High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

被引：1089

作者：

Hart, Traver ^{[1
]}

Chandrashekhar, Megha ^{[1
,2
]}

Aregger, Michael ^{[1
]}

Steinhart, Zachary ^{[3
,4
]}

Brown, Kevin R. ^{[1
]}

MacLeod, Graham ^{[3
,4
]}

Mis, Monika ^{[3
,4
]}

Zimmermann, Michal ^{[6
]}

Fradet-Turcotte, Amelie ^{[6
]}

Sun, Song ^{[1
,2
,8
,10
]}

Mero, Patricia ^{[1
]}

Dirks, Peter ^{[2
,9
]}

Sidhu, Sachdev ^{[1
,2
]}

Roth, Frederick P. ^{[1
,2
,6
,10
,11
,12
]}

Rissland, Olivia S. ^{[2
,7
]}

Durocher, Daniel ^{[2
,6
]}

Angers, Stephane ^{[3
,4
,5
]}

Moffat, Jason ^{[1
,2
,11
]}

机构：

[1] Donnelly Ctr, Toronto, ON M5S 3E1, Canada

[2] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A1, Canada

[3] Univ Toronto, Dept Pharmaceut Sci, Toronto, ON M5S 1A1, Canada

[4] Univ Toronto, Leslie Dan Fac Pharm, Toronto, ON M5S 1A1, Canada

[5] Univ Toronto, Dept Biochem, Toronto, ON M5S 1A1, Canada

[6] Mt Sinai Hosp, Lunenfeld Tanenbaum Res Inst, Toronto, ON M5G 1X5, Canada

[7] Hosp Sick Children, Res Inst, Mol Struct & Funct Program, Toronto, ON M5G 0A4, Canada

[8] Uppsala Univ, Dept Med Biochem & Microbiol, SE-75123 Uppsala, Sweden

[9] Hosp Sick Children, Div Neurosurg, Program Dev & Stem Cell Biol, Toronto, ON M5G 1X8, Canada

[10] Univ Toronto, Dept Comp Sci, Toronto, ON M5G 1X8, Canada

[11] Canadian Inst Adv Res, Toronto, ON M5G 1Z8, Canada

[12] Dana Farber Canc Inst, Ctr Canc Syst Biol, Boston, MA 02215 USA

来源：

CELL | 2015年 / 163卷 / 06期

基金：

瑞士国家科学基金会; 瑞典研究理事会;

关键词：

SACCHAROMYCES-CEREVISIAE GENOME; MITOCHONDRIAL PROTEIN-SYNTHESIS; HUMAN-CELLS; RNAI SCREENS; INHIBITION; MAP; P53; VULNERABILITIES; OXAZOLIDINONES; ENDONUCLEASE;

D O I：

10.1016/j.cell.2015.11.015

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context-dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.

引用

页码：1515 / 1526

页数：12

共 47 条

[1] Epigenetic and genetic features of 24 colon cancer cell lines [J].

Ahmed, D. ;

Eide, P. W. ;

Eilertsen, I. A. ;

Danielsen, S. A. ;

Eknaes, M. ;

Hektoen, M. ;

Lind, G. E. ;

Lothe, R. A. .

ONCOGENESIS, 2013, 2 :e71-e71

[2] A human MAP kinase interactome [J].

Bandyopadhyay, Sourav ;

Chiang, Chih-yuan ;

Srivastava, Jyoti ;

Gersten, Merril ;

White, Suhaila ;

Bell, Russell ;

Kurschner, Cornelia ;

Martin, Christopher H. ;

Smoot, Mike ;

Sahasrabudhe, Sudhir ;

Barber, Diane L. ;

Chanda, Sumit K. ;

Ideker, Trey .

NATURE METHODS, 2010, 7 (10) :801-U50

[3] The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity [J].

