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Doni Jayavelu N, Altman MC, Benson B, Dufort MJ, Vanderwall ER, Rich LM, White MP, Becker PM, Togias A, Jackson DJ, Debley JS. Type 2 inflammation reduces SARS-CoV-2 replication in the airway epithelium in allergic asthma through functional alteration of ciliated epithelial cells. J Allergy Clin Immunol 2023; 152:56-67. [PMID: 37001649 PMCID: PMC10052850 DOI: 10.1016/j.jaci.2023.03.021] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/05/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023]
Abstract
BACKGROUND Despite well-known susceptibilities to other respiratory viral infections, individuals with allergic asthma have shown reduced susceptibility to severe coronavirus disease 2019 (COVID-19). OBJECTIVE We sought to identify mechanisms whereby type 2 inflammation in the airway protects against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by using bronchial airway epithelial cells (AECs) from aeroallergen-sensitized children with asthma and healthy nonsensitized children. METHODS We measured SARS-CoV-2 replication and ACE2 protein and performed bulk and single-cell RNA sequencing of ex vivo infected AEC samples with SARS-CoV-2 infection and with or without IL-13 treatment. RESULTS We observed that viral replication was lower in AECs from children with allergic asthma than those from in healthy nonsensitized children and that IL-13 treatment reduced viral replication only in children with allergic asthma and not in healthy children. Lower viral transcript levels were associated with a downregulation of functional pathways of the ciliated epithelium related to differentiation as well as cilia and axoneme production and function, rather than lower ACE2 expression or increases in goblet cells or mucus secretion pathways. Moreover, single-cell RNA sequencing identified specific subsets of relatively undifferentiated ciliated epithelium (which are common in allergic asthma and highly responsive to IL-13) that directly accounted for impaired viral replication. CONCLUSION Our results identify a novel mechanism of innate protection against SARS-CoV-2 in allergic asthma that provides important molecular and clinical insights during the ongoing COVID-19 pandemic.
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Affiliation(s)
- Naresh Doni Jayavelu
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, Wash
| | - Matthew C Altman
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, Wash; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, Wash.
| | - Basilin Benson
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, Wash
| | - Matthew J Dufort
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, Wash
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Maria P White
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, Md
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, Md
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash; Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, University of Washington, Seattle, Wash
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2
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Powell WT, Rich LM, Vanderwall ER, White MP, Debley JS. Temperature synchronisation of circadian rhythms in primary human airway epithelial cells from children. BMJ Open Respir Res 2022; 9:9/1/e001319. [PMID: 36198442 PMCID: PMC9535174 DOI: 10.1136/bmjresp-2022-001319] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/24/2022] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION Cellular circadian rhythms regulate immune pathways and inflammatory responses that mediate human disease such as asthma. Circadian rhythms in the lung may also contribute to exacerbations of chronic diseases such as asthma by regulating observed rhythms in mucus production, bronchial reactivity, airway inflammation and airway resistance. Primary human airway epithelial cells (AECs) are commonly used to model human lung diseases, such as asthma, with circadian symptoms, but a method for synchronising circadian rhythms in AECs has not been developed, and the presence of circadian rhythms in human AECs remains uninvestigated. METHODS We used temperature cycling to synchronise circadian rhythms in undifferentiated and differentiated primary human AECs. Reverse transcriptase-quantitative PCR was used to measure expression of the core circadian clock genes ARNTL, CLOCK, CRY1, CRY2, NR1D1, NR1D2, PER1 and PER2. RESULTS Following temperature synchronisation, the core circadian genes ARNTL, CRY1, CRY2, NR1D1, NR1D2, PER1 and PER2 maintained endogenous 24-hour rhythms under constant conditions. Following serum shock, the core circadian genes ARNTL, NR1D1 and NR1D2 demonstrated rhythmic expression. Following temperature synchronisation, CXCL8 demonstrated rhythmic circadian expression. CONCLUSIONS Temperature synchronised circadian rhythms in AECs differentiated at an air-liquid interface can serve as a model to investigate circadian rhythms in pulmonary diseases.
