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Updated: Mar 20, 2026
Genome-Wide CRISPR Screen for Unveiling Radiosensitive and Radioresistant Genes
Published on: May 23, 2025
CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for
Diana M Munoz1, Pamela J Cassiani1, Li Li1
1Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
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.
Insights
CRISPR screens effectively identify cancer dependencies by causing full gene inactivation, but false positives arise in amplified genomic regions. This highlights the need for careful validation in unstable cancer lines.
Area of Science:
- Genomics
- Cancer Biology
- Molecular Biology
Background:
- CRISPR/Cas9 technology offers a novel approach for systematic gene function analysis.
- RNA interference (RNAi) and CRISPR screens are used to identify cancer dependencies.
Purpose of the Study:
- To compare the efficacy of CRISPR and RNAi loss-of-function screens for identifying cancer dependencies.
- To investigate potential false-positive hits in CRISPR screens, especially in aneuploid cancer models.
- To develop strategies for defining essential protein domains using CRISPR tiling screens.
Main Methods:
- Comparative analysis of CRISPR dropout screens versus RNAi screens across multiple cancer cell lines.
- CRISPR tiling screens to assess the impact of targeting specific protein domains.
- Evaluation of CRISPR screen performance in aneuploid cancer models with genomic amplifications.
Main Results:
- CRISPR dropout screens identified more lethal genes than RNAi, suggesting full gene inactivation is crucial for dependency identification.
- A class of false-positive hits was observed in aneuploid cancer models, where all genes in amplified regions, including non-expressed ones, were flagged as lethal.
- CRISPR tiling screens revealed that targeting essential domains yields the strongest lethality phenotypes, offering a method to map functional protein regions.
Conclusions:
- CRISPR screens are powerful tools for identifying cancer-essential genes but require careful control for false positives in chromosomally unstable cancer types.
- The findings provide critical insights for optimizing the application of CRISPR screens in systematic cancer target identification.
- Understanding CRISPR screen liabilities, particularly in regions of genome amplification, is essential for reliable results.
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