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Chen DY, Turcinovic J, Feng S, Kenney DJ, Chin CV, Choudhary MC, Conway HL, Semaan M, Close BJ, Tavares AH, Seitz S, Khan N, Kapell S, Crossland NA, Li JZ, Douam F, Baker SC, Connor JH, Saeed M. Cell culture systems for isolation of SARS-CoV-2 clinical isolates and generation of recombinant virus. iScience 2023; 26:106634. [PMID: 37095858 PMCID: PMC10083141 DOI: 10.1016/j.isci.2023.106634] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/22/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023] Open
Abstract
A simple and robust cell culture system is essential for generating authentic SARS-CoV-2 stocks for evaluation of viral pathogenicity, screening of antiviral compounds, and preparation of inactivated vaccines. Evidence suggests that Vero E6, a cell line commonly used in the field to grow SARS-CoV-2, does not support efficient propagation of new viral variants and triggers rapid cell culture adaptation of the virus. We generated a panel of 17 human cell lines overexpressing SARS-CoV-2 entry factors and tested their ability to support viral infection. Two cell lines, Caco-2/AT and HuH-6/AT, demonstrated exceptional susceptibility, yielding highly concentrated virus stocks. Notably, these cell lines were more sensitive than Vero E6 cells in recovering SARS-CoV-2 from clinical specimens. Further, Caco-2/AT cells provided a robust platform for producing genetically reliable recombinant SARS-CoV-2 through a reverse genetics system. These cellular models are a valuable tool for the study of SARS-CoV-2 and its continuously emerging variants.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Shuchen Feng
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Devin J Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Chue Vin Chin
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Manish C Choudhary
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Hasahn L Conway
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Marc Semaan
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Brianna J Close
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Scott Seitz
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Sebastian Kapell
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
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2
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Chen DY, Chin CV, Kenney D, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O'Connell AK, Adams S, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation. Nature 2023; 615:143-150. [PMID: 36630998 DOI: 10.1038/s41586-023-05697-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [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: 03/16/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
The SARS-CoV-2 Omicron variant is more immune evasive and less virulent than other major viral variants that have so far been recognized1-12. The Omicron spike (S) protein, which has an unusually large number of mutations, is considered to be the main driver of these phenotypes. Here we generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron (BA.1 lineage) in the backbone of an ancestral SARS-CoV-2 isolate, and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escaped vaccine-induced humoral immunity, mainly owing to mutations in the receptor-binding motif; however, unlike naturally occurring Omicron, it efficiently replicated in cell lines and primary-like distal lung cells. Similarly, in K18-hACE2 mice, although virus bearing Omicron S caused less severe disease than the ancestral virus, its virulence was not attenuated to the level of Omicron. Further investigation showed that mutating non-structural protein 6 (nsp6) in addition to the S protein was sufficient to recapitulate the attenuated phenotype of Omicron. This indicates that although the vaccine escape of Omicron is driven by mutations in S, the pathogenicity of Omicron is determined by mutations both in and outside of the S protein.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Chue Vin Chin
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Hasahn L Conway
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Manish C Choudhary
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K O'Connell
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Scott Adams
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Alexandra Herrmann
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Armin Ensser
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Markus Bosmann
- The Pulmonary Center and Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jonathan Z Li
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yachana Kataria
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
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3
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Chen DY, Kenney D, Chin CV, Tavares AH, Khan N, Conway HL, Liu G, Choudhary MC, Gertje HP, O'Connell AK, Kotton DN, Herrmann A, Ensser A, Connor JH, Bosmann M, Li JZ, Gack MU, Baker SC, Kirchdoerfer RN, Kataria Y, Crossland NA, Douam F, Saeed M. Role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron. bioRxiv 2023:2022.10.13.512134. [PMID: 36263066 PMCID: PMC9580375 DOI: 10.1101/2022.10.13.512134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The recently identified, globally predominant SARS-CoV-2 Omicron variant (BA.1) is highly transmissible, even in fully vaccinated individuals, and causes attenuated disease compared with other major viral variants recognized to date. The Omicron spike (S) protein, with an unusually large number of mutations, is considered the major driver of these phenotypes. We generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron in the backbone of an ancestral SARS-CoV-2 isolate and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escapes vaccine-induced humoral immunity, mainly due to mutations in the receptor binding motif (RBM), yet unlike naturally occurring Omicron, efficiently replicates in cell lines and primary-like distal lung cells. In K18-hACE2 mice, while Omicron causes mild, non-fatal infection, the Omicron S-carrying virus inflicts severe disease with a mortality rate of 80%. This indicates that while the vaccine escape of Omicron is defined by mutations in S, major determinants of viral pathogenicity reside outside of S.
