1
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Ogega CO, Skinner NE, Schoenle MV, Wilcox XE, Frumento N, Wright DA, Paul HT, Sinnis-Bourozikas A, Clark KE, Figueroa A, Bjorkman PJ, Ray SC, Flyak AI, Bailey JR. Convergent evolution and targeting of diverse E2 epitopes by human broadly neutralizing antibodies are associated with HCV clearance. Immunity 2024; 57:890-903.e6. [PMID: 38518779 DOI: 10.1016/j.immuni.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/21/2023] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
The early appearance of broadly neutralizing antibodies (bNAbs) in serum is associated with spontaneous hepatitis C virus (HCV) clearance, but to date, the majority of bNAbs have been isolated from chronically infected donors. Most of these bNAbs use the VH1-69 gene segment and target the envelope glycoprotein E2 front layer. Here, we performed longitudinal B cell receptor (BCR) repertoire analysis on an elite neutralizer who spontaneously cleared multiple HCV infections. We isolated 10,680 E2-reactive B cells, performed BCR sequencing, characterized monoclonal B cell cultures, and isolated bNAbs. In contrast to what has been seen in chronically infected donors, the bNAbs used a variety of VH genes and targeted at least three distinct E2 antigenic sites, including sites previously thought to be non-neutralizing. Diverse front-layer-reactive bNAb lineages evolved convergently, acquiring breadth-enhancing somatic mutations. These findings demonstrate that HCV clearance-associated bNAbs are genetically diverse and bind distinct antigenic sites that should be the target of vaccine-induced bNAbs.
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Affiliation(s)
- Clinton O Ogega
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole E Skinner
- Division of Infectious Diseases, Department of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Center for Vaccines and Immunity, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Marta V Schoenle
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Xander E Wilcox
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Nicole Frumento
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Desiree A Wright
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Harry T Paul
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ariadne Sinnis-Bourozikas
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kaitlyn E Clark
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexis Figueroa
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stuart C Ray
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew I Flyak
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.
| | - Justin R Bailey
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Barnes CO, Jette CA, Abernathy ME, Dam KMA, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West AP, Bjorkman PJ. Author Correction: SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 2024; 628:E2. [PMID: 38565636 DOI: 10.1038/s41586-024-07344-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Affiliation(s)
- Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Claudia A Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan E Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shannon R Esswein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrey G Malyutin
- Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Naima G Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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3
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Kubinski HC, Despres HW, Johnson BA, Schmidt MM, Jaffrani SA, Mills MG, Lokugamage K, Dumas CM, Shirley DJ, Estes LK, Pekosz A, Crothers JW, Roychoudhury P, Greninger AL, Jerome KR, Di Genova BM, Walker DH, Ballif BA, Ladinsky MS, Bjorkman PJ, Menachery VD, Bruce EA. Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation. bioRxiv 2024:2024.03.08.584120. [PMID: 38559000 PMCID: PMC10979914 DOI: 10.1101/2024.03.08.584120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of Spike are not well studied, the entire viral genome is undergoing evolutionary selection, particularly the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a disulfide bond and a stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both in vitro and in vivo. Finally, we demonstrate that the N:G215C virus packages more nucleocapsid per virion and that individual virions are larger, with elongated morphologies.
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Affiliation(s)
- Hannah C. Kubinski
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Hannah W. Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Madaline M. Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Sara A. Jaffrani
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Caroline M. Dumas
- Department of Biology, University of Vermont 109 Carrigan Drive, 120A Marsh Life Sciences, Burlington VT 05404, USA
| | - David J. Shirley
- Faraday, Inc. Data Science Department. Burlington VT, 05405, USA
| | - Leah K. Estes
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, MD College of Medicine, University of Vermont, Burlington, VT, USA
| | - Pavitra Roychoudhury
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Bruno Martorelli Di Genova
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bryan A. Ballif
- Department of Biology, University of Vermont 109 Carrigan Drive, 120A Marsh Life Sciences, Burlington VT 05404, USA
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA. 91125, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA. 91125, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Emily A. Bruce
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
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4
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Wang E, Cohen AA, Caldera LF, Keeffe JR, Rorick AV, Aida YM, Gnanapragasam PN, Bjorkman PJ, Chakraborty AK. Designed mosaic nanoparticles enhance cross-reactive immune responses in mice. bioRxiv 2024:2024.02.28.582544. [PMID: 38464322 PMCID: PMC10925254 DOI: 10.1101/2024.02.28.582544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
1Using computational methods, we designed 60-mer nanoparticles displaying SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs) by (i) creating RBD sequences with 6 mutations in the SARS-COV-2 WA1 RBD that were predicted to retain proper folding and abrogate antibody responses to variable epitopes (mosaic-2COMs; mosaic-5COM), and (ii) selecting 7 natural sarbecovirus RBDs (mosaic-7COM). These antigens were compared with mosaic-8b, which elicits cross-reactive antibodies and protects from sarbecovirus challenges in animals. Immunizations in naïve and COVID-19 pre-vaccinated mice revealed that mosaic-7COM elicited higher binding and neutralization titers than mosaic-8b and related antigens. Deep mutational scanning showed that mosaic-7COM targeted conserved RBD epitopes. Mosaic-2COMs and mosaic-5COM elicited higher titers than homotypic SARS-CoV-2 Beta RBD-nanoparticles and increased potencies against some SARS-CoV-2 variants than mosaic-7COM. However, mosaic-7COM elicited more potent responses against zoonotic sarbecoviruses and highly mutated Omicrons. These results support using mosaic-7COM to protect against highly mutated SARS-CoV-2 variants and zoonotic sarbecoviruses with spillover potential.
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Affiliation(s)
- Eric Wang
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- These authors contributed equally
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- These authors contributed equally
| | - Luis F. Caldera
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- These authors contributed equally
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Annie V. Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Yusuf M. Aida
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Present address: School of Clinical Medicine, University of Cambridge, Hills Rd, Cambridge, CB2 0SP, UK
| | | | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Arup K. Chakraborty
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
- Lead contact
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5
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Cohen AA, Keeffe JR, Schiepers A, Dross SE, Greaney AJ, Rorick AV, Gao H, Gnanapragasam PN, Fan C, West AP, Ramsingh AI, Erasmus JH, Pata JD, Muramatsu H, Pardi N, Lin PJ, Baxter S, Cruz R, Quintanar-Audelo M, Robb E, Serrano-Amatriain C, Magneschi L, Fotheringham IG, Fuller DH, Victora GD, Bjorkman PJ. Mosaic sarbecovirus vaccination elicits cross-reactive responses in pre-immunized animals. bioRxiv 2024:2024.02.08.576722. [PMID: 38370696 PMCID: PMC10871317 DOI: 10.1101/2024.02.08.576722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Immunization with mosaic-8b [60-mer nanoparticles presenting 8 SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs)] elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated effects of prior COVID-19 vaccinations in non-human primates and mice on sarbecovirus response breadths elicited by mosaic-8b, admix-8b (8 homotypics), and homotypic SARS-CoV-2, finding greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate-mapping in which antibodies derived from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b- and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced with mosaic-8b boosting, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19 vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential.
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Affiliation(s)
- Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Ariën Schiepers
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Sandra E. Dross
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Allison J. Greaney
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Annie V. Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | - Janice D. Pata
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany, Albany, NY, 12201, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Scott Baxter
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Rita Cruz
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Martina Quintanar-Audelo
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
- Present address: Centre for Inflammation Research and Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Ellis Robb
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | | | - Leonardo Magneschi
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Ian G. Fotheringham
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Deborah H. Fuller
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Gabriel D. Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Lead contact
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6
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Dam KMA, Fan C, Yang Z, Bjorkman PJ. Publisher Correction: Intermediate conformations of CD4-bound HIV-1 Env heterotrimers. Nature 2024; 626:E7. [PMID: 38243106 PMCID: PMC10849941 DOI: 10.1038/s41586-024-07082-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Affiliation(s)
- Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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7
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Abstract
HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120 and gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops1-4 and in fully saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops3-9. To investigate changes resulting from substoichiometric CD4 binding, we solved single-particle cryo-electron microscopy (cryo-EM) structures of soluble, native-like heterotrimeric Envs bound to one or two CD4 molecules. Most of the Env trimers bound to one CD4 adopted the closed, prefusion Env state, with a minority exhibiting a heterogeneous partially open Env conformation. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state10 that showed gp120 outward rotation but maintained the prefusion three-stranded gp120 bridging sheet with only partial V1V2 displacement and V3 exposure. We conclude that most of the engagements with one CD4 molecule were insufficient to stimulate CD4-induced conformational changes, whereas binding two CD4 molecules led to Env opening in CD4-bound protomers only. The substoichiometric CD4-bound soluble Env heterotrimer structures resembled counterparts derived from a cryo-electron tomography study of complexes between virion-bound Envs and membrane-anchored CD4 (ref. 11), validating their physiological relevance. Together, these results illuminate intermediate conformations of HIV-1 Env and illustrate its structural plasticity.
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Affiliation(s)
- Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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8
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Horns F, Martinez JA, Fan C, Haque M, Linton JM, Tobin V, Santat L, Maggiolo AO, Bjorkman PJ, Lois C, Elowitz MB. Engineering RNA export for measurement and manipulation of living cells. Cell 2023; 186:3642-3658.e32. [PMID: 37437570 PMCID: PMC10528933 DOI: 10.1016/j.cell.2023.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/08/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
A system for programmable export of RNA molecules from living cells would enable both non-destructive monitoring of cell dynamics and engineering of cells capable of delivering executable RNA programs to other cells. We developed genetically encoded cellular RNA exporters, inspired by viruses, that efficiently package and secrete cargo RNA molecules from mammalian cells within protective nanoparticles. Exporting and sequencing RNA barcodes enabled non-destructive monitoring of cell population dynamics with clonal resolution. Further, by incorporating fusogens into the nanoparticles, we demonstrated the delivery, expression, and functional activity of exported mRNA in recipient cells. We term these systems COURIER (controlled output and uptake of RNA for interrogation, expression, and regulation). COURIER enables measurement of cell dynamics and establishes a foundation for hybrid cell and gene therapies based on cell-to-cell delivery of RNA.