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Affiliation(s)
- Weston T Powell
- Seattle Children's Research Institute, Seattle, Washington, USA,Department of Pediatrics, University of Washington, Seattle, Washington, USA,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Lucille M Rich
- Seattle Children's Research Institute, Seattle, Washington, USA,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Elizabeth R Vanderwall
- Seattle Children's Research Institute, Seattle, Washington, USA,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Maria P White
- Seattle Children's Research Institute, Seattle, Washington, USA,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jason S Debley
- Seattle Children's Research Institute, Seattle, Washington, USA,Department of Pediatrics, University of Washington, Seattle, Washington, USA,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
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3
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Hale M, Netland J, Chen Y, Thouvenel CD, Smith KN, Rich LM, Vanderwall ER, Miranda MC, Eggenberger J, Hao L, Watson MJ, Mundorff CC, Rodda LB, King NP, Guttman M, Gale M, Abraham J, Debley JS, Pepper M, Rawlings DJ. Correction: IgM antibodies derived from memory B cells are potent cross-variant neutralizers of SARS-CoV-2. J Exp Med 2022; 219:jem.2022084908172022c. [PMID: 36036783 PMCID: PMC9441922 DOI: 10.1084/jem.2022084908172022c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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4
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Hale M, Netland J, Chen Y, Thouvenel CD, Smith KN, Rich LM, Vanderwall ER, Miranda MC, Eggenberger J, Hao L, Watson MJ, Mundorff CC, Rodda LB, King NP, Guttman M, Gale M, Abraham J, Debley JS, Pepper M, Rawlings DJ. IgM antibodies derived from memory B cells are potent cross-variant neutralizers of SARS-CoV-2. J Exp Med 2022; 219:213384. [PMID: 35938988 PMCID: PMC9365875 DOI: 10.1084/jem.20220849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/22/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
Humoral immunity to SARS-CoV-2 can be supplemented with polyclonal sera from convalescent donors or an engineered monoclonal antibody (mAb) product. While pentameric IgM antibodies are responsible for much of convalescent sera's neutralizing capacity, all available mAbs are based on the monomeric IgG antibody subtype. We now show that IgM mAbs derived from immune memory B cell receptors are potent neutralizers of SARS-CoV-2. IgM mAbs outperformed clonally identical IgG antibodies across a range of affinities and SARS-CoV-2 receptor-binding domain epitopes. Strikingly, efficacy against SARS-CoV-2 viral variants was retained for IgM but not for clonally identical IgG. To investigate the biological role for IgM memory in SARS-CoV-2, we also generated IgM mAbs from antigen-experienced IgM+ memory B cells in convalescent donors, identifying a potent neutralizing antibody. Our results highlight the therapeutic potential of IgM mAbs and inform our understanding of the role for IgM memory against a rapidly mutating pathogen.
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Affiliation(s)
- Malika Hale
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Jason Netland
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Yu Chen
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | - Marcos C. Miranda
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Linhui Hao
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Michael J. Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | | | - Lauren B. Rodda
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA,Department of Immunology, University of Washington School of Medicine, Seattle, WA,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA,Correspondence to David J. Rawlings:
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5
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Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Herlands L, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. eLife 2021; 10:73027. [PMID: 34874007 PMCID: PMC8651292 DOI: 10.7554/elife.73027] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/07/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of SARS-CoV-2 variants threatens current vaccines and therapeutic antibodies and urgently demands powerful new therapeutics that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain, and the S2 subunit, to identify new nanobody binding sites that may reflect novel mechanisms of viral neutralization. Structural mapping and functional assays show that indeed these highly stable monovalent nanobodies potently inhibit SARS-CoV-2 infection, display numerous neutralization mechanisms, are effective against emerging variants of concern, and are resistant to mutational escape. Rational combinations of these nanobodies that bind to distinct sites within and between spike subunits exhibit extraordinary synergy and suggest multiple tailored therapeutic and prophylactic strategies.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States.,Department of Chemistry, St. John's University, Queens, United States
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Magdalena Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States
| | - Nicholas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, United States
| | - Jacob B Jiler
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | | | | | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States.,Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, United States
