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Cell
01 07, 2021;184 (1): 76-91.e13.

Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection.

Jin Wei, Mia Madel Alfajaro, Peter C DeWeirdt, Ruth E Hanna, William J Lu-Culligan, Wesley L Cai, Madison S Strine, Shang-Min Zhang, Vincent R Graziano, Cameron O Schmitz, Jennifer S Chen, Madeleine C Mankowski, Renata B Filler, Neal G Ravindra, Victor Gasque, Fernando J de Miguel, Ajinkya Patil, Huacui Chen, Kasopefoluwa Y Oguntuyo, Laura Abriola, Yulia V Surovtseva, Robert C Orchard, Benhur Lee, Brett D Lindenbach, Katerina Politi, David van Dijk, Cigall Kadoch, Matthew D Simon, Qin Yan, John G Doench, Craig B Wilen
Author Information
  1. Jin Wei: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
  2. Mia Madel Alfajaro: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
  3. Peter C DeWeirdt: Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  4. Ruth E Hanna: Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  5. William J Lu-Culligan: Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
  6. Wesley L Cai: Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
  7. Madison S Strine: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
  8. Shang-Min Zhang: Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
  9. Vincent R Graziano: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
  10. Cameron O Schmitz: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
  11. Jennifer S Chen: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
  12. Madeleine C Mankowski: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
  13. Renata B Filler: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA.
  14. Neal G Ravindra: Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA.
  15. Victor Gasque: Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA.
  16. Fernando J de Miguel: Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
  17. Ajinkya Patil: Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  18. Huacui Chen: Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
  19. Kasopefoluwa Y Oguntuyo: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
  20. Laura Abriola: Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA.
  21. Yulia V Surovtseva: Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA.
  22. Robert C Orchard: Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
  23. Benhur Lee: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
  24. Brett D Lindenbach: Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA.
  25. Katerina Politi: Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA.
  26. David van Dijk: Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA.
  27. Cigall Kadoch: Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  28. Matthew D Simon: Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
  29. Qin Yan: Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
  30. John G Doench: Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: jdoench@broadinstitute.org.
  31. Craig B Wilen: Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA. Electronic address: craig.wilen@yale.edu.
PMID: 33147444 DOI: 10.1016/j.cell.2020.10.028

Abstract

Identification of host genes essential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may reveal novel therapeutic targets and inform our understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), bat CoV HKU5 expressing the SARS-CoV-1 spike, and vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike. We identified known SARS-CoV-2 host factors, including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways, including HMGB1 and the SWI/SNF chromatin remodeling complex, that are SARS lineage and pan-coronavirus specific, respectively. We show that HMGB1 regulates ACE2 expression and is critical for entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small-molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. This identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS lineage-specific and pan-CoV host factors that regulate susceptibility to highly pathogenic CoVs.

Keywords

COVID-19 CRISPR screen Epigenetics HMGB1 MERS-CoV Middle East Respiratory Syndrome SARS-CoV-2 SWI/SNF complex Severe Acute Respiratory Syndrome

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Grants

  1. R01 AI123449/NIAID NIH HHS
  2. T32 AI007019/NIAID NIH HHS
  3. T32 GM007223/NIGMS NIH HHS
  4. UL1 TR001863/NCATS NIH HHS
  5. F30 HL149151/NHLBI NIH HHS
  6. R01 AI148467/NIAID NIH HHS
  7. R21 AI157835/NIAID NIH HHS
  8. T32 GM007205/NIGMS NIH HHS
  9. F31 AI54739/NIAID NIH HHS
  10. P50 CA121974/NCI NIH HHS
  11. K08 AI128043/NIAID NIH HHS
  12. R01 AI087925/NIAID NIH HHS
  13. F31 DA054739/NIDA NIH HHS
  14. U19 AI133524/NIAID NIH HHS
  15. T32 CA193200/NCI NIH HHS
  16. R00 DK116666/NIDDK NIH HHS
  17. F31 AI154739/NIAID NIH HHS
  18. P50 CA196530/NCI NIH HHS

MeSH Term

Angiotensin-Converting Enzyme 2
Animals
COVID-19
Cell Line
Chlorocebus aethiops
Clustered Regularly Interspaced Short Palindromic Repeats
Coronavirus
Coronavirus Infections
Gene Knockout Techniques
Gene Regulatory Networks
Genome-Wide Association Study
HEK293 Cells
HMGB1 Protein
Host-Pathogen Interactions
Humans
SARS-CoV-2
Vero Cells
Virus Internalization

Chemicals

HMGB1 Protein
Angiotensin-Converting Enzyme 2
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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