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Affiliation(s)
- Felix Horns
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Joe A Martinez
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mehernaz Haque
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - James M Linton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Victoria Tobin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leah Santat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ailiena O Maggiolo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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9
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Hoffmann MAG, Yang Z, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Nakatomi LM, Storm KN, Moon WJ, Lin PJC, West AP, Bjorkman PJ. ESCRT recruitment to SARS-CoV-2 spike induces virus-like particles that improve mRNA vaccines. Cell 2023; 186:2380-2391.e9. [PMID: 37146611 PMCID: PMC10121106 DOI: 10.1016/j.cell.2023.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/28/2023] [Accepted: 04/17/2023] [Indexed: 05/07/2023]
Abstract
Prime-boost regimens for COVID-19 vaccines elicit poor antibody responses against Omicron-based variants and employ frequent boosters to maintain antibody levels. We present a natural infection-mimicking technology that combines features of mRNA- and proteinnanoparticle-based vaccines through encoding self-assembling enveloped virus-like particles (eVLPs). eVLP assembly is achieved by inserting an ESCRT- and ALIX-binding region (EABR) into the SARS-CoV-2 spike cytoplasmic tail, which recruits ESCRT proteins to induce eVLP budding from cells. Purified spike-EABR eVLPs presented densely arrayed spikes and elicited potent antibody responses in mice. Two immunizations with mRNA-LNP encoding spike-EABR elicited potent CD8+ T cell responses and superior neutralizing antibody responses against original and variant SARS-CoV-2 compared with conventional spike-encoding mRNA-LNP and purified spike-EABR eVLPs, improving neutralizing titers >10-fold against Omicron-based variants for 3 months post-boost. Thus, EABR technology enhances potency and breadth of vaccine-induced responses through antigen presentation on cell surfaces and eVLPs, enabling longer-lasting protection against SARS-CoV-2 and other viruses.
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Affiliation(s)
- Magnus A G Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Leesa M Nakatomi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kaya N Storm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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10
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Shrock EL, Timms RT, Kula T, Mena EL, West AP, Guo R, Lee IH, Cohen AA, McKay LGA, Bi C, Keerti, Leng Y, Fujimura E, Horns F, Li M, Wesemann DR, Griffiths A, Gewurz BE, Bjorkman PJ, Elledge SJ. Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses. Science 2023; 380:eadc9498. [PMID: 37023193 PMCID: PMC10273302 DOI: 10.1126/science.adc9498] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023]
Abstract
Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant "public epitopes" at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition. Systematic analysis of antibody-antigen structures uncovered 18 human and 21 partially overlapping mouse germline-encoded amino acid-binding (GRAB) motifs within heavy and light V gene segments that in case studies proved critical for public epitope recognition. GRAB motifs represent a fundamental component of the immune system's architecture that promotes recognition of pathogens and leads to species-specific public antibody responses that can exert selective pressure on pathogens.
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Affiliation(s)
- Ellen L. Shrock
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
| | - Richard T. Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
- Present address: Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Elijah L. Mena
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rui Guo
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - I-Hsiu Lee
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lindsay G. A. McKay
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Caihong Bi
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Keerti
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric Fujimura
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Felix Horns
- Department of Bioengineering, Department of Applied Physics, Chan Zuckerberg Biohub and Stanford University, Stanford, CA 94305, USA
| | - Mamie Li
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Duane R. Wesemann
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139 USA
| | - Anthony Griffiths
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Benjamin E. Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
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11
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Braet SM, Buckley TSC, Venkatakrishnan V, Dam KMA, Bjorkman PJ, Anand GS. Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk with altered NTD dynamics. eLife 2023; 12:82584. [PMID: 36929749 PMCID: PMC10049203 DOI: 10.7554/elife.82584] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
SARS-CoV-2 emergent variants are characterized by increased viral fitness and each shows multiple mutations predominantly localized to the spike (S) protein. Here, amide hydrogen/deuterium exchange mass spectrometry has been applied to track changes in S dynamics from multiple SARS-CoV-2 variants. Our results highlight large differences across variants at two loci with impacts on S dynamics and stability. A significant enhancement in stabilization first occurred with the emergence of D614G S followed by smaller, progressive stabilization in subsequent variants. Stabilization preceded altered dynamics in the N-terminal domain, wherein Omicron BA.1 S showed the largest magnitude increases relative to other preceding variants. Changes in stabilization and dynamics resulting from S mutations detail the evolutionary trajectory of S in emerging variants. These carry major implications for SARS-CoV-2 viral fitness and offer new insights into variant-specific therapeutic development.
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Affiliation(s)
- Sean M Braet
- Department of Chemistry, Pennsylvania State University, University Park, United States
| | - Theresa S C Buckley
- Department of Chemistry, Pennsylvania State University, University Park, United States
| | - Varun Venkatakrishnan
- Department of Chemistry, Pennsylvania State University, University Park, United States
| | - Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
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12
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Cable J, Balachandran S, Daley-Bauer LP, Rustagi A, Antony F, Frere JJ, Strampe J, Kedzierska K, Cannon JL, McGargill MA, Weiskopf D, Mettelman RC, Niessl J, Thomas PG, Briney B, Valkenburg SA, Bloom JD, Bjorkman PJ, Iketani S, Rappazzo CG, Crooks CM, Crofts KF, Pöhlmann S, Krammer F, Sant AJ, Nabel GJ, Schultz-Cherry S. Viral immunity: Basic mechanisms and therapeutic applications-a Keystone Symposia report. Ann N Y Acad Sci 2023; 1521:32-45. [PMID: 36718537 DOI: 10.1111/nyas.14960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Viruses infect millions of people each year. Both endemic viruses circulating throughout the population as well as novel epidemic and pandemic viruses pose ongoing threats to global public health. Developing more effective tools to address viruses requires not only in-depth knowledge of the virus itself but also of our immune system's response to infection. On June 29 to July 2, 2022, researchers met for the Keystone symposium "Viral Immunity: Basic Mechanisms and Therapeutic Applications." This report presents concise summaries from several of the symposium presenters.
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Affiliation(s)
| | - Siddharth Balachandran
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Lisa P Daley-Bauer
- Department of Microbiology and Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Ferrin Antony
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Justin J Frere
- East Harlem Health Outreach Partnership; Department of Medical Education; and Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jamie Strampe
- Bioinformatics Program, Boston University and National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Judy L Cannon
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, California, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Julia Niessl
- Department of Medicine, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - Jesse D Bloom
- Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Microbiology and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | | | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kali F Crofts
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center and Faculty of Biology and Psychology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrea J Sant
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gary J Nabel
- Modex Therapeutics Inc., an OPKO Health Company, Natick, Massachusetts, USA
| | - Stacey Schultz-Cherry
- Department of Laboratory Medicine and Department of Immunology, Yale University School of Medicine, New Haven, Connecticut, USA
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13
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Hills RA, Kit Tan T, Cohen AA, Keeffe JR, Keeble AH, Gnanapragasam PN, Storm KN, Hill ML, Liu S, Gilbert-Jaramillo J, Afzal M, Napier A, James WS, Bjorkman PJ, Townsend AR, Howarth M. Multiviral Quartet Nanocages Elicit Broad Anti-Coronavirus Responses for Proactive Vaccinology. bioRxiv 2023:2023.02.24.529520. [PMID: 36865256 PMCID: PMC9980174 DOI: 10.1101/2023.02.24.529520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Defending against future pandemics may require vaccine platforms that protect across a range of related pathogens. The presentation of multiple receptor-binding domains (RBDs) from evolutionarily-related viruses on a nanoparticle scaffold elicits a strong antibody response to conserved regions. Here we produce quartets of tandemly-linked RBDs from SARS-like betacoronaviruses coupled to the mi3 nanocage through a SpyTag/SpyCatcher spontaneous reaction. These Quartet Nanocages induce a high level of neutralizing antibodies against several different coronaviruses, including against viruses not represented on the vaccine. In animals primed with SARS-CoV-2 Spike, boost immunizations with Quartet Nanocages increased the strength and breadth of an otherwise narrow immune response. Quartet Nanocages are a strategy with potential to confer heterotypic protection against emergent zoonotic coronavirus pathogens and facilitate proactive pandemic protection.
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Affiliation(s)
- Rory A. Hills
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony H. Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | | | - Kaya N. Storm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michelle L. Hill
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Javier Gilbert-Jaramillo
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Madeeha Afzal
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Amy Napier
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - William S. James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alain R. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
- Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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14
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Gristick HB, Hartweger H, Loewe M, van Schooten J, Ramos V, Oliviera TY, Nishimura Y, Koranda NS, Wall A, Yao KH, Poston D, Gazumyan A, Wiatr M, Horning M, Keeffe JR, Hoffmann MA, Yang Z, Abernathy ME, Dam KMA, Gao H, Gnanapragasam PN, Kakutani LM, Pavlovitch-Bedzyk AJ, Seaman MS, Howarth M, McGuire AT, Stamatatos L, Martin MA, West AP, Nussenzweig MC, Bjorkman PJ. CD4 binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wild-type animals. Sci Immunol 2023; 8:eade6364. [PMID: 36763635 PMCID: PMC10202037 DOI: 10.1126/sciimmunol.ade6364] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023]
Abstract
Passive transfer of broadly neutralizing anti-HIV-1 antibodies (bNAbs) protects against infection, and therefore, eliciting bNAbs by vaccination is a major goal of HIV-1 vaccine efforts. bNAbs that target the CD4 binding site (CD4bs) on HIV-1 Env are among the most broadly active, but to date, responses elicited against this epitope in vaccinated animals have lacked potency and breadth. We hypothesized that CD4bs bNAbs resembling the antibody IOMA might be easier to elicit than other CD4bs antibodies that exhibit higher somatic mutation rates, a difficult-to-achieve mechanism to accommodate Env's N276gp120 N-glycan, and rare five-residue light chain complementarity-determining region 3. As an initial test of this idea, we developed IOMA germline-targeting Env immunogens and evaluated a sequential immunization regimen in transgenic mice expressing germline-reverted IOMA. These mice developed CD4bs epitope-specific responses with heterologous neutralization, and cloned antibodies overcame neutralization roadblocks, including accommodating the N276gp120 glycan, with some neutralizing selected HIV-1 strains more potently than IOMA. The immunization regimen also elicited CD4bs-specific responses in mice containing polyclonal antibody repertoires as well as rabbits and rhesus macaques. Thus, germline targeting of IOMA-class antibody precursors represents a potential vaccine strategy to induce CD4bs bNAbs.
