1
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Weinberg ZY, Soliman SS, Kim MS, Chen IP, Ott M, El-Samad H. De novo-designed minibinders expand the synthetic biology sensing repertoire. bioRxiv 2024:2024.01.12.575267. [PMID: 38293112 PMCID: PMC10827046 DOI: 10.1101/2024.01.12.575267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Synthetic and chimeric receptors capable of recognizing and responding to user-defined antigens have enabled "smart" therapeutics based on engineered cells. These cell engineering tools depend on antigen sensors which are most often derived from antibodies. Advances in the de novo design of proteins have enabled the design of protein binders with the potential to target epitopes with unique properties and faster production timelines compared to antibodies. Building upon our previous work combining a de novo-designed minibinder of the Spike protein of SARS-CoV-2 with the synthetic receptor synNotch (SARSNotch), we investigated whether minibinders can be readily adapted to a diversity of cell engineering tools. We show that the Spike minibinder LCB1 easily generalizes to a next-generation proteolytic receptor SNIPR that performs similarly to our previously reported SARSNotch. LCB1-SNIPR successfully enables the detection of live SARS-CoV-2, an improvement over SARSNotch which can only detect cell-expressed Spike. To test the generalizability of minibinders to diverse applications, we tested LCB1 as an antigen sensor for a chimeric antigen receptor (CAR). LCB1-CAR enabled CD8+ T cells to cytotoxically target Spike-expressing cells. Our findings suggest that minibinders represent a novel class of antigen sensors that have the potential to dramatically expand the sensing repertoire of cell engineering tools.
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Affiliation(s)
| | | | - Matthew S. Kim
- Tetrad Gradudate Program, UCSF, San Francisco CA
- Cell Design Institute, San Francisco CA
| | - Irene P. Chen
- Gladstone Institutes, San Francisco CA
- Department of Medicine, UCSF, San Francisco CA
| | - Melanie Ott
- Gladstone Institutes, San Francisco CA
- Department of Medicine, UCSF, San Francisco CA
- Chan Zuckerberg Biohub–San Francisco, San Francisco CA
| | - Hana El-Samad
- Department of Biochemistry & Biophysics, UCSF, San Francisco CA
- Cell Design Institute, San Francisco CA
- Chan Zuckerberg Biohub–San Francisco, San Francisco CA
- Altos Labs, San Francisco CA
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2
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Suryawanshi RK, Taha TY, McCavitt-Malvido M, Silva I, Khalid MM, Syed AM, Chen IP, Saldhi P, Sreekumar B, Montano M, Foresythe K, Tabata T, Kumar GR, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Kojima N, Arellanor T, Bussanich A, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Wang Y, Ghazarian S, Davis G, Rodriguez D, Doudna J, Spraggon L, Chiu CY, Ott M. Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination. Emerg Microbes Infect 2023; 12:2270071. [PMID: 37869789 PMCID: PMC10619466 DOI: 10.1080/22221751.2023.2270071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
The emergence of SARS-CoV-2 recombinants is of particular concern as they can result in a sudden increase in immune evasion due to antigenic shift. Recent recombinants XBB and XBB.1.5 have higher transmissibility than previous recombinants such as "Deltacron." We hypothesized that immunity to a SARS-CoV-2 recombinant depends on prior exposure to its parental strains. To test this hypothesis, we examined whether Delta or Omicron (BA.1 or BA.2) immunity conferred through infection, vaccination, or breakthrough infection could neutralize Deltacron and XBB/XBB.1.5 recombinants. We found that Delta, BA.1, or BA.2 breakthrough infections provided better immune protection against Deltacron and its parental strains than did the vaccine booster. None of the sera were effective at neutralizing the XBB lineage or its parent BA.2.75.2, except for the sera from the BA.2 breakthrough group. These results support our hypothesis. In turn, our findings underscore the importance of multivalent vaccines that correspond to the antigenic profile of circulating variants of concern and of variant-specific diagnostics that may guide public health and individual decisions in response to emerging SARS-CoV-2 recombinants.
