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Volumn 568, Issue 7753, 2019, Pages 511-516

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(25)  Behan, Fiona M a,b   Iorio, Francesco a,b,c   Picco, Gabriele a   Gonçalves, Emanuel a   Beaver, Charlotte M a   Migliardi, Giorgia d,e   Santos, Rita f   Rao, Yanhua g   Sassi, Francesco d   Pinnelli, Marika d,e   Ansari, Rizwan a   Harper, Sarah a   Jackson, David Adam a   McRae, Rebecca a   Pooley, Rachel a   Wilkinson, Piers a   van der Meer, Dieudonne a   Dow, David b,f   Buser Doepner, Carolyn b,g   Bertotti, Andrea d,e   more..

d IRCCS   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; BIOLOGICAL MARKER; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; TRANSCRIPTION FACTOR GATA 3; TUMOR MARKER; WERNER SYNDROME ATP DEPENDENT HELICASE;

EID: 85064233743     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/s41586-019-1103-9     Document Type: Article
Times cited : (811)

References (47)
  • 1
    • 84880452562 scopus 로고    scopus 로고
    • Genomics-driven oncology: framework for an emerging paradigm
    • Garraway, L. A. Genomics-driven oncology: framework for an emerging paradigm. J. Clin. Oncol. 31, 1806–1814 (2013).
    • (2013) J. Clin. Oncol. , vol.31 , pp. 1806-1814
    • Garraway, L.A.1
  • 2
    • 85020279899 scopus 로고    scopus 로고
    • Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients
    • COI: 1:CAS:528:DC%2BC2sXntFKitLo%3D
    • Zehir, A. et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat. Med. 23, 703–713 (2017).
    • (2017) Nat. Med. , vol.23 , pp. 703-713
    • Zehir, A.1
  • 3
    • 84892153139 scopus 로고    scopus 로고
    • Clinical development success rates for investigational drugs
    • COI: 1:CAS:528:DC%2BC2cXkvFyjsA%3D%3D
    • Hay, M., Thomas, D. W., Craighead, J. L., Economides, C. & Rosenthal, J. Clinical development success rates for investigational drugs. Nat. Biotechnol. 32, 40–51 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 40-51
    • Hay, M.1    Thomas, D.W.2    Craighead, J.L.3    Economides, C.4    Rosenthal, J.5
  • 4
    • 84898665052 scopus 로고    scopus 로고
    • Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR–guide RNA library
    • COI: 1:CAS:528:DC%2BC3sXhvFylsL%2FF
    • Koike-Yusa, H., Li, Y., Tan, E.-P., Del Castillo Velasco-Herrera, M. & Yusa, K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR–guide RNA library. Nat. Biotechnol. 32, 267–273 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 267-273
    • Koike-Yusa, H.1    Li, Y.2    Tan, E.-P.3    Del Castillo Velasco-Herrera, M.4    Yusa, K.5
  • 5
    • 85035771254 scopus 로고    scopus 로고
    • Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells
    • COI: 1:CAS:528:DC%2BC2sXhslehtrjI
    • Meyers, R. M. et al. Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779–1784 (2017).
    • (2017) Nat. Genet. , vol.49 , pp. 1779-1784
    • Meyers, R.M.1
  • 6
    • 85059794862 scopus 로고    scopus 로고
    • Cell Model Passports—a hub for clinical, genetic and functional datasets of preclinical cancer models
    • van der Meer, D. et al. Cell Model Passports—a hub for clinical, genetic and functional datasets of preclinical cancer models. Nucleic Acids Res. 47, D923–D929 (2019).
    • (2019) Nucleic Acids Res. , vol.47 , pp. D923-D929
    • van der Meer, D.1
  • 7
    • 84979649916 scopus 로고    scopus 로고
    • A landscape of pharmacogenomic interactions in cancer
    • COI: 1:CAS:528:DC%2BC28XhtFCiu73L
    • Iorio, F. et al. A landscape of pharmacogenomic interactions in cancer. Cell 166, 740–754 (2016).