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Affiliation(s)
- Harry B. Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Maximilian Loewe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jelle van Schooten
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y. Oliviera
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases,National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas S. Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Abigail Wall
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Poston
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marie Wiatr
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marcel Horning
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Magnus A.G. Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Morgan E. Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Leesa M. Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Andrew T. McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Malcolm A. Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases,National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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15
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DeLaitsch AT, Liendo N, Bjorkman PJ. Designing occluded-open Env-based immunogens for HIV-1. Biophys J 2023; 122:472a. [PMID: 36784426 DOI: 10.1016/j.bpj.2022.11.2532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Nathaniel Liendo
- California Institute of Technology, Pasadena, CA, USA; St. Mary's University, San Antonio, TX, USA
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16
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Dam KMA, Fan C, Yang Z, Bjorkman PJ. Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations. bioRxiv 2023:2023.01.27.525985. [PMID: 36747804 PMCID: PMC9900888 DOI: 10.1101/2023.01.27.525985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120/gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops, and in fully-saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops. To investigate changes resulting from sub-stoichiometric CD4 binding, we solved 3.4Å and 3.9Å single-particle cryo-EM structures of soluble, native-like Envs bound to one or two CD4 molecules. Env trimer bound to one CD4 adopted the closed, prefusion Env state. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state that included gp120 outward rotation but maintained the prefusion, three-stranded gp120 bridging sheet and showed only partial V1V2 displacement and V3 exposure. We conclude that engagement of one CD4 molecule was insufficient to stimulate CD4-induced conformational changes, while binding two CD4 molecules led to Env opening in CD4-bound protomers only. Together, these results illuminate HIV-1 Env intermediate conformations and illustrate the structural plasticity of HIV-1 Env.
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Affiliation(s)
- Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Department of Molecular and Cell Biology, University of California, 13 Berkeley, CA 94720, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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17
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Huang KYA, Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Tan TK, Rijal P, Vester SK, Hills RA, Howarth M, Keeffe JR, Cohen AA, Kakutani LM, Wu YM, Shahed-Al-Mahmud M, Chou YC, Bjorkman PJ, Townsend AR, Ma C. Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2. Nat Commun 2023; 14:311. [PMID: 36658148 PMCID: PMC9852238 DOI: 10.1038/s41467-023-35949-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.
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Affiliation(s)
- Kuan-Ying A Huang
- Graduate Institute of Immunology and Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Xiaorui Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Hong Thuy Vy Nguyen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Lisa Schimanski
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Pramila Rijal
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Susan K Vester
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Rory A Hills
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Yi-Min Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | | | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Alain R Townsend
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
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18
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Hoffmann MAG, Yang Z, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Nakatomi LM, Storm KN, Moon WJ, Lin PJ, Bjorkman PJ. ESCRT recruitment to mRNA-encoded SARS-CoV-2 spike induces virus-like particles and enhanced antibody responses. bioRxiv 2022:2022.12.26.521940. [PMID: 36597535 PMCID: PMC9810232 DOI: 10.1101/2022.12.26.521940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Prime-boost regimens for COVID-19 vaccines elicit poor antibody responses against Omicron-based variants and employ frequent boosters to maintain antibody levels. We present a natural infection-mimicking technology that combines features of mRNA- and protein nanoparticle-based vaccines through encoding self-assembling enveloped virus-like particles (eVLPs). eVLP assembly is achieved by inserting an ESCRT- and ALIX-binding region (EABR) into the SARS-CoV-2 spike cytoplasmic tail, which recruits ESCRT proteins to induce eVLP budding from cells. Purified spike-EABR eVLPs presented densely-arrayed spikes and elicited potent antibody responses in mice. Two immunizations with mRNA-LNP encoding spike-EABR elicited potent CD8+ T-cell responses and superior neutralizing antibody responses against original and variant SARS-CoV-2 compared to conventional spike-encoding mRNA-LNP and purified spike-EABR eVLPs, improving neutralizing titers >10-fold against Omicron-based variants for three months post-boost. Thus, EABR technology enhances potency and breadth of vaccine-induced responses through antigen presentation on cell surfaces and eVLPs, enabling longer-lasting protection against SARS-CoV-2 and other viruses.
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Affiliation(s)
- Magnus A. G. Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Leesa M. Nakatomi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kaya N. Storm
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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19
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Fan C, Cohen AA, Park M, Hung AFH, Keeffe JR, Gnanapragasam PNP, Lee YE, Gao H, Kakutani LM, Wu Z, Kleanthous H, Malecek KE, Williams JC, Bjorkman PJ. Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes. Immunity 2022; 55:2419-2435.e10. [PMID: 36370711 PMCID: PMC9606073 DOI: 10.1016/j.immuni.2022.10.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/07/2022] [Accepted: 10/24/2022] [Indexed: 01/21/2023]
Abstract
Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.
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Affiliation(s)
- Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Miso Park
- Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | | | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ziyan Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Kathryn E Malecek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John C Williams
- Department of Molecular Medicine, City of Hope, Duarte, CA 91010, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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20
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Barnes CO, Schoofs T, Gnanapragasam PN, Golijanin J, Huey-Tubman KE, Gruell H, Schommers P, Suh-Toma N, Lee YE, Cetrulo Lorenzi JC, Piechocka-Trocha A, Scheid JF, West AP, Walker BD, Seaman MS, Klein F, Nussenzweig MC, Bjorkman PJ. A naturally arising broad and potent CD4-binding site antibody with low somatic mutation. Sci Adv 2022; 8:eabp8155. [PMID: 35960796 PMCID: PMC9374330 DOI: 10.1126/sciadv.abp8155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.
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Affiliation(s)
- Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Till Schoofs
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
| | | | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nina Suh-Toma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu Erica Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Johannes F. Scheid
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Corresponding author. (M.C.N.); (P.J.B.)
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Corresponding author. (M.C.N.); (P.J.B.)
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21
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Cohen AA, van Doremalen N, Greaney AJ, Andersen H, Sharma A, Starr TN, Keeffe JR, Fan C, Schulz JE, Gnanapragasam PNP, Kakutani LM, West AP, Saturday G, Lee YE, Gao H, Jette CA, Lewis MG, Tan TK, Townsend AR, Bloom JD, Munster VJ, Bjorkman PJ. Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models. Science 2022; 377:eabq0839. [PMID: 35857620 PMCID: PMC9273039 DOI: 10.1126/science.abq0839] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/29/2022] [Indexed: 12/12/2022]
Abstract
To combat future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants, including Omicrons, and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.
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Affiliation(s)
- Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | | | | | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jonathan E. Schulz
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | | | - Leesa M. Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Greg Saturday
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Tiong K. Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Alain R. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, Oxford OX3 9DS, UK
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Vincent J. Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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22
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Bozhanova NG, Flyak AI, Brown BP, Ruiz SE, Salas J, Rho S, Bombardi RG, Myers L, Soto C, Bailey JR, Crowe JE, Bjorkman PJ, Meiler J. Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals. Nat Commun 2022; 13:3178. [PMID: 35676279 PMCID: PMC9177688 DOI: 10.1038/s41467-022-30865-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/20/2022] [Indexed: 12/14/2022] Open
Abstract
Despite recent success in hepatitis C virus (HCV) treatment using antivirals, an HCV vaccine is still needed to prevent reinfections in treated patients, to avert the emergence of drug-resistant strains, and to provide protection for people with no access to the antiviral therapeutics. The early production of broadly neutralizing antibodies (bNAbs) associates with HCV clearance. Several potent bNAbs bind a conserved HCV glycoprotein E2 epitope using an unusual heavy chain complementarity determining region 3 (HCDR3) containing an intra-loop disulfide bond. Isolation of additional structurally-homologous bNAbs would facilitate the recognition of key determinants of such bNAbs and guide rational vaccine design. Here we report the identification of new antibodies containing an HCDR3 disulfide bond motif using computational screening with the Rosetta software. Using the newly-discovered and already-known members of this antibody family, we review the required HCDR3 amino acid composition and propose determinants for the bent versus straight HCDR3 loop conformation observed in these antibodies.
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Affiliation(s)
- Nina G. Bozhanova
- grid.152326.10000 0001 2264 7217Department of Chemistry, Vanderbilt University, Nashville, TN 37235 USA ,grid.152326.10000 0001 2264 7217Center for Structural Biology, Vanderbilt University, Nashville, TN 37235 USA
| | - Andrew I. Flyak
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Benjamin P. Brown
- grid.152326.10000 0001 2264 7217Department of Chemistry, Vanderbilt University, Nashville, TN 37235 USA ,grid.152326.10000 0001 2264 7217Center for Structural Biology, Vanderbilt University, Nashville, TN 37235 USA
| | - Stormy E. Ruiz
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA ,grid.21107.350000 0001 2171 9311Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Jordan Salas
- grid.21107.350000 0001 2171 9311Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Semi Rho
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Robin G. Bombardi
- grid.412807.80000 0004 1936 9916Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232 USA
| | - Luke Myers
- grid.412807.80000 0004 1936 9916Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232 USA
| | - Cinque Soto
- grid.412807.80000 0004 1936 9916Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232 USA ,grid.412807.80000 0004 1936 9916Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232 USA
| | - Justin R. Bailey
- grid.21107.350000 0001 2171 9311Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - James E. Crowe
- grid.412807.80000 0004 1936 9916Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232 USA ,grid.412807.80000 0004 1936 9916Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232 USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232 USA
| | - Pamela J. Bjorkman
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Jens Meiler
- grid.152326.10000 0001 2264 7217Department of Chemistry, Vanderbilt University, Nashville, TN 37235 USA ,grid.152326.10000 0001 2264 7217Center for Structural Biology, Vanderbilt University, Nashville, TN 37235 USA ,grid.9647.c0000 0004 7669 9786Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103 Germany
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23
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Cohen AA, van Doremalen N, Greaney AJ, Andersen H, Sharma A, Starr TN, Keeffe JR, Fan C, Schulz JE, Gnanapragasam PN, Kakutani LM, West AP, Saturday G, Lee YE, Gao H, Jette CA, Lewis MG, Tan TK, Townsend AR, Bloom JD, Munster VJ, Bjorkman PJ. Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models. bioRxiv 2022:2022.03.25.485875. [PMID: 35378752 PMCID: PMC8978945 DOI: 10.1101/2022.03.25.485875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To combat future SARS-CoV-2 variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles presenting randomly-arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against conserved/relatively-occluded, rather than variable/immunodominant/exposed, epitopes. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD-nanoparticles in mice and macaques, observing stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants including Omicron and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest mosaic-8 RBD-nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.