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Affiliation(s)
| | | | | | | | | | - Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Irene P. Chen
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | - Kafaya Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | | | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Amelia Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jennifer Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | | | - Charles Y. Chiu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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3
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Ma T, Suryawanshi RK, Miller SR, Ly KK, Thomas R, Elphick N, Yin K, Luo X, Kaliss N, Chen IP, Montano M, Sreekumar B, Standker L, Münch J, Heath Damron F, Palop JJ, Ott M, Roan NR. Post-acute immunological and behavioral sequelae in mice after Omicron infection. bioRxiv 2023:2023.06.05.543758. [PMID: 37333294 PMCID: PMC10274741 DOI: 10.1101/2023.06.05.543758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Progress in understanding long COVID and developing effective therapeutics is hampered in part by the lack of suitable animal models. Here we used ACE2-transgenic mice recovered from Omicron (BA.1) infection to test for pulmonary and behavioral post-acute sequelae. Through in-depth phenotyping by CyTOF, we demonstrate that naïve mice experiencing a first Omicron infection exhibit profound immune perturbations in the lung after resolving acute infection. This is not observed if mice were first vaccinated with spike-encoding mRNA. The protective effects of vaccination against post-acute sequelae were associated with a highly polyfunctional SARS-CoV-2-specific T cell response that was recalled upon BA.1 breakthrough infection but not seen with BA.1 infection alone. Without vaccination, the chemokine receptor CXCR4 was uniquely upregulated on multiple pulmonary immune subsets in the BA.1 convalescent mice, a process previously connected to severe COVID-19. Taking advantage of recent developments in machine learning and computer vision, we demonstrate that BA.1 convalescent mice exhibited spontaneous behavioral changes, emotional alterations, and cognitive-related deficits in context habituation. Collectively, our data identify immunological and behavioral post-acute sequelae after Omicron infection and uncover a protective effect of vaccination against post-acute pulmonary immune perturbations.
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Affiliation(s)
- Tongcui Ma
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | | | - Stephanie R. Miller
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Katie K. Ly
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Reuben Thomas
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Natalie Elphick
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Kailin Yin
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Xiaoyu Luo
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Nick Kaliss
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Irene P Chen
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco; San Francisco, CA, USA
- Department of Medicine, University of California San Francisco; San Francisco, CA, USA
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | | | | | - Ludger Standker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - F. Heath Damron
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown WV, USA
| | - Jorge J. Palop
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Melanie Ott
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco; San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nadia R. Roan
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
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4
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Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio 2023; 14:e0088923. [PMID: 37294090 PMCID: PMC10470529 DOI: 10.1128/mbio.00889-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 06/10/2023] Open
Abstract
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2-positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls. These results were confirmed and extended in the K18-humanized angiotensin-converting enzyme 2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the USA), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2, it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | - Preston Tasoff
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | | | - Victoria Wong Murray
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | - Jordan E. Bisanz
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
| | - Yulin Hswen
- Department of Epidemiology and Biostatistics and the Bakar Computational Health Institute, University of California San Francisco, San Francisco, California, USA
| | - Connie W. Y. Ha
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | - Irene P. Chen
- Gladstone Institutes, San Francisco, California, USA
| | - Susan V. Lynch
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
- Department of Pediatrics, University of California San Francisco, University of California, San Francisco, California, USA
| | - Melanie Ott
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Gladstone Institutes, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
| | - Sulggi Lee
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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5
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Kim IJ, Lee YH, Khalid MM, Chen IP, Zhang Y, Ott M, Verdin E. SARS-CoV-2 protein ORF8 limits expression levels of Spike antigen and facilitates immune evasion of infected host cells. J Biol Chem 2023; 299:104955. [PMID: 37354973 PMCID: PMC10289268 DOI: 10.1016/j.jbc.2023.104955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
Recovery from COVID-19 depends on the ability of the host to effectively neutralize virions and infected cells, a process largely driven by antibody-mediated immunity. However, with the newly emerging variants that evade Spike-targeting antibodies, re-infections and breakthrough infections are increasingly common. A full characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mechanisms counteracting antibody-mediated immunity is therefore needed. Here, we report that ORF8 is a virally encoded SARS-CoV-2 factor that controls cellular Spike antigen levels. We show that ORF8 limits the availability of mature Spike by inhibiting host protein synthesis and retaining Spike at the endoplasmic reticulum, reducing cell-surface Spike levels and recognition by anti-SARS-CoV-2 antibodies. In conditions of limited Spike availability, we found ORF8 restricts Spike incorporation during viral assembly, reducing Spike levels in virions. Cell entry of these virions then leaves fewer Spike molecules at the cell surface, limiting antibody recognition of infected cells. Based on these findings, we propose that SARS-CoV-2 variants may adopt an ORF8-dependent strategy that facilitates immune evasion of infected cells for extended viral production.
