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Updated: Mar 15, 2026
Genome-Wide CRISPR Screen for Unveiling Radiosensitive and Radioresistant Genes
Published on: May 23, 2025
Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening
Michael K Kiessling1, Sven Schuierer2, Silke Stertz3
1Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland.
Background:
Genome-wide CRISPR-Cas9 dropout screens can identify genes whose knockout affects cell viability. Recent CRISPR screens detected thousands of essential genes required for cellular survival and key cellular processes; however discovering novel lineage-specific genetic dependencies from the many hits still remains a challenge.
Results:
To assess whether CRISPR-Cas9 dropout screens can help identify cancer dependencies, we screened two human cancer cell lines carrying known and distinct oncogenic mutations using a genome-wide sgRNA library. We found that the gRNA targeting the driver mutation EGFR was one of the highest-ranking candidates in the EGFR-mutant HCC-827 lung adenocarcinoma cell line. Likewise, sgRNAs for NRAS and MAP2K1 (MEK1), a downstream kinase of mutant NRAS, were identified among the top hits in the NRAS-mutant neuroblastoma cell line CHP-212. Depletion of these genes targeted by the sgRNAs strongly correlated with the sensitivity to specific kinase inhibitors of the EGFR or RAS pathway in cell viability assays. In addition, we describe other dependencies such as TBK1 in HCC-827 cells and TRIB2 in CHP-212 cells which merit further investigation.
Conclusions:
We show that genome-wide CRISPR dropout screens are suitable for the identification of oncogenic drivers and other essential genes.
Insights
Genome-wide CRISPR screens identify essential genes for cell survival. This study demonstrates their utility in pinpointing cancer-specific genetic dependencies, including oncogenic drivers like EGFR and NRAS.
Area of Science:
- Genomics
- Cancer Biology
- Molecular Genetics
Background:
- Genome-wide CRISPR-Cas9 dropout screens identify genes crucial for cell viability and function.
- Discovering lineage-specific genetic dependencies from large-scale CRISPR screens remains a challenge.
Purpose of the Study:
- To evaluate the effectiveness of CRISPR-Cas9 dropout screens in identifying cancer-specific dependencies.
- To validate the screen's ability to detect known oncogenic drivers.
Main Methods:
- Screening of two human cancer cell lines with distinct oncogenic mutations using a genome-wide sgRNA library.
- Analysis of gene targeting by sgRNAs and correlation with cell viability assays and pathway-specific inhibitors.
Main Results:
- CRISPR screens successfully identified the driver mutation EGFR in an EGFR-mutant lung adenocarcinoma cell line (HCC-827).
- NRAS and MAP2K1 (MEK1) were identified as top hits in an NRAS-mutant neuroblastoma cell line (CHP-212).
- Gene depletion correlated with sensitivity to specific kinase inhibitors, validating the identified dependencies.
Conclusions:
- Genome-wide CRISPR dropout screens are effective for identifying oncogenic drivers.
- These screens are suitable for discovering essential genes and potential therapeutic targets in cancer.
