High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines

Nature Biotechnology

Volumn 34, Issue 4, 2016, Pages 419-423

  Yu, Channing ^a,b,c   Mannan, Aristotle M ^a   Yvone, Griselda Metta ^a,f   Ross, Kenneth N ^a,f,g   Zhang, Yan Ling ^a   Marton, Melissa A ^a   Taylor, Bradley R ^a   Crenshaw, Andrew ^a   Gould, Joshua Z ^a   Tamayo, Pablo ^a   Weir, Barbara A ^a   Tsherniak, Aviad ^a   Wong, Bang ^a   Garraway, Levi A ^a,b,c   Shamji, Alykhan F ^a   Palmer, Michelle A ^a,f,h   Foley, Michael A ^a,f,i   Winckler, Wendy ^a   Schreiber, Stuart L ^a,d,e   Kung, Andrew L ^b,c,f,j   Golub, Todd R ^a,b,c,d,e   more..

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d HARVARD UNIVERSITY   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g MASSACHUSETTS GENERAL HOSPITAL   (United States)

^h IMMUNOGEN INC   (United States)

ⁱ Tri Institutional Therapeutics Discovery Institute Inc   (United States)

^j Department of Medicine   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; CYTOLOGY; DIAGNOSIS; DISEASES; MIXTURES; PRISMS; TUMORS;

AURORA KINASE; CANCER CELL LINES; CELL KILLING; CELL LINES; ERLOTINIB; HIGH THROUGHPUT; SPECIFIC INHIBITORS; TUMOR CELL LINES;

CELLS;

AURORA B KINASE; AURORA C KINASE; ERLOTINIB;

ADENOCARCINOMA CELL LINE; ANIMAL CELL; ARTICLE; CANCER CELL LINE; CANCER SCREENING; CELL ASSAY; CELL KILLING; DNA BARCODING; GENE DOSAGE; GENE EXPRESSION; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; HIGH THROUGHPUT SCREENING; LUNG ADENOCARCINOMA; MOUSE; NEOPLASM; NONHUMAN; PRIORITY JOURNAL; PRISM ASSAY; ANIMAL; CLASSIFICATION; DRUG RESISTANCE; GENETICS; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; TUMOR CELL LINE;

ANIMALS; CELL LINE, TUMOR; DNA BARCODING, TAXONOMIC; DRUG RESISTANCE, NEOPLASM; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; NEOPLASMS;

EID: 84963614599     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3460     Document Type: Article

References (26)

1. McDermott, U., et al. Identification of genotype-correlated sensitivity to selective kinase inhibitors by using high-throughput tumor cell line profiling. Proc. Natl. Acad. Sci. USA 104, 19936-19941 (2007).
2. Sos, M.L., et al. Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. J. Clin. Invest. 119, 1727-1740 (2009).
3. Barretina, J., et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012).
4. Garnett, M.J., et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483, 570-575 (2012).
5. Sharma, S.V., Haber, D.A. & Settleman, J. Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents. Nat. Rev. Cancer 10, 241-253 (2010).
6. Abaan, O.D., et al. The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Res. 73, 4372-4382 (2013).
7. Basu, A., et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell 154, 1151-1161 (2013).
8. Turner, N.C. & Reis-Filho, J.S. Genetic heterogeneity and cancer drug resistance. Lancet Oncol. 13, e178-e185 (2012).
9. Peck, D., et al. A method for high-throughput gene expression signature analysis. Genome Biol. 7, R61 (2006).
10. Du, J., et al. Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy. Nat. Biotechnol. 27, 77-83 (2009).
11. Muellner, M.K., et al. A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer. Nat. Chem. Biol. 7, 787-793 (2011).
12. Koivunen, J.P., et al. EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer. Clin. Cancer Res. 14, 4275-4283 (2008).
13. http://www.broadinstitute.org/ccle.
14. Wilhelm, S.M., et al. Preclinical overview of sorafenib, a multikinase inhibitor that targets both Raf and VEGF and PDGF receptor tyrosine kinase signaling. Mol. Cancer Ther. 7, 3129-3140 (2008).
15. Flaherty, K.T., et al. METRIC Study Group. Improved survival with MEK inhibition in BRAF-mutated melanoma. N. Engl. J. Med. 367, 107-114 (2012).
16. Comer, E., et al. Fragment-based domain shuffling approach for the synthesis of pyran-based macrocycles. Proc. Natl. Acad. Sci. USA 108, 6751-6756 (2011).
17. Lowe, J.T., et al. Synthesis and profiling of a diverse collection of azetidine-based scaffolds for the development of CNS-focused lead-like libraries. J. Org. Chem. 77, 7187-7211 (2012).
18. Marcaurelle, L.A., et al. An aldol-based build/couple/pair strategy for the synthesis of medium- and large-sized rings: discovery of macrocyclic histone deacetylase inhibitors. J. Am. Chem. Soc. 132, 16962-16976 (2010).
19. Schreiber, S.L., et al. Cancer Target Discovery and Development Network. Towards patient-based cancer therapeutics. Nat. Biotechnol. 28, 904-906 (2010).
20. Zhang, X.D. Illustration of SSMD, z score, SSMD∗, z∗ score, and t statistic for hit selection in RNAi high-throughput screens. J. Biomol. Screen. 16, 775-785 (2011).
21. Andrews, P.D., Knatko, E., Moore, W.J. & Swedlow, J.R. Mitotic mechanics: the auroras come into view. Curr. Opin. Cell Biol. 15, 672-683 (2003).
22. Carmena, M. & Earnshaw, W.C. The cellular geography of aurora kinases. Nat. Rev. Mol. Cell Biol. 4, 842-854 (2003).
23. Ditchfield, C., et al. Aurora B couples chromosome alignment with anaphase by targeting BubR1, Mad2, and Cenp-E to kinetochores. J. Cell Biol. 161, 267-280 (2003).
24. Davis, M.I., et al. Comprehensive analysis of kinase inhibitor selectivity. Nat. Biotechnol. 29, 1046-1051 (2011).
25. Karaman, M.W., et al. A quantitative analysis of kinase inhibitor selectivity. Nat. Biotechnol. 26, 127-132 (2008).
26. Korn, J.M., et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet. 40, 1253-1260 (2008).