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Affiliation(s)
- Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, California, United States.
| | - Yong-Ho Lee
- Buck Institute for Research on Aging, Novato, California, United States; Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Irene P Chen
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Yini Zhang
- Buck Institute for Research on Aging, Novato, California, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States; Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, United States.
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6
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Taha TY, Suryawanshi RK, Chen IP, Correy GJ, McCavitt-Malvido M, O’Leary PC, Jogalekar MP, Diolaiti ME, Kimmerly GR, Tsou CL, Gascon R, Montano M, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo. PLoS Pathog 2023; 19:e1011614. [PMID: 37651466 PMCID: PMC10499221 DOI: 10.1371/journal.ppat.1011614] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/13/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the role of Mac1 catalytic activity in viral replication, we generated recombinant viruses and replicons encoding a catalytically inactive NSP3 Mac1 domain by mutating a critical asparagine in the active site. While substitution to alanine (N40A) reduced catalytic activity by ~10-fold, mutations to aspartic acid (N40D) reduced activity by ~100-fold relative to wild-type. Importantly, the N40A mutation rendered Mac1 unstable in vitro and lowered expression levels in bacterial and mammalian cells. When incorporated into SARS-CoV-2 molecular clones, the N40D mutant only modestly affected viral fitness in immortalized cell lines, but reduced viral replication in human airway organoids by 10-fold. In mice, the N40D mutant replicated at >1000-fold lower levels compared to the wild-type virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection. Our data validate the critical role of SARS-CoV-2 NSP3 Mac1 catalytic activity in viral replication and as a promising therapeutic target to develop antivirals.
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Affiliation(s)
- Taha Y. Taha
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Rahul K. Suryawanshi
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Irene P. Chen
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Galen J. Correy
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Maria McCavitt-Malvido
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Patrick C. O’Leary
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Manasi P. Jogalekar
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Morgan E. Diolaiti
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Gabriella R. Kimmerly
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Chia-Lin Tsou
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Ronnie Gascon
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Mauricio Montano
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Luis Martinez-Sobrido
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Alan Ashworth
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - James S. Fraser
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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7
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Taha TY, Suryawanshi RK, Chen IP, Correy GJ, O'Leary PC, Jogalekar MP, McCavitt-Malvido M, Diolaiti ME, Kimmerly GR, Tsou CL, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo. bioRxiv 2023:2023.04.18.537104. [PMID: 37131711 PMCID: PMC10153184 DOI: 10.1101/2023.04.18.537104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the therapeutic potential of Mac1 inhibition, we generated recombinant viruses and replicons encoding a catalytically inactive NSP3 Mac1 domain by mutating a critical asparagine in the active site. While substitution to alanine (N40A) reduced catalytic activity by ~10-fold, mutations to aspartic acid (N40D) reduced activity by ~100-fold relative to wildtype. Importantly, the N40A mutation rendered Mac1 unstable in vitro and lowered expression levels in bacterial and mammalian cells. When incorporated into SARS-CoV-2 molecular clones, the N40D mutant only modestly affected viral fitness in immortalized cell lines, but reduced viral replication in human airway organoids by 10-fold. In mice, N40D replicated at >1000-fold lower levels compared to the wildtype virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection and showed no signs of lung pathology. Our data validate the SARS-CoV-2 NSP3 Mac1 domain as a critical viral pathogenesis factor and a promising target to develop antivirals.
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Affiliation(s)
- Taha Y Taha
- Gladstone Institutes, San Francisco, CA 94158
| | | | - Irene P Chen
- Gladstone Institutes, San Francisco, CA 94158
- University of California San Francisco, San Francisco, CA 94158
| | - Galen J Correy
- University of California San Francisco, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
| | | | | | | | | | | | | | | | - Nevan J Krogan
- University of California San Francisco, San Francisco, CA 94158
| | - Alan Ashworth
- University of California San Francisco, San Francisco, CA 94158
| | - James S Fraser
- University of California San Francisco, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158
- University of California San Francisco, San Francisco, CA 94158
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158
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8
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Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Renuka Kumar G, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. Nat Commun 2023; 14:2308. [PMID: 37085489 PMCID: PMC10120482 DOI: 10.1038/s41467-023-37787-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 04/23/2023] Open
Abstract
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (~30 kb). Here, we present a plasmid-based viral genome assembly and rescue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.
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Affiliation(s)
- Taha Y Taha
- Gladstone Institutes, San Francisco, CA, USA.
