1
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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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2
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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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3
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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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4
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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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5
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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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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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Jette CA, Cohen AA, Gnanapragasam PN, 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. bioRxiv 2021:2021.04.23.441195. [PMID: 33948592 PMCID: PMC8095199 DOI: 10.1101/2021.04.23.441195] [Citation(s) in RCA: 15] [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] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many anti-SARS-CoV-2 neutralizing antibodies target the ACE2-binding site on viral spike receptor-binding domains (RBDs). The most 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 usually show only weak neutralization potencies. We characterized two class 4 anti-RBD antibodies derived from COVID-19 donors that exhibited broad recognition and potent neutralization of zoonotic coronavirus and SARS-CoV-2 variants. C118-RBD and C022-RBD structures revealed CDRH3 mainchain H-bond interactions that extended an RBD β-sheet, thus reducing sensitivity to RBD sidechain changes, and epitopes that extended from the cryptic epitope to occlude ACE2 binding. A C118-spike trimer structure revealed rotated RBDs to allow cryptic epitope access 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
| | - 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
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
- 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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15
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Cohen AA, Yang Z, Gnanapragasam PNP, Ou S, Dam KMA, Wang H, Bjorkman PJ. Construction, characterization, and immunization of nanoparticles that display a diverse array of influenza HA trimers. PLoS One 2021; 16:e0247963. [PMID: 33661993 PMCID: PMC7932532 DOI: 10.1371/journal.pone.0247963] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 09/13/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
Current influenza vaccines do not elicit broadly protective immune responses against multiple strains. New strategies to focus the humoral immune response to conserved regions on influenza antigens are therefore required for recognition by broadly neutralizing antibodies. It has been suggested that B-cells with receptors that recognize conserved epitopes would be preferentially stimulated through avidity effects by mosaic particles presenting multiple forms of a variable antigen. We adapted SpyCatcher-based platforms, AP205 virus-like particles (VLPs) and mi3 nanoparticles (NPs), to covalently co-display SpyTagged hemagglutinin (HA) trimers from group 1 and group 2 influenza A strains. Here we show successful homotypic and heterotypic conjugation of up to 8 different HA trimers to both VLPs and NPs. We characterized the HA-VLPs and HA-NPs by cryo-electron tomography to derive the average number of conjugated HAs and their separation distances on particles, and compared immunizations of mosaic and homotypic particles in wild-type mice. Both types of HA particles elicited strong antibody responses, but the mosaic particles did not consistently elicit broader immune responses than mixtures of homotypic particles. We conclude that covalent attachment of HAs from currently-circulating influenza strains represents a viable alternative to current annual influenza vaccine strategies, but in the absence of further modifications, is unlikely to represent a method for making a universal influenza vaccine.
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Affiliation(s)
- Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Priyanthi N. P. Gnanapragasam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Susan Ou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Haoqing Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
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16
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Cohen AA, Gnanapragasam PNP, Lee YE, Hoffman PR, Ou S, Kakutani LM, Keeffe JR, Wu HJ, Howarth M, West AP, Barnes CO, Nussenzweig MC, Bjorkman PJ. Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice. Science 2021; 371:735-741. [PMID: 33436524 PMCID: PMC7928838 DOI: 10.1126/science.abf6840] [Citation(s) in RCA: 257] [Impact Index Per Article: 85.7] [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: 11/12/2020] [Accepted: 01/07/2021] [Indexed: 12/14/2022]
Abstract
Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs relative to sera from immunizations with homotypic SARS-CoV-2-RBD nanoparticles or COVID-19 convalescent human plasmas. Moreover, after priming, sera from mosaic RBD-immunized mice neutralized heterologous pseudotyped coronaviruses as well as or better than sera from homotypic SARS-CoV-2-RBD nanoparticle immunizations, demonstrating no loss of immunogenicity against particular RBDs resulting from co-display. A single immunization with mosaic RBD nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses.
