Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions

被引：249

作者：

Shen, John Paul ^{[1
,2
,3
,4
]}

Zhao, Dongxin ^{[3
,4
,5
]}

Sasik, Roman ^{[6
]}

Luebeck, Jens ^{[7
]}

Birmingham, Amanda ^{[6
]}

Bojorquez-Gomez, Ana ^{[1
]}

Licon, Katherine ^{[1
]}

Klepper, Kristin ^{[1
]}

Pekin, Daniel ^{[1
]}

Beckett, Alex N. ^{[1
]}

Sanchez, Kyle Salinas ^{[1
]}

Thomas, Alex ^{[7
,8
]}

Kuo, Chih-Chung ^{[5
]}

Du, Dan ^{[3
,4
,9
]}

Roguev, Assen ^{[3
,4
,10
]}

Lewis, Nathan E. ^{[8
,11
]}

Chang, Aaron N. ^{[6
]}

Kreisberg, Jason F. ^{[1
,3
,4
]}

Krogan, Nevan ^{[3
,4
,10
]}

Qi, Lei ^{[3
,4
,12
]}

Ideker, Trey ^{[1
,2
,3
,4
,6
]}

Mali, Prashant ^{[2
,3
,4
,5
]}

机构：

[1] Univ Calif San Diego, Dept Med, Div Genet, La Jolla, CA 92093 USA

[2] Moores UCSD Canc Ctr, La Jolla, CA 92093 USA

[3] Canc Cell Map Initiat, La Jolla, CA 92037 USA

[4] Canc Cell Map Initiat, San Francisco, CA 94143 USA

[5] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[6] Univ Calif San Diego, Ctr Computat Biol & Bioinformat, La Jolla, CA 92093 USA

[7] Univ Calif San Diego, Bioinformat & Syst Biol Program, La Jolla, CA 92093 USA

[8] Univ Calif San Diego, Novo Nordisk Ctr Biosustainabil, La Jolla, CA 92093 USA

[9] Univ Calif San Francisco, Dept Cell & Tissue Biol, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, San Francisco, CA 94143 USA

[10] Univ Calif San Francisco, Dept Cellular & Mol Pharmacol, San Francisco, CA 94143 USA

[11] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA

[12] Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA

来源：

NATURE METHODS | 2017年 / 14卷 / 06期

关键词：

FALSE DISCOVERY RATE; NETWORKS; CAS9; FITNESS; YEAST;

D O I：

10.1038/nmeth.4225

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We developed a systematic approach to map human genetic networks by combinatorial CRISPR Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies.

引用

页码：573 / +

页数：9

共 50 条

[41] High-throughput screens in mammalian cells using the CRISPR-Cas9 system
Peng, Jingyu
Zhou, Yuexin
Zhu, Shiyou
Wei, Wensheng
FEBS JOURNAL, 2015, 282 (11) : 2089 - 2096
[42] Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing
Dirk Heckl
Monika S Kowalczyk
David Yudovich
Roger Belizaire
Rishi V Puram
Marie E McConkey
Anne Thielke
Jon C Aster
Aviv Regev
Benjamin L Ebert
Nature Biotechnology, 2014, 32 : 941 - 946
[43] The MyLO CRISPR-Cas9 toolkit: a markerless yeast localization and overexpression CRISPR-Cas9 toolkit
Bean, Bjorn D. M.
Whiteway, Malcolm
Martin, Vincent J. J.
G3-GENES GENOMES GENETICS, 2022, 12 (08):
[44] Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification
Deans, Richard M.
Morgens, David W.
Okesli, Ayse
Pillay, Sirika
Horlbeck, Max A.
Kampmann, Martin
Gilbert, Luke A.
Li, Amy
Mateo, Roberto
Smith, Mark
Glenn, Jeffrey S.
Carette, Jan E.
Khosla, Chaitan
Bassik, Michael C.
NATURE CHEMICAL BIOLOGY, 2016, 12 (05) : 361 - +
[45] Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification
Deans R.M.
Morgens D.W.
Ökesli A.
Pillay S.
Horlbeck M.A.
Kampmann M.
Gilbert L.A.
Li A.
Mateo R.
Smith M.
Glenn J.S.
Carette J.E.
Khosla C.
Bassik M.C.
Nature Chemical Biology, 2016, 12 (5) : 361 - 366
[46] Mapping the Boundary of DNA Unwinding in CRISPR-Cas9 Target Recognition
Liu, Yukang
Li, Yue
Tangprasertchai, Narin
Qin, Peter Z.
BIOPHYSICAL JOURNAL, 2020, 118 (03) : 224A - 224A
[47] CRISPR-Cas9 screens identify regulators of antibody-drug conjugate toxicity
Tsui, C. Kimberly
Barfield, Robyn M.
Fischer, Curt R.
Morgens, David W.
Li, Amy
Smith, Benjamin A. H.
Gray, Melissa Anne
Bertozzi, Carolyn R.
Rabuka, David
Bassik, Michael C.
NATURE CHEMICAL BIOLOGY, 2019, 15 (10) : 949 - +
[48] Functional dissection of human mitotic genes using CRISPR-Cas9 tiling screens
Herman, Jacob A.
Arora, Sonali
Carter, Lucas
Zhu, Jun
Biggins, Sue
Paddison, Patrick J.
GENES & DEVELOPMENT, 2022, 36 (7-8) : 495 - 510
[49] New bioinformatics workflow of genome-wide CRISPR-Cas9 knockout screens
Zhao, Yue
Wu, Xue
Wang, Yuru
Au, Kin Fai
Cheng, Lijun
Li, Lang
CANCER RESEARCH, 2020, 80 (16)
[50] Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing
Heck, Dirk
Kowalczyk, Monika S.
Yudovich, David
Belizaire, Roger
Puram, Rishi V.
McConkey, Marie E.
Thielke, Anne
Aster, Jon C.
Regev, Aviv
Ebert, Benjamin L.
NATURE BIOTECHNOLOGY, 2014, 32 (09) : 941 - 946

← 1 2 3 4 5 →