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States.,Department of Biochemistry, University of Washington, Seattle, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
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6
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Vanderwall ER, Barrow KA, Rich LM, Read DF, Trapnell C, Okoloko O, Ziegler SF, Hallstrand TS, White MP, Debley JS. Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication. bioRxiv 2021. [PMID: 34845445 DOI: 10.1101/2021.11.20.469409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Common alphacoronaviruses and human rhinoviruses (HRV) induce type I and III interferon (IFN) responses important to limiting viral replication in the airway epithelium. In contrast, highly pathogenic betacoronaviruses including SARS-CoV-2 may evade or antagonize RNA-induced IFN I/III responses. METHODS In airway epithelial cells (AECs) from children and older adults we compared IFN I/III responses to SARS-CoV-2 and HRV-16, and assessed whether pre-infection with HRV-16, or pretreatment with recombinant IFN-β or IFN-λ, modified SARS-CoV-2 replication. Bronchial AECs from children (ages 6-18 yrs.) and older adults (ages 60-75 yrs.) were differentiated ex vivo to generate organotypic cultures. In a biosafety level 3 (BSL-3) facility, cultures were infected with SARS-CoV-2 or HRV-16, and RNA and protein was harvested from cell lysates 96 hrs. following infection and supernatant was collected 48 and 96 hrs. following infection. In additional experiments cultures were pre-infected with HRV-16, or pre-treated with recombinant IFN-β1 or IFN-λ2 before SARS-CoV-2 infection. RESULTS Despite significant between-donor heterogeneity SARS-CoV-2 replicated 100 times more efficiently than HRV-16. IFNB1, INFL2, and CXCL10 gene expression and protein production following HRV-16 infection was significantly greater than following SARS-CoV-2. IFN gene expression and protein production were inversely correlated with SARS-CoV-2 replication. Treatment of cultures with recombinant IFNβ1 or IFNλ2, or pre-infection of cultures with HRV-16, markedly reduced SARS-CoV-2 replication. DISCUSSION In addition to marked between-donor heterogeneity in IFN responses and viral replication, SARS-CoV-2 elicits a less robust IFN response in primary AEC cultures than does rhinovirus, and heterologous rhinovirus infection, or treatment with recombinant IFN-β1 or IFN-λ2, markedly reduces SARS-CoV-2 replication.
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Okoloko O, Vanderwall ER, Rich LM, White MP, Reeves SR, Harrington WE, Barrow KA, Debley JS. Effect of Angiotensin-Converting-Enzyme Inhibitor and Angiotensin II Receptor Antagonist Treatment on ACE2 Expression and SARS-CoV-2 Replication in Primary Airway Epithelial Cells. Front Pharmacol 2021; 12:765951. [PMID: 34867390 PMCID: PMC8641911 DOI: 10.3389/fphar.2021.765951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/02/2021] [Indexed: 01/08/2023] Open
Abstract
Rationale: SARS-CoV-2 gains entrance to airway epithelial cells (AECs) through binding of the viral spike protein to the angiotensin-converting enzyme 2 (ACE2) on the cell surface. However, ACE2 also converts angiotensin II into angiotensin-(1-7) and counterbalances the renin-angiotensin-aldosterone system, with resultant protective effects in the cardiovascular system. Some data suggest that two common antihypertension medications (angiotensin II receptor antagonists, ARBs; and angiotensin-converting-enzyme inhibitors, ACEIs) may increase ACE2 expression in heart and kidney cells, fueling debate about how these widely used medications may modulate SARS-CoV-2 infectivity and risk of COVID-19. Aim: Determine whether exposure of bronchial AECs to the ARB losartan or the ACEI captopril modulate expression of ACE2 by AECs, SARS CoV2 replication, or expression of proinflammatory cytokines and type I and III interferon (IFN) responses. Methods: Primary bronchial AECs from children and adults (n = 19; Ages 8-75 yrs) were differentiated ex vivo at an air-liquid interface to generate organotypic cultures. Cultures were treated with captopril (1 μM) or losartan (2 μM) with culture media changes starting 72 h before infection with SARS-CoV-2. In a biosafety level 3 (BSL-3) facility, cultures were infected with SARS-CoV-2 isolate USA-WA1/2020 at a multiplicity of infection (MOI) of 0.5. At 96 h following infection, RNA and protein were isolated. SARS-CoV-2 replication in cultures was assessed with quantitative PCR (qPCR). ACE2, IL-6, IL-1B, IFNB1, and IFNL2 expression were assessed by qPCR. Results: Neither captopril nor losartan treatment significantly changed ACE2, IL-6, IL-1B, IFNB1, or IFNL2 expression by AECs as compared to SARS-CoV-2 infected AEC cultures without captopril or losartan treatment. At 96 h following infection, SARS-CoV-2 copy number/ng RNA was not significantly different between untreated AEC cultures, cultures treated with captopril, or cultures treated with losartan. Conclusion: These findings suggest that at the level of the airway epithelium neither the ACEI captopril or ARB losartan significantly modify expression of the SARS-CoV-2 entry factor ACE2, nor does either medication increase replication SARS-CoV-2 replication. This ex vivo data is reassuring and is consistent with evolving clinical data suggesting ACEIs and ARBs do not increase the risk for poor prognosis with COVID-19 and may actually reduce the risk of COVID-19 disease.
