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Target Discovery for Precision Medicine Using High-Throughput Genome Engineering

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Precision Medicine, CRISPR, and Genome Engineering

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1016))

Abstract

Over the past few years, programmable RNA-guided nucleases such as the CRISPR/Cas9 system have ushered in a new era of precision genome editing in diverse model systems and in human cells. Functional screens using large libraries of RNA guides can interrogate a large hypothesis space to pinpoint particular genes and genetic elements involved in fundamental biological processes and disease-relevant phenotypes. Here, we review recent high-throughput CRISPR screens (e.g. loss-of-function, gain-of-function, and targeting noncoding elements) and highlight their potential for uncovering novel therapeutic targets, such as those involved in cancer resistance to small molecular drugs and immunotherapies, tumor evolution, infectious disease, inborn genetic disorders, and other therapeutic challenges.

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References

  1. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013;339:823–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Cho SW, Kim S, Kim JM, Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol. 2013;31:230–2.

    Article  CAS  PubMed  Google Scholar 

  4. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–21.

    Article  CAS  PubMed  Google Scholar 

  5. Lieber MR, Ma Y, Pannicke U, Schwarz K. Mechanism and regulation of human non-homologous DNA end-joining. Nat Rev Mol Cell Biol. 2003;4:712–20.

    Article  CAS  PubMed  Google Scholar 

  6. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343:84–7.

    Article  CAS  PubMed  Google Scholar 

  7. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014;343:80–4.

    Article  CAS  PubMed  Google Scholar 

  8. Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc. 2017;12:828–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc. 2013;8:2180–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJ, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G. Comparison of Cas9 activators in multiple species. Nat Methods. 2016;13:563–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Klann TS, Black JB, Chellappan M, Safi A, Song L, Hilton IB, Crawford GE, Reddy TE, Gersbach CA. CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nat Biotechnol. 2017;35:561.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol. 2017;15:169–82.

    Article  CAS  PubMed  Google Scholar 

  13. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013;154:442–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014;32:670–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Sripathy SP, Stevens J, Schultz DC. The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression. Mol Cell Biol. 2006;26:8623–38.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS. Genome-scale CRISPR-mediated control of gene repression and activation. Cell. 2014;159:647–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science. 2016;354:769–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK. CRISPR RNA-guided activation of endogenous human genes. Nat Methods. 2013;10:977–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW, Guilak F, Crawford GE, Reddy TE, Gersbach CA. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods. 2013;10:973–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, Iyer EPR, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, Weiss R, Aach J, Collins JJ, Church GM. Highly efficient Cas9-mediated transcriptional programming. Nat Methods. 2015;12:326–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hilton IB, D’Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, Gersbach CA. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015;33:510–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Dominguez AA, Lim WA, Qi LS. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol. 2016;17:5–15.

    Article  CAS  PubMed  Google Scholar 

  23. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, Hsu PD, Habib N, Gootenberg JS, Nishimasu H, Nureki O, Zhang F. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature. 2015;517:583–8.

    Article  CAS  PubMed  Google Scholar 

  25. Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell. 2015;160:339–50.

    Article  CAS  PubMed  Google Scholar 

  26. Feng J, Fan G. The role of DNA methylation in the central nervous system and neuropsychiatric disorders. Int Rev Neurobiol. 2009;89:67–84.

    Article  CAS  PubMed  Google Scholar 

  27. Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Dadon D, Young RA, Jaenisch R. Editing DNA methylation in the mammalian genome. Cell. 2016;167:233–247 e217.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533:420–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Hess GT, Fresard L, Han K, Lee CH, Li A, Cimprich KA, Montgomery SB, Bassik MC. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods. 2016;13:1036–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhu S, Li W, Liu J, Chen CH, Liao Q, Xu P, Xu H, Xiao T, Cao Z, Peng J, Yuan P, Brown M, Liu XS, Wei W. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol. 2016;34:1279–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015;527:192–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F. High-resolution interrogation of functional elements in the noncoding genome. Science. 2016;353:1545–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galacteros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet. 2017;49:625.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Wong AS, Choi GC, Cui CH, Pregernig G, Milani P, Adam M, Perli SD, Kazer SW, Gaillard A, Hermann M, Shalek AK, Fraenkel E, Lu TK. Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. Proc Natl Acad Sci. 2016;113:2544–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163:759–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fonfara I, Richter H, Bratovic M, Le Rhun A, Charpentier E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature. 2016;532:517–21.

