Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors

Katherine Chan; Adrian Granda Farias; Hunsang Lee; Furkan Guvenc; Patricia Mero; Kevin R Brown; Henry Ward; Maximilian Billmann; Kamaldeep Aulakh; Audrey Astori; Shahan Haider; Edyta Marcon; Ulrich Braunschweig; Shuye Pu; Andrea Habsid; Amy Hin Yan Tong; Natasha Christie-Holmes; Patrick Budylowski; Ayoob Ghalami; Samira Mubareka; Finlay Maguire; Arinjay Banerjee; Karen L Mossman; Jack Greenblatt; Scott D Gray-Owen; Brian Raught; Benjamin J Blencowe; Mikko Taipale; Chad Myers; Jason Moffat

doi:10.1016/j.heliyon.2022.e12744

Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors

Heliyon. 2023 Jan;9(1):e12744. doi: 10.1016/j.heliyon.2022.e12744. Epub 2022 Dec 30.

Authors

Katherine Chan¹, Adrian Granda Farias^{1

2}, Hunsang Lee¹, Furkan Guvenc², Patricia Mero¹, Kevin R Brown¹, Henry Ward³, Maximilian Billmann³, Kamaldeep Aulakh¹, Audrey Astori⁴, Shahan Haider¹, Edyta Marcon¹, Ulrich Braunschweig¹, Shuye Pu¹, Andrea Habsid¹, Amy Hin Yan Tong¹, Natasha Christie-Holmes⁵, Patrick Budylowski², Ayoob Ghalami⁶, Samira Mubareka^{7

8}, Finlay Maguire^{9

10}, Arinjay Banerjee¹¹, Karen L Mossman¹², Jack Greenblatt^{1

2}, Scott D Gray-Owen², Brian Raught⁴, Benjamin J Blencowe^{1

2}, Mikko Taipale^{1

2}, Chad Myers³, Jason Moffat^{1

2

13}

Affiliations

¹ Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1.
² Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8.
³ Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
⁴ Princess Margaret Cancer Center, Toronto, Ontario, Canada.
⁵ Combined Containment Level 3 Unit, Temerty Faculty of Medicine, University of Toronto Toronto, Ontario, Canada, M5S3E1.
⁶ Office of Environmental Health & Safety, University of Toronto, Toronto, Ontario, Canada.
⁷ Sunnybrook Research Institute, Toronto, Ontario, Canada, M5S3E1.
⁸ Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada.
⁹ Department of Community Health and Epidemiology, Faculty of Medicine Dalhousie University, Halifax, Nova Scotia, Canada.
¹⁰ Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.
¹¹ Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
¹² Department of Medicine, McMaster University, Hamilton, Ontario, Canada.
¹³ Institute for Biomedical Engineering, Rosebrugh Building, 164 College Street, Room 407, University of Toronto, Toronto, Ontario, Canada, M5S3G9.

Abstract

SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection and replication. If druggable, host factor dependencies may present an attractive strategy for anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens in Vero E6 cells and four human cell lines including Calu-3, UM-UC-4, HEK-293 and HuH-7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while other host genes identified were largely cell line specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, immune-related pathways, and chromatin modification. Notably, the chromatin modifier gene KMT2C in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed.

Keywords: ACE2; CRISPR screens; Genome-wide loss-of-function; Host factors; SARS-CoV-2.