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Affiliation(s)
- Alexander A Cohen
- 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
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susan Ou
- 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
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hung-Jen Wu
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anthony P West
- 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
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, 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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17
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Cohen AA, Gnanapragasam PNP, Lee YE, Hoffman PR, Ou S, Kakutani LM, Keeffe JR, Wu HJ, Howarth M, West AP, Barnes CO, Nussenzweig MC, Bjorkman PJ. Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice. bioRxiv 2021. [PMID: 33236016 PMCID: PMC7685334 DOI: 10.1101/2020.11.17.387092] [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] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protection against SARS-CoV-2 and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor-binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles; 4–8 distinct RBDs). Mice immunized with RBD-nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic-RBD-nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs compared to sera from immunizations with homotypic SARS-CoV-2–RBD-nanoparticles or COVID-19 convalescent human plasmas. Moreover, sera from mosaic-RBD–immunized mice neutralized heterologous pseudotyped coronaviruses equivalently or better after priming than sera from homotypic SARS-CoV-2–RBD-nanoparticle immunizations, demonstrating no immunogenicity loss against particular RBDs resulting from co-display. A single immunization with mosaic-RBD-nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses. One sentence summary: Nanoparticle strategy for pan-sarbecovirus vaccine Immunizing with nanoparticles displaying diverse coronavirus RBDs elicits cross-reactive and neutralizing antibody responses.
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Affiliation(s)
- Alexander A Cohen
- 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
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susan Ou
- 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
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hung-Jen Wu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony P West
- 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
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, 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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18
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Fulop T, Larbi A, Hirokawa K, Cohen AA, Witkowski JM. Immunosenescence is both functional/adaptive and dysfunctional/maladaptive. Semin Immunopathol 2020; 42:521-536. [PMID: 32930852 PMCID: PMC7490574 DOI: 10.1007/s00281-020-00818-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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: 06/01/2020] [Accepted: 08/24/2020] [Indexed: 01/08/2023]
Abstract
Alterations in the immune system with aging are considered to underlie many age-related diseases. However, many elderly individuals remain healthy until even a very advanced age. There is also an increase in numbers of centenarians and their apparent fitness. We should therefore change our unilaterally detrimental consideration of age-related immune changes. Recent data taking into consideration the immunobiography concept may allow for meaningful distinctions among various aging trajectories. This implies that the aging immune system has a homeodynamic characteristic balanced between adaptive and maladaptive aspects. The survival and health of an individual depends from the equilibrium of this balance. In this article, we highlight which parts of the aging of the immune system may be considered adaptive in contrast to those that may be maladaptive.
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Affiliation(s)
- T Fulop
- Department of Geriatrics, Faculty of Medicine, Research Center on Aging, University of Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
- Research Center on Aging, Faculty of Medicine and Health Sciences, University of Sherbrooke, 3001, 12th Avenue North, Sherbrooke, Quebec, J1H 5N4, Canada.
