Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting

Andrew J. Aguirre, Robin M. Meyers, Barbara A. Weir, Francisca Vazquez, Cheng Zhong Zhang, Uri Ben-David, April Cook, Gavin Ha, William F. Harrington, Mihir B. Doshi, Maria Kost-Alimova, Stanley Gill, Han Xu, Levi D. Ali, Guozhi Jiang, Sasha Pantel, Yenarae Lee, Amy Goodale, Andrew D. Cherniack, Coyin OhGregory Kryukov, Glenn S. Cowley, Levi A. Garraway, Kimberly Stegmaier, Charles W. Roberts, Todd R. Golub, Matthew Meyerson, David E. Root, Aviad Tsherniak, William C. Hahn

Research output: Contribution to journalArticlepeer-review

382 Scopus citations


The CRISPR/Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome-scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy-number gain, CRISPR/Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G 2 cell-cycle arrest. By examining single-guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR/Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR/Cas9 elicits a gene-independent antiproliferative cell response. This effect has important practical implications for the interpretation of CRISPR/Cas9 screening data and confounds the use of this technology for the identification of essential genes in amplified regions. SIGNIFICANCE: We found that the number of CRISPR/Cas9-induced DNA breaks dictates a geneindependent antiproliferative response in cells. These observations have practical implications for using CRISPR/Cas9 to interrogate cancer gene function and illustrate that cancer cells are highly sensitive to site-specific DNA damage, which may provide a path to novel therapeutic strategies.

Original languageEnglish
Pages (from-to)914-929
Number of pages16
JournalCancer Discovery
Issue number8
StatePublished - Aug 2016
Externally publishedYes


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