    • (2016) Cell , vol.166 , pp. 740-754
    • Iorio, F.1
  • 8
    • 84949233942 scopus 로고    scopus 로고
    • High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities
    • COI: 1:CAS:528:DC%2BC2MXhvFagur7I
    • Hart, T. et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163, 1515–1526 (2015).
    • (2015) Cell , vol.163 , pp. 1515-1526
    • Hart, T.1
  • 9
    • 85027283916 scopus 로고    scopus 로고
    • Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens
    • COI: 1:CAS:528:DC%2BC1cXisVKhtrrP
    • Hart, T. et al. Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens. G3 (Bethesda) 7, 2719–2727 (2017).
    • (2017) G3 (Bethesda) , vol.7 , pp. 2719-2727
    • Hart, T.1
  • 10
    • 84994850910 scopus 로고    scopus 로고
    • A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia
    • COI: 1:CAS:528:DC%2BC28XhslSntLjM
    • Tzelepis, K. et al. A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia. Cell Rep. 17, 1193–1205 (2016).
    • (2016) Cell Rep. , vol.17 , pp. 1193-1205
    • Tzelepis, K.1
  • 11
    • 84892749369 scopus 로고    scopus 로고
    • Genetic screens in human cells using the CRISPR–Cas9 system
    • COI: 1:CAS:528:DC%2BC2cXkslOq
    • Wang, T., Wei, J. J., Sabatini, D. M. & Lander, E. S. Genetic screens in human cells using the CRISPR–Cas9 system. Science 343, 80–84 (2014).
    • (2014) Science , vol.343 , pp. 80-84
    • Wang, T.1    Wei, J.J.2    Sabatini, D.M.3    Lander, E.S.4
  • 12
    • 85026428627 scopus 로고    scopus 로고
    • Project DRIVE: a compendium of cancer dependencies and synthetic lethal relationships uncovered by large-scale, deep RNAi screening
    • COI: 1:CAS:528:DC%2BC2sXht1GisLvI
    • McDonald, E. R. III et al. Project DRIVE: a compendium of cancer dependencies and synthetic lethal relationships uncovered by large-scale, deep RNAi screening. Cell 170, 577–592 (2017).
    • (2017) Cell , vol.170 , pp. 577-592
    • McDonald, E.R.1
  • 13
    • 84954357527 scopus 로고    scopus 로고
    • PI3K inhibitors as new cancer therapeutics: implications for clinical trial design
    • COI: 1:CAS:528:DC%2BC1cXlvFyqsr4%3D
    • Massacesi, C. et al. PI3K inhibitors as new cancer therapeutics: implications for clinical trial design. OncoTargets Ther. 9, 203–210 (2016).
    • (2016) OncoTargets Ther. , vol.9 , pp. 203-210
    • Massacesi, C.1
  • 14
    • 85046037741 scopus 로고    scopus 로고
    • Approaches to target tractability assessment — a practical perspective
    • COI: 1:CAS:528:DC%2BC1cXislSmtb8%3D
    • Brown, K. K. et al. Approaches to target tractability assessment — a practical perspective. MedChemComm 9, 606–613 (2018).
    • (2018) MedChemComm , vol.9 , pp. 606-613
    • Brown, K.K.1
  • 15
    • 85026414383 scopus 로고    scopus 로고
    • Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway
    • COI: 1:CAS:528:DC%2BC2sXhtFaqt73P
    • Viswanathan, V. S. et al. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature 547, 453–457 (2017).
    • (2017) Nature , vol.547 , pp. 453-457
    • Viswanathan, V.S.1
  • 16
    • 69249209608 scopus 로고    scopus 로고
    • RecQ helicases: multifunctional genome caretakers
    • COI: 1:CAS:528:DC%2BD1MXpsVersL4%3D
    • Chu, W. K. & Hickson, I. D. RecQ helicases: multifunctional genome caretakers. Nat. Rev. Cancer 9, 644–654 (2009).