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4
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Fuchs SY, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway. J Virol 2021; 95:e0086221. [PMID: 34260266 PMCID: PMC8428404 DOI: 10.1128/jvi.00862-21] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we generated a panel of phenotypically diverse, SARS-CoV-2-infectible human cell lines representing different body organs and performed longitudinal survey of cellular proteins and pathways broadly affected by the virus. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cells and primary-like cardiomyocytes, and found that SARS-CoV-2 targeted the proximal pathway components, including Janus kinase 1 (JAK1), tyrosine kinase 2 (Tyk2), and the interferon receptor subunit 1 (IFNAR1), resulting in cellular desensitization to type I IFN. Detailed mechanistic investigation of IFNAR1 showed that the protein underwent ubiquitination upon SARS-CoV-2 infection. Furthermore, chemical inhibition of JAK kinases enhanced infection of stem cell-derived cultures, indicating that the virus benefits from inhibiting the JAK-STAT pathway. These findings suggest that the suppression of interferon signaling is a mechanism widely used by the virus to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19. IMPORTANCE SARS-CoV-2 can infect various organs in the human body, but the molecular interface between the virus and these organs remains unexplored. In this study, we generated a panel of highly infectible human cell lines originating from various body organs and employed these cells to identify cellular processes commonly or distinctly disrupted by SARS-CoV-2 in different cell types. One among the universally impaired processes was interferon signaling. Systematic analysis of this pathway in diverse culture systems showed that SARS-CoV-2 targets the proximal JAK-STAT pathway components, destabilizes the type I interferon receptor though ubiquitination, and consequently renders the infected cells resistant to type I interferon. These findings illuminate how SARS-CoV-2 can continue to propagate in different tissues even in the presence of a disseminated innate immune response.
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Affiliation(s)
- Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Brianna J. Close
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Raghuveera K. Goel
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Benjamin Blum
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Alexander H. Tavares
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Devin Kenney
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Hasahn L. Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Vipul C. Chitalia
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Boston Veterans Affairs Healthcare System, Boston, Massachusetts, USA
- Institute of Medical Engineering and Sciences, MA Institute of Technology, Cambridge, Massachusetts, USA
| | - Nicholas A. Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Susan C. Baker
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois, USA
| | - Serge Y. Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John H. Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
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Nageswara Rao D, Zephyr J, Henes M, Chan ET, Matthew AN, Hedger AK, Conway HL, Saeed M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A. Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants. J Med Chem 2021; 64:11972-11989. [PMID: 34405680 PMCID: PMC9228641 DOI: 10.1021/acs.jmedchem.1c00554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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] [Indexed: 02/07/2023]
Abstract
The three pan-genotypic HCV NS3/4A protease inhibitors (PIs) currently in clinical use-grazoprevir, glecaprevir, and voxilaprevir-are quinoxaline-based P2-P4 macrocycles and thus exhibit similar resistance profiles. Using our quinoxaline-based P1-P3 macrocyclic lead compounds as an alternative chemical scaffold, we explored structure-activity relationships (SARs) at the P2 and P4 positions to develop pan-genotypic PIs that avoid drug resistance. A structure-guided strategy was used to design and synthesize two series of compounds with different P2 quinoxalines in combination with diverse P4 groups of varying sizes and shapes, with and without fluorine substitutions. Our SAR data and cocrystal structures revealed the interplay between the P2 and P4 groups, which influenced inhibitor binding and the overall resistance profile. Optimizing inhibitor interactions in the S4 pocket led to PIs with excellent antiviral activity against clinically relevant PI-resistant HCV variants and genotype 3, providing potential pan-genotypic inhibitors with improved resistance profiles.
