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1
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Hie BL, Shanker VR, Xu D, Bruun TUJ, Weidenbacher PA, Tang S, Wu W, Pak JE, Kim PS. Efficient evolution of human antibodies from general protein language models. Nat Biotechnol 2024; 42:275-283. [PMID: 37095349 PMCID: PMC10869273 DOI: 10.1038/s41587-023-01763-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/28/2023] [Indexed: 04/26/2023]
Abstract
Natural evolution must explore a vast landscape of possible sequences for desirable yet rare mutations, suggesting that learning from natural evolutionary strategies could guide artificial evolution. Here we report that general protein language models can efficiently evolve human antibodies by suggesting mutations that are evolutionarily plausible, despite providing the model with no information about the target antigen, binding specificity or protein structure. We performed language-model-guided affinity maturation of seven antibodies, screening 20 or fewer variants of each antibody across only two rounds of laboratory evolution, and improved the binding affinities of four clinically relevant, highly mature antibodies up to sevenfold and three unmatured antibodies up to 160-fold, with many designs also demonstrating favorable thermostability and viral neutralization activity against Ebola and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudoviruses. The same models that improve antibody binding also guide efficient evolution across diverse protein families and selection pressures, including antibiotic resistance and enzyme activity, suggesting that these results generalize to many settings.
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Affiliation(s)
- Brian L Hie
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Varun R Shanker
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Theodora U J Bruun
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Payton A Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter S Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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2
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Li C, Lee A, Grigoryan L, Arunachalam PS, Scott MKD, Trisal M, Wimmers F, Sanyal M, Weidenbacher PA, Feng Y, Adamska JZ, Valore E, Wang Y, Verma R, Reis N, Dunham D, O'Hara R, Park H, Luo W, Gitlin AD, Kim P, Khatri P, Nadeau KC, Pulendran B. Mechanisms of innate and adaptive immunity to the Pfizer-BioNTech BNT162b2 vaccine. Nat Immunol 2022; 23:543-555. [PMID: 35288714 PMCID: PMC8989677 DOI: 10.1038/s41590-022-01163-9] [Citation(s) in RCA: 168] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/17/2022] [Indexed: 01/26/2023]
Abstract
Despite the success of the BNT162b2 mRNA vaccine, the immunological mechanisms that underlie its efficacy are poorly understood. Here we analyzed the innate and adaptive responses to BNT162b2 in mice, and show that immunization stimulated potent antibody and antigen-specific T cell responses, as well as strikingly enhanced innate responses after secondary immunization, which was concurrent with enhanced serum interferon (IFN)-γ levels 1 d following secondary immunization. Notably, we found that natural killer cells and CD8+ T cells in the draining lymph nodes are the major producers of this circulating IFN-γ. Analysis of knockout mice revealed that induction of antibody and T cell responses to BNT162b2 was not dependent on signaling via Toll-like receptors 2, 3, 4, 5 and 7 nor inflammasome activation, nor the necroptosis or pyroptosis cell death pathways. Rather, the CD8+ T cell response induced by BNT162b2 was dependent on type I interferon-dependent MDA5 signaling. These results provide insights into the molecular mechanisms by which the BNT162b2 vaccine stimulates immune responses.
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Affiliation(s)
- Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Audrey Lee
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Lilit Grigoryan
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Madeleine K D Scott
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry & Stanford, ChEM-H, Stanford University, Stanford, CA, USA
| | - Payton A Weidenbacher
- Department of Biochemistry & Stanford, ChEM-H, Stanford University, Stanford, CA, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Julia Z Adamska
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Erika Valore
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Yanli Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Rohit Verma
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Noah Reis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Diane Dunham
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA
| | - Ruth O'Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Helen Park
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Wei Luo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alexander D Gitlin
- Department of Physiological Chemistry, Genentech, South San Francisco, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Kim
- Department of Biochemistry & Stanford, ChEM-H, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford, CA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Chang SE, Feng A, Meng W, Apostolidis SA, Mack E, Artandi M, Barman L, Bennett K, Chakraborty S, Chang I, Cheung P, Chinthrajah S, Dhingra S, Do E, Finck A, Gaano A, Geßner R, Giannini HM, Gonzalez J, Greib S, Gündisch M, Hsu AR, Kuo A, Manohar M, Mao R, Neeli I, Neubauer A, Oniyide O, Powell AE, Puri R, Renz H, Schapiro J, Weidenbacher PA, Wittman R, Ahuja N, Chung HR, Jagannathan P, James JA, Kim PS, Meyer NJ, Nadeau KC, Radic M, Robinson WH, Singh U, Wang TT, Wherry EJ, Skevaki C, Luning Prak ET, Utz PJ. New-onset IgG autoantibodies in hospitalized patients with COVID-19. Nat Commun 2021; 12:5417. [PMID: 34521836 PMCID: PMC8440763 DOI: 10.1038/s41467-021-25509-3] [Citation(s) in RCA: 222] [Impact Index Per Article: 74.0] [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: 02/02/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