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | - Hannah S Martin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Stacia Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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9
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Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Kumar GR, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. bioRxiv 2023:2023.01.31.525914. [PMID: 36798416 PMCID: PMC9934579 DOI: 10.1101/2023.01.31.525914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (30kb). Here, we designed a plasmid-based viral genome assembly and resc ue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.
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10
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Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. bioRxiv 2022:2022.12.07.519508. [PMID: 36523400 PMCID: PMC9753784 DOI: 10.1101/2022.12.07.519508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila . Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.
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11
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Abstract
Proteins of the bromodomain and exterminal domain (BET) family mediate critical host functions such as cell proliferation, transcriptional regulation, and the innate immune response, which makes them preferred targets for viruses. These multidomain proteins are best known as transcriptional effectors able to read acetylated histone and non-histone proteins through their tandem bromodomains. They also contain other short motif-binding domains such as the extraterminal domain, which recognizes transcriptional regulatory proteins. Here, we describe how different viruses have evolved to hijack or disrupt host BET protein function through direct interactions with BET family members to support their own propagation. The network of virus-BET interactions emerges as highly intricate, which may complicate the use of small-molecule BET inhibitors-currently in clinical development for the treatment of cancer and cardiovascular diseases-to treat viral infections.
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Affiliation(s)
- Irene P. Chen
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Correspondence:
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12
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Zandian M, Chen IP, Byrareddy SN, Fujimori DG, Ott M, Kutateladze TG. Catching BETs by viruses. Biochim Biophys Acta Gene Regul Mech 2022; 1865:194859. [PMID: 35985635 PMCID: PMC9381978 DOI: 10.1016/j.bbagrm.2022.194859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022]
Abstract
Viruses use diverse tactics to hijack host cellular machineries to evade innate immune responses and maintain their life cycles. Being critical transcriptional regulators, human BET proteins are prominent targets of a growing number of viruses. The BET proteins associate with chromatin through the interaction of their bromodomains with acetylated histones, whereas the carboxy-terminal domains of these proteins contain docking sites for various human co-transcriptional regulators. The same docking sites however can be occupied by viral proteins that exploit the BET proteins to anchor their genome components to chromatin in the infected host cell. In this review we highlight the pathological functions of the BET proteins upon viral infection, focusing on the mechanisms underlying their direct interactions with viral proteins, such as the envelope protein from SARS-CoV-2.
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Affiliation(s)
- Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Irene P Chen
- Gladstone Institutes, and Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Danica Galonić Fujimori
- Quantitative Biosciences Institute, and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Melanie Ott
- Gladstone Institutes, and Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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13
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Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Soveg FW, Gross JD, Krogan NJ, Jerome KR, Schilling B, Ott M, Verdin E. SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein. PLoS Pathog 2022; 18:e1010811. [PMID: 36095012 PMCID: PMC9499238 DOI: 10.1371/journal.ppat.1010811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 09/22/2022] [Accepted: 08/18/2022] [Indexed: 12/27/2022] Open
Abstract
SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response, independently of the Mitochondrial Antiviral Signaling Protein MAVS. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.
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Affiliation(s)
- Marius Walter
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Irene P. Chen
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Albert Vallejo-Gracia
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Olga Bielska
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Victor L. Lam
- University of California San Francisco, San Francisco, California, United States of America
| | - Jennifer M. Hayashi
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Andrew Cruz
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Frank W. Soveg
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - John D. Gross
- University of California San Francisco, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, United States of America
| | - Nevan J. Krogan
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, United States of America
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States of America
- University of California San Francisco, San Francisco, California, United States of America
- QBI COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, United States of America
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14
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Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Gascon R, Tsou CL, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Morris MK, Wadford D, Hanson C, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna JA, Ott M. Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination. Nature 2022; 607:351-355. [PMID: 35584773 PMCID: PMC9279157 DOI: 10.1038/s41586-022-04865-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [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: 01/13/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
SARS-CoV-2 Delta and Omicron are globally relevant variants of concern. Although individuals infected with Delta are at risk of developing severe lung disease, infection with Omicron often causes milder symptoms, especially in vaccinated individuals1,2. The question arises of whether widespread Omicron infections could lead to future cross-variant protection, accelerating the end of the pandemic. Here we show that without vaccination, infection with Omicron induces a limited humoral immune response in mice and humans. Sera from mice overexpressing the human ACE2 receptor and infected with Omicron neutralize only Omicron, but not other variants of concern, whereas broader cross-variant neutralization was observed after WA1 and Delta infections. Unlike WA1 and Delta, Omicron replicates to low levels in the lungs and brains of infected animals, leading to mild disease with reduced expression of pro-inflammatory cytokines and diminished activation of lung-resident T cells. Sera from individuals who were unvaccinated and infected with Omicron show the same limited neutralization of only Omicron itself. By contrast, Omicron breakthrough infections induce overall higher neutralization titres against all variants of concern. Our results demonstrate that Omicron infection enhances pre-existing immunity elicited by vaccines but, on its own, may not confer broad protection against non-Omicron variants in unvaccinated individuals.
