CRISPR/Cas9 library screening for drug target discovery

Journal of Human Genetics

Volumn 63, Issue 2, 2018, Pages 179-186

  Kurata, Morito ^a,b   Yamamoto, Kouhei ^a   Moriarity, Branden S ^b,c   Kitagawa, Masanobu ^a   Largaespada, David A ^b,c,d  

^a TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

CRISPR-CAS9 SYSTEM; DNA LIBRARY; DRUG SCREENING; GENE TARGETING; GENETIC SCREENING; HUMAN; NONHUMAN; REVIEW; RNA SEQUENCE; SINGLE CELL ANALYSIS; TUMOR GENE; ANIMAL; CRISPR CAS SYSTEM; DRUG DELIVERY SYSTEM; DRUG DEVELOPMENT; GENE LIBRARY; PROCEDURES;

ANIMALS; CRISPR-CAS SYSTEMS; DRUG DELIVERY SYSTEMS; DRUG DISCOVERY; GENE LIBRARY; HUMANS;

EID: 85034585650     PISSN: 14345161     EISSN: 1435232X     Source Type: Journal    
DOI: 10.1038/s10038-017-0376-9     Document Type: Review

References (49)

1. 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.
2. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR. Science. 2013; 339: 819-23.
3. Cheng AW, Wang H, Yang H, Shi L, Katz Y, Theunissen TW, et al. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res. 2013; 23: 1163-71.
4. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013; 152: 1173-83.
5. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013; 154: 442-51.
6. Lin S, Ewen-Campen B, Ni X, Housden BE, Perrimon N. In vivo transcriptional activation using CRISPR/Cas9 in Drosophila. Genetics. 2015; 201: 433-42.
7. Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature. 2015; 517: 583-8.
8. Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell. 2014; 159: 635-46.
9. Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, et al. Epigenome editing by a CRISPRCas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015; 33: 510-7.
10. Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, et al. Comparison of Cas9 activators in multiple species. Nat Methods. 2016; 13: 563-7.
11. Nakamura T. Retroviral insertional mutagenesis identifies oncogene cooperation. Cancer Sci. 2005; 96: 7-12.
12. Largaespada DA. Transposon-mediated mutagenesis of somatic cells in the mouse for cancer gene identification. Methods. 2009; 49: 282-6.
13. Westbrook TF, Martin ES, Schlabach MR, Leng Y, Liang AC, Feng B, et al. A genetic screen for candidate tumor suppressors identifies REST. Cell. 2005; 121: 837-48.
14. Kolfschoten IG, van Leeuwen B, Berns K, Mullenders J, Beijersbergen RL, Bernards R, et al. A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell. 2005; 121: 849-58.
15. Ngo VN, Davis RE, Lamy L, Yu X, Zhao H, Lenz G, et al. A lossof-function RNA interference screen for molecular targets in cancer. Nature. 2006; 441: 106-10.
16. Schlabach MR, Luo J, Solimini NL, Hu G, Xu Q, Li MZ, et al. Cancer proliferation gene discovery through functional genomics. Science. 2008; 319: 620-4.
17. Ranzani M, Annunziato S, Calabria A, Brasca S, Benedicenti F, Gallina P, et al. Lentiviral vector-based insertional mutagenesis identifies genes involved in the resistance to targeted anticancer therapies. Mol. Ther. 2014; 22: 2056-68.
18. Chen L, Stuart L, Ohsumi TK, Burgess S, Varshney GK, Dastur A, et al. Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics. BMC Cancer. 2013; 13: 93
19. Khorashad JS, Eiring AM, Mason CC, Gantz KC, Bowler AD, Redwine HM, et al. shRNA library screening identifies nucleocytoplasmic transport as a mediator of BCR-ABL1 kinase-independent resistance. Blood. 2015; 125: 1772-81.
20. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014; 343: 84-7.
21. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014; 343: 80-4.
22. Kurata M, Rathe SK, Bailey NJ, Aumann NK, Jones JM, Veldhuijzen GW, et al. Using genome-wide CRISPR library screening with library resistant DCK to find new sources of Ara-C drug resistance in AML. Sci Rep. 2016; 6: 36199.
23. 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.
24. 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.