    • (2009) Nat. Rev. Cancer , vol.9 , pp. 644-654
    • Chu, W.K.1    Hickson, I.D.2
  • 17
    • 85020420753 scopus 로고    scopus 로고
    • A molecular portrait of microsatellite instability across multiple cancers
    • COI: 1:CAS:528:DC%2BC2sXpsVCisro%3D
    • Cortes-Ciriano, I., Lee, S., Park, W.-Y., Kim, T.-M. & Park, P. J. A molecular portrait of microsatellite instability across multiple cancers. Nat. Commun. 8, 15180 (2017).
    • (2017) Nat. Commun. , vol.8
    • Cortes-Ciriano, I.1    Lee, S.2    Park, W.-Y.3    Kim, T.-M.4    Park, P.J.5
  • 18
    • 54249144723 scopus 로고    scopus 로고
    • Genetic instability caused by loss of MutS homologue 3 in human colorectal cancer
    • COI: 1:CAS:528:DC%2BD1cXht1CmsbrK
    • Haugen, A. C. et al. Genetic instability caused by loss of MutS homologue 3 in human colorectal cancer. Cancer Res. 68, 8465–8472 (2008).
    • (2008) Cancer Res. , vol.68 , pp. 8465-8472
    • Haugen, A.C.1
  • 19
    • 33745084835 scopus 로고    scopus 로고
    • WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing
    • COI: 1:CAS:528:DC%2BD28XltFWlsrs%3D
    • Perry, J. J. P. et al. WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nat. Struct. Mol. Biol. 13, 414–422 (2006).
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 414-422
    • Perry, J.J.P.1
  • 20
    • 11244258888 scopus 로고    scopus 로고
    • The enzymatic activities of the Werner syndrome protein are disabled by the amino acid polymorphism R834C
    • COI: 1:CAS:528:DC%2BD2cXhtFeis7jN
    • Kamath-Loeb, A. S., Welcsh, P., Waite, M., Adman, E. T. & Loeb, L. A. The enzymatic activities of the Werner syndrome protein are disabled by the amino acid polymorphism R834C. J. Biol. Chem. 279, 55499–55505 (2004).
    • (2004) J. Biol. Chem. , vol.279 , pp. 55499-55505
    • Kamath-Loeb, A.S.1    Welcsh, P.2    Waite, M.3    Adman, E.T.4    Loeb, L.A.5
  • 21
    • 85013814402 scopus 로고    scopus 로고
    • Residues in the RecQ C-terminal domain of the human Werner Syndrome helicase are involved in unwinding G-quadruplex DNA
    • COI: 1:CAS:528:DC%2BC2sXjtlyqtbw%3D
    • Ketkar, A., Voehler, M., Mukiza, T. & Eoff, R. L. Residues in the RecQ C-terminal domain of the human Werner Syndrome helicase are involved in unwinding G-quadruplex DNA. J. Biol. Chem. 292, 3154–3163 (2017).
    • (2017) J. Biol. Chem. , vol.292 , pp. 3154-3163
    • Ketkar, A.1    Voehler, M.2    Mukiza, T.3    Eoff, R.L.4
  • 22
    • 85064214826 scopus 로고    scopus 로고
    • WRN helicase is a synthetic lethal target in microsatellite unstable cancers
    • Chan, E. M. et al. WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 10.1038/s41586-019-1102-x (2019).
    • (2019) Nature
    • Chan, E.M.1
  • 23
    • 34848881418 scopus 로고    scopus 로고
    • Physical and functional interactions between Werner syndrome helicase and mismatch-repair initiation factors
    • COI: 1:CAS:528:DC%2BD2sXhtFWhsr7N
    • Saydam, N. et al. Physical and functional interactions between Werner syndrome helicase and mismatch-repair initiation factors. Nucleic Acids Res. 35, 5706–5716 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. 5706-5716
    • Saydam, N.1
  • 24
    • 62849091779 scopus 로고    scopus 로고
    • The Werner syndrome helicase/exonuclease processes mobile D-loops through branch migration and degradation
    • Opresko, P. L., Sowd, G. & Wang, H. The Werner syndrome helicase/exonuclease processes mobile D-loops through branch migration and degradation. PLoS ONE 4, e4825 (2009).
