Cornerstones of CRISPR-Cas in drug discovery and therapy

Nature Reviews Drug Discovery

Volumn 16, Issue 2, 2017, Pages 89-100

  Fellmann, Christof ^a   Gowen, Benjamin G ^a   Lin, Pei Chun ^a,b   Doudna, Jennifer A ^a,c   Corn, Jacob E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CRISPR ASSOCIATED PROTEIN;

BIOLOGICAL MODEL; BIOTECHNOLOGY; CELL THERAPY; CRISPR CAS SYSTEM; DRUG IDENTIFICATION; DRUG RESEARCH; DRUG THERAPY; EX VIVO STUDY; FUNCTIONAL GENOMICS; GENE CONTROL; GENE EDITING; GENE SEQUENCE; GENE THERAPY; GENETIC DISORDER; GENETIC ENGINEERING; GENETIC SCREENING; HUMAN; MEDICAL INFORMATION; MOLECULAR BIOLOGY; MOLECULAR GENETICS; NONHUMAN; PATIENT SAFETY; PHYSICAL DISEASE; REVIEW; T LYMPHOCYTE; VALIDATION STUDY; ANIMAL; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DRUG DEVELOPMENT; DRUG EFFECTS; TRENDS;

ANIMALS; BIOMARKERS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; DRUG DISCOVERY; DRUG THERAPY; GENETIC ENGINEERING; GENETIC THERAPY; HUMANS;

EID: 85007179090     PISSN: 14741776     EISSN: 14741784     Source Type: Journal    
DOI: 10.1038/nrd.2016.238     Document Type: Review

References (159)

1. Crick, F. Central dogma of molecular biology. Nature 227, 561-563 (1970).
2. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
3. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826 (2013).
4. Jinek, M. et al. RNA-programmed genome editing in human cells. eLife 2, e00471 (2013).
5. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
6. Cho, S. W., Kim, S., Kim, J. M. & Kim, J.-S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol. 31, 230-232 (2013). References 2-6 describe the development and first use of the CRISPR-Cas9 system for genome editing in mammalian cells.
7. Cox, D. B. T., Platt, R. J. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med. 21, 121-131 (2015).
8. Hopkins, A. L. & Groom, C. R. The druggable genome. Nat. Rev. Drug Discov. 1, 727-730 (2002).
9. Wright, A. V., Nuñez, J. K. & Doudna, J. A. Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering. Cell 164, 29-44 (2016).
10. Doudna, J. A. & Charpentier, E. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).
11. Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278 (2014).
12. Moore, J. K. & Haber, J. E. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 2164-2173 (1996).
13. Guirouilh-Barbat, J. et al. Impact of the KU80 pathway on NHEJ-induced genome rearrangements in mammalian cells. Mol. Cell 14, 611-623 (2004).
14. Roth, D. B. & Wilson, J. H. Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. Mol. Cell. Biol. 6, 4295-4304 (1986).
15. Resnick, M. A. The repair of double-strand breaks in DNA; a model involving recombination. J. Theor. Biol. 59, 97-106 (1976).
16. Orr-Weaver, T. L., Szostak, J. W. & Rothstein, R. J. Yeast transformation: a model system for the study of recombination. Proc. Natl Acad. Sci. USA 78, 6354-6358 (1981).
17. Szostak, J. W., Orr-Weaver, T. L., Rothstein, R. J. & Stahl, F. W. The double-strand-break repair model for recombination. Cell 33, 25-35 (1983).
18. Lin, F. L., Sperle, K. & Sternberg, N. Model for homologous recombination during transfer of DNA into mouse L cells: role for DNA ends in the recombination process. Mol. Cell. Biol. 4, 1020-1034 (1984).
19. Jasin, M., de Villiers, J., Weber, F. & Schaffner, W. High frequency of homologous recombination in mammalian cells between endogenous and introduced SV40 genomes. Cell 43, 695-703 (1985).
20. Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647-661 (2014).
21. Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583-588 (2015).
22. Gilbert, L. A. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442-451 (2013). References 20-22 describe the development and application of CRISPRi and CRISPRa.
23. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519-525 (2012).
24. The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).
25. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2013).
26. The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
27. The Cancer Genome Atlas Research Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
28. Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012).
29. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636-640 (2004).
30. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
31. Thon, N., Kreth, S. & Kreth, F.-W. Personalized treatment strategies in glioblastoma: MGMT promoter methylation status. Onco. Targets Ther. 6, 1363-1372 (2013).
32. Shirasawa, S., Furuse, M., Yokoyama, N. & Sasazuki, T. Altered growth of human colon cancer cell lines disrupted at activated Ki-ras. Science 260, 85-88 (1993).
33. Sur, S. et al. A panel of isogenic human cancer cells suggests a therapeutic approach for cancers with inactivated p53. Proc. Natl Acad. Sci. USA 106, 3964-3969 (2009).
34. Torrance, C. J., Agrawal, V., Vogelstein, B. & Kinzler, K. W. Use of isogenic human cancer cells for high-throughput screening and drug discovery. Nat. Biotechnol. 19, 940-945 (2001).
35. Yun, J. et al. Glucose deprivation contributes to the development of KRAS pathway mutations in tumor cells. Science 325, 1555-1559 (2009).
36. Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281-2308 (2013).
37. Schumann, K. et al. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc. Natl Acad. Sci. USA 112, 10437-10442 (2015). This paper demonstrates high-efficiency editing of primary human cells using Cas9 RNPs.
38. Grobarczyk, B., Franco, B., Hanon, K. & Malgrange, B. Generation of isogenic human iPS cell line precisely corrected by genome editing using the CRISPR/Cas9 system. Stem Cell Rev. 11, 774-787 (2015).
39. Matano, M. et al. Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids. Nat. Med. 21, 256-262 (2015).
40. Drost, J. et al. Sequential cancer mutations in cultured human intestinal stem cells. Nature 521, 43-47 (2015).
41. Carette, J. E. et al. Haploid genetic screens in human cells identify host factors used by pathogens. Science 326, 1231-1235 (2009).
42. Carette, J. E. et al. Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. Nature 477, 340-343 (2011).
43. Shi, J. et al. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat. Biotechnol. 33, 661-667 (2015). This article shows how CRISPRn-mediated targeting of functional protein domains improves knockout screening.
44. Kasap, C., Elemento, O. & Kapoor, T. M. DrugTargetSeqR: a genomics-And CRISPR-Cas9-based method to analyze drug targets. Nat. Chem. Biol. 10, 626-628 (2014).
45. Smurnyy, Y. et al. DNA sequencing and CRISPR-Cas9 gene editing for target validation in mammalian cells. Nat. Chem. Biol. 10, 623-625 (2014).
46. Chen, J., Ye, Y., Sun, H. & Shi, G. Association between KRAS codon 13 mutations and clinical response to anti-EGFR treatment in patients with metastatic colorectal cancer: results from a meta-Analysis. Cancer Chemother. Pharmacol. 71, 265-272 (2013).
47. Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558 (2013).
48. Paix, A. et al. Scalable and versatile genome editing using linear DNAs with microhomology to Cas9 Sites in Caenorhabditis elegans. Genetics 198, 1347-1356 (2014).
49. Paix, A., Schmidt, H. & Seydoux, G. Cas9-Assisted recombineering in C. elegans: genome editing using in vivo assembly of linear DNAs. Nucleic Acids Res. 44, e128 (2016).
50. Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L. & Corn, J. E. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat. Biotechnol. 34, 339-344 (2016). Here, mechanism-guided design of ssDNA templates is used for efficient HDR.
51. Paquet, D. et al. Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9. Nature 533, 125-129 (2016).
52. Nakade, S. et al. Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9. Nat. Commun. 5, 5560 (2014).
53. Sakuma, T., Nakade, S., Sakane, Y., Suzuki, K.-I. T. & Yamamoto, T. MMEJ-Assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems. Nat. Protoc. 11, 118-133 (2016).
54. Suzuki, K. et al. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540, 144-149 (2016).
55. He, X. et al. Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair. Nucleic Acids Res. 44, e85 (2016)
56. Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420-424 (2016).
57. Nishida, K. et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353, aaf8729 (2016). References 56 and 57 show the engineering of chimeric Cas enzymes for position-specific base editing.
58. Cheung, H. W. et al. Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Proc. Natl Acad. Sci. USA 108, 12372-12377 (2011).
59. Fellmann, C. & Lowe, S. W. Stable RNA interference rules for silencing. Nat. Cell Biol. 16, 10-18 (2014).
60. Deans, R. M. et al. Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification. Nat. Chem. Biol. 12, 361-366 (2016).