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Affiliation(s)
- Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | | | | | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jonathan E. Schulz
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | | | - Leesa M. Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Greg Saturday
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Tiong K. Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Alain R. Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Chinese Academy of Medical Sciences, Oxford Institute, University of Oxford, Oxford OX3 9DS, UK
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Vincent J. Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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24
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Yang Z, Dam KMA, Bridges MD, Hoffmann MAG, DeLaitsch AT, Gristick HB, Escolano A, Gautam R, Martin MA, Nussenzweig MC, Hubbell WL, Bjorkman PJ. Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer. Nat Commun 2022; 13:732. [PMID: 35136084 PMCID: PMC8826976 DOI: 10.1038/s41467-022-28424-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/24/2022] [Indexed: 11/09/2022] Open
Abstract
Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an ‘occluded-open’ conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts. Neutralizing antibodies (bNAbs) against HIV-1 are exclusively directed against the viral envelope protein (Env) and mainly target Env in a closed, prefusion state. Here, Yang et al. structurally characterize two heterologously-neutralizing CD4-binding site (CD4bs) antibodies isolated from sequentially immunized macaques, and show that these antibodies recognize the CD4bs on Env trimers in an „occluded-open‟ conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4.
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Affiliation(s)
- Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael D Bridges
- Jules Stein Eye Institute, University of California, Los Angeles, CA, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Magnus A G Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew T DeLaitsch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Malcolm A Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, CA, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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25
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Weber T, Potthoff J, Bizu S, Labuhn M, Dold L, Schoofs T, Horning M, Ercanoglu MS, Kreer C, Gieselmann L, Vanshylla K, Langhans B, Janicki H, Ströh LJ, Knops E, Nierhoff D, Spengler U, Kaiser R, Bjorkman PJ, Krey T, Bankwitz D, Pfeifer N, Pietschmann T, Flyak AI, Klein F. Analysis of antibodies from HCV elite neutralizers identifies genetic determinants of broad neutralization. Immunity 2022; 55:341-354.e7. [PMID: 34990590 PMCID: PMC10089621 DOI: 10.1016/j.immuni.2021.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/21/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
The high genetic diversity of hepatitis C virus (HCV) complicates effective vaccine development. We screened a cohort of 435 HCV-infected individuals and found that 2%-5% demonstrated outstanding HCV-neutralizing activity. From four of these patients, we isolated 310 HCV antibodies, including neutralizing antibodies with exceptional breadth and potency. High neutralizing activity was enabled by the use of the VH1-69 heavy-chain gene segment, somatic mutations within CDRH1, and CDRH2 hydrophobicity. Structural and mutational analyses revealed an important role for mutations replacing the serines at positions 30 and 31, as well as the presence of neutral and hydrophobic residues at the tip of the CDRH3. Based on these characteristics, we computationally created a de novo antibody with a fully synthetic VH1-69 heavy chain that efficiently neutralized multiple HCV genotypes. Our findings provide a deep understanding of the generation of broadly HCV-neutralizing antibodies that can guide the design of effective vaccine candidates.
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Affiliation(s)
- Timm Weber
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Julian Potthoff
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sven Bizu
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Maurice Labuhn
- Twincore, Centre for Experimental and Clinical Infection Research, Institute of Experimental Virology, 30625 Hannover, Germany
| | - Leona Dold
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Department of Internal Medicine I, University Hospital of Bonn, 53127 Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Till Schoofs
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Marcel Horning
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Meryem S Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Bettina Langhans
- Department of Internal Medicine I, University Hospital of Bonn, 53127 Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Luisa J Ströh
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Elena Knops
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Dirk Nierhoff
- Department of Gastroenterology and Hepatology, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
| | - Ulrich Spengler
- Department of Internal Medicine I, University Hospital of Bonn, 53127 Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Rolf Kaiser
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany; Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany; Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, 23562 Luebeck, Germany; Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Riems, 23562 Luebeck, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Dorothea Bankwitz
- Twincore, Centre for Experimental and Clinical Infection Research, Institute of Experimental Virology, 30625 Hannover, Germany
| | - Nico Pfeifer
- Methods in Medical Informatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Thomas Pietschmann
- Twincore, Centre for Experimental and Clinical Infection Research, Institute of Experimental Virology, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30625 Hannover, Germany
| | - Andrew I Flyak
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany; Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University of Cologne, 50931 Cologne, Germany.
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26
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Tanaka S, Olson CA, Barnes CO, Higashide W, Gonzalez M, Taft J, Richardson A, Martin-Fernandez M, Bogunovic D, Gnanapragasam PNP, Bjorkman PJ, Spilman P, Niazi K, Rabizadeh S, Soon-Shiong P. Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Cell Rep 2022; 38:110348. [PMID: 35114110 PMCID: PMC8769934 DOI: 10.1016/j.celrep.2022.110348] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/06/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022] Open
Abstract
The increasing prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identify a set of antibodies against SARS-CoV-2 spike (S) proteins and characterize the structures of nAbs that recognize epitopes in the S1 subunit of the S glycoprotein. These structural studies reveal distinct binding modes for several antibodies, including the targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interact with angiotensin-converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. Further, we engineer a potent ACE2-blocking nAb to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is an approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.
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Affiliation(s)
- Shiho Tanaka
- ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA
| | - C Anders Olson
- ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA.
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Wendy Higashide
- ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA
| | - Marcos Gonzalez
- ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA
| | - Justin Taft
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA
| | - Ashley Richardson
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA
| | - Marta Martin-Fernandez
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA
| | - Dusan Bogunovic
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA
| | - Priyanthi N P Gnanapragasam
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Patricia Spilman
- ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA
| | - Kayvan Niazi
- ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA
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27
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Needham BD, Funabashi M, Adame MD, Wang Z, Boktor JC, Haney J, Wu WL, Rabut C, Ladinsky MS, Hwang SJ, Guo Y, Zhu Q, Griffiths JA, Knight R, Bjorkman PJ, Shapiro MG, Geschwind DH, Holschneider DP, Fischbach MA, Mazmanian SK. A gut-derived metabolite alters brain activity and anxiety behaviour in mice. Nature 2022; 602:647-653. [PMID: 35165440 PMCID: PMC9170029 DOI: 10.1038/s41586-022-04396-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/02/2022] [Indexed: 12/14/2022]
Abstract
Integration of sensory and molecular inputs from the environment shapes animal behaviour. A major site of exposure to environmental molecules is the gastrointestinal tract, in which dietary components are chemically transformed by the microbiota1 and gut-derived metabolites are disseminated to all organs, including the brain2. In mice, the gut microbiota impacts behaviour3, modulates neurotransmitter production in the gut and brain4,5, and influences brain development and myelination patterns6,7. The mechanisms that mediate the gut-brain interactions remain poorly defined, although they broadly involve humoral or neuronal connections. We previously reported that the levels of the microbial metabolite 4-ethylphenyl sulfate (4EPS) were increased in a mouse model of atypical neurodevelopment8. Here we identified biosynthetic genes from the gut microbiome that mediate the conversion of dietary tyrosine to 4-ethylphenol (4EP), and bioengineered gut bacteria to selectively produce 4EPS in mice. 4EPS entered the brain and was associated with changes in region-specific activity and functional connectivity. Gene expression signatures revealed altered oligodendrocyte function in the brain, and 4EPS impaired oligodendrocyte maturation in mice and decreased oligodendrocyte-neuron interactions in ex vivo brain cultures. Mice colonized with 4EP-producing bacteria exhibited reduced myelination of neuronal axons. Altered myelination dynamics in the brain have been associated with behavioural outcomes7,9-14. Accordingly, we observed that mice exposed to 4EPS displayed anxiety-like behaviours, and pharmacological treatments that promote oligodendrocyte differentiation prevented the behavioural effects of 4EPS. These findings reveal that a gut-derived molecule influences complex behaviours in mice through effects on oligodendrocyte function and myelin patterning in the brain.
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Affiliation(s)
- Brittany D Needham
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Masanori Funabashi
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
- Translational Research Department, Daiichi Sankyo RD Novare Co Ltd, Tokyo, Japan
| | - Mark D Adame
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhuo Wang
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joseph C Boktor
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jillian Haney
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Wei-Li Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Claire Rabut
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Son-Jong Hwang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yumei Guo
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Jessica A Griffiths
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel P Holschneider
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Viterbi School of Engineering, Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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28
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Cable J, Rappuoli R, Klemm EJ, Kang G, Mutreja A, Wright GJ, Pizza M, Castro SA, Hoffmann JP, Alter G, Carfi A, Pollard AJ, Krammer F, Gupta RK, Wagner CE, Machado V, Modjarrad K, Corey L, B Gilbert P, Dougan G, Lurie N, Bjorkman PJ, Chiu C, Nemes E, Gordon SB, Steer AC, Rudel T, Blish CA, Sandberg JT, Brennan K, Klugman KP, Stuart LM, Madhi SA, Karp CL. Innovative vaccine approaches-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1511:59-86. [PMID: 35029310 DOI: 10.1111/nyas.14739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022]
Abstract
The rapid development of COVID-19 vaccines was the result of decades of research to establish flexible vaccine platforms and understand pathogens with pandemic potential, as well as several novel changes to the vaccine discovery and development processes that partnered industry and governments. And while vaccines offer the potential to drastically improve global health, low-and-middle-income countries around the world often experience reduced access to vaccines and reduced vaccine efficacy. Addressing these issues will require novel vaccine approaches and platforms, deeper insight how vaccines mediate protection, and innovative trial designs and models. On June 28-30, 2021, experts in vaccine research, development, manufacturing, and deployment met virtually for the Keystone eSymposium "Innovative Vaccine Approaches" to discuss advances in vaccine research and development.
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Affiliation(s)
| | | | | | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK.,Department of Biology, Hull York Medical School, and York Biomedical Research Institute, University of York, York, UK
| | | | - Sowmya Ajay Castro
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joseph P Hoffmann
- Departments of Pediatrics and Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts.,Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Florian Krammer
- The Tisch Cancer Institute and Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK.,Africa Health Research Institute, Durban, South Africa
| | - Caroline E Wagner
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Viviane Machado
- Measles and Respiratory Viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Lawrence Corey
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Lurie
- Coalition for Epidemic Preparedness Innovations, Oslo, Norway.,Harvard Medical School, Boston, Massachusetts
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Elisa Nemes
- Division of Immunology, Department of Pathology, South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Andrew C Steer
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Department of General Medicine, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Thomas Rudel
- Microbiology Biocenter, University of Würzburg, Würzburg, Germany
| | - Catherine A Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford Immunology Program, Stanford University School of Medicine, Stanford, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - John Tyler Sandberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kiva Brennan
- National Children's Research Centre, Crumlin and School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Lynda M Stuart
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
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29
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Vanshylla K, Fan C, Wunsch M, Poopalasingam N, Meijers M, Kreer C, Kleipass F, Ruchnewitz D, Ercanoglu MS, Gruell H, Münn F, Pohl K, Janicki H, Nolden T, Bartl S, Stein SC, Augustin M, Dewald F, Gieselmann L, Schommers P, Schulz TF, Sander LE, Koch M, Łuksza M, Lässig M, Bjorkman PJ, Klein F. Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers. Cell Host Microbe 2022; 30:69-82.e10. [PMID: 34973165 PMCID: PMC8683262 DOI: 10.1016/j.chom.2021.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/08/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023]
Abstract
A fraction of COVID-19 convalescent individuals mount a potent antibody response to SARS-CoV-2 with cross-reactivity to SARS-CoV-1. To uncover their humoral response in detail, we performed single B cell analysis from 10 SARS-CoV-2 elite neutralizers. We isolated and analyzed 126 monoclonal antibodies, many of which were sarbecovirus cross-reactive, with some displaying merbecovirus- and embecovirus-reactivity. Several isolated broadly neutralizing antibodies were effective against B.1.1.7, B.1.351, B.1.429, B.1.617, and B.1.617.2 variants and 19 prominent potential escape sites. Furthermore, assembly of 716,806 SARS-CoV-2 sequences predicted emerging escape variants, which were also effectively neutralized. One of these broadly neutralizing potent antibodies, R40-1G8, is a IGHV3-53 RBD-class-1 antibody. Remarkably, cryo-EM analysis revealed that R40-1G8 has a flexible binding mode, targeting both "up" and "down" conformations of the RBD. Given the threat of emerging SARS-CoV-2 variants, we demonstrate that elite neutralizers are a valuable source for isolating ultrapotent antibody candidates to prevent and treat SARS-CoV-2 infection.