Barretina, Jordi ;

Caponigro, Giordano ;

Stransky, Nicolas ;

Venkatesan, Kavitha ;

Margolin, Adam A. ;

Kim, Sungjoon ;

Wilson, Christopher J. ;

Lehar, Joseph ;

Kryukov, Gregory V. ;

Sonkin, Dmitriy ;

Reddy, Anupama ;

Liu, Manway ;

Murray, Lauren ;

Berger, Michael F. ;

Monahan, John E. ;

Morais, Paula ;

Meltzer, Jodi ;

Korejwa, Adam ;

Jane-Valbuena, Judit ;

Mapa, Felipa A. ;

Thibault, Joseph ;

Bric-Furlong, Eva ;

Raman, Pichai ;

Shipway, Aaron ;

Engels, Ingo H. ;

Cheng, Jill ;

Yu, Guoying K. ;

Yu, Jianjun ;

Aspesi, Peter, Jr. ;

de Silva, Melanie ;

Jagtap, Kalpana ;

Jones, Michael D. ;

Wang, Li ;

Hatton, Charles ;

Palescandolo, Emanuele ;

Gupta, Supriya ;

Mahan, Scott ;

Sougnez, Carrie ;

Onofrio, Robert C. ;

Liefeld, Ted ;

MacConaill, Laura ;

Winckler, Wendy ;

Reich, Michael ;

Li, Nanxin ;

Mesirov, Jill P. ;

Gabriel, Stacey B. ;

Getz, Gad ;

Ardlie, Kristin ;

Chan, Vivien ;

Myer, Vic E. .

NATURE, 2012, 483 (7391) :603-607

[4] Extension of life-span by introduction of telomerase into normal human cells [J].

Bodnar, AG ;

Ouellette, M ;

Frolkis, M ;

Holt, SE ;

Chiu, CP ;

Morin, GB ;

Harley, CB ;

Shay, JW ;

Lichtsteiner, S ;

Wright, WE .

SCIENCE, 1998, 279 (5349) :349-352

[5] An ecosystem of cancer cell line factories to support a cancer dependency map [J].

Boehm, Jesse S. ;

Golub, Todd R. .

NATURE REVIEWS GENETICS, 2015, 16 (07) :373-374

[6] Organoid Models of Human and Mouse Ductal Pancreatic Cancer [J].

Boj, Sylvia F. ;

Hwang, Chang-Il ;

Baker, Lindsey A. ;

Chio, Iok In Christine ;

Engle, Dannielle D. ;

Corbo, Vincenzo ;

Jager, Myrthe ;

Ponz-Sarvise, Mariano ;

Tiriac, Herve ;

Spector, Mona S. ;

Gracanin, Ana ;

Oni, Tobiloba ;

Yu, Kenneth H. ;

van Boxtel, Ruben ;

Huch, Meritxell ;

Rivera, Keith D. ;

Wilson, John P. ;

Feigin, Michael E. ;

Oehlund, Daniel ;

Handly-Santana, Abram ;

Ardito-Abraham, Christine M. ;

Ludwig, Michael ;

Elyada, Ela ;

Alagesan, Brinda ;

Biffi, Giulia ;

Yordanov, Georgi N. ;

Delcuze, Bethany ;

Creighton, Brianna ;

Wright, Kevin ;

Park, Youngkyu ;

Morsink, Folkert H. M. ;

Molenaar, I. Quintus ;

Rinkes, Inne H. Borel ;

Cuppen, Edwin ;

Hao, Yuan ;

Jin, Ying ;

Nijman, Isaac J. ;

Iacobuzio-Donahue, Christine ;

Leach, Steven D. ;

Pappin, Darryl J. ;

Hammell, Molly ;

Klimstra, David S. ;

Basturk, Olca ;

Hruban, Ralph H. ;

Offerhaus, George Johan ;

Vries, Robert G. J. ;

Clevers, Hans ;

Tuveson, David A. .

CELL, 2015, 160 (1-2) :324-338

[7] Effects of metformin and other biguanides on oxidative phosphorylation in mitochondria [J].

Bridges, Hannah R. ;

Jones, Andrew J. Y. ;

Pollak, Michael N. ;

Hirst, Judy .

BIOCHEMICAL JOURNAL, 2014, 462 :475-487

[8]

Castellano Esther, 2011, Genes Cancer, V2, P261, DOI 10.1177/1947601911408079

[9] Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis [J].

Chen, Sidi ;

Sanjana, Neville E. ;

Zheng, Kaijie ;

Shalem, Ophir ;

Lee, Kyungheon ;

Shi, Xi ;

Scott, David A. ;

Song, Jun ;

Pan, Jen Q. ;

Weissleder, Ralph ;

Lee, Hakho ;

Zhang, Feng ;

Sharp, Phillip A. .

CELL, 2015, 160 (06) :1246-1260

[10] Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease [J].

Cho, Seung Woo ;

Kim, Sojung ;

Kim, Jong Min ;

Kim, Jin-Soo .

NATURE BIOTECHNOLOGY, 2013, 31 (03) :230-232

← 1 2 3 4 5 →