CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions.
CRISPR/Cas9 has emerged as a powerful new tool to systematically probe gene function. We compared the performance of CRISPR to RNAi-based loss-of-function screens for the identification of cancer dependencies across multiple cancer cell lines. CRISPR dropout screens consistently identified more lethal genes than RNAi, implying that the identification of many cellular dependencies may require full gene inactivation. However, in two aneuploid cancer models, we found that all genes within highly amplified regions, including nonexpressed genes, scored as lethal by CRISPR, revealing an unanticipated class of false-positive hits. In addition, using a CRISPR tiling screen, we found that sgRNAs targeting essential domains generate the strongest lethality phenotypes and thus provide a strategy to rapidly define the protein domains required for cancer dependence. Collectively, these findings not only demonstrate the utility of CRISPR screens in the identification of cancer-essential genes, but also reveal the need to carefully control for false-positive results in chromosomally unstable cancer lines.



We show in this study that CRISPR-based screens have a significantly lower false-negative rate compared with RNAi-based screens, but have specific liabilities particularly in the interrogation of regions of genome amplification. Therefore, this study provides critical insights for applying CRISPR-based screens toward the systematic identification of new cancer targets. Cancer Discov; 6(8); 900-13. ©2016 AACR.See related commentary by Sheel and Xue, p. 824See related article by Aguirre et al., p. 914This article is highlighted in the In This Issue feature, p. 803.
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Diana M
DM
Munoz
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Pamela J
PJ
Cassiani
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Li
L
Li
Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Eric
E
Billy
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Joshua M
JM
Korn
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Michael D
MD
Jones
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Javad
J
Golji
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
David A
DA
Ruddy
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Kristine
K
Yu
Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Gregory
G
McAllister
Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Antoine
A
DeWeck
Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Dorothee
D
Abramowski
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Jessica
J
Wan
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Matthew D
MD
Shirley
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Sarah Y
SY
Neshat
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Daniel
D
Rakiec
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Rosalie
R
de Beaumont
Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Odile
O
Weber
Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Audrey
A
Kauffmann
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
E Robert
ER
McDonald
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Nicholas
N
Keen
Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Francesco
F
Hofmann
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
William R
WR
Sellers
Oncology Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Tobias
T
Schmelzle
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
Frank
F
Stegmeier
Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts. mschlabach@ksqtx.com.
Michael R
MR
Schlabach
D064113:CRISPR-Cas Systems; D045744:Cell Line, Tumor; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D005784:Gene Amplification; D056726:Genetic Association Studies; D015894:Genome, Human; D023281:Genomics / Q000379:methods / Q000592:standards; D057166:High-Throughput Screening Assays; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D000094704:RNA, Guide, CRISPR-Cas Systems / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D015203:Reproducibility of Results
D000094704:RNA, Guide, CRISPR-Cas Systems; D034741:RNA, Small Interfering