RRC ID 64989
Author Munoz DM, Cassiani PJ, Li L, Billy E, Korn JM, Jones MD, Golji J, Ruddy DA, Yu K, McAllister G, DeWeck A, Abramowski D, Wan J, Shirley MD, Neshat SY, Rakiec D, de Beaumont R, Weber O, Kauffmann A, McDonald ER 3rd, Keen N, Hofmann F, Sellers WR, Schmelzle T, Stegmeier F, Schlabach MR.
Title CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions.
Journal Cancer Discov
Abstract UNLABELLED: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.
SIGNIFICANCE: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.
Volume 6(8)
Pages 900-13
Published 2016-8-1
DOI 10.1158/2159-8290.CD-16-0178
PII 2159-8290.CD-16-0178
PMID 27260157
MeSH CRISPR-Cas Systems* Cell Line, Tumor Clustered Regularly Interspaced Short Palindromic Repeats* Gene Amplification* Genetic Association Studies Genome, Human* Genomics* / methods Genomics* / standards High-Throughput Screening Assays Humans Neoplasms / genetics* Phenotype Polymorphism, Single Nucleotide Quantitative Trait Loci RNA, Guide, Kinetoplastida / genetics RNA, Small Interfering / genetics Reproducibility of Results
IF 29.497
Human and Animal Cells MKN45(RCB1001)