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Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

View ORCID ProfileRyan A. Flynn, Julia A. Belk, Yanyan Qi, Yuki Yasumoto, Cameron O. Schmitz, Maxwell R. Mumbach, Aditi Limaye, Jin Wei, Mia Madel Alfajaro, Kevin R. Parker, Howard Y. Chang, Tamas L. Horvath, Jan E. Carette, Carolyn Bertozzi, Craig B. Wilen, View ORCID ProfileAnsuman T. Satpathy
doi: https://doi.org/10.1101/2020.10.06.327445
Ryan A. Flynn
1Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA
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  • ORCID record for Ryan A. Flynn
  • For correspondence: raflynn@stanford.edu craig.wilen@yale.edu satpathy@stanford.edu
Julia A. Belk
2Department of Computer Science, Stanford University, Stanford, CA
3Department of Pathology, Stanford University, Stanford, CA
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Yanyan Qi
3Department of Pathology, Stanford University, Stanford, CA
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Yuki Yasumoto
4Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT
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Cameron O. Schmitz
5Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
6Department of Immunobiology, Yale School of Medicine, New Haven, CT
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Maxwell R. Mumbach
7Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
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Aditi Limaye
3Department of Pathology, Stanford University, Stanford, CA
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Jin Wei
5Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
6Department of Immunobiology, Yale School of Medicine, New Haven, CT
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Mia Madel Alfajaro
5Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
6Department of Immunobiology, Yale School of Medicine, New Haven, CT
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Kevin R. Parker
7Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
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Howard Y. Chang
7Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
8Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
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Tamas L. Horvath
4Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT
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Jan E. Carette
9Department of Microbiology and Immunology, Stanford University, Stanford, CA
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Carolyn Bertozzi
1Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA
8Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
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Craig B. Wilen
5Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
6Department of Immunobiology, Yale School of Medicine, New Haven, CT
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  • For correspondence: raflynn@stanford.edu craig.wilen@yale.edu satpathy@stanford.edu
Ansuman T. Satpathy
3Department of Pathology, Stanford University, Stanford, CA
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  • ORCID record for Ansuman T. Satpathy
  • For correspondence: raflynn@stanford.edu craig.wilen@yale.edu satpathy@stanford.edu
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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a pandemic with growing global mortality. There is an urgent need to understand the molecular pathways required for host infection and anti-viral immunity. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with viral ChIRP-MS data from three other positive-sense RNA viruses defined pan-viral and SARS-CoV-2-specific host interactions. Functional interrogation of these factors with a genome-wide CRISPR screen revealed that the vast majority of viral RNA-binding proteins protect the host from virus-induced cell death, and we identified known and novel anti-viral proteins that regulate SARS-CoV-2 pathogenicity. Finally, our RNA-centric approach demonstrated a physical connection between SARS-CoV-2 RNA and host mitochondria, which we validated with functional and electron microscopy data, providing new insights into a more general virus-specific protein logic for mitochondrial interactions. Altogether, these data provide a comprehensive catalogue of SARS-CoV-2 RNA-host protein interactions, which may inform future studies to understand the mechanisms of viral pathogenesis, as well as nominate host pathways that could be targeted for therapeutic benefit.

Highlights

  • · ChIRP-MS of SARS-CoV-2 RNA identifies a comprehensive viral RNA-host protein interaction network during infection across two species

  • · Comparison to RNA-protein interaction networks with Zika virus, dengue virus, and rhinovirus identify SARS-CoV-2-specific and pan-viral RNA protein complexes and highlights distinct intracellular trafficking pathways

  • · Intersection of ChIRP-MS and genome-wide CRISPR screens identify novel SARS-CoV-2-binding proteins with pro- and anti-viral function

  • · Viral RNA-RNA and RNA-protein interactions reveal specific SARS-CoV-2-mediated mitochondrial dysfunction during infection

Competing Interest Statement

K.R.P., H.Y.C., and A.T.S. are co-founders of Cartography Biosciences. A.T.S. is a co-founder of Immunai and receives research funding from Arsenal Biosciences, Sonoma Biotherapeutics, and Allogene Therapeutics. H.Y.C. is a co-founder of Accent Therapeutics, Boundless Bio, and an advisor for 10x Genomics, Arsenal Biosciences, and Spring Discovery. Yale University (C.B.W.) has a patent pending related to this work entitled: Compounds and Compositions for Treating, Ameliorating, and/or Preventing SARS-CoV-2 Infection and/or Complications Thereof. Yale University has committed to rapidly executable non-exclusive royalty-free licenses to intellectual property rights for the purpose of making and distributing products to prevent, diagnose and treat COVID-19 infection during the pandemic and for a short period thereafter.

Footnotes

  • Lead Contact: raflynn{at}stanford.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection
Ryan A. Flynn, Julia A. Belk, Yanyan Qi, Yuki Yasumoto, Cameron O. Schmitz, Maxwell R. Mumbach, Aditi Limaye, Jin Wei, Mia Madel Alfajaro, Kevin R. Parker, Howard Y. Chang, Tamas L. Horvath, Jan E. Carette, Carolyn Bertozzi, Craig B. Wilen, Ansuman T. Satpathy
bioRxiv 2020.10.06.327445; doi: https://doi.org/10.1101/2020.10.06.327445
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Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection
Ryan A. Flynn, Julia A. Belk, Yanyan Qi, Yuki Yasumoto, Cameron O. Schmitz, Maxwell R. Mumbach, Aditi Limaye, Jin Wei, Mia Madel Alfajaro, Kevin R. Parker, Howard Y. Chang, Tamas L. Horvath, Jan E. Carette, Carolyn Bertozzi, Craig B. Wilen, Ansuman T. Satpathy
bioRxiv 2020.10.06.327445; doi: https://doi.org/10.1101/2020.10.06.327445

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