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Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

2016; American Association for Cancer Research; Volume: 6; Issue: 8 Linguagem: Inglês

10.1158/2159-8290.cd-16-0154

2159-8290

Andrew J. Aguirre, Robin M. Meyers, Barbara A. Weir, Francisca Vázquez, 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 Oh, Gregory V. Kryukov, Glenn S. Cowley, Levi A. Garraway, Kimberly Stegmaier, Charles W.M. Roberts, Todd R. Golub, Matthew Meyerson, David E. Root, Aviad Tsherniak, William C. Hahn,

Advanced biosensing and bioanalysis techniques

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 G2 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.