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Affiliation(s)
- Kanika Vanshylla
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marie Wunsch
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nareshkumar Poopalasingam
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Matthijs Meijers
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Christoph Kreer
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Franziska Kleipass
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Meryem S. Ercanoglu
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Friederike Münn
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Kai Pohl
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Hanna Janicki
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | | | - Simone Bartl
- Vira Therapeutics GmbH, 6063 Rum, Austria,Boehringer Ingelheim International GmbH, Ingelheim, Germany
| | - Saskia C. Stein
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Max Augustin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Felix Dewald
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Marta Łuksza
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany,Corresponding author
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30
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Ogega CO, Skinner NE, Flyak AI, Clark KE, Board NL, Bjorkman PJ, Crowe JE, Cox AL, Ray SC, Bailey JR. B cell overexpression of FCRL5 and PD-1 is associated with low antibody titers in HCV infection. PLoS Pathog 2022; 18:e1010179. [PMID: 34990486 PMCID: PMC8769295 DOI: 10.1371/journal.ppat.1010179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/19/2022] [Accepted: 12/07/2021] [Indexed: 11/25/2022] Open
Abstract
Antibodies targeting the hepatitis C virus (HCV) envelope glycoprotein E2 are associated with delayed disease progression, and these antibodies can also facilitate spontaneous clearance of infection in some individuals. However, many infected people demonstrate low titer and delayed anti-E2 antibody responses. Since a goal of HCV vaccine development is induction of high titers of anti-E2 antibodies, it is important to define the mechanisms underlying these suboptimal antibody responses. By staining lymphocytes with a cocktail of soluble E2 (sE2) glycoproteins, we detected HCV E2-specific (sE2+) B cells directly ex vivo at multiple acute infection timepoints in 29 HCV-infected subjects with a wide range of anti-E2 IgG titers, including 17 persistently infected subjects and 12 subjects with spontaneous clearance of infection. We performed multi-dimensional flow cytometric analysis of sE2+ and E2-nonspecific (sE2-) class-switched B cells (csBC). In sE2+ csBC from both persistence and clearance subjects, frequencies of resting memory B cells (rMBC) were reduced, frequencies of activated MBC (actMBC) and tissue-like MBC (tlMBC) were increased, and expression of FCRL5, an IgG receptor, was significantly upregulated. Across all subjects, plasma anti-E2 IgG levels were positively correlated with frequencies of sE2+ rMBC and sE2+ actMBC, while anti-E2 IgG levels were negatively correlated with levels of FCRL5 expression on sE2+ rMBC and PD-1 expression on sE2+ actMBC. Upregulation of FCRL5 on sE2+ rMBC and upregulation of PD-1 on sE2+ actMBC may limit anti-E2 antibody production in vivo. Strategies that limit upregulation of these molecules could potentially generate higher titers of protective antibodies against HCV or other pathogens. Antiviral immunity relies on production of protective immunoglobulin G (IgG) by B cells, but many hepatitis C virus (HCV)-infected individuals have very low levels of HCV-specific IgG in their serum. Elucidating mechanisms underlying this suboptimal IgG expression remains paramount in guiding therapeutic and vaccine strategies. In this study, we developed a highly specific method to capture HCV-specific B cells and characterized their surface protein expression. Two proteins analyzed were Fc receptor-like protein 5 (FCRL5), a cell surface receptor for IgG, and programmed cell death protein-1 (PD-1), a marker of lymphocyte activation and exhaustion. We measured serum levels of anti-HCV IgG in these subjects and demonstrated that overexpression of FCRL5 and PD-1 on memory B cells was associated with reduced anti-E2 IgG levels. This study uses HCV as a viral model, but the findings may be applicable to many viral infections, and they offer new potential targets to enhance antiviral IgG production.
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Affiliation(s)
- Clinton O. Ogega
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, Maryland, United States of America
| | - Nicole E. Skinner
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, Maryland, United States of America
| | - Andrew I. Flyak
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, California, United States of America
| | - Kaitlyn E. Clark
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, Maryland, United States of America
| | - Nathan L. Board
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, Maryland, United States of America
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, California, United States of America
| | - James E. Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, Tennessee, United States of America
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, Tennessee, United States of America
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, Tennessee, United States of America
| | - Andrea L. Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, Maryland, United States of America
| | - Stuart C. Ray
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, Maryland, United States of America
| | - Justin R. Bailey
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, Maryland, United States of America
- * E-mail:
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31
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Escolano A, Gristick HB, Gautam R, DeLaitsch AT, Abernathy ME, Yang Z, Wang H, Hoffmann MAG, Nishimura Y, Wang Z, Koranda N, Kakutani LM, Gao H, Gnanapragasam PNP, Raina H, Gazumyan A, Cipolla M, Oliveira TY, Ramos V, Irvine DJ, Silva M, West AP, Keeffe JR, Barnes CO, Seaman MS, Nussenzweig MC, Martin MA, Bjorkman PJ. Sequential immunization of macaques elicits heterologous neutralizing antibodies targeting the V3-glycan patch of HIV-1 Env. Sci Transl Med 2021; 13:eabk1533. [PMID: 34818054 DOI: 10.1126/scitranslmed.abk1533] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew T DeLaitsch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Morgan E Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Haoqing Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Magnus A G Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leesa M Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Henna Raina
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Darrell J Irvine
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Murillo Silva
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Malcolm A Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Abernathy ME, Gristick HB, Vielmetter J, Keeffe JR, Gnanapragasam PNP, Lee YE, Escolano A, Gautam R, Seaman MS, Martin MA, Nussenzweig MC, Bjorkman PJ. Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope. NPJ Vaccines 2021; 6:126. [PMID: 34697307 PMCID: PMC8545924 DOI: 10.1038/s41541-021-00387-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/01/2021] [Indexed: 11/09/2022] Open
Abstract
HIV-1 vaccine design aims to develop an immunogen that elicits broadly neutralizing antibodies against a desired epitope, while eliminating responses to off-target regions of HIV-1 Env. We report characterization of Ab1245, an off-target antibody against the Env gp120-gp41 interface, from V3-glycan patch immunogen-primed and boosted macaques. A 3.7 Å cryo-EM structure of an Ab1245-Env complex reveals one Ab1245 Fab binding asymmetrically to Env trimer at the gp120-gp41 interface using its long CDRH3 to mimic regions of gp41. The mimicry includes positioning of a CDRH3 methionine into the gp41 tryptophan clasp, resulting in displacement of the fusion peptide and fusion peptide-proximal region. Despite fusion peptide displacement, Ab1245 is non-neutralizing even at high concentrations, raising the possibility that only two fusion peptides per trimer are required for viral-host membrane fusion. These structural analyses facilitate immunogen design to prevent elicitation of Ab1245-like antibodies that block neutralizing antibodies against the fusion peptide.
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Affiliation(s)
- Morgan E. Abernathy
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Harry B. Gristick
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Jost Vielmetter
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Jennifer R. Keeffe
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Priyanthi N. P. Gnanapragasam
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Yu E. Lee
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | | | - Rajeev Gautam
- grid.419681.30000 0001 2164 9667Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Present Address: Virology Branch, Basic Research Section, NIAID, NIH. 5601 Fisher’s Lane, Rockville, MD 20892 USA
| | - Michael S. Seaman
- grid.239395.70000 0000 9011 8547Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA USA
| | - Malcolm A. Martin
- grid.419681.30000 0001 2164 9667Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, New York, 10065 USA ,grid.134907.80000 0001 2166 1519Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065 USA
| | - Pamela J. Bjorkman
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
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Abernathy ME, Dam KMA, Esswein SR, Jette CA, Bjorkman PJ. How Antibodies Recognize Pathogenic Viruses: Structural Correlates of Antibody Neutralization of HIV-1, SARS-CoV-2, and Zika. Viruses 2021; 13:2106. [PMID: 34696536 PMCID: PMC8537525 DOI: 10.3390/v13102106] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
The H1N1 pandemic of 2009-2010, MERS epidemic of 2012, Ebola epidemics of 2013-2016 and 2018-2020, Zika epidemic of 2015-2016, and COVID-19 pandemic of 2019-2021, are recent examples in the long history of epidemics that demonstrate the enormous global impact of viral infection. The rapid development of safe and effective vaccines and therapeutics has proven vital to reducing morbidity and mortality from newly emerging viruses. Structural biology methods can be used to determine how antibodies elicited during infection or vaccination target viral proteins and identify viral epitopes that correlate with potent neutralization. Here we review how structural and molecular biology approaches have contributed to our understanding of antibody recognition of pathogenic viruses, specifically HIV-1, SARS-CoV-2, and Zika. Determining structural correlates of neutralization of viruses has guided the design of vaccines, monoclonal antibodies, and small molecule inhibitors in response to the global threat of viral epidemics.
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Affiliation(s)
- Morgan E. Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (M.E.A.); (K.-M.A.D.); (C.A.J.)
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (M.E.A.); (K.-M.A.D.); (C.A.J.)
| | - Shannon R. Esswein
- David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA;
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (M.E.A.); (K.-M.A.D.); (C.A.J.)
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; (M.E.A.); (K.-M.A.D.); (C.A.J.)