61. Jae, L. T. et al. Lassa virus entry requires a trigger-induced receptor switch. Science 344, 1506-1510 (2014).
62. Blomen, V. A. et al. Gene essentiality and synthetic lethality in haploid human cells. Science 350, 1092-1096 (2015).
63. Hart, T. et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163, 1515-1526 (2015).
64. Wang, T. et al. Identification and characterization of essential genes in the human genome. Science 350, 1096-1101 (2015).
65. Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87 (2014).
66. Koike-Yusa, H., Li, Y., Tan, E.-P., Velasco-Herrera, M. D. C. & Yusa, K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat. Biotechnol. 32, 267-273 (2014). References 65 and 66 are pioneering genome-wide CRISPRn screens.
67. Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184-191 (2016). This article describes the development of an improved sgRNA design tool.
68. Munoz, D. M. et al. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer Discov. 6, 900-913 (2016).
69. Aguirre, A. J. et al. Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting. Cancer Discov. 6, 914-929 (2016). References 64, 68 and 69 show that CRISPR-Cas9 can generate false-positive effects at amplified loci.
70. Morgens, D. W., Deans, R. M., Li, A. & Bassik, M. C. Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nat. Biotechnol. 34, 634-636 (2016).
71. Marceau, C. D. et al. Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature 535, 159-163 (2016).
72. Chen, S. et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 160, 1246-1260 (2015).
73. Mandegar, M. A. et al. CRISPR interference efficiently induces specific and reversible gene silencing in human iPSCs. Cell Stem Cell 18, 541-553 (2016).
74. Kampmann, M. et al. Next-generation libraries for robust RNA interference-based genome-wide screens. Proc. Natl Acad. Sci. USA 112, E3384-E3391 (2015).
75. Tanenbaum, M. E., Gilbert, L. A., Qi, L. S., Weissman, J. S. & Vale, R. D. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159, 635-646 (2014).
76. Hilton, I. B. et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33, 510-517 (2015).
77. Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339-350 (2015).
78. Chavez, A. et al. Highly efficient Cas9-mediated transcriptional programming. Nat. Methods 12, 326-328 (2015).
79. Chakraborty, S. et al. A CRISPR/Cas9-based system for reprogramming cell lineage specification. Stem Cell Rep. 3, 940-947 (2014).
80. Cheng, A. W. et al. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res. 23, 1163-1171 (2013).
81. Chavez, A. et al. Comparison of Cas9 activators in multiple species. Nat. Methods 13, 563-567 (2016).
82. Sidik, S. M. et al. A genome-wide CRISPR screen in Toxoplasma identifies essential apicomplexan genes. Cell 166, 1423-1435.e12 (2016).
83. Canver, M. C. et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527, 192-197 (2015).
84. Korkmaz, G. et al. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat. Biotechnol. 34, 192-198 (2016).
85. Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910-918 (2013).
86. Yang, H. et al. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154, 1370-1379 (2013). References 85 and 86 show one-step generation of multi-Allelic genetically engineered mouse models.
87. Chen, S., Lee, B., Lee, A. Y.-F., Modzelewski, A. J. & He, L. Highly efficient mouse genome editing by CRISPR ribonucleoprotein electroporation of zygotes. J. Biol. Chem. 291, 14457-14467 (2016).
88. Wang, W. et al. Delivery of Cas9 protein into mouse zygotes through a series of electroporation dramatically increases the efficiency of model creation. J. Genet. Genomics 43, 319-327 (2016).
89. Qin, W. et al. Efficient CRISPR/Cas9-mediated genome editing in mice by zygote electroporation of nuclease. Genetics 200, 423-430 (2015). References 87-89 show direct zygote editing by electroporation of Cas9 RNP or Cas9 mRNA and sgRNA.
90. Premsrirut, P. K. K. et al. A rapid and scalable system for studying gene function in mice using conditional RNA interference. Cell 145, 145-158 (2011).
91. Beard, C., Hochedlinger, K., Plath, K., Wutz, A. & Jaenisch, R. Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis 44, 23-28 (2006).
92. Nagy, A. et al. Embryonic stem cells alone are able to support fetal development in the mouse. Development 110, 815-821 (1990).