    Article  CAS  PubMed  Google Scholar 

  37. Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol. 2017;35:31–4.

    Article  CAS  PubMed  Google Scholar 

  38. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353:aaf5573.

    Article  PubMed  PubMed Central  Google Scholar 

  39. East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. 2016;538:270–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. de Bono JS, Ashworth A. Translating cancer research into targeted therapeutics. Nature. 2010;467:543–9.

    Article  PubMed  Google Scholar 

  41. Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med. 2015;372:793–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, Lander ES, Sabatini DM. Identification and characterization of essential genes in the human genome. Science. 2015;350:1096–101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, Mis M, Zimmermann M, Fradet-Turcotte A, Sun S, Mero P, Dirks P, Sidhu S, Roth FP, Rissland OS, Durocher D, Angers S, Moffat J. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell. 2015;163:1515–26.

    Article  CAS  PubMed  Google Scholar 

  44. Hong AL, Tseng YY, Cowley GS, Jonas O, Cheah JH, Kynnap BD, Doshi MB, Oh C, Meyer SC, Church AJ, Gill S, Bielski CM, Keskula P, Imamovic A, Howell S, Kryukov GV, Clemons PA, Tsherniak A, Vazquez F, Crompton BD, Shamji AF, Rodriguez-Galindo C, Janeway KA, Roberts CW, Stegmaier K, van Hummelen P, Cima MJ, Langer RS, Garraway LA, Schreiber SL, Root DE, Hahn WC, Boehm JS. Integrated genetic and pharmacologic interrogation of rare cancers. Nat Commun. 2016;7:11987.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 2015;160:1246–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Xu C, Qi X, Du X, Zou H, Gao F, Feng T, Lu H, Li S, An X, Zhang L, Wu Y, Liu Y, Li N, Capecchi MR, Wu S. piggyBac mediates efficient in vivo CRISPR library screening for tumorigenesis in mice. Proc Natl Acad Sci U S A. 2017;114:722–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Pagliarini R, Shao W, Sellers WR. Oncogene addiction: pathways of therapeutic response, resistance, and road maps toward a cure. EMBO Rep. 2015;16:280–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Kurata M, Rathe SK, Bailey NJ, Aumann NK, Jones JM, Veldhuijzen GW, Moriarity BS, Largaespada DA. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Ruiz S, Mayor-Ruiz C, Lafarga V, Murga M, Vega-Sendino M, Ortega S, Fernandez-Capetillo O. A genome-wide CRISPR screen identifies CDC25A as a determinant of sensitivity to ATR inhibitors. Mol Cell. 2016;62:307–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017;14:573.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Dang CV. MYC on the path to cancer. Cell. 2012;149:22–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Sen DR, Kaminski J, Barnitz RA, Kurachi M, Gerdemann U, Yates KB, Tsao HW, Godec J, LaFleur MW, Brown FD, Tonnerre P, Chung RT, Tully DC, Allen TM, Frahm N, Lauer GM, Wherry EJ, Yosef N, Haining WN. The epigenetic landscape of T cell exhaustion. Science. 2016;354:1165–9.