| | - A Larbi
- Biology of Aging Program and Immunomonitoring Platform, Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Biopolis, Singapore, 138648, Singapore
| | - K Hirokawa
- Institute of Health and Life Science, Tokyo and Nito-memory Nakanosogo Hospital, Department of Pathology, Tokyo Med. Dent. University, Tokyo, Japan
| | - A A Cohen
- Department of Family Medicine, Faculty of Medicine, Research Center on Aging, University of Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - J M Witkowski
- Department of Pathophysiology, Medical University of Gdansk, Gdansk, Poland
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19
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Levine M, Cohen AA. ADVANCING GEROSCIENCE: NEW METHODS FOR GENOMIC EPIDEMIOLOGY OF AGING. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.230] [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: 11/13/2022] Open
Affiliation(s)
- M Levine
- Yale School of Medicine, New Haven, Connecticut
| | - A A Cohen
- Universite de Sherbrooke, St-Denis-de-Brompton, Quebec
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20
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Cohen AA, Dufour F, Jacques P. BROAD-SCALE, MULTI-SYSTEM DYSREGULATION OF GENE EXPRESSION: TOWARD CLINICAL QUANTIFICATION OF AGING. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.232] [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: 11/12/2022] Open
Affiliation(s)
- A A Cohen
- Universite de Sherbrooke, St-Denis-de-Brompton, Quebec, Canada
| | - F Dufour
- Department of Biology, University of Sherbrooke, Sherbrooke, QC, Canada
| | - P Jacques
- National Institute on Aging, Baltimore, Maryland, United States
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21
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Vanasse A, Blais L, Courteau J, Cohen AA, Roberge P, Larouche A, Grignon S, Fleury MJ, Lesage A, Demers MF, Roy MA, Carrier JD, Delorme A. Comparative effectiveness and safety of antipsychotic drugs in schizophrenia treatment: a real-world observational study. Acta Psychiatr Scand 2016; 134:374-384. [PMID: 27404582 DOI: 10.1111/acps.12621] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The objective was to compare, in a real-world setting, the risk of mental and physical health events associated with different antipsychotic drugs (clozapine, olanzapine, risperidone, quetiapine and first-generation antipsychotics) in patients with SZ. METHODS This is a retrospective cohort study using administrative data. Outcome measures included any mental health event (suicide, hospitalization or emergency visit for mental disorders) and physical health event (death other than suicide, hospitalization or emergency visit for physical disorders). Cox proportional hazard models were used to estimate the hazard ratios of the events associated with the use of the different antipsychotic drugs. RESULTS The cohort included 18 869 adult patients living in the province of Quebec (Canada) with SZ and starting antipsychotic drugs between January 1998 and December 2005. Results show that quetiapine and not using any antipsychotics were associated with an increased risk of mental and physical health events as compared to other drugs. The second finding is the confirmation of better performance of clozapine. The results were robust across sensitivity analyses. CONCLUSION Both findings call for an international public health and drug agencies surveillance of 'real-world' antipsychotic medication to ensure the optimal choices in treatment guidelines for SZ.
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Affiliation(s)
- A Vanasse
- Département de médecine de famille et de médecine d'urgence, Université de Sherbrooke, Sherbrooke, QC, Canada. .,PRIMUS Group, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada.
| | - L Blais
- Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| | - J Courteau
- PRIMUS Group, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - A A Cohen
- Département de médecine de famille et de médecine d'urgence, Université de Sherbrooke, Sherbrooke, QC, Canada.,PRIMUS Group, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - P Roberge
- Département de médecine de famille et de médecine d'urgence, Université de Sherbrooke, Sherbrooke, QC, Canada.,PRIMUS Group, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - A Larouche
- PRIMUS Group, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - S Grignon
- Département de Psychiatrie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - M-J Fleury
- Douglas Mental Health University Institute, McGill University, Montréal, QC, Canada
| | - A Lesage
- Centre de recherche de l'Institut universitaire en santé mentale de Montréal, Montréal, QC, Canada
| | - M-F Demers
- Faculté de pharmacie, Université Laval, Québec, QC, Canada.,Centre de recherche de l'Institut universitaire en santé mentale de Québec (CRIUSMQ), Québec, QC, Canada
| | - M-A Roy
- Centre de recherche de l'Institut universitaire en santé mentale de Québec (CRIUSMQ), Québec, QC, Canada
| | - J-D Carrier
- PRIMUS Group, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - A Delorme
- Direction de la santé mentale, Ministère de la santé et des services sociaux du Québec, Québec, QC, Canada
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22
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Watson H, Cohen AA, Isaksson C. A theoretical model of the evolution of actuarial senescence under environmental stress. Exp Gerontol 2015; 71:80-8. [PMID: 26335620 PMCID: PMC4710637 DOI: 10.1016/j.exger.2015.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 01/16/2023]
Abstract