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Affiliation(s)
- Desaboini Nageswara Rao
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Elise T Chan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ashley N Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Adam K Hedger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Hasahn L Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts 02118, United States
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts 02118, United States
| | - Alicia Newton
- Monogram Biosciences, South San Francisco, California 94080, United States
| | | | - Wei Huang
- Monogram Biosciences, South San Francisco, California 94080, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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6
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Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Gallagher KME, Bauer MR, Taylor HB, Dunn WA, Tarr C, Sidney J, Rachimi S, Conway HL, Katsis K, Wang Y, Leistritz-Edwards D, Durkin MR, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Carulli IP, Chea VA, Chandrashekar A, Bozkus CC, Carrington M, Bhardwaj N, Barouch DH, Sette A, Maus MV, Rice CM, Clauser KR, Keskin DB, Pregibon DC, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs. Cell 2021; 184:3962-3980.e17. [PMID: 34171305 PMCID: PMC8173604 DOI: 10.1016/j.cell.2021.05.046] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [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: 10/12/2020] [Revised: 04/21/2021] [Accepted: 05/27/2021] [Indexed: 01/23/2023]
Abstract
T cell-mediated immunity plays an important role in controlling SARS-CoV-2 infection, but the repertoire of naturally processed and presented viral epitopes on class I human leukocyte antigen (HLA-I) remains uncharacterized. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two cell lines at different times post infection using mass spectrometry. We found HLA-I peptides derived not only from canonical open reading frames (ORFs) but also from internal out-of-frame ORFs in spike and nucleocapsid not captured by current vaccines. Some peptides from out-of-frame ORFs elicited T cell responses in a humanized mouse model and individuals with COVID-19 that exceeded responses to canonical peptides, including some of the strongest epitopes reported to date. Whole-proteome analysis of infected cells revealed that early expressed viral proteins contribute more to HLA-I presentation and immunogenicity. These biological insights, as well as the discovery of out-of-frame ORF epitopes, will facilitate selection of peptides for immune monitoring and vaccine development.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | - Leah R Pearlman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Kathleen M E Gallagher
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah B Taylor
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Suzanna Rachimi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hasahn L Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Katelin Katsis
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Yuntong Wang
- Repertoire Immune Medicines, Cambridge, MA 02139, USA
| | | | | | - Christopher H Tomkins-Tinch
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Matteo Gentili
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Keith D Rivera
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Isabel P Carulli
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vipheaviny A Chea
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Cansu Cimen Bozkus
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Nina Bhardwaj
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Dan H Barouch
- Harvard Medical School, Boston, MA 02115, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Marcela V Maus
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Derin B Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA; Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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7
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Kapell S, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 desensitizes host cells to interferon through inhibition of the JAK-STAT pathway. bioRxiv 2020. [PMID: 33140044 DOI: 10.1101/2020.10.27.358259] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we performed global proteomic analysis of the virus-host interface in a newly established panel of phenotypically diverse, SARS-CoV-2-infectable human cell lines representing different body organs. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cell lines and primary-like cardiomyocytes, and found that several pathway components were targeted by SARS-CoV-2 leading to cellular desensitization to interferon. These findings indicate that the suppression of interferon signaling is a mechanism widely used by SARS-CoV-2 in diverse tissues to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19.
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8
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Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Bauer MR, Taylor HB, Conway HL, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Keskin DB, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. bioRxiv 2020. [PMID: 33024965 PMCID: PMC7536868 DOI: 10.1101/2020.10.02.324145] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class I human leukocyte antigen (HLA-I) can reveal epitopes for recognition by cytotoxic T cells and potential incorporation into vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not captured by current vaccines. Proteomics analyses of infected cells revealed that SARS-CoV-2 may interfere with antigen processing and immune signaling pathways. Based on the endogenously processed and presented viral peptides that we identified, we estimate that a pool of 24 peptides would provide one or more peptides for presentation by at least one HLA allele in 99% of the human population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.