    • (2009) PLoS ONE , vol.4
    • Opresko, P.L.1    Sowd, G.2    Wang, H.3
  • 25
    • 0035158640 scopus 로고    scopus 로고
    • SGS1, the Saccharomyces cerevisiae homologue of BLM and WRN, suppresses genome instability and homeologous recombination
    • COI: 1:CAS:528:DC%2BD3MXis1yrtA%3D%3D
    • Myung, K., Datta, A., Chen, C. & Kolodner, R. D. SGS1, the Saccharomyces cerevisiae homologue of BLM and WRN, suppresses genome instability and homeologous recombination. Nat. Genet. 27, 113–116 (2001).
    • (2001) Nat. Genet. , vol.27 , pp. 113-116
    • Myung, K.1    Datta, A.2    Chen, C.3    Kolodner, R.D.4
  • 26
    • 84932628341 scopus 로고    scopus 로고
    • PD-1 blockade in tumors with mismatch-repair deficiency
    • COI: 1:CAS:528:DC%2BC2MXhtFyrsbrI
    • Le, D. T. et al. PD-1 blockade in tumors with mismatch-repair deficiency. N. Engl. J. Med. 372, 2509–2520 (2015).
    • (2015) N. Engl. J. Med. , vol.372 , pp. 2509-2520
    • Le, D.T.1
  • 27
    • 85026422523 scopus 로고    scopus 로고
    • Defining a cancer dependency map
    • COI: 1:CAS:528:DC%2BC2sXht1GisLjP
    • Tsherniak, A. et al. Defining a cancer dependency map. Cell 170, 564–576 (2017).
    • (2017) Cell , vol.170 , pp. 564-576
    • Tsherniak, A.1
  • 28
    • 85011268687 scopus 로고    scopus 로고
    • Gene essentiality profiling reveals gene networks and synthetic lethal interactions with oncogenic Ras
    • COI: 1:CAS:528:DC%2BC2sXitFehtrc%3D
    • Wang, T. et al. Gene essentiality profiling reveals gene networks and synthetic lethal interactions with oncogenic Ras. Cell 168, 890–903 (2017).
    • (2017) Cell , vol.168 , pp. 890-903
    • Wang, T.1
  • 29
    • 84964727289 scopus 로고    scopus 로고
    • AuPairWise: a method to estimate RNA-seq replicability through co-expression
    • Home (25 Doggett St
    • Ballouz, S. & Gillis, J. AuPairWise: a method to estimate RNA-seq replicability through co-expression. PLOS Comput. Biol. 12, e1004868 (2016). Home (25 Doggett St)
    • (2016) PLOS Comput. Biol. , vol.12
    • Ballouz, S.1    Gillis, J.2
  • 30
    • 84963595182 scopus 로고    scopus 로고
    • BAGEL: a computational framework for identifying essential genes from pooled library screens
    • Hart, T. & Moffat, J. BAGEL: a computational framework for identifying essential genes from pooled library screens. BMC Bioinformatics 17, 164 (2016).
    • (2016) BMC Bioinformatics , vol.17
    • Hart, T.1    Moffat, J.2
  • 31
    • 0036125672 scopus 로고    scopus 로고
    • The human ribosomal protein genes: sequencing and comparative analysis of 73 genes
    • COI: 1:CAS:528:DC%2BD38XitFSlt7c%3D
    • Yoshihama, M. et al. The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. Genome Res. 12, 379–390 (2002).
    • (2002) Genome Res. , vol.12 , pp. 379-390
    • Yoshihama, M.1
  • 32
    • 85051579665 scopus 로고    scopus 로고
    • Unsupervised correction of gene-independent cell responses to CRISPR–Cas9 targeting
    • Iorio, F. et al. Unsupervised correction of gene-independent cell responses to CRISPR–Cas9 targeting. BMC Genomics 19, 604 (2018).
    • (2018) BMC Genomics , vol.19
    • Iorio, F.1
  • 33
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • COI: 1:CAS:528:DC%2BC3cXhsVahs7bI
    • Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
    • (2010) Genome Biol. , vol.11
    • Anders, S.1    Huber, W.2
  • 34
    • 84982918709 scopus 로고    scopus 로고
    • Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting
    • COI: 1:CAS:528:DC%2BC28Xht12mur7O
    • Aguirre, A. J. et al. Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting. Cancer Discov. 6, 914–929 (2016).