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34
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Jette CA, Cohen AA, Gnanapragasam PNP, Muecksch F, Lee YE, Huey-Tubman KE, Schmidt F, Hatziioannou T, Bieniasz PD, Nussenzweig MC, West AP, Keeffe JR, Bjorkman PJ, Barnes CO. Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies. Cell Rep 2021; 36:109760. [PMID: 34534459 PMCID: PMC8423902 DOI: 10.1016/j.celrep.2021.109760] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/05/2021] [Accepted: 09/01/2021] [Indexed: 01/21/2023] Open
Abstract
Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding domains (RBDs). Potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly emergent zoonotic sarbecoviruses and variants, but they usually show only weak neutralization potencies. Here, we characterize two class 4 anti-RBD antibodies derived from coronavirus disease 2019 (COVID-19) donors that exhibit breadth and potent neutralization of zoonotic coronaviruses and SARS-CoV-2 variants. C118-RBD and C022-RBD structures reveal orientations that extend from the cryptic epitope to occlude ACE2 binding and CDRH3-RBD main-chain H-bond interactions that extend an RBD β sheet, thus reducing sensitivity to RBD side-chain changes. A C118-spike trimer structure reveals rotated RBDs that allow access to the cryptic epitope and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.
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Affiliation(s)
- Claudia A Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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35
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Ullah I, Prévost J, Ladinsky MS, Stone H, Lu M, Anand SP, Beaudoin-Bussières G, Symmes K, Benlarbi M, Ding S, Gasser R, Fink C, Chen Y, Tauzin A, Goyette G, Bourassa C, Medjahed H, Mack M, Chung K, Wilen CB, Dekaban GA, Dikeakos JD, Bruce EA, Kaufmann DE, Stamatatos L, McGuire AT, Richard J, Pazgier M, Bjorkman PJ, Mothes W, Finzi A, Kumar P, Uchil PD. Live imaging of SARS-CoV-2 infection in mice reveals that neutralizing antibodies require Fc function for optimal efficacy. Immunity 2021; 54:2143-2158.e15. [PMID: 34453881 PMCID: PMC8372518 DOI: 10.1016/j.immuni.2021.08.015] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/27/2021] [Accepted: 08/11/2021] [Indexed: 12/29/2022]
Abstract
Neutralizing antibodies (NAbs) are effective in treating COVID-19, but the mechanism of immune protection is not fully understood. Here, we applied live bioluminescence imaging (BLI) to monitor the real-time effects of NAb treatment during prophylaxis and therapy of K18-hACE2 mice intranasally infected with SARS-CoV-2-nanoluciferase. Real-time imaging revealed that the virus spread sequentially from the nasal cavity to the lungs in mice and thereafter systemically to various organs including the brain, culminating in death. Highly potent NAbs from a COVID-19 convalescent subject prevented, and also effectively resolved, established infection when administered within three days. In addition to direct neutralization, depletion studies indicated that Fc effector interactions of NAbs with monocytes, neutrophils, and natural killer cells were required to effectively dampen inflammatory responses and limit immunopathology. Our study highlights that both Fab and Fc effector functions of NAbs are essential for optimal in vivo efficacy against SARS-CoV-2.
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Affiliation(s)
- Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Helen Stone
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Kelly Symmes
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Corby Fink
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Alexandra Tauzin
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | | | | | | | - Matthias Mack
- Universitätsklinikum Regensburg, Innere Medizin II - Nephrologie, Regensburg 93042, Germany
| | - Kunho Chung
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Craig B Wilen
- Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Gregory A Dekaban
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5B7, Canada; Molecluar Medicine Research Laboratories, Robarts Research Institute, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Emily A Bruce
- Division of Immunobiology, Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405. USA
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Center, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Center, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA.
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36
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Tanaka S, Anders Olson C, Barnes CO, Higashide W, Gonzalez M, Taft J, Richardson A, Martin-Fernandez M, Bogunovic D, Gnanapragasam PNP, Bjorkman PJ, Spilman P, Niazi K, Rabizadeh S, Soon-Shiong P. Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display. bioRxiv 2021:2021.09.14.460356. [PMID: 34545362 PMCID: PMC8452091 DOI: 10.1101/2021.09.14.460356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The increasing prevalence of SARS-CoV-2 variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly-reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identified a set of antibodies against SARS-CoV-2 spike (S) proteins and characterized the structures of nAbs that recognized epitopes in the S1 subunit of the S glycoprotein. These structural studies revealed distinct binding modes for several antibodies, including targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interacts with angiotensin- converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. A potent ACE2-blocking nAb was further engineered to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is a promising approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.
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37
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Brune KD, Liekniņa I, Sutov G, Morris AR, Jovicevic D, Kalniņš G, Kazāks A, Kluga R, Kastaljana S, Zajakina A, Jansons J, Skrastiņa D, Spunde K, Cohen AA, Bjorkman PJ, Morris HR, Suna E, Tārs K. N-Terminal Modification of Gly-His-Tagged Proteins with Azidogluconolactone. Chembiochem 2021; 22:3199-3207. [PMID: 34520613 DOI: 10.1002/cbic.202100381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/13/2021] [Indexed: 01/07/2023]
Abstract
Site-specific protein modifications are vital for biopharmaceutical drug development. Gluconoylation is a non-enzymatic, post-translational modification of N-terminal HisTags. We report high-yield, site-selective in vitro α-aminoacylation of peptides, glycoproteins, antibodies, and virus-like particles (VLPs) with azidogluconolactone at pH 7.5 in 1 h. Conjugates slowly hydrolyse, but diol-masking with borate esters inhibits reversibility. In an example, we multimerise azidogluconoylated SARS-CoV-2 receptor-binding domain (RBD) onto VLPs via click-chemistry, to give a COVID-19 vaccine. Compared to yeast antigen, HEK-derived RBD was immunologically superior, likely due to observed differences in glycosylation. We show the benefits of ordered over randomly oriented multimeric antigen display, by demonstrating single-shot seroconversion and best virus-neutralizing antibodies. Azidogluconoylation is simple, fast and robust chemistry, and should accelerate research and development.
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Affiliation(s)
- Karl D Brune
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Ilva Liekniņa
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Grigorij Sutov
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Lab Group LT, UAB, Vilnius, Lithuania
| | - Alexander R Morris
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Lab Group LT, UAB, Vilnius, Lithuania.,BioPharmaSpec Ltd., Suite 3.1, Lido Medical Centre, St. Saviour, JE2 7LA, UK
| | - Dejana Jovicevic
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Andris Kazāks
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Rihards Kluga
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Sabine Kastaljana
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Anna Zajakina
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Dace Skrastiņa
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Karīna Spunde
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Howard R Morris
- BioPharmaSpec Ltd., Suite 3.1, Lido Medical Centre, St. Saviour, JE2 7LA, UK.,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Edgars Suna
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
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38
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Muecksch F, Weisblum Y, Barnes CO, Schmidt F, Schaefer-Babajew D, Wang Z, C Lorenzi JC, Flyak AI, DeLaitsch AT, Huey-Tubman KE, Hou S, Schiffer CA, Gaebler C, Da Silva J, Poston D, Finkin S, Cho A, Cipolla M, Oliveira TY, Millard KG, Ramos V, Gazumyan A, Rutkowska M, Caskey M, Nussenzweig MC, Bjorkman PJ, Hatziioannou T, Bieniasz PD. Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations. Immunity 2021; 54:1853-1868.e7. [PMID: 34331873 PMCID: PMC8323339 DOI: 10.1016/j.immuni.2021.07.008] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/26/2021] [Accepted: 07/12/2021] [Indexed: 12/23/2022]
Abstract
Antibodies elicited by infection accumulate somatic mutations in germinal centers that can increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) Spike receptor-binding domain (RBD)-specific antibodies from 5 individuals shortly after infection and later in convalescence to determine the impact of maturation over months. In addition to increased affinity and neutralization potency, antibody evolution changed the mutational pathways for the acquisition of viral resistance and restricted neutralization escape options. For some antibodies, maturation imposed a requirement for multiple substitutions to enable escape. For certain antibodies, affinity maturation enabled the neutralization of circulating SARS-CoV-2 variants of concern and heterologous sarbecoviruses. Antibody-antigen structures revealed that these properties resulted from substitutions that allowed additional variability at the interface with the RBD. These findings suggest that increasing antibody diversity through prolonged or repeated antigen exposure may improve protection against diversifying SARS-CoV-2 populations, and perhaps against other pandemic threat coronaviruses.
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MESH Headings
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity/immunology
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Epitopes/chemistry
- Epitopes/immunology
- Host-Pathogen Interactions/immunology
- Humans
- Models, Molecular
- Mutation
- Neutralization Tests
- Protein Binding
- Protein Conformation
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Structure-Activity Relationship
- Virulence/genetics
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Affiliation(s)
- Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Andrew I Flyak
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew T DeLaitsch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Justin Da Silva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Poston
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Magdalena Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute.
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute.
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Jacobs JL, Bain W, Naqvi A, Staines B, Castanha PMS, Yang H, Boltz VF, Barratt-Boyes S, Marques ETA, Mitchell SL, Methé B, Olonisakin TF, Haidar G, Burke TW, Petzold E, Denny T, Woods CW, McVerry BJ, Lee JS, Watkins SC, St Croix CM, Morris A, Kearney MF, Ladinsky MS, Bjorkman PJ, Kitsios GD, Mellors JW. Severe Acute Respiratory Syndrome Coronavirus 2 Viremia Is Associated With Coronavirus Disease 2019 Severity and Predicts Clinical Outcomes. Clin Infect Dis 2021; 74:1525-1533. [PMID: 34374761 PMCID: PMC9070832 DOI: 10.1093/cid/ciab686] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA (vRNA) is detected in the bloodstream of some patients with coronavirus disease 2019 (COVID-19), but it is not clear whether this RNAemia reflects viremia (ie, virus particles) and how it relates to host immune responses and outcomes. METHODS SARS-CoV-2 vRNA was quantified in plasma samples from observational cohorts of 51 COVID-19 patients including 9 outpatients, 19 hospitalized (non-intensive care unit [ICU]), and 23 ICU patients. vRNA levels were compared with cross-sectional indices of COVID-19 severity and prospective clinical outcomes. We used multiple imaging methods to visualize virions in plasma. RESULTS SARS-CoV-2 vRNA was detected in plasma of 100%, 52.6%, and 11.1% of ICU, non-ICU, and outpatients, respectively. Virions were detected in plasma pellets using electron tomography and immunostaining. Plasma vRNA levels were significantly higher in ICU > non-ICU > outpatients (P < .0001); for inpatients, plasma vRNA levels were strongly associated with higher World Health Organization (WHO) score at admission (P = .01), maximum WHO score (P = .002), and discharge disposition (P = .004). A plasma vRNA level >6000 copies/mL was strongly associated with mortality (hazard ratio, 10.7). Levels of vRNA were significantly associated with several inflammatory biomarkers (P < .01) but not with plasma neutralizing antibody titers (P = .8). CONCLUSIONS Visualization of virus particles in plasma indicates that SARS-CoV-2 RNAemia is due, at least in part, to viremia. The levels of SARS-CoV-2 RNAemia correlate strongly with disease severity, patient outcome, and specific inflammatory biomarkers but not with neutralizing antibody titers.