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Affiliation(s)
- Oghenemega Okoloko
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Elizabeth R. Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Maria P. White
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Stephen R. Reeves
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children’s Hospital, University of Washington, Seattle, WA, United States
| | - Whitney E. Harrington
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, Division of Infectious Disease, Seattle Children’s Hospital, University of Washington, Seattle, WA, United States
| | - Kaitlyn A. Barrow
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children’s Hospital, University of Washington, Seattle, WA, United States
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8
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Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2. bioRxiv 2021:2021.04.08.438911. [PMID: 33851164 PMCID: PMC8043454 DOI: 10.1101/2021.04.08.438911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/12/2022]
Abstract
Despite the great promise of vaccines, the COVID-19 pandemic is ongoing and future serious outbreaks are highly likely, so that multi-pronged containment strategies will be required for many years. Nanobodies are the smallest naturally occurring single domain antigen binding proteins identified to date, possessing numerous properties advantageous to their production and use. We present a large repertoire of high affinity nanobodies against SARS-CoV-2 Spike protein with excellent kinetic and viral neutralization properties, which can be strongly enhanced with oligomerization. This repertoire samples the epitope landscape of the Spike ectodomain inside and outside the receptor binding domain, recognizing a multitude of distinct epitopes and revealing multiple neutralization targets of pseudoviruses and authentic SARS-CoV-2, including in primary human airway epithelial cells. Combinatorial nanobody mixtures show highly synergistic activities, and are resistant to mutational escape and emerging viral variants of concern. These nanobodies establish an exceptional resource for superior COVID-19 prophylactics and therapeutics.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Magda Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nicolas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sarah Keegan
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Jacob B Jiler
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Theodora Hatziioannou
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
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Barrow KA, Rich LM, Vanderwall ER, Reeves SR, Rathe JA, White MP, Debley JS. Inactivation of Material from SARS-CoV-2-Infected Primary Airway Epithelial Cell Cultures. Methods Protoc 2021; 4:mps4010007. [PMID: 33430421 PMCID: PMC7839057 DOI: 10.3390/mps4010007] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/25/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Given that the airway epithelium is the initial site of infection, study of primary human airway epithelial cells (AEC) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will be crucial to improved understanding of viral entry factors and innate immune responses to the virus. Centers for Disease Control and Prevention (CDC) guidance recommends work with live SARS-CoV-2 in cell culture be conducted in a Biosafety Level 3 (BSL-3) laboratory. To facilitate downstream assays of materials from experiments there is a need for validated protocols for SARS-CoV-2 inactivation to facilitate safe transfer of material out of a BSL-3 laboratory. We propagated stocks of SARS-CoV-2, then evaluated the effectiveness of heat (65 °C) or ultraviolet (UV) light inactivation. We infected differentiated human primary AECs with SARS-CoV-2, then tested protocols designed to inactivate SARS-CoV-2 in supernatant, protein isolate, RNA, and cells fixed for immunohistochemistry by exposing Vero E6 cells to materials isolated/treated using these protocols. Heating to 65 °C for 10 min or exposing to UV light fully inactivated SARS-CoV-2. Furthermore, we found in SARS-CoV-2-infected primary AEC cultures that treatment of supernatant with UV light, isolation of RNA with Trizol®, isolation of protein using a protocol including sodium dodecyl sulfate (SDS) 0.1% and Triton X100 1%, and fixation of AECs using 10% formalin and Triton X100 1%, each fully inactivated SARS-CoV-2.
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Affiliation(s)
- Kaitlyn A. Barrow
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA; (K.A.B.); (L.M.R.); (E.R.V.); (S.R.R.); (M.P.W.)
| | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA; (K.A.B.); (L.M.R.); (E.R.V.); (S.R.R.); (M.P.W.)
| | - Elizabeth R. Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA; (K.A.B.); (L.M.R.); (E.R.V.); (S.R.R.); (M.P.W.)
| | - Stephen R. Reeves
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA; (K.A.B.); (L.M.R.); (E.R.V.); (S.R.R.); (M.P.W.)
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children’s Hospital, University of Washington, Seattle, WA 98101, USA
| | - Jennifer A. Rathe
- Department of Pediatrics, Division of Infectious Disease, Seattle Children’s Hospital, University of Washington, Seattle, WA 98101, USA;
| | - Maria P. White
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA; (K.A.B.); (L.M.R.); (E.R.V.); (S.R.R.); (M.P.W.)
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA; (K.A.B.); (L.M.R.); (E.R.V.); (S.R.R.); (M.P.W.)
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children’s Hospital, University of Washington, Seattle, WA 98101, USA
- Correspondence:
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