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

Research paper by Andrew J AJ Aguirre, Robin M RM Meyers, Barbara A BA Weir, Francisca F Vazquez, Cheng-Zhong CZ Zhang, Uri U Ben-David, April A Cook, Gavin G Ha, William F WF Harrington, Mihir B MB Doshi, Maria M Kost-Alimova, Stanley S Gill, Han H Xu, Levi D LD Ali, Guozhi G Jiang, et al.

Indexed on: 05 Jun '16Published on: 05 Jun '16Published in: Cancer discovery


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 anti-proliferative cell response. This effect has important practical implications for interpretation of CRISPR-Cas9 screening data and confounds the use of this technology for identification of essential genes in amplified regions.