Free-living organisms are exposed to a wide range of stressors, all of which can disrupt components of stress-related and detoxification physiology. The subsequent accumulation of somatic damage is widely believed to play a major role in the evolution of senescence. Organisms have evolved sophisticated physiological regulatory mechanisms to maintain homeostasis in response to environmental perturbations, but these systems are likely to be constrained in their ability to optimise robustness to multiple stressors due to functional correlations among related traits. While evolutionary change can accelerate due to human ecological impacts, it remains to be understood how exposure to multiple environmental stressors could affect senescence rates and subsequently population dynamics and fitness. We used a theoretical evolutionary framework to quantify the potential consequences for the evolution of actuarial senescence in response to exposure to simultaneous physiological stressors – one versus multiple and additive versus synergistic – in a hypothetical population of avian “urban adapters”. In a model in which multiple stressors have additive effects on physiology, species may retain greater capacity to recover, or respond adaptively, to environmental challenges. However, in the presence of high synergy, physiological dysregulation suddenly occurs, leading to a rapid increase in age-dependent mortality and subsequent population collapse. Our results suggest that, if the synergistic model is correct, population crashes in environmentally-stressed species could happen quickly and with little warning, as physiological thresholds of stress resistance are overcome. Environmental stressors challenge physiological systems linked to senescence. Various scenarios of stress exposure were simulated on a hypothetical “urban adapter”. Actuarial senescence increased rapidly in synergistic models of stress. Wild populations may be at greater risk of collapse than demography alone suggests. An explicit model of how stressors affect physiology underlying ageing is required.
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Affiliation(s)
- H Watson
- Evolutionary Ecology Unit, Biology Department, Ecology Building, Lund University, SE-22362 Lund, Sweden
| | - A A Cohen
- Groupe de recherche PRIMUS, Department of Family Medicine, University of Sherbrooke, Sherbrooke, Québec J1J 3H5, Canada
| | - C Isaksson
- Evolutionary Ecology Unit, Biology Department, Ecology Building, Lund University, SE-22362 Lund, Sweden.
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23
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Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R, Cohen-Saidon C, Liron Y, Kam Z, Cohen L, Danon T, Perzov N, Alon U. Dynamic proteomics of individual cancer cells in response to a drug. Science 2008; 322:1511-6. [PMID: 19023046 DOI: 10.1126/science.1160165] [Citation(s) in RCA: 432] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Why do seemingly identical cells respond differently to a drug? To address this, we studied the dynamics and variability of the protein response of human cancer cells to a chemotherapy drug, camptothecin. We present a dynamic-proteomics approach that measures the levels and locations of nearly 1000 different endogenously tagged proteins in individual living cells at high temporal resolution. All cells show rapid translocation of proteins specific to the drug mechanism, including the drug target (topoisomerase-1), and slower, wide-ranging temporal waves of protein degradation and accumulation. However, the cells differ in the behavior of a subset of proteins. We identify proteins whose dynamics differ widely between cells, in a way that corresponds to the outcomes-cell death or survival. This opens the way to understanding molecular responses to drugs in individual cells.
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Affiliation(s)
- A A Cohen
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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24
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Cohen AA, Shatzmiller SE. Localization and quantitative evaluation of potent local binding sites on the accessible Lennard-jones surface. J Comput Chem 1995. [DOI: 10.1002/jcc.540161203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Cohen AA, Shatzmiller SE. Implementation of artificial intelligence for automatic drug design. I. Stepwise computation of the interactive drug-design sequence. J Comput Chem 1994. [DOI: 10.1002/jcc.540151209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Cohen AA, Shatzmiller SE. Structure design: an artificial intelligence-based method for the design of molecules under geometrical constraints. J Mol Graph 1993; 11:166-73. [PMID: 8110662 DOI: 10.1016/0263-7855(93)80068-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This study presents an algorithm that implements artificial-intelligence techniques for automated, and site-directed drug design. The aim of the method is to link two or more predetermined functional groups into a sensible molecular structure. The proposed designing process mimics the classical manual design method, in which the drug designer sits in front of the computer screen and with the aid of computer graphics attempts to design the new drug. Therefore, the key principle of the algorithm is the parameterization of some criteria that affect the decision-making process carried out by the drug designer. This parameterization is based on the generation of weighting factors that reflect the knowledge and knowledge-based intuition of the drug designer, and thus add further rationalization to the drug design process. The proposed algorithm has been shown to yield a large variety of different structures, of which the drug designer may choose the most sensible. Performance tests indicate that with the proper set of parameters, the method generates a new structure within a short time.
