibody required for protection. Finally, while antibody feedback limited responses to the PfCSP repeat region in vaccinated volunteers, potentially protective subdominant responses to PfCSP C-terminal regions expanded with subsequent boosts. These data suggest that antibody feedback drives the diversification of immune responses and that vaccination for malaria will require targeting multiple antigens.
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48
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Foglierini M, Pappas L, Lanzavecchia A, Corti D, Perez L. AncesTree: An interactive immunoglobulin lineage tree visualizer. PLoS Comput Biol 2020; 16:e1007731. [PMID: 32649725 PMCID: PMC7375605 DOI: 10.1371/journal.pcbi.1007731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 07/22/2020] [Accepted: 06/14/2020] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing of human immunoglobulin genes allows analysis of antibody repertoires and the reconstruction of clonal lineage evolution. The study of antibodies (Abs) affinity maturation is of specific interest to understand the generation of Abs with high affinity or broadly neutralizing activities. Moreover, phylogenic analysis enables the identification of the key somatic mutations required to achieve optimal antigen binding. The Immcantation framework provides a start-to-finish set of analytical methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) data. Furthermore, Immcantation's Change-O package has developed IgPhyML, an algorithm designed to build specifically immunoglobulin (Ig) phylogenic trees. Meanwhile Phylip, an algorithm that has been originally developed for applications in ecology and macroevolution, can also be used for the phylogenic reconstruction of antibodies maturation pathway. To complement Ig lineages made by IgPhyML or Dnaml (Phylip), we developed AncesTree, a graphic user interface (GUI) that aims to give researchers the opportunity to interactively explore antibodies clonal evolution. AncesTree displays interactive immunoglobulins phylogenic tree, Ig related mutations and sequence alignments using additional information coming from specialized antibody tools. The GUI is a Java standalone application allowing interaction with Ig tree that can run under Windows, Linux and Mac OS.
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Affiliation(s)
- Mathilde Foglierini
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Leontios Pappas
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Laurent Perez
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
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49
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Nouri N, Kleinstein SH. Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. PLoS Comput Biol 2020; 16:e1007977. [PMID: 32574157 PMCID: PMC7347241 DOI: 10.1371/journal.pcbi.1007977] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 07/09/2020] [Accepted: 05/21/2020] [Indexed: 01/11/2023] Open
Abstract
Adaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of identifying and tracking B cell clonal expansions during adaptive immune responses. Members of a B cell clone are descended from a common ancestor and share the same initial V(D)J rearrangement, but their B cell receptor (BCR) sequence may differ due to the accumulation of somatic hypermutations (SHMs). Clonal relationships are learned from AIRR-seq data by analyzing the BCR sequence, with the most common methods focused on the highly diverse junction region. However, clonally related cells often share SHMs which have been accumulated during affinity maturation. Here, we investigate whether shared SHMs in the V and J segments of the BCR can be leveraged along with the junction sequence to improve the ability to identify clonally related sequences. We develop independent distance functions that capture junction similarity and shared mutations, and combine these in a spectral clustering framework to infer the BCR clonal relationships. Using both simulated and experimental data, we show that this model improves both the sensitivity and specificity for identifying B cell clones. Source code for this method is freely available in the SCOPer (Spectral Clustering for clOne Partitioning) R package (version 0.2 or newer) in the Immcantation framework: www.immcantation.org under the AGPLv3 license.
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Affiliation(s)
- Nima Nouri
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Center for Medical Informatics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Center for Medical Informatics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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50
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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 2020; 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: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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