    Article  CAS  PubMed  Google Scholar 

  53. Ott PA, Hodi FS, Kaufman HL, Wigginton JM, Wolchok JD. Combination immunotherapy: a road map. J Immunother Cancer. 2017;5:16.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Golden RJ, Chen B, Li T, Braun J, Manjunath H, Chen X, Wu J, Schmid V, Chang TC, Kopp F, Ramirez-Martinez A, Tagliabracci VS, Chen ZJ, Xie Y, Mendell JT. An Argonaute phosphorylation cycle promotes microRNA-mediated silencing. Nature. 2017;542:197–202.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Kataoka K, Shiraishi Y, Takeda Y, Sakata S, Matsumoto M, Nagano S, Maeda T, Nagata Y, Kitanaka A, Mizuno S, Tanaka H, Chiba K, Ito S, Watatani Y, Kakiuchi N, Suzuki H, Yoshizato T, Yoshida K, Sanada M, Itonaga H, Imaizumi Y, Totoki Y, Munakata W, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Masuda K, Minato N, Kashiwase K, Izutsu K, Takaori-Kondo A, Miyazaki Y, Takahashi S, Shibata T, Kawamoto H, Akatsuka Y, Shimoda K, Takeuchi K, Seya T, Miyano S, Ogawa S. Aberrant PD-L1 expression through 3′-UTR disruption in multiple cancers. Nature. 2016;534:402–6.

    Article  CAS  PubMed  Google Scholar 

  56. Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P. Global trends in emerging infectious diseases. Nature. 2008;451:990–3.

    Article  CAS  PubMed  Google Scholar 

  57. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, Wei W. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature. 2014;509:487–91.

    Article  CAS  PubMed  Google Scholar 

  58. Coburn B, Sekirov I, Finlay BB. Type III secretion systems and disease. Clin Microbiol Rev. 2007;20:535–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Blondel CJ, Park JS, Hubbard TP, Pacheco AR, Kuehl CJ, Walsh MJ, Davis BM, Gewurz BE, Doench JG, Waldor MK. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Mackenzie JS, Gubler DJ, Petersen LR. Emerging flaviviruses: the spread and resurgence of Japanese encephalitis, West Nile and dengue viruses. Nat Med. 2004;10:S98–S109.

    Article  CAS  PubMed  Google Scholar 

  61. Petersen LR, Jamieson DJ, Powers AM, Honein MA. Zika virus. N Engl J Med. 2016;374:1552–63.

    Article  CAS  PubMed  Google Scholar 

  62. Simmonds P. Genetic diversity and evolution of hepatitis C virus--15 years on. J Gen Virol. 2004;85:3173–88.

    Article  CAS  PubMed  Google Scholar 

  63. Ma H, Dang Y, Wu Y, Jia G, Anaya E, Zhang J, Abraham S, Choi JG, Shi G, Qi L, Manjunath N, Wu H. A CRISPR-based screen identifies genes essential for West-Nile-virus-induced cell death. Cell Rep. 2015;12:673–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Zhang R, Miner JJ, Gorman MJ, Rausch K, Ramage H, White JP, Zuiani A, Zhang P, Fernandez E, Zhang Q, Dowd KA, Pierson TC, Cherry S, Diamond MS. A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. Nature. 2016;535:164–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, Swaminathan K, Mata MA, Elias JE, Sarnow P, Carette JE. Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature. 2016;535:159–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltran W, Piechocka-Trocha A, Krogan NJ, Marson A, Sabatini DM, Lander ES, Hacohen N, Walker BDA. Genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nat Genet. 2017;49:193–203.

    Article  CAS  PubMed  Google Scholar 

  67. Falagas ME, Lourida P, Poulikakos P, Rafailidis PI, Tansarli GS. Antibiotic treatment of infections due to carbapenem-resistant Enterobacteriaceae: systematic evaluation of the available evidence. Antimicrob Agents Chemother. 2014;58:654–63.

    Article  PubMed  PubMed Central  Google Scholar 

  68. Schito GC. The importance of the development of antibiotic resistance in Staphylococcus aureus. Clin Microbiol Infect. 2006;12(Suppl 1):3–8.