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Affiliation(s)
- A A Cohen
- Tel-Aviv University, School of Chemistry, Ramat-Aviv, Israel
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27
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Cohen AA, Daru V, Covelli G, Gonzalez M, Villamayor R, Tronge JE. Hemodynamic effects of intravenous flecainide in acute noncomplicated myocardial infarction. Am Heart J 1985; 110:1193-6. [PMID: 4072876 DOI: 10.1016/0002-8703(85)90011-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hemodynamic and ECG effects of intravenous flecainide were assessed in 10 patients with acute myocardial infarction and no symptoms or signs of heart failure. The dose was 2 mg/kg injected over a 15-minute period. R-R interval did not change, but PR interval and QRS increased significantly, 28% (p less than 0.0005) and 20% (p less than 0.05), respectively. Duration of P wave also increased significantly, 15% (p less than 0.02). Pulmonary wedge pressure increased 29% (p less than 0.005) and cardiac index and left ventricular stroke work index decreased 9% (p less than 0.05) and 20% (p less than 0.05), respectively. No significant change in mean aortic pressure and systemic vascular resistance occurred. Thus, intravenous flecainide has a mild and transient negative inotropic effect in patients with noncomplicated acute myocardial infarction. It did not induce ventricular failure in this group of patients but should be administered cautiously to patients with overt heart failure or severe conduction defects.
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Feldstein CA, Vilches AR, Oliveri AO, Cohen AA, Burucua JE. [Etiology of electrocardiographic disorders in cerebrovascular accidents I) Changes in acid-base balance and kalemia]. Rev Clin Esp 1978; 149:37-9. [PMID: 674752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Feldstein CA, Vilches AR, Olivieri AO, Cohen AA, Burucua JE. [Electrocardiographic changes in diseases of the central nervous system]. Rev Clin Esp 1978; 149:33-6. [PMID: 674751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Feldstein CA, Vilches AR, Olivieri AO, Cohen AA, Burucua JE. [Etiology of the electrocardiographic disorders in cerebrovascular accidents and brain tumors. II) Clinico-anatomical correlation study]. Rev Clin Esp 1978; 149:41-4. [PMID: 674753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Cohen AA, Nelson CJ, Bromberg SM, Pravda M, Ferrand EF, Leone G. Symptom reporting during recent publicized and unpublicized air pollution episodes. Am J Public Health 1974; 64:442-9. [PMID: 4818083 PMCID: PMC1775458 DOI: 10.2105/ajph.64.5.442] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Shy CM, Hasselblad V, Burton RM, Nelson CJ, Cohen AA. Air pollution effects on ventilatory function of US schoolchildren. Results of studies in Cincinnati, Chattanooga, and New York. Arch Environ Health 1973; 27:124-8. [PMID: 4722866 DOI: 10.1080/00039896.1973.10666339] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Obenour WH, Stevens PM, Cohen AA, McCutchen JJ. The causes of abnormal pulmonary function in Parkinson's disease. Am Rev Respir Dis 1972; 105:382-7. [PMID: 5011667 DOI: 10.1164/arrd.1972.105.3.382] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Glasser SP, Cohen AA, Stevens PM. Blood pressure in pulmonary fibrosis. Ann Intern Med 1970; 73:341. [PMID: 5454274 DOI: 10.7326/0003-4819-73-2-341_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Cohen AA, Cohen SR. Programs for delinquent boys in three East European countries. Children 1968; 15:158-60. [PMID: 5663453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Capp AB, Cohen AA, Campos JA, Pannunzio Filho M, Coutinho AR, Silva P. [Pristinamycine in staphylococcal infections]. Hospital (Rio J) 1966; 69:283-92. [PMID: 5295659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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