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

Abstract

<div>Abstract<p>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<sub>2</sub> 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.</p><p><b>Significance:</b> We found that the number of CRISPR/Cas9-induced DNA breaks dictates a gene-independent 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. <i>Cancer Discov; 6(8); 914–29. ©2016 AACR.</i></p><p><i>See related commentary by Sheel and Xue, p. 824</i>.</p><p><i>See related article by Munoz et al., p. 900</i>.</p><p>This article is highlighted in the In This Issue feature, p. 803</p></div>