Heliyon (Jan 2023)
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
Affiliations
- Katherine Chan
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1; Corresponding author.
- Adrian Granda Farias
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1; Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
- Hunsang Lee
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Furkan Guvenc
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
- Patricia Mero
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Kevin R. Brown
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Henry Ward
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Kamaldeep Aulakh
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Audrey Astori
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
- Shahan Haider
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Edyta Marcon
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Ulrich Braunschweig
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Shuye Pu
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Andrea Habsid
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Amy Hin Yan Tong
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1
- Natasha Christie-Holmes
- Combined Containment Level 3 Unit, Temerty Faculty of Medicine, University of Toronto Toronto, Ontario, Canada, M5S3E1
- Patrick Budylowski
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
- Ayoob Ghalami
- Office of Environmental Health & Safety, University of Toronto, Toronto, Ontario, Canada
- Samira Mubareka
- Sunnybrook Research Institute, Toronto, Ontario, Canada, M5S3E1; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
- Finlay Maguire
- Department of Community Health and Epidemiology, Faculty of Medicine Dalhousie University, Halifax, Nova Scotia, Canada; Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
- Arinjay Banerjee
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Karen L. Mossman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Jack Greenblatt
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1; Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
- Scott D. Gray-Owen
- Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
- Brian Raught
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
- Benjamin J. Blencowe
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1; Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
- Mikko Taipale
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1; Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8
- Chad Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Jason Moffat
- Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1; Department of Molecular Genetics, 1 King's College Circle, University of Toronto, Toronto, Ontario, Canada, M5S1A8; Institute for Biomedical Engineering, Rosebrugh Building, 164 College Street, Room 407, University of Toronto, Toronto, Ontario, Canada, M5S3G9; Corresponding author. Donnelly Center, 160 College Street, University of Toronto, Toronto, Ontario, Canada, M5S3E1.
- Journal volume & issue
-
Vol. 9,
no. 1
p. e12744
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.