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Affiliation(s)
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
| | - Tongcui Ma
- Gladstone Institutes, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Camille R Simoneau
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Pei-Yi Chen
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Mauricio Montano
- Gladstone Institutes, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
| | | | | | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amelia Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Noah Kojima
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | | | - Ashley F George
- Gladstone Institutes, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaohui Fang
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Anesthesia, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Mazharul Maishan
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Anesthesia, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Matthay
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Anesthesia, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | | | - Debra Wadford
- California Department of Public Health, Richmond, CA, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA, USA
| | - Warner C Greene
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Nadia R Roan
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
| | - Charles Y Chiu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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15
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Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Khalid MM, Taha TY, Tabata T, Hayashi JM, Soveg FW, Carlson-Stevermer J, Gupta M, Zhang MY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Fujimori DG, Ott M. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. Cell Rep 2022; 40:111088. [PMID: 35839775 PMCID: PMC9234021 DOI: 10.1016/j.celrep.2022.111088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/27/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
Inhibitors of bromodomain and extraterminal domain (BET) proteins are possible anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here we show that BET proteins should not be inactivated therapeutically because they are critical antiviral factors at the post-entry level. Depletion of BRD3 or BRD4 in cells overexpressing ACE2 exacerbates SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible “histone mimetic.” E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
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Affiliation(s)
- Irene P Chen
- Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA
| | - James E Longbotham
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Mir M Khalid
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Taha Y Taha
- Gladstone Institutes, San Francisco, CA 94158, USA
| | | | | | | | | | - Meghna Gupta
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Meng Yao Zhang
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Victor L Lam
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yang Li
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zanlin Yu
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erron W Titus
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amy Diallo
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer Oki
- Synthego Corporation, 3696 Haven Avenue, Suite A, Menlo Park, CA 94063, USA
| | - Kevin Holden
- Synthego Corporation, 3696 Haven Avenue, Suite A, Menlo Park, CA 94063, USA
| | - Nevan Krogan
- Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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16
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Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna J, Ott M. Limited Cross-Variant Immunity after Infection with the SARS-CoV-2 Omicron Variant Without Vaccination. medRxiv 2022. [PMID: 35075459 DOI: 10.1101/2022.01.13.22269243] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
SARS-CoV-2 Delta and Omicron strains are the most globally relevant variants of concern (VOCs). While individuals infected with Delta are at risk to develop severe lung disease 1 , Omicron infection causes less severe disease, mostly upper respiratory symptoms 2,3 . The question arises whether rampant spread of Omicron could lead to mass immunization, accelerating the end of the pandemic. Here we show that infection with Delta, but not Omicron, induces broad immunity in mice. While sera from Omicron-infected mice only neutralize Omicron, sera from Delta-infected mice are broadly effective against Delta and other VOCs, including Omicron. This is not observed with the WA1 ancestral strain, although both WA1 and Delta elicited a highly pro-inflammatory cytokine response and replicated to similar titers in the respiratory tracts and lungs of infected mice as well as in human airway organoids. Pulmonary viral replication, pro-inflammatory cytokine expression, and overall disease progression are markedly reduced with Omicron infection. Analysis of human sera from Omicron and Delta breakthrough cases reveals effective cross-variant neutralization induced by both viruses in vaccinated individuals. Together, our results indicate that Omicron infection enhances preexisting immunity elicited by vaccines, but on its own may not induce broad, cross-neutralizing humoral immunity in unvaccinated individuals.
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17
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Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Gross JD, Krogan NJ, Schilling B, Ott M, Verdin E. SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein. bioRxiv 2022:2022.01.04.474979. [PMID: 35018374 PMCID: PMC8750649 DOI: 10.1101/2022.01.04.474979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 stably interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.
