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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 08
ISSN2159-8290
KeywordsCell Line, Tumor, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems, DNA Cleavage, DNA Copy Number Variations, DNA Damage, G2 Phase Cell Cycle Checkpoints, Gene Amplification, Gene Dosage, Gene Editing, Gene Expression, Gene Knockout Techniques, Gene Targeting, Genes, Essential, Genomics, High-Throughput Screening Assays, Humans, RNA, Guide
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 ListU01 CA199253 / CA / NCI NIH HHS / United States
R01 CA130988 / CA / NCI NIH HHS / United States
P01 CA154303 / CA / NCI NIH HHS / United States
U01 CA176058 / CA / NCI NIH HHS / United States
UL1 TR001102 / TR / NCATS NIH HHS / United States