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Affiliation(s)
- Jana L Jacobs
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brittany Staines
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Priscila M S Castanha
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Haopu Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,School of Medicine, Tsinghua University, Beijing, China
| | - Valerie F Boltz
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Simon Barratt-Boyes
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Ernesto T A Marques
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Stephanie L Mitchell
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tolani F Olonisakin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ghady Haidar
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Thomas Denny
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Chris W Woods
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Claudette M St Croix
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Correspondence: John W. Mellors, Division of Infectious Diseases, University of Pittsburgh, Scaife Hall, Suite 818, 3550 Terrace Street, Pittsburgh, PA 15261 USA ()
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40
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West AP, Wertheim JO, Wang JC, Vasylyeva TI, Havens JL, Chowdhury MA, Gonzalez E, Fang CE, Di Lonardo SS, Hughes S, Rakeman JL, Lee HH, Barnes CO, Gnanapragasam PNP, Yang Z, Gaebler C, Caskey M, Nussenzweig MC, Keeffe JR, Bjorkman PJ. Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Nat Commun 2021; 12:4886. [PMID: 34373458 PMCID: PMC8352861 DOI: 10.1038/s41467-021-25168-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/28/2021] [Indexed: 02/02/2023] Open
Abstract
Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage.
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Affiliation(s)
- Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jade C Wang
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Tetyana I Vasylyeva
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jennifer L Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Moinuddin A Chowdhury
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Edimarlyn Gonzalez
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Courtney E Fang
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Steve S Di Lonardo
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Scott Hughes
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Jennifer L Rakeman
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Henry H Lee
- Pandemic Response Laboratory, Long Island City, NY, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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41
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West AP, Wertheim JO, Wang JC, Vasylyeva TI, Havens JL, Chowdhury MA, Gonzalez E, Fang CE, Di Lonardo SS, Hughes S, Rakeman JL, Lee HH, Barnes CO, Gnanapragasam PNP, Yang Z, Gaebler C, Caskey M, Nussenzweig MC, Keeffe JR, Bjorkman PJ. Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Nat Commun 2021. [PMID: 34373458 DOI: 10.1101/2021.02.14.431043v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage.
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Affiliation(s)
- Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jade C Wang
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Tetyana I Vasylyeva
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jennifer L Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Moinuddin A Chowdhury
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Edimarlyn Gonzalez
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Courtney E Fang
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Steve S Di Lonardo
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Scott Hughes
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Jennifer L Rakeman
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Henry H Lee
- Pandemic Response Laboratory, Long Island City, NY, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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42
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Garber AI, Kupper M, Laetsch DR, Weldon SR, Ladinsky MS, Bjorkman PJ, McCutcheon JP. The Evolution of Interdependence in a Four-Way Mealybug Symbiosis. Genome Biol Evol 2021; 13:evab123. [PMID: 34061185 PMCID: PMC8331144 DOI: 10.1093/gbe/evab123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 01/03/2023] Open
Abstract
Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrient-poor plant sap diets. Some mealybugs have a single betaproteobacterial endosymbiont, a Candidatus Tremblaya species (hereafter Tremblaya) that alone provides the insect with its required nutrients. Other mealybugs have two nutritional endosymbionts that together provision these same nutrients, where Tremblaya has gained a gammaproteobacterial partner that resides in its cytoplasm. Previous work had established that Pseudococcus longispinus mealybugs maintain not one but two species of gammaproteobacterial endosymbionts along with Tremblaya. Preliminary genomic analyses suggested that these two gammaproteobacterial endosymbionts have large genomes with features consistent with a relatively recent origin as insect endosymbionts, but the patterns of genomic complementarity between members of the symbiosis and their relative cellular locations were unknown. Here, using long-read sequencing and various types of microscopy, we show that the two gammaproteobacterial symbionts of P. longispinus are mixed together within Tremblaya cells, and that their genomes are somewhat reduced in size compared with their closest nonendosymbiotic relatives. Both gammaproteobacterial genomes contain thousands of pseudogenes, consistent with a relatively recent shift from a free-living to an endosymbiotic lifestyle. Biosynthetic pathways of key metabolites are partitioned in complex interdependent patterns among the two gammaproteobacterial genomes, the Tremblaya genome, and horizontally acquired bacterial genes that are encoded on the mealybug nuclear genome. Although these two gammaproteobacterial endosymbionts have been acquired recently in evolutionary time, they have already evolved codependencies with each other, Tremblaya, and their insect host.
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Affiliation(s)
- Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Maria Kupper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephanie R Weldon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Mark S Ladinsky
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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Hensley MK, Bain WG, Jacobs J, Nambulli S, Parikh U, Cillo A, Staines B, Heaps A, Sobolewski MD, Rennick LJ, Macatangay BJC, Klamar-Blain C, Kitsios GD, Methé B, Somasundaram A, Bruno TC, Cardello C, Shan F, Workman C, Ray P, Ray A, Lee J, Sethi R, Schwarzmann WE, Ladinsky MS, Bjorkman PJ, Vignali DA, Duprex WP, Agha ME, Mellors JW, McCormick KD, Morris A, Haidar G. Intractable Coronavirus Disease 2019 (COVID-19) and Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Replication in a Chimeric Antigen Receptor-Modified T-Cell Therapy Recipient: A Case Study. Clin Infect Dis 2021; 73:e815-e821. [PMID: 33507235 PMCID: PMC7929077 DOI: 10.1093/cid/ciab072] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Indexed: 11/23/2022] Open
Abstract
A chimeric antigen receptor-modified T-cell therapy recipient developed severe coronavirus disease 2019, intractable RNAemia, and viral replication lasting >2 months. Premortem endotracheal aspirate contained >2 × 1010 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copies/mL and infectious virus. Deep sequencing revealed multiple sequence variants consistent with intrahost virus evolution. SARS-CoV-2 humoral and cell-mediated immunity were minimal. Prolonged transmission from immunosuppressed patients is possible.
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Affiliation(s)
- Matthew K Hensley
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William G Bain
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Jana Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Urvi Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anthony Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Brittany Staines
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michele D Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Linda J Rennick
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bernard J C Macatangay
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cynthia Klamar-Blain
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ashwin Somasundaram
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Division of Hematology, Oncology, Department of Internal Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Feng Shan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Creg Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anuradha Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Janet Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rahil Sethi
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William E Schwarzmann
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dario A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mounzer E Agha
- Division of Hematology, Oncology, Department of Internal Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin D McCormick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ghady Haidar
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Greaney AJ, Starr TN, Barnes CO, Weisblum Y, Schmidt F, Caskey M, Gaebler C, Cho A, Agudelo M, Finkin S, Wang Z, Poston D, Muecksch F, Hatziioannou T, Bieniasz PD, Robbiani DF, Nussenzweig MC, Bjorkman PJ, Bloom JD. Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies. Nat Commun 2021; 12:4196. [PMID: 34234131 PMCID: PMC8263750 DOI: 10.1038/s41467-021-24435-8] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022] Open
Abstract
Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasmas, including plasmas from individuals from whom some of the antibodies were isolated. While the binding of polyclonal plasma antibodies are affected by mutations across multiple RBD epitopes, the plasma-escape maps most resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.
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Affiliation(s)
- Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Daniel Poston
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Paul D Bieniasz
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Michel C Nussenzweig
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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45
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Haugh KA, Ladinsky MS, Ullah I, Stone HM, Pi R, Gilardet A, Grunst MW, Kumar P, Bjorkman PJ, Mothes W, Uchil PD. In vivo imaging of retrovirus infection reveals a role for Siglec-1/CD169 in multiple routes of transmission. eLife 2021; 10:64179. [PMID: 34223819 PMCID: PMC8298093 DOI: 10.7554/elife.64179] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/15/2021] [Indexed: 12/12/2022] Open
Abstract
Early events in retrovirus transmission are determined by interactions between incoming viruses and frontline cells near entry sites. Despite their importance for retroviral pathogenesis, very little is known about these events. We developed a bioluminescence imaging (BLI)-guided multiscale imaging approach to study these events in vivo. Engineered murine leukemia reporter viruses allowed us to monitor individual stages of retrovirus life cycle including virus particle flow, virus entry into cells, infection and spread for retroorbital, subcutaneous, and oral routes. BLI permitted temporal tracking of orally administered retroviruses along the gastrointestinal tract as they traversed the lumen through Peyer’s patches to reach the draining mesenteric sac. Importantly, capture and acquisition of lymph-, blood-, and milk-borne retroviruses spanning three routes was promoted by a common host factor, the I-type lectin CD169, expressed on sentinel macrophages. These results highlight how retroviruses co-opt the immune surveillance function of tissue-resident sentinel macrophages for establishing infection.
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Affiliation(s)
- Kelsey A Haugh
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, United States
| | - Helen M Stone
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States
| | - Ruoxi Pi
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States
| | - Alexandre Gilardet
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States
| | - Michael W Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, United States
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States
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46
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Ullah I, Prévost J, Ladinsky MS, Stone H, Lu M, Anand SP, Beaudoin-Bussières G, Symmes K, Benlarbi M, Ding S, Gasser R, Fink C, Chen Y, Tauzin A, Goyette G, Bourassa C, Medjahed H, Mack M, Chung K, Wilen CB, Dekaban GA, Dikeakos JD, Bruce EA, Kaufmann DE, Stamatatos L, McGuire AT, Richard J, Pazgier M, Bjorkman PJ, Mothes W, Finzi A, Kumar P, Uchil PD. Live Imaging of SARS-CoV-2 Infection in Mice Reveals Neutralizing Antibodies Require Fc Function for Optimal Efficacy. bioRxiv 2021. [PMID: 33791699 DOI: 10.1101/2021.03.22.436337] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Neutralizing antibodies (NAbs) are effective in treating COVID-19 but the mechanism of immune protection is not fully understood. Here, we applied live bioluminescence imaging (BLI) to monitor the real-time effects of NAb treatment in prophylaxis and therapy of K18-hACE2 mice intranasally infected with SARS-CoV-2-nanoluciferase. We could visualize virus spread sequentially from the nasal cavity to the lungs and thereafter systemically to various organs including the brain, which culminated in death. Highly potent NAbs from a COVID-19 convalescent subject prevented, and also effectively resolved, established infection when administered within three days. In addition to direct Fab-mediated neutralization, Fc effector interactions of NAbs with monocytes, neutrophils and natural killer cells were required to effectively dampen inflammatory responses and limit immunopathology. Our study highlights that both Fab and Fc effector functions of NAbs are essential for optimal in vivo efficacy against SARS-CoV-2.