93. Nagy, A., Rossant, J., Nagy, R., Abramow-Newerly, W. & Roder, J. C. Derivation of completely cell culture-derived mice from early-passage embryonic stem cells. Proc. Natl Acad. Sci. USA 90, 8424-8428 (1993).
94. Sanchez-Rivera, F. J. et al. Rapid modelling of cooperating genetic events in cancer through somatic genome editing. Nature 516, 428-431 (2014). References 94 and 95 describe somatic gene editing in mice.
95. Xue, W. et al. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature 514, 380-384 (2014).
96. Sanchez-Rivera, F. J., Jacks, T., Sánchez-Rivera, F. J. & Jacks, T. Applications of the CRISPR-Cas9 system in cancer biology. Nat. Rev. Cancer 15, 387-395 (2015).
97. Yin, H. et al. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat. Biotechnol. 32, 551-553 (2014).
98. Tabebordbar, M. et al. In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science 351, 407-411 (2016).
99. Long, C. et al. Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy. Science 351, 400-403 (2016).
100. Nelson, C. E. et al. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science 351, 403-407 (2016).
101. Maddalo, D. et al. In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system. Nature 516, 423-427 (2014).
102. Choi, P. S. & Meyerson, M. Targeted genomic rearrangements using CRISPR/Cas technology. Nat. Commun. 5, 3728 (2014). References 101 and 102 describe the in situ generation of somatic chromosomal rearrangements.
103. DuPage, M. & Jacks, T. Genetically engineered mouse models of cancer reveal new insights about the antitumor immune response. Curr. Opin. Immunol. 25, 192-199 (2013).
104. Li, D. et al. Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat. Biotechnol. 31, 681-683 (2013).
105. Zou, Q. et al. Generation of gene-target dogs using CRISPR/Cas9 system. J. Mol. Cell Biol. 7, 580-583 (2015).
106. Niu, Y. et al. Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell 156, 836-843 (2014). This article describes the pioneering application of gene editing with Cas9 in non-human primates.
107. Chen, Y. et al. Functional disruption of the dystrophin gene in rhesus monkey using CRISPR/Cas9. Hum. Mol. Genet. 24, 3764-3774 (2015).
108. Yang, L. et al. Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science 350, 1101-1104 (2015).
109. Matsuoka, Y., Lamirande, E. W. & Subbarao, K. The ferret model for influenza. Curr. Protoc. Microbiol. http://dx.doi.org/10.1002/9780471729259.mc15g02s13 (2009).
110. Clark, S., Hall, Y. & Williams, A. Animal models of tuberculosis: guinea pigs. Cold Spring Harb. Perspect. Med. 5, a018572 (2015).
111. Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187-197 (2015).
112. Crosetto, N. et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat. Methods 10, 361-365 (2013).
113. Kuscu, C., Arslan, S., Singh, R., Thorpe, J. & Adli, M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 32, 677-683 (2014).
114. Gori, J. L. et al. Delivery and specificity of CRISPR-Cas9 genome editing technologies for human gene therapy. Hum. Gene Ther. 26, 443-451 (2015).
115. O'Geen, H., Yu, A. S. & Segal, D. J. How specific is CRISPR/Cas9 really? Curr. Opin. Chem. Biol. 29, 72-78 (2015).
116. Bolukbasi, M. F., Gupta, A. & Wolfe, S. A. Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery. Nat. Methods 13, 41-50 (2016).
117. Hsu, P. D. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827-832 (2013).
118. Lin, Y. et al. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res. 42, 7473-7485 (2014).
119. Stemmer, M., Thumberger, T., Del Sol Keyer, M., Wittbrodt, J. & Mateo, J. L. CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS ONE 10, e0124633 (2015).
120. Bae, S., Park, J. & Kim, J.-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475 (2014).
121. Heigwer, F., Kerr, G. & Boutros, M. E-CRISP: fast CRISPR target site identification. Nat. Methods 11, 122-123 (2014).
122. Haeussler, M. et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 17, 148 (2016).
123. Labun, K., Montague, T. G., Gagnon, J. A., Thyme, S. B. & Valen, E. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res. 44, W272-W276 (2016).
124. Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833-838 (2013).
125. Ran, F. A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380-1389 (2013).
126. Guilinger, J. P., Thompson, D. B. & Liu, D. R. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat. Biotechnol. 32, 577-582 (2014).
