CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions

清脆的 生物 计算生物学 基因 遗传学 癌症 表型 功能(生物学) RNA干扰 基因组 鉴定(生物学) 损失函数 遗传筛选 核糖核酸 植物
作者
Diana M. Munoz,Pamela J. Cassiani,Li Li,Éric Billy,Joshua M. Korn,Michael D. Jones,Javad Golji,David A. Ruddy,Kristine Yu,Gregory McAllister,Antoine DeWeck,Dorothée Abramowski,Jessica Wan,Matthew D. Shirley,Sarah Y. Neshat,Daniel P. Rakiec,Rosalie de Beaumont,Odile Weber,Audrey Kauffmann,Ellice McDonald,Nicholas Keen,Francesco Hofmann,William R. Sellers,Tobias Schmelzle,Frank Stegmeier,Michael R. Schlabach
出处
期刊:Cancer Discovery [American Association for Cancer Research]
卷期号:6 (8): 900-913 被引量:320
标识
DOI:10.1158/2159-8290.cd-16-0178
摘要

Abstract 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. 824. See related article by Aguirre et al., p. 914. This article is highlighted in the In This Issue feature, p. 803

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