    • (2016) Cancer Discov. , vol.6 , pp. 914-929
    • Aguirre, A.J.1
  • 35
    • 84996567029 scopus 로고    scopus 로고
    • MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
    • Li, W. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 15, 554 (2014).
    • (2014) Genome Biol. , vol.15
    • Li, W.1
  • 36
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    • COI: 1:CAS:528:DC%2BD2MXht1ShtrnO
    • Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 37
    • 24044522270 scopus 로고    scopus 로고
    • BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
    • COI: 1:CAS:528:DC%2BD2MXovVKru74%3D
    • Durinck, S. et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21, 3439–3440 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 3439-3440
    • Durinck, S.1
  • 38
    • 78651332286 scopus 로고    scopus 로고
    • Pathway Commons, a web resource for biological pathway data
    • COI: 1:CAS:528:DC%2BC3sXivF2msb0%3D
    • Cerami, E. G. et al. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 39, D685–D690 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. D685-D690
    • Cerami, E.G.1
  • 39
    • 85046621112 scopus 로고    scopus 로고
    • Pathway-based dissection of the genomic heterogeneity of cancer hallmarks’ acquisition with SLAPenrich
    • Iorio, F. et al. Pathway-based dissection of the genomic heterogeneity of cancer hallmarks’ acquisition with SLAPenrich. Sci. Rep. 8, 6713 (2018).
    • (2018) Sci. Rep. , vol.8
    • Iorio, F.1
  • 40
    • 84878682420 scopus 로고    scopus 로고
    • The Genotype-Tissue Expression (GTEx) project
    • GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580–585 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 580-585
  • 41
    • 85045837625 scopus 로고    scopus 로고
    • GDSCTools for mining pharmacogenomic interactions in cancer
    • COI: 1:CAS:528:DC%2BC1cXitlGkurjJ
    • Cokelaer, T. et al. GDSCTools for mining pharmacogenomic interactions in cancer. Bioinformatics 34, 1226–1228 (2018).
    • (2018) Bioinformatics , vol.34 , pp. 1226-1228
    • Cokelaer, T.1
  • 42
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • COI: 1:CAS:528:DC%2BD3sXmtlyktbY%3D
    • Storey, J. D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 9440–9445 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 43
    • 84874969184 scopus 로고    scopus 로고
    • PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
    • COI: 1:CAS:528:DC%2BC38XhvV2ktrrP
    • Mi, H., Muruganujan, A. & Thomas, P. D. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 41, D377–D386 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D377-D386
    • Mi, H.1    Muruganujan, A.2    Thomas, P.D.3
  • 44
    • 84896735766 scopus 로고    scopus 로고
    • voom: precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15, R29 (2014).
    • (2014) Genome Biol. , vol.15
    • Law, C.W.1    Chen, Y.2    Shi, W.3    Smyth, G.K.4
  • 45
    • 85041469991 scopus 로고    scopus 로고
    • Transcription factor activities enhance markers of drug sensitivity in cancer
    • COI: 1:CAS:528:DC%2BC1cXitVWnsbY%3D
    • Garcia-Alonso, L. et al. Transcription factor activities enhance markers of drug sensitivity in cancer. Cancer Res. 78, 769–780 (2018).
    • (2018) Cancer Res. , vol.78 , pp. 769-780
    • Garcia-Alonso, L.1
  • 46
    • 84926507971 scopus 로고    scopus 로고
    • limma powers differential expression analyses for RNA-sequencing and microarray studies
    • Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
    • (2015) Nucleic Acids Res. , vol.43
    • Ritchie, M.E.1
  • 47
    • 85027944392 scopus 로고    scopus 로고
    • LAS: a software platform to support oncological data management
    • Baralis, E., Bertotti, A., Fiori, A. & Grand, A. LAS: a software platform to support oncological data management. J. Med. Syst. 36, 81–90 (2012).
    • (2012) J. Med. Syst. , vol.36 , pp. 81-90
    • Baralis, E.1    Bertotti, A.2    Fiori, A.3    Grand, A.4


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