COVID-19 is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. Here we develop three protein arrays to measure IgG autoantibodies associated with connective tissue diseases, anti-cytokine antibodies, and anti-viral antibody responses in serum from 147 hospitalized COVID-19 patients. Autoantibodies are identified in approximately 50% of patients but in less than 15% of healthy controls. When present, autoantibodies largely target autoantigens associated with rare disorders such as myositis, systemic sclerosis and overlap syndromes. A subset of autoantibodies targeting traditional autoantigens or cytokines develop de novo following SARS-CoV-2 infection. Autoantibodies track with longitudinal development of IgG antibodies recognizing SARS-CoV-2 structural proteins and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
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Affiliation(s)
- Sarah Esther Chang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sokratis A Apostolidis
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elisabeth Mack
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Maja Artandi
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford CROWN Clinic, Stanford University School of Medicine, Stanford, CA, USA
| | - Linda Barman
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Kate Bennett
- Molecular Pathology and Imaging Core, Department of Medicine, Gastroenterology Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Iris Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon Chinthrajah
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaurya Dhingra
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Evan Do
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Amanda Finck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Gaano
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Reinhard Geßner
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Heather M Giannini
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Joyce Gonzalez
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Greib
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Margrit Gündisch
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
| | - Alex Ren Hsu
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Kuo
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Monali Manohar
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rong Mao
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andreas Neubauer
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Oluwatosin Oniyide
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abigail E Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, USA
| | - Rajan Puri
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Harald Renz
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany
- Member of the Universities of Giessen and Marburg Lung Center (UGMLC), and the German Center for Lung Research (DZL), Giessen, Germany
| | - Jeffrey Schapiro
- TPMG Regional Reference Laboratory, Kaiser Permanente Northern California, Berkeley, CA, USA
| | - Payton A Weidenbacher
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, USA
| | - Richard Wittman
- Department of Medicine, Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Neera Ahuja
- Department of Medicine, Division of Hospital Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ho-Ryun Chung
- Institute for Medical Bioinformatics and Biostatistics, Philipps University Marburg, Marburg, Germany
| | - Prasanna Jagannathan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Judith A James
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Peter S Kim
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nuala J Meyer
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kari C Nadeau
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - William H Robinson
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Upinder Singh
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany.
- Member of the Universities of Giessen and Marburg Lung Center (UGMLC), and the German Center for Lung Research (DZL), Giessen, Germany.
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
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4
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Chang SE, Feng A, Meng W, Apostolidis SA, Mack E, Artandi M, Barman L, Bennett K, Chakraborty S, Chang I, Cheung P, Chinthrajah S, Dhingra S, Do E, Finck A, Gaano A, Geßner R, Giannini HM, Gonzalez J, Greib S, Gündisch M, Hsu AR, Kuo A, Manohar M, Mao R, Neeli I, Neubauer A, Oniyide O, Powell AE, Puri R, Renz H, Schapiro JM, Weidenbacher PA, Wittman R, Ahuja N, Chung HR, Jagannathan P, James J, Kim PS, Meyer NJ, Nadeau K, Radic M, Robinson WH, Singh U, Wang TT, Wherry EJ, Skevaki C, Prak ETL, Utz PJ. New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19. medRxiv 2021. [PMID: 33532787 DOI: 10.1101/2021.01.27.21250559] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. We developed three different protein arrays to measure hallmark IgG autoantibodies associated with Connective Tissue Diseases (CTDs), Anti-Cytokine Antibodies (ACA), and anti-viral antibody responses in 147 hospitalized COVID-19 patients in three different centers. Autoantibodies were identified in approximately 50% of patients, but in <15% of healthy controls. When present, autoantibodies largely targeted autoantigens associated with rare disorders such as myositis, systemic sclerosis and CTD overlap syndromes. Anti-nuclear antibodies (ANA) were observed in ∼25% of patients. Patients with autoantibodies tended to demonstrate one or a few specificities whereas ACA were even more prevalent, and patients often had antibodies to multiple cytokines. Rare patients were identified with IgG antibodies against angiotensin converting enzyme-2 (ACE-2). A subset of autoantibodies and ACA developed de novo following SARS-CoV-2 infection while others were transient. Autoantibodies tracked with longitudinal development of IgG antibodies that recognized SARS-CoV-2 structural proteins such as S1, S2, M, N and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. COVID-19 patients with one or more autoantibodies tended to have higher levels of antibodies against SARS-CoV-2 Nonstructural Protein 1 (NSP1) and Methyltransferase (ME). We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
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5
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Powell A, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice. ACS Cent Sci 2021; 7:183-199. [PMID: 33527087 PMCID: PMC7805605 DOI: 10.1021/acscentsci.0c01405] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 05/05/2023]
