High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

Traver Hart; Megha Chandrashekhar; Michael Aregger; Zachary Steinhart; Kevin R Brown; Graham MacLeod; Monika Mis; Michal Zimmermann; Amelie Fradet-Turcotte; Song Sun; Patricia Mero; Peter Dirks; Sachdev Sidhu; Frederick P Roth; Olivia S Rissland; Daniel Durocher; Stephane Angers; Jason Moffat

doi:10.1016/j.cell.2015.11.015

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

Cell. 2015 Dec 3;163(6):1515-26. doi: 10.1016/j.cell.2015.11.015. Epub 2015 Nov 25.

Authors

Traver Hart¹, Megha Chandrashekhar², Michael Aregger¹, Zachary Steinhart³, Kevin R Brown¹, Graham MacLeod³, Monika Mis³, Michal Zimmermann⁴, Amelie Fradet-Turcotte⁴, Song Sun⁵, Patricia Mero¹, Peter Dirks⁶, Sachdev Sidhu², Frederick P Roth⁷, Olivia S Rissland⁸, Daniel Durocher⁹, Stephane Angers¹⁰, Jason Moffat¹¹

Affiliations

¹ Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada.
² Donnelly Centre, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada.
³ Department of Pharmaceutical Sciences and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S1A1, Canada.
⁴ The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada.
⁵ 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.
⁶ 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.
⁷ 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.
⁸ 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.
⁹ Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G1X5, Canada.
¹⁰ 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.
¹¹ 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.

PMID: 26627737
DOI: 10.1016/j.cell.2015.11.015

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bayes Theorem
CRISPR-Cas Systems
Cell Line, Tumor
Gene Knockout Techniques
Gene Library
Genes, Essential*
Humans
Mutation

Associated data

GEO/GSE75189

Grants and funding

CIHR-342551/Canadian Institutes of Health Research/Canada