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Affiliation(s)
- Marius Walter
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Albert Vallejo-Gracia
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Olga Bielska
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Victor L Lam
- University of California San Francisco, San Francisco, CA, United States
| | - Jennifer M Hayashi
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Andrew Cruz
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA, United States
| | - John D Gross
- University of California San Francisco, San Francisco, CA, United States
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, United States
| | - Nevan J Krogan
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, United States
| | | | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, United States
- University of California San Francisco, San Francisco, CA, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, United States
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18
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Syed AM, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Spraggon L, Taha TY, Tabata T, Chen IP, Ott M, Doudna JA. Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles. medRxiv 2022. [PMID: 34981067 PMCID: PMC8722610 DOI: 10.1101/2021.12.20.21268048] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Omicron SARS-CoV-2 virus contains extensive sequence changes relative to the earlier arising B.1, B.1.1 and Delta SARS-CoV-2 variants that have unknown effects on viral infectivity and response to existing vaccines. Using SARS-CoV-2 virus-like particles (SC2-VLPs), we examined mutations in all four structural proteins and found that Omicron showed increased infectivity relative to B.1, B.1.1 and similar to Delta, a property conferred by S and N protein mutations. Thirty-eight antisera samples from individuals vaccinated with tozinameran (Pfizer/BioNTech), elasomeran (Moderna), Johnson & Johnson vaccines and convalescent sera from unvaccinated COVID-19 survivors had moderately to dramatically reduced efficacy to prevent cell transduction by VLPs containing the Omicron mutations. The Pfizer/BioNTech and Moderna vaccine antisera showed strong neutralizing activity against VLPs possessing the ancestral spike protein (B.1, B.1.1), with 3-fold reduced efficacy against Delta and 15-fold lower neutralization against Omicron VLPs. Johnson & Johnson antisera showed minimal neutralization of any of the VLPs tested. Furthermore, the monoclonal antibody therapeutics Casirivimab and Imdevimab had robust neutralization activity against B.1, B.1.1 or Delta VLPs but no detectable neutralization of Omicron VLPs. Our results suggest that Omicron is at least as efficient at assembly and cell entry as Delta, and the antibody response triggered by existing vaccines or previous infection, at least prior to boost, will have limited ability to neutralize Omicron. In addition, some currently available monoclonal antibodies will not be useful in treating Omicron-infected patients.
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19
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Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science 2021; 374:1626-1632. [PMID: 34735219 PMCID: PMC9005165 DOI: 10.1126/science.abl6184] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023]
Abstract
Efforts to determine why new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants demonstrate improved fitness have been limited to analyzing mutations in the spike (S) protein with the use of S-pseudotyped particles. In this study, we show that SARS-CoV-2 virus-like particles (SC2-VLPs) can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and at multiple steps in the viral life cycle. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202→arginine (S202R) and arginine-203→methionine (R203M) mutations each produced >50 times as much virus. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation).
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Affiliation(s)
- Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Taha Y. Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Takako Tabata
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Irene P. Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Alison Ciling
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Mir M. Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Katarzyna M. Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Melanie Ott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, CA, USA
| | - Jennifer A. Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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20
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Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Carlson-Stevermer J, Gupta M, Zhang MY, Soveg FW, Hayashi JM, Taha TY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Galonić Fujimori D, Ott M. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. bioRxiv 2021. [PMID: 34816261 DOI: 10.1101/2021.11.14.468537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Inhibitors of Bromodomain and Extra-terminal domain (BET) proteins are possible anti-SARS-CoV-2 prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here, we show that BET proteins should not be inactivated therapeutically as they are critical antiviral factors at the post-entry level. Knockouts of BRD3 or BRD4 in cells overexpressing ACE2 exacerbate SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection, and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible "histone mimetic." E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
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21
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Vallejo-Gracia A, Chen IP, Perrone R, Besnard E, Boehm D, Battivelli E, Tezil T, Krey K, Raymond KA, Hull PA, Walter M, Habrylo I, Cruz A, Deeks S, Pillai S, Verdin E, Ott M. FOXO1 promotes HIV latency by suppressing ER stress in T cells. Nat Microbiol 2020; 5:1144-1157. [PMID: 32541947 PMCID: PMC7483895 DOI: 10.1038/s41564-020-0742-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/15/2020] [Indexed: 01/13/2023]
Abstract
Quiescence is a hallmark of CD4+ T cells latently infected with human immunodeficiency virus 1 (HIV-1). While reversing this quiescence is an effective approach to reactivate latent HIV from T cells in culture, it can cause deleterious cytokine dysregulation in patients. As a key regulator of T-cell quiescence, FOXO1 promotes latency and suppresses productive HIV infection. We report that, in resting T cells, FOXO1 inhibition impaired autophagy and induced endoplasmic reticulum (ER) stress, thereby activating two associated transcription factors: activating transcription factor 4 (ATF4) and nuclear factor of activated T cells (NFAT). Both factors associate with HIV chromatin and are necessary for HIV reactivation. Indeed, inhibition of protein kinase R-like ER kinase, an ER stress sensor that can mediate the induction of ATF4, and calcineurin, a calcium-dependent regulator of NFAT, synergistically suppressed HIV reactivation induced by FOXO1 inhibition. Thus, our studies uncover a link of FOXO1, ER stress and HIV infection that could be therapeutically exploited to selectively reverse T-cell quiescence and reduce the size of the latent viral reservoir.