Abstract
The development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines, and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
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Affiliation(s)
- Abigail
E. Powell
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Kaiming Zhang
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Shaogeng Tang
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Payton A. Weidenbacher
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Shanshan Li
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Tho D. Pham
- Department
of Pathology, Stanford University, Stanford, California 94305, United States
- Stanford
Blood Center, Palo Alto, California 94304, United States
| | - John E. Pak
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
| | - Wah Chiu
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Peter S. Kim
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
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6
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Gray MA, Stanczak MA, Mantuano NR, Xiao H, Pijnenborg JFA, Malaker SA, Miller CL, Weidenbacher PA, Tanzo JT, Ahn G, Woods EC, Läubli H, Bertozzi CR. Targeted glycan degradation potentiates the anticancer immune response in vivo. Nat Chem Biol 2020; 16:1376-1384. [PMID: 32807964 PMCID: PMC7727925 DOI: 10.1038/s41589-020-0622-x] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [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: 05/23/2019] [Accepted: 07/08/2020] [Indexed: 12/24/2022]
Abstract
Currently approved immune checkpoint inhibitor therapies targeting the PD-1 and CTLA-4 receptor pathways are powerful treatment options for certain cancers; however, most patients across cancer types still fail to respond. Consequently, there is interest in discovering and blocking alternative pathways that mediate immune suppression. One such mechanism is an upregulation of sialoglycans in malignancy, which has been recently shown to inhibit immune cell activation through multiple mechanisms and therefore represents a targetable glycoimmune checkpoint. Since these glycans are not canonically druggable, we designed an αHER2 antibody-sialidase conjugate that potently and selectively strips diverse sialoglycans from breast cancer cells. In syngeneic breast cancer models, desialylation enhanced immune cell infiltration and activation and prolonged the survival of mice, an effect that was dependent on expression of the Siglec-E checkpoint receptor found on tumor-infiltrating myeloid cells. Thus, antibody-sialidase conjugates represent a promising modality for glycoimmune checkpoint therapy.
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MESH Headings
- Allografts
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/metabolism
- B7-H1 Antigen/genetics
- B7-H1 Antigen/immunology
- Cell Line, Tumor
- Humans
- Hydrolysis
- Immunoconjugates/chemistry
- Immunoconjugates/metabolism
- Immunoconjugates/pharmacology
- Immunotherapy/methods
- Killer Cells, Natural/cytology
- Killer Cells, Natural/immunology
- Melanoma, Experimental/genetics
- Melanoma, Experimental/immunology
- Melanoma, Experimental/mortality
- Melanoma, Experimental/therapy
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Models, Molecular
- Molecular Targeted Therapy
- Neuraminidase/chemistry
- Neuraminidase/genetics
- Neuraminidase/immunology
- Polysaccharides/chemistry
- Polysaccharides/immunology
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/immunology
- Protein Binding
- Protein Interaction Domains and Motifs
- Protein Structure, Secondary
- Receptor, ErbB-2/chemistry
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/immunology
- Sialic Acid Binding Immunoglobulin-like Lectins/chemistry
- Sialic Acid Binding Immunoglobulin-like Lectins/genetics
- Sialic Acid Binding Immunoglobulin-like Lectins/immunology
- Survival Analysis
- T-Lymphocytes/cytology
- T-Lymphocytes/immunology
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Affiliation(s)
- Melissa A Gray
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Michal A Stanczak
- Cancer Immunology Laboratory, Department of Biomedicine, University Hospital, Basel, Switzerland
- Division of Oncology, Department of Internal Medicine, University Hospital, Basel, Switzerland
| | - Natália R Mantuano
- Cancer Immunology Laboratory, Department of Biomedicine, University Hospital, Basel, Switzerland
- Division of Oncology, Department of Internal Medicine, University Hospital, Basel, Switzerland
| | - Han Xiao
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Caitlyn L Miller
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Julia T Tanzo
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Green Ahn
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Elliot C Woods
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Heinz Läubli
- Cancer Immunology Laboratory, Department of Biomedicine, University Hospital, Basel, Switzerland
- Division of Oncology, Department of Internal Medicine, University Hospital, Basel, Switzerland
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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Powell AE, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice. bioRxiv 2020:2020.08.28.272518. [PMID: 32869030 PMCID: PMC7457616 DOI: 10.1101/2020.08.28.272518] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 12/17/2022]
Abstract
Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
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Affiliation(s)
- Abigail E. Powell
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Kaiming Zhang
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Shaogeng Tang
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Payton A. Weidenbacher
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Shanshan Li
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Tho D. Pham
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Stanford Blood Center, Palo Alto, CA 94304, USA
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Wah Chiu
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Peter S. Kim
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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