CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions

Cancer Discovery

Volumn 6, Issue 8, 2016, Pages 900-913

  Munoz, Diana M ^a   Cassiani, Pamela J ^a   Li, Li ^a   Billy, Eric ^b   Korn, Joshua M ^a   Jones, Michael D ^a   Golji, Javad ^a   Ruddy, David A ^a   Yu, Kristine ^a   McAllister, Gregory ^a   Deweck, Antoine ^b   Abramowski, Dorothee ^b   Wan, Jessica ^a   Shirley, Matthew D ^a   Neshat, Sarah Y ^a   Rakiec, Daniel ^a   De Beaumont, Rosalie ^a   Weber, Odile ^b   Kauffmann, Audrey ^b   Robert McDonald, E ^a   Keen, Nicholas ^a   Hofmann, Francesco ^b   Sellers, William R ^a   Schmelzle, Tobias ^b   Stegmeier, Frank ^a   Schlabach, Michael R ^a   more..

^a NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; LENTIVIRUS VECTOR; SHORT HAIRPIN RNA; GUIDE RNA; SMALL INTERFERING RNA;

ARTICLE; CANCER CELL LINE; CANCER SUSCEPTIBILITY; CELL CYCLE ASSAY; CELL PROLIFERATION ASSAY; CELL VIABILITY ASSAY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; ESSENTIAL GENE; FALSE POSITIVE RESULT; GENE AMPLIFICATION; GENE FUNCTION; HUMAN; HUMAN CELL; LETHAL GENE; LOSS OF FUNCTION MUTATION; PHENOTYPE; POLYMERASE CHAIN REACTION; RNA INTERFERENCE; SCREENING TEST; SEQUENCE ANALYSIS; WESTERN BLOTTING; CRISPR CAS SYSTEM; GENETIC ASSOCIATION STUDY; GENETICS; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN GENOME; NEOPLASM; PROCEDURES; QUANTITATIVE TRAIT LOCUS; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARDS; TUMOR CELL LINE;

CELL LINE, TUMOR; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; GENE AMPLIFICATION; GENETIC ASSOCIATION STUDIES; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; NEOPLASMS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; RNA, GUIDE; RNA, SMALL INTERFERING;

EID: 84982913128     PISSN: 21598274     EISSN: 21598290     Source Type: Journal    
DOI: 10.1158/2159-8290.CD-16-0178     Document Type: Article

References (31)

