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Cancer Discov DOI:10.1158/2159-8290.CD-16-0154

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

Publication TypeJournal Article
Year of Publication2016
AuthorsAguirre, AJ, Meyers, RM, Weir, BA, Vazquez, F, Zhang, C-Z, Ben-David, U, Cook, A, Ha, G, Harrington, WF, Doshi, MB, Kost-Alimova, M, Gill, S, Xu, H, Ali, LD, Jiang, G, Pantel, S, Lee, Y, Goodale, A, Cherniack, AD, Oh, C, Kryukov, G, Cowley, GS, Garraway, LA, Stegmaier, K, Roberts, CW, Golub, TR, Meyerson, M, Root, DE, Tsherniak, A, Hahn, WC
JournalCancer Discov
Volume6
Issue8
Pages914-29
Date Published2016 Aug
ISSN2159-8290
Abstract

UNLABELLED: 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.

SIGNIFICANCE: 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. Cancer Discov; 6(8); 914-29. ©2016 AACR.See related commentary by Sheel and Xue, p. 824See related article by Munoz et al., p. 900This article is highlighted in the In This Issue feature, p. 803.

DOI10.1158/2159-8290.CD-16-0154
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/27260156?dopt=Abstract

Alternate JournalCancer Discov
PubMed ID27260156
PubMed Central IDPMC4972686
Grant ListR01 CA130988 / CA / NCI NIH HHS / United States
U01 CA176058 / CA / NCI NIH HHS / United States
U01 CA199253 / CA / NCI NIH HHS / United States