    Article  CAS  PubMed  Google Scholar 

  69. Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CH, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA. A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell. 2016;165:1493–506.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Sidik SM, Huet D, Ganesan SM, Huynh MH, Wang T, Nasamu AS, Thiru P, Saeij JP, Carruthers VB, Niles JC, Lourido S. A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes. Cell. 2016;166:1423–1435 e1412.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Weatherall DJ. The inherited diseases of hemoglobin are an emerging global health burden. Blood. 2010;115:4331–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Uda M, Galanello R, Sanna S, Lettre G, Sankaran VG, Chen W, Usala G, Busonero F, Maschio A, Albai G, Piras MG, Sestu N, Lai S, Dei M, Mulas A, Crisponi L, Naitza S, Asunis I, Deiana M, Nagaraja R, Perseu L, Satta S, Cipollina MD, Sollaino C, Moi P, Hirschhorn JN, Orkin SH, Abecasis GR, Schlessinger D, Cao A. Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia. Proc Natl Acad Sci U S A. 2008;105:1620–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Chow J, Rahman J, Achermann JC, Dattani MT, Rahman S. Mitochondrial disease and endocrine dysfunction. Nat Rev Endocrinol. 2017;13:92–104.

    Article  CAS  PubMed  Google Scholar 

  74. Jain IH, Zazzeron L, Goli R, Alexa K, Schatzman-Bone S, Dhillon H, Goldberger O, Peng J, Shalem O, Sanjana NE, Zhang F, Goessling W, Zapol WM, Mootha VK. Hypoxia as a therapy for mitochondrial disease. Science. 2016;352:54–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Arroyo JD, Jourdain AA, Calvo SE, Ballarano CA, Doench JG, Root DE, Mootha VK. A genome-wide CRISPR death screen identifies genes essential for oxidative phosphorylation. Cell Metab. 2016;24:875–85.

    Article  CAS  PubMed  Google Scholar 

  76. Ohh M, Park CW, Ivan M, Hoffman MA, Kim TY, Huang LE, Pavletich N, Chau V, Kaelin WG. Ubiquitination of hypoxia-inducible factor requires direct binding to the beta-domain of the von Hippel-Lindau protein. Nat Cell Biol. 2000;2:423–7.

    Article  CAS  PubMed  Google Scholar 

  77. Barrow JJ, Balsa E, Verdeguer F, Tavares CD, Soustek MS, Hollingsworth LR t, Jedrychowski M, Vogel R, Paulo JA, Smeitink J, Gygi SP, Doench J, Root DE, Puigserver P. Bromodomain inhibitors correct bioenergetic deficiency caused by mitochondrial disease complex I mutations. Mol Cell. 2016;64:163–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Pickrell JK. Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Am J Hum Genet. 2014;94:559–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Xie S, Duan J, Li B, Zhou P, Hon GC. Multiplexed engineering and analysis of combinatorial enhancer activity in single cells. Mol Cell. 2017;66:285–299 e285.

    Article  CAS  PubMed  Google Scholar 

  80. Adamson B, Norman TM, Jost M, Cho MY, Nunez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell. 2016;167:1867–1882e1821.

    Article  CAS  PubMed  Google Scholar 

  81. Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A. Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell. 2016;167:1853–1866e1817.

    Article  CAS  PubMed  Google Scholar 

  82. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A, Amit I. Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq. Cell. 2016;167:1883–1896e1815.

    Article  CAS  PubMed  Google Scholar 

  83. Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, Schuster LC, Kuchler A, Alpar D, Bock C. Pooled CRISPR screening with single-cell transcriptome readout. Nat Methods. 2017;14:297–301.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Canver MC, Bauer DE, Dass A, Yien YY, Chung J, Masuda T, Maeda T, Paw BH, Orkin SH. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J Biol Chem. 2014;289:21312–24.

