title: High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.
abstract: The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context-dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada.
authors.forename: Traver
authors.initials: T
authors.lastname: Hart
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada.
authors.forename: Megha
authors.initials: M
authors.lastname: Chandrashekhar
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Aregger
authors.affiliation: Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada.
authors.forename: Zachary
authors.initials: Z
authors.lastname: Steinhart
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada.
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Brown
authors.affiliation: Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada.
authors.forename: Graham
authors.initials: G
authors.lastname: MacLeod
authors.affiliation: Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada.
authors.forename: Monika
authors.initials: M
authors.lastname: Mis
authors.affiliation: The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada.
authors.forename: Michal
authors.initials: M
authors.lastname: Zimmermann
authors.affiliation: The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada.
authors.forename: Amelie
authors.initials: A
authors.lastname: Fradet-Turcotte
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE-75123, Sweden; Department of Computer Science, University of Toronto, Toronto, ON M5G1X8, Canada.
authors.forename: Song
authors.initials: S
authors.lastname: Sun
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada.
authors.forename: Patricia
authors.initials: P
authors.lastname: Mero
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Program in Developmental and Stem Cell Biology, Division of Neurosurgery, Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G1X8, Canada.
authors.forename: Peter
authors.initials: P
authors.lastname: Dirks
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada.
authors.forename: Sachdev
authors.initials: S
authors.lastname: Sidhu
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5G1X8, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada; Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors.forename: Frederick P
authors.initials: FP
authors.lastname: Roth
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G0A4, Canada.
authors.forename: Olivia S
authors.initials: OS
authors.lastname: Rissland
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada.
authors.forename: Daniel
authors.initials: D
authors.lastname: Durocher
authors.affiliation: Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S1A1, Canada.
authors.forename: Stephane
authors.initials: S
authors.lastname: Angers
authors.affiliation: Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G1Z8, Canada. Electronic address: j.moffat@utoronto.ca.
authors.forename: Jason
authors.initials: J
authors.lastname: Moffat
mesh_terms: D001499:Bayes Theorem; D064113:CRISPR-Cas Systems; D045744:Cell Line, Tumor; D055786:Gene Knockout Techniques; D015723:Gene Library; D020043:Genes, Essential; D006801:Humans; D009154:Mutation