1. Cowley GS., Weir BA., Vazquez F., Tamayo P., Scott JA., Rusin S., et al. Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. Sci Data 2014. 1. 140035.
2. Hoffman GR., Rahal R., Buxton F., Xiang K., McAllister G., Frias E., et al. Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers. Proc Natl Acad Sci U S A 2014. 111. 3128–33.
3. Sigoillot FD., Lyman S., Huckins JF., Adamson B., Chung E., Quattrochi B., et al. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat Methods 2012. 9. 363–6.
4. Hsu PD., Lander ES., Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014. 157. 1262–78.
5. Jinek M., East A., Cheng A., Lin S., Ma E., Doudna J. RNA-programmed genome editing in human cells. eLife 2013. 2. e00471.
6. Shi J., Wang E., Milazzo JP., Wang Z., Kinney JB., Vakoc CR. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol 2015. 33. 661–7.
7. Wang T., Wei JJ., Sabatini DM., Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2014. 343. 80–4.
8. Wang T., Birsoy K., Hughes NW., Krupczak KM., Post Y., Wei JJ., et al. Identification and characterization of essential genes in the human genome. Science 2015. 350. 1096–101.
9. Hart T., Chandrashekhar M., Aregger M., Steinhart Z., Brown KR., MacLeod G., et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 2015. 163. 1515–26.
10. Finn RD., Tate J., Mistry J., Coggill PC., Sammut SJ., Hotz HR., et al. The Pfam protein families database. Nucleic Acids Res 2008. 36. D281–8.
11. Cong L., Ran FA., Cox D., Lin S., Barretto R., Habib N., et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013; 339: 819–23.
12. Schmidt EV. The role of c-myc in cellular growth control. Oncogene 1999. 18. 2988–96.
13. Raab M., Kappel S., Kramer A., Sanhaji M., Matthess Y., Kurunci- Csacsko E., et al. Toxicity modelling of Plk1-targeted therapies in genetically engineered mice and cultured primary mammalian cells. Nat Commun 2011. 2. 395.
14. Segditsas S., Tomlinson I. Colorectal cancer and genetic alterations in the Wnt pathway. Oncogene 2006. 25. 7531–7.
15. Nunez F., Bravo S., Cruzat F., Montecino M., De Ferrari GV. Wnt/betacatenin signaling enhances cyclooxygenase-2 (COX2) transcriptional activity in gastric cancer cells. PLoS ONE 2011. 6. e18562.
16. Arva NC., Talbott KE., Okoro DR., Brekman A., Qiu WG., Bargonetti J. Disruption of the p53-Mdm2 complex by Nutlin-3 reveals different cancer cell phenotypes. Ethn Dis 2008. 18. S2–1–8.
17. Hulsken J., Birchmeier W., Behrens J. E-cadherin and APC compete for the interaction with beta-catenin and the cytoskeleton. J Cell Biol 1994. 127. 2061–9.
18. Vangamudi B., Paul TA., Shah PK., Kost-Alimova M., Nottebaum L., Shi X., et al. The SMARCA2/4 ATPase domain surpasses the bromodomain as a drug target in SWI/SNF-mutant cancers: Insights from cDNA rescue and PFI-3 inhibitor studies. Cancer Res 2015. 75. 3865–78.
19. Zender L., Xue W., Zuber J., Semighini CP., Krasnitz A., Ma B., et al. An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell 2008. 135. 852–64.
20. Tsai SQ., Zheng Z., Nguyen NT., Liebers M., Topkar VV., Thapar V., et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 2015. 33. 187–97.
21. Gilbert LA., Horlbeck MA., Adamson B., Villalta JE., Chen Y., Whitehead EH., et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 2014. 159. 647–61.
22. Fellmann C., Lowe SW. Stable RNA interference rules for silencing. Nat Cell Biol 2014. 16. 10–8.
23. Gentric G., Desdouets C. Polyploidization in liver tissue. Am J Pathol 2014. 184. 322–31.
24. Doench JG., Hartenian E., Graham DB., Tothova Z., Hegde M., Smith I., et al. Rational design of highly active sgRNAs for CRISPR-Cas9- mediated gene inactivation. Nat Biotechnol 2014. 32. 1262–7.
25. Mali P., Yang L., Esvelt KM., Aach J., Guell M., DiCarlo JE., et al. RNA-guided human genome engineering via Cas9. Science 2013. 339. 823–6.
26. Huesken D., Lange J., Mickanin C., Weiler J., Asselbergs F., Warner J., et al. Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol 2005; 23: 995–1001.
27. Arpino JA., Reddington SC., Halliwell LM., Rizkallah PJ., Jones DD. Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure. Structure 2014; 22: 889–98.
28. Barretina J., Caponigro G., Stransky N., Venkatesan K., Margolin AA., Kim S., et al. The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012. 483. 603–7.
29. Chen B., Gilbert LA., Cimini BA., Schnitzbauer J., Zhang W., Li GW., et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 2013. 155. 1479–91.
30. Weber E., Engler C., Gruetzner R., Werner S., Marillonnet S. A modular cloning system for standardized assembly of multigene constructs. PLoS ONE 2011. 6. e16765.
31. Dow LE., Fisher J., O’Rourke KP., Muley A., Kastenhuber ER., Livshits G., et al. Inducible in vivo genome editing with CRISPR-Cas9. Nat Biotechnol 2015. 33. 390–4.