25. Tzelepis K, KoikeYusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, et al. A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia. Cell Rep. 2016; 17: 1193-205.
26. 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.
27. Ledford H. Cancer: rhe Ras renaissance. Nature. 2015; 520: 278-80.
28. Wang T, Yu H, Hughes NW, Liu B, Kendirli A, Klein K, et al. Gene essentiality profiling reveals gene networks and synthetic lethal interactions with oncogenic Ras. Cell. 2017; 168: 890-903. e15
29. Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, et al. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Elife. 2016: 5. https://doi. org/10. 7554/eLife. 19760.
30. Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, et al. CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells. Science. 355. https://doi. org/10. 1126/science. aah7111.
31. Wong AS, Choi GC, Cui CH, Pregernig G, Milani P, Adam M, et al. Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. Proc Natl Acad Sci USA. 2016; 113: 2544-9.
32. Han K, Jeng EE, Hess GT, Morgens DW, Li A, Bassik MC. Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions. Nat Biotechnol. 2017; 35: 463-74.
33. Zhu S, Li W, Liu J, Chen CH, Liao Q, Xu P, et al. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol. 2016; 34: 1279-86.
34. Junker JP, van Oudenaarden A. Every cell is special: genomewide studies add a new dimension to single-cell biology. Cell. 2014; 157: 8-11.
35. Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, et al. Pooled CRISPR screening with single-cell transcriptome readout. Nat Methods. 2017 14: 297-301.
36. Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, et al. Perturb-Seq: dissecting molecular circuits with scalable single-cell rna profiling of pooled genetic screens. Cell. 2016; 167: 1853-66. e17.
37. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, et al. Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq. Cell. 2016; 167: 1883-96. e15.
38. Sanjana NE, Shalem O, Zhang F. Improved vectors and genomewide libraries for CRISPR screening. Nat Methods. 2014; 11: 783-84.
39. Jain IH, Zazzeron L, Goli R, Alexa K, Schatzman Bone S, Dhillon H, et al. Hypoxia as a therapy for mitochondrial disease. Science. 2016; 352: 54-61.
40. Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, et al. Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature. 2016; 535: 159-63.
41. Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016; 34: 184-91.
42. Blondel CJ, Park JS, Hubbard TP, Pacheco AR, Kuehl CJ, Walsh MJ, et al. CRISPR/Cas9 screens reveal requirements for host cell sulfation and fucosylation in bacterial type iii secretion system-mediated cytotoxicity. Cell Host Microbe. 2016; 20: 226-37.
43. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, et al. Highthroughput screening of a CRISPR. Nature. 2014; 509: 487-91.
44. Ma H, Dang Y, Wu Y, Jia G, Anaya E, Zhang J, et al. A CRISPRbased screen identifies genes essential for West Nile virus-induced cell death. Cell Rep. 2015; 12: 673-83.
45. Kim HS, Lee K, Bae S, Park J, Lee CK, Kim M, et al. CRISPR/Cas9-mediated gene-knockout screens and target identification via whole genome sequencing uncover host genes required for picornavirus infection. J Biol Chem. 2017; 292: 10664-71.
46. Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe Molina P, Monel B, et al. A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nat Genet. 2017; 49: 193-203.
47. Koike-Yusa H, Li Y, Tan EP, Velasco-Herrera Mdel C, Yusa K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol. 2014; 32: 267-73.
48. Haga K, Fujimoto A, Takai-Todaka R, Miki M, Doan YH, Murakami K, et al. Functional receptor molecules CD300lf and CD300ld within the CD300 family enable murine noroviruses to infect cells. Proc Natl Acad Sci USA. 2016; 113: E6248-55.
49. Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 2015; 160: 1246-60.