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47
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Scheid JF, Barnes CO, Eraslan B, Hudak A, Keeffe JR, Cosimi LA, Brown EM, Muecksch F, Weisblum Y, Zhang S, Delorey T, Woolley AE, Ghantous F, Park SM, Phillips D, Tusi B, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Rzasa K, Hatziioanno T, Durney MA, Gu X, Tada T, Landau NR, West AP, Rozenblatt-Rosen O, Seaman MS, Baden LR, Graham DB, Deguine J, Bieniasz PD, Regev A, Hung D, Bjorkman PJ, Xavier RJ. B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell 2021; 184:3205-3221.e24. [PMID: 34015271 PMCID: PMC8064835 DOI: 10.1016/j.cell.2021.04.032] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/26/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell sorting with single-cell VDJ and RNA sequencing (RNA-seq) and mAb structures to characterize B cell responses against SARS-CoV-2. We show that the SARS-CoV-2-specific B cell repertoire consists of transcriptionally distinct B cell populations with cells producing potently neutralizing antibodies (nAbs) localized in two clusters that resemble memory and activated B cells. Cryo-electron microscopy structures of selected nAbs from these two clusters complexed with SARS-CoV-2 spike trimers show recognition of various receptor-binding domain (RBD) epitopes. One of these mAbs, BG10-19, locks the spike trimer in a closed conformation to potently neutralize SARS-CoV-2, the recently arising mutants B.1.1.7 and B.1.351, and SARS-CoV and cross-reacts with heterologous RBDs. Together, our results characterize transcriptional differences among SARS-CoV-2-specific B cells and uncover cross-neutralizing Ab targets that will inform immunogen and therapeutic design against coronaviruses.
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MESH Headings
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/metabolism
- Antigen-Antibody Reactions
- B-Lymphocytes/cytology
- B-Lymphocytes/metabolism
- B-Lymphocytes/virology
- COVID-19/pathology
- COVID-19/virology
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Gene Expression Profiling
- Humans
- Immunoglobulin A/immunology
- Immunoglobulin Variable Region/chemistry
- Immunoglobulin Variable Region/genetics
- Protein Domains/immunology
- Protein Multimerization
- Protein Structure, Quaternary
- SARS-CoV-2/immunology
- SARS-CoV-2/isolation & purification
- SARS-CoV-2/metabolism
- Sequence Analysis, RNA
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Johannes F Scheid
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Basak Eraslan
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew Hudak
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lisa A Cosimi
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric M Brown
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Frauke Muecksch
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Shuting Zhang
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Toni Delorey
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ann E Woolley
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Fadi Ghantous
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Sung-Moo Park
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Devan Phillips
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Betsabeh Tusi
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Kara Rzasa
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Theodora Hatziioanno
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Michael A Durney
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Xiebin Gu
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Lindsey R Baden
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel B Graham
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jacques Deguine
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Paul D Bieniasz
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Deborah Hung
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ramnik J Xavier
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, Aydillo T, Parigi TL, Ladinsky MS, Ramos I, Dunleavy K, Lee B, Dixon RE, Chen ST, Martinez-Delgado G, Nagula S, Bruce EA, Ko HM, Glicksberg BS, Nadkarni G, Pujadas E, Reidy J, Naymagon S, Grinspan A, Ahmad J, Tankelevich M, Bram Y, Gordon R, Sharma K, Houldsworth J, Britton GJ, Chen-Liaw A, Spindler MP, Plitt T, Wang P, Cerutti A, Faith JJ, Colombel JF, Kenigsberg E, Argmann C, Merad M, Gnjatic S, Harpaz N, Danese S, Cordon-Cardo C, Rahman A, Schwartz RE, Kumta NA, Aghemo A, Bjorkman PJ, Petralia F, van Bakel H, Garcia-Sastre A, Mehandru S. Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms. Gastroenterology 2021; 160:2435-2450.e34. [PMID: 33676971 PMCID: PMC7931673 DOI: 10.1053/j.gastro.2021.02.056] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of COVID-19, we investigated intestinal infection with SARS-CoV-2, its effect on pathogenesis, and clinical significance. METHODS Human intestinal biopsy tissues were obtained from patients with COVID-19 (n = 19) and uninfected control individuals (n = 10) for microscopic examination, cytometry by time of flight analyses, and RNA sequencing. Additionally, disease severity and mortality were examined in patients with and without GI symptoms in 2 large, independent cohorts of hospitalized patients in the United States (N = 634) and Europe (N = 287) using multivariate logistic regressions. RESULTS COVID-19 case patients and control individuals in the biopsy cohort were comparable for age, sex, rates of hospitalization, and relevant comorbid conditions. SARS-CoV-2 was detected in small intestinal epithelial cells by immunofluorescence staining or electron microscopy in 15 of 17 patients studied. High-dimensional analyses of GI tissues showed low levels of inflammation, including down-regulation of key inflammatory genes including IFNG, CXCL8, CXCL2, and IL1B and reduced frequencies of proinflammatory dendritic cells compared with control individuals. Consistent with these findings, we found a significant reduction in disease severity and mortality in patients presenting with GI symptoms that was independent of sex, age, and comorbid illnesses and despite similar nasopharyngeal SARS-CoV-2 viral loads. Furthermore, there was reduced levels of key inflammatory proteins in circulation in patients with GI symptoms. CONCLUSIONS These data highlight the absence of a proinflammatory response in the GI tract despite detection of SARS-CoV-2. In parallel, reduced mortality in patients with COVID-19 presenting with GI symptoms was observed. A potential role of the GI tract in attenuating SARS-CoV-2-associated inflammation needs to be further examined.
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Affiliation(s)
- Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Minami Tokuyama
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tommaso L Parigi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Irene Ramos
- Department of Neurology and Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Katie Dunleavy
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brian Lee
- Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York
| | - Rebekah E Dixon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Steven T Chen
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gustavo Martinez-Delgado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Satish Nagula
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emily A Bruce
- Division of Immunobiology, Department of Medicine, University of Vermont, Larner College of Medicine, Burlington, Vermont
| | - Huaibin M Ko
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Girish Nadkarni
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elisabet Pujadas
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jason Reidy
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Steven Naymagon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ari Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jawad Ahmad
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Ronald Gordon
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Keshav Sharma
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jane Houldsworth
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Matthew P Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tamar Plitt
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Catalan Institute for Research and Advanced Studies, Barcelona, Spain; Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean-Frederic Colombel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ephraim Kenigsberg
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Noam Harpaz
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Carlos Cordon-Cardo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adeeb Rahman
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Nikhil A Kumta
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alessio Aghemo
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Adolfo Garcia-Sastre
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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49
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Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, van Nimwegen E, Worobey M, Relman DA. Investigate the origins of COVID-19. Science 2021; 372:694. [PMID: 33986172 PMCID: PMC9520851 DOI: 10.1126/science.abj0016] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Jesse D Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Yujia Alina Chan
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Ralph S Baric
- Department of Epidemiology and Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Benjamin E Deverman
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - David N Fisman
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ravindra Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Marc Lipsitch
- Department of Immunology and Infectious Diseases and Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ruslan Medzhitov
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Richard A Neher
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California, Berkeley, CA 94720, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Tim Stearns
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - David A Relman
- Department of Medicine and Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Center for International Security and Cooperation, Stanford University, Stanford, CA 94305, USA
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50
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Agudelo M, Palus M, Keeffe JR, Bianchini F, Svoboda P, Salát J, Peace A, Gazumyan A, Cipolla M, Kapoor T, Guidetti F, Yao KH, Elsterová J, Teislerová D, Chrdle A, Hönig V, Oliveira T, West AP, Lee YE, Rice CM, MacDonald MR, Bjorkman PJ, Růžek D, Robbiani DF, Nussenzweig MC. Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease. J Exp Med 2021; 218:e20210236. [PMID: 33831141 PMCID: PMC8040517 DOI: 10.1084/jem.20210236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is an emerging human pathogen that causes potentially fatal disease with no specific treatment. Mouse monoclonal antibodies are protective against TBEV, but little is known about the human antibody response to infection. Here, we report on the human neutralizing antibody response to TBEV in a cohort of infected and vaccinated individuals. Expanded clones of memory B cells expressed closely related anti-envelope domain III (EDIII) antibodies in both groups of volunteers. However, the most potent neutralizing antibodies, with IC50s below 1 ng/ml, were found only in individuals who recovered from natural infection. These antibodies also neutralized other tick-borne flaviviruses, including Langat, louping ill, Omsk hemorrhagic fever, Kyasanur forest disease, and Powassan viruses. Structural analysis revealed a conserved epitope near the lateral ridge of EDIII adjoining the EDI-EDIII hinge region. Prophylactic or early therapeutic antibody administration was effective at low doses in mice that were lethally infected with TBEV.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/administration & dosage
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Cells, Cultured
- Cohort Studies
- Cross Reactions/immunology
- Encephalitis Viruses, Tick-Borne/drug effects
- Encephalitis Viruses, Tick-Borne/immunology
- Encephalitis Viruses, Tick-Borne/physiology
- Encephalitis, Tick-Borne/immunology
- Encephalitis, Tick-Borne/prevention & control
- Encephalitis, Tick-Borne/virology
- Epitopes/immunology
- Female
- Humans
- Immunoglobulin G/administration & dosage
- Immunoglobulin G/immunology
- Mice, Inbred BALB C
- Sequence Homology, Amino Acid
- Survival Analysis
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/immunology
- Mice
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Affiliation(s)
- Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Filippo Bianchini
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Pavel Svoboda
- Veterinary Research Institute, Brno, Czech Republic
- Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Jiří Salát
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Avery Peace
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Tania Kapoor
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Francesca Guidetti
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Jana Elsterová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | | | - Aleš Chrdle
- Hospital České Budějovice, České Budějovice, Czech Republic
- Faculty of Social and Health Sciences, University of South Bohemia, České Budějovice, Czech Republic
- Royal Liverpool University Hospital, Liverpool, UK
| | - Václav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Margaret R. MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Daniel Růžek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY
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