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Affiliation(s)
- Albert Vallejo-Gracia
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, USA
- University of California San Francisco, San Francisco, CA, USA
| | - Irene P Chen
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, USA
- University of California San Francisco, San Francisco, CA, USA
| | | | - Emilie Besnard
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Daniela Boehm
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, USA
- University of California San Francisco, San Francisco, CA, USA
| | | | - Tugsan Tezil
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Karsten Krey
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, USA
- Ludwig Maximilian University, Munich, Germany
| | | | - Philip A Hull
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, USA
| | - Marius Walter
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Ireneusz Habrylo
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, USA
- University of California San Francisco, San Francisco, CA, USA
| | - Andrew Cruz
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Steven Deeks
- University of California San Francisco, San Francisco, CA, USA
| | - Satish Pillai
- University of California San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Eric Verdin
- University of California San Francisco, San Francisco, CA, USA
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, USA.
- University of California San Francisco, San Francisco, CA, USA.
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22
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Pérez R, Cuadrado A, Chen IP, Puchta H, Jouve N, De Bustos A. The Rad50 genes of diploid and polyploid wheat species. Analysis of homologue and homoeologue expression and interactions with Mre11. Theor Appl Genet 2011; 122:251-262. [PMID: 20827456 DOI: 10.1007/s00122-010-1440-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 08/25/2010] [Indexed: 05/29/2023]
Abstract
The MRN complex plays a central role in the DNA repair pathways of eukaryotic cells and takes part in many other processes, including cell cycle checkpoint signalling, meiosis, DNA replication and telomere maintenance. This complex is formed by the interaction of the products of the Mre11, Rad50 and Nbs1 genes. This paper reports the molecular characterization, expression and interactions of the Rad50 gene in several wheat species with different levels of ploidy. The homoeologous Rad50 wheat genes were found to show a high level of conservation. Most of the RAD50 domains and motifs previously described in other species were also present in wheat RAD50; these proteins are therefore likely to have similar functions. Interactions between the RAD50 wheat proteins and their MRE11 counterparts in the MRN complex were observed. The level of expression of Rad50 in each of the species examined was determined and compared with those previously reported for the Mre11 genes. In some cases similar levels of expression were seen, as expected. The expression of the RAD50 homoeologous genes was assessed in two polyploid wheat species using quantitative PCR. In both cases, an overexpression of the Rad50B gene was detected. Although the results indicate the maintenance of function of these species' three homoeologous Rad50 genes, the biased expression of Rad50B might indicate ongoing silencing of one or both other homoeologues in polyploid wheat. To assess the consequences of such silencing on the formation of the MRN complex, the interactions between individual homoeologues of Rad50 and their genomic counterpart Mre11 genes were examined. The results indicate the inexistence of genomic specificity in the interactions between these genes. This would guarantee the formation of an MRN complex in wheat.