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9
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Ejemel M, Li Q, Hou S, Schiller ZA, Tree JA, Wallace A, Amcheslavsky A, Kurt Yilmaz N, Buttigieg KR, Elmore MJ, Godwin K, Coombes N, Toomey JR, Schneider R, Ramchetty AS, Close BJ, Chen DY, Conway HL, Saeed M, Ganesa C, Carroll MW, Cavacini LA, Klempner MS, Schiffer CA, Wang Y. A cross-reactive human IgA monoclonal antibody blocks SARS-CoV-2 spike-ACE2 interaction. Nat Commun 2020; 11:4198. [PMID: 32826914 PMCID: PMC7442812 DOI: 10.1038/s41467-020-18058-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [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: 05/05/2020] [Accepted: 08/03/2020] [Indexed: 01/19/2023] Open
Abstract
COVID-19 caused by SARS-CoV-2 has become a global pandemic requiring the development of interventions for the prevention or treatment to curtail mortality and morbidity. No vaccine to boost mucosal immunity, or as a therapeutic, has yet been developed to SARS-CoV-2. In this study, we discover and characterize a cross-reactive human IgA monoclonal antibody, MAb362. MAb362 binds to both SARS-CoV and SARS-CoV-2 spike proteins and competitively blocks ACE2 receptor binding, by overlapping the ACE2 structural binding epitope. Furthermore, MAb362 IgA neutralizes both pseudotyped SARS-CoV and SARS-CoV-2 in 293 cells expressing ACE2. When converted to secretory IgA, MAb326 also neutralizes authentic SARS-CoV-2 virus while the IgG isotype shows no neutralization. Our results suggest that SARS-CoV-2 specific IgA antibodies, such as MAb362, may provide effective immunity against SARS-CoV-2 by inducing mucosal immunity within the respiratory system, a potentially critical feature of an effective vaccine. Here, Ejemel et al. report the identification and characterization of a cross-neutralizing human IgA monoclonal antibody, named MAb362, that binds the receptor-binding domain of SARS-CoV-2 Spike, blocking its interaction with the ACE2 host receptor.
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Affiliation(s)
- Monir Ejemel
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Qi Li
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Shurong Hou
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Boston, MA, USA
| | - Zachary A Schiller
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Julia A Tree
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Aaron Wallace
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Alla Amcheslavsky
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Nese Kurt Yilmaz
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Boston, MA, USA
| | - Karen R Buttigieg
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Michael J Elmore
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Kerry Godwin
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Naomi Coombes
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Jacqueline R Toomey
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Ryan Schneider
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Anudeep S Ramchetty
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Brianna J Close
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Da-Yuan Chen
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Hasahn L Conway
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Chandrashekar Ganesa
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Lisa A Cavacini
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA.
| | - Mark S Klempner
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA.
| | - Celia A Schiffer
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Boston, MA, USA.
| | - Yang Wang
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA.
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10
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Ejemel M, Li Q, Hou S, Schiller ZA, Wallace AL, Amcheslavsky A, Yilmaz NK, Toomey JR, Schneider R, Close BJ, Chen DY, Conway HL, Mohsan S, Cavacini LA, Klempner MS, Schiffer CA, Wang Y. IgA MAb blocks SARS-CoV-2 Spike-ACE2 interaction providing mucosal immunity. bioRxiv 2020. [PMID: 32511396 DOI: 10.1101/2020.05.15.096719] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
COVID-19 caused by SARS-CoV-2 has become a global pandemic requiring the development of interventions for the prevention or treatment to curtail mortality and morbidity. No vaccine to boost mucosal immunity or as a therapeutic has yet been developed to SARS-CoV-2. In this study we discover and characterize a cross-reactive human IgA monoclonal antibody, MAb362. MAb362 binds to both SARS-CoV and SARS-CoV-2 spike proteins and competitively blocks hACE2 receptor binding, by completely overlapping the hACE2 structural binding epitope. Furthermore, MAb362 IgA neutralizes both pseudotyped SARS-CoV and SARS-CoV-2 in human epithelial cells expressing hACE2. SARS-CoV-2 specific IgA antibodies, such as MAb362, may provide effective immunity against SARS-CoV-2 by inducing mucosal immunity within the respiratory system, a potentially critical feature of an effective vaccine.
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