    Article  PubMed  PubMed Central  Google Scholar 

  85. Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi MB, Kost-Alimova M, Gill S, Xu H, Ali LD, Jiang G, Pantel S, Lee Y, Goodale A, Cherniack AD, Oh C, Kryukov G, Cowley GS, Garraway LA, Stegmaier K, Roberts CW, Golub TR, Meyerson M, Root DE, Tsherniak A, Hahn WC. Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting. Cancer Discov. 2016;6:914–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Wu Y, Zhou L, Wang X, Lu J, Zhang R, Liang X, Wang L, Deng W, Zeng YX, Huang H, Kang T. A genome-scale CRISPR-Cas9 screening method for protein stability reveals novel regulators of Cdc25A. Cell Discov. 2016;2:16014.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Ohnishi S, Cooper J, Patel M, McKerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, McDermott U, Saez-Rodriguez J, Huntly BJ, Iorio F, Pina C, Vassiliou GS, Yusa K. A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia. Cell Rep. 2016;17:1193–205.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Erb MA, Scott TG, Li BE, Xie H, Paulk J, Seo HS, Souza A, Roberts JM, Dastjerdi S, Buckley DL, Sanjana NE, Shalem O, Nabet B, Zeid R, Offei-Addo NK, Dhe-Paganon S, Zhang F, Orkin SH, Winter GE, Bradner JE. Transcription control by the ENL YEATS domain in acute leukaemia. Nature. 2017;543:270.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Wallace J, Hu R, Mosbruger TL, Dahlem TJ, Stephens WZ, Rao DS, Round JL, O’Connell RM. Genome-wide CRISPR-Cas9 screen identifies MicroRNAs that regulate myeloid leukemia cell growth. PLoS One. 2016;11:e0153689.

    Article  PubMed  PubMed Central  Google Scholar 

  90. Shi J, Wang E, Milazzo JP, Wang Z, Kinney JB, Vakoc CR. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol. 2015;33:661–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Gayle S, Landrette S, Beeharry N, Conrad C, Hernandez M, Beckett P, Ferguson SM, Mandelkern T, Zheng M, Xu T, Rothberg J, Lichenstein H. Identification of apilimod as a first-in-class PIKfyve kinase inhibitor for treatment of B-cell non-Hodgkin lymphoma. Blood. 2017;129:1768.

    Article  CAS  PubMed  Google Scholar 

  92. Katigbak A, Cencic R, Robert F, Senecha P, Scuoppo C, Pelletier J. A CRISPR/Cas9 functional screen identifies rare tumor suppressors. Sci Rep. 2016;6:38968.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Song CQ, Li Y, Mou H, Moore J, Park A, Pomyen Y, Hough S, Kennedy Z, Fischer A, Yin H, Anderson DG, Conte D Jr, Zender L, Wang XW, Thorgeirsson S, Weng Z, Xue W, Genome-wide CRISPR. Screen identifies regulators of MAPK as suppressors of liver tumors in mice. Gastroenterology. 2016;152:1161.

    Article  PubMed  Google Scholar 

  94. Kiessling MK, Schuierer S, Stertz S, Beibel M, Bergling S, Knehr J, Carbone W, de Valliere C, Tchinda J, Bouwmeester T, Seuwen K, Rogler G, Roma G. Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening. BMC Genomics. 2016;17:723.

    Article  PubMed  PubMed Central  Google Scholar 

  95. Phelps MP, Bailey JN, Vleeshouwer-Neumann T, Chen EY. CRISPR screen identifies the NCOR/HDAC3 complex as a major suppressor of differentiation in rhabdomyosarcoma. Proc Natl Acad Sci U S A. 2016;113:15090–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R, Agami R. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat Biotechnol. 2016;34:192–8.

    Article  CAS  PubMed  Google Scholar 

  97. Steinhart Z, Pavlovic Z, Chandrashekhar M, Hart T, Wang X, Zhang X, Robitaille M, Brown KR, Jaksani S, Overmeer R, Boj SF, Adams J, Pan J, Clevers H, Sidhu S, Moffat J, Angers S, Genome-wide CRISPR. Screens reveal a Wnt-FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors. Nat Med. 2017;23:60–8.

    Article  CAS  PubMed  Google Scholar 

  98. 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.

    Article  CAS  PubMed  Google Scholar 

  99. Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell. 2015;162:675–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Virreira Winter S, Zychlinsky A, Bardoel BW. Genome-wide CRISPR screen reveals novel host factors required for Staphylococcus aureus Alpha-hemolysin-mediated toxicity. Sci Rep. 2016;6:24242.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Guo, X., Chitale, P., Sanjana, N.E. (2017). Target Discovery for Precision Medicine Using High-Throughput Genome Engineering. In: Tsang, S. (eds) Precision Medicine, CRISPR, and Genome Engineering. Advances in Experimental Medicine and Biology, vol 1016. Springer, Cham. https://doi.org/10.1007/978-3-319-63904-8_7

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