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Affiliation(s)
- R Pérez
- Department of Cell Biology and Genetics, University of Alcalá, Alcalá de Henares, Spain
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23
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Chen IP, Mathis P, Koepke J, Michel H. Uphill electron transfer in the tetraheme cytochrome subunit of the Rhodopseudomonas viridis photosynthetic reaction center: evidence from site-directed mutagenesis. Biochemistry 2000; 39:3592-602. [PMID: 10736158 DOI: 10.1021/bi992443p] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cytochrome (cyt) subunit of the photosynthetic reaction center from Rhodopseudomonas viridis contains four heme groups in a linear arrangement in the spatial order heme1, heme2, heme4, and heme3. Heme3 is the direct electron donor to the photooxidized primary electron donor (special pair, P(+)). This heme has the highest redox potential (E(m)) among the hemes in the cyt subunit. The E(m) of heme3 has been specifically lowered by site-directed mutagenesis in which the Arg residue at the position of 264 of the cyt was replaced by Lys. The mutation decreases the E(m) of heme3 from +380 to +270 mV, i.e., below that of heme2 (+320 mV). In addition, a blue shift of the alpha-band was found to accompany the mutation. The assignment of the lowered E(m) and the shifted alpha-band to heme3 was confirmed by spectroscopic measurements on RC crystals. The structure of the mutant RC has been determined by X-ray crystallography. No remarkable differences were found in the structure apart from the mutated residue itself. The velocity of the electron transfer (ET) from the tetraheme cyt to P(+) was measured under several redox conditions by following the rereduction of P(+) at 1283 nm after a laser flash. Heme3 donates an electron to P(+) with t(1/2) = 105 ns, i.e., faster than in the wild-type reaction center (t(1/2) = 190 ns), as expected from the larger driving force. The main feature is that a phase with t(1/2) approximately 2 micros dominates when heme3 is oxidized but heme2 is reduced. We conclude that the ET from heme2 to heme3 has a t(1/2) of approximately 2 micros, i.e., the same as in the WT, despite the fact that the reaction is endergonic by 50 meV instead of exergonic by 60 meV. We propose that the reaction kinetics is limited by the very uphill ET from heme2 to heme4, the DeltaG degrees of which is about the same (+230 meV) in both cases. The interpretation is further supported by measurements of the activation energy (216 meV in the wild-type, 236 meV in the mutant) and by approximate calculations of ET rates. Altogether these results demonstrate that the ET from heme2 to heme3 is stepwise, starting with a first very endergonic step from heme2 to heme4.
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Affiliation(s)
- I P Chen
- Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60528 Frankfurt am Main, Germany
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24
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Abstract
A recombination-deficient strain of the phototrophic bacterium Rhodopseudomonas viridis was constructed for the homologous expression of modified photosynthetic reaction center genes. The R. viridis recA gene was cloned and subsequently deleted from the R. viridis genome. The cloned R. viridis recA gene shows high identity to known recA genes and was able to complement the Rec- phenotype of a Rhizobium meliloti recA strain. The constructed R. viridis recA strain showed the general Rec- phenotype, i.e., increased sensitivity to DNA damage and severely impaired recombination ability. The latter property of this strain will be of advantage in particular for expression of modified, nonfunctional photosynthetic reaction centers which are not as yet available.
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Affiliation(s)
- I P Chen
- Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany
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25
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Abstract
Distracting attention away from the location of an adaptation figure reduces the positional shift of a displaced test figure in the figural aftereffect (FAE). Participants performed an alignment task after adaptation involving various manipulations of spatial attention. In 1 condition, participants counted how often numbers occurred in an alphanumeric sequence presented during adaptation. (The sequence also appeared in a comparison condition, but no attention was required.) The FAE was reduced when the alphanumeric sequence attended to was in the center of the display while the adaptation figure was 3 degrees eccentric but not when the pattern was superimposed on the adaptation figure. Forced attention to 1 feature of the adaptation figure, its orientation, did not reduce the FAE (Experiment 3). To obtain a maximum FAE, the span of attention must cover the adaptation figure.
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Affiliation(s)
- S L Yeh
- Department of Psychology, University of California, Berkeley 94720, USA
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26
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Abstract
Distracting attention away from the location of an adaptation figure reduces the positional shift of a displaced test figure in the figural aftereffect (FAE). Participants performed an alignment task after adaptation involving various manipulations of spatial attention. In 1 condition, participants counted how often numbers occurred in an alphanumeric sequence presented during adaptation. (The sequence also appeared in a comparison condition, but no attention was required.) The FAE was reduced when the alphanumeric sequence attended to was in the center of the display while the adaptation figure was 3 degrees eccentric but not when the pattern was superimposed on the adaptation figure. Forced attention to 1 feature of the adaptation figure, its orientation, did not reduce the FAE (Experiment 3). To obtain a maximum FAE, the span of attention must cover the adaptation figure.
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Affiliation(s)
- S L Yeh
- Department of Psychology, University of California, Berkeley 94720, USA
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