127. Tsai, S. Q. et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat. Biotechnol. 32, 569-576 (2014).
128. Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M. & Joung, J. K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32, 279-284 (2014).
129. Kleinstiver, B. P. et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523, 481-485 (2015).
130. Slaymaker, I. M. et al. Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84-88 (2016). References 129 and 130 describe the development of a Cas9 nuclease with reduced off-target activity.
131. Kleinstiver, B. P. et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490-495 (2016).
132. Davis, K. M., Pattanayak, V., Thompson, D. B., Zuris, J. A. & Liu, D. R. Small molecule-triggered Cas9 protein with improved genome-editing specificity. Nat. Chem. Biol. 11, 316-318 (2015).
133. Nihongaki, Y., Kawano, F., Nakajima, T. & Sato, M. Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat. Biotechnol. 33, 755-760 (2015).
134. Oakes, B. L. et al. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nat. Biotechnol. 34, 646-651 (2016).
135. Maus, M. V., Grupp, S. A., Porter, D. L. & June, C. H. Antibody-modified T cells: CARs take the front seat for hematologic malignancies. Blood 123, 2625-2635 (2014).
136. Torikai, H. et al. A foundation for universal T-cell based immunotherapy: T cells engineered to express a CD19-specific chimeric-Antigen-receptor and eliminate expression of endogenous TCR. Blood 119, 5697-5705 (2012).
137. Qasim, W. et al. First clinical application of TALEN engineered universal CAR19 T cells in B-ALL. Blood 126, 2046 (2015).
138. Torikai, H. et al. Toward eliminating HLA class I expression to generate universal cells from allogeneic donors. Blood 122, 1341-1349 (2013).
139. Lloyd, A., Vickery, O. N. & Laugel, B. Beyond the antigen receptor: editing the genome of T-cells for cancer adoptive cellular therapies. Front. Immunol. 4, 221 (2013).
140. Hoos, A. Development of immuno-oncology drugs-from CTLA4 to PD1 to the next generations. Nat. Rev. Drug Discov. 15, 235-247 (2016).
141. Cyranoski, D. CRISPR gene-editing tested in a person for the first time. Nature 539, 479 (2016).
142. Sadelain, M., Papapetrou, E. P. & Bushman, F. D. Safe harbours for the integration of new DNA in the human genome. Nat. Rev. Cancer 12, 51-58 (2012).
143. Kalos, M. & June, C. H. Adoptive T cell transfer for cancer immunotherapy in the era of synthetic biology. Immunity 39, 49-60 (2013).
144. Tebas, P. et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N. Engl. J. Med. 370, 901-910 (2014).
145. Hütter, G. et al. Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N. Engl. J. Med. 360, 692-698 (2009).
146. Perez, E. E. et al. Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat. Biotechnol. 26, 808-816 (2008).
147. Holt, N. et al. Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo. Nat. Biotechnol. 28, 839-847 (2010). References 144 and 147 use ex vivo gene editing with ZFNs for HIV therapy.
148. Yang, L. et al. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 41, 9049-9061 (2013).
149. Mandal, P. K. et al. Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell 15, 643-652 (2014).
150. Hoban, M. D. et al. Correction of the sickle cell disease mutation in human hematopoietic stem/progenitor cells. Blood 125, 2597-2604 (2015).
151. Wang, J. et al. Homology-driven genome editing in hematopoietic stem and progenitor cells using ZFN mRNA and AAV6 donors. Nat. Biotechnol. 33, 1256-1263 (2015).
152. DeWitt, M. A. et al. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci. Transl Med. 8, 360ra134 (2016).
153. Cao, A. & Galanello, R. Beta-thalassemia. Genet. Med. 12, 61-76 (2010).
154. Bauer, D. E. et al. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science 342, 253-257 (2013).
155. Vierstra, J. et al. Functional footprinting of regulatory DNA. Nat. Methods 12, 927-930 (2015).
156. Roberts, S. A. et al. Engineering Factor Viii for hemophilia gene therapy. J. Genet. Syndr. Gene Ther. 1, S1-006 (2011).
157. Stripecke, R. et al. Immune response to green fluorescent protein: implications for gene therapy. Gene Ther. 6, 1305-1312 (1999).
158. Cavazzana, M. et al. Outcomes of gene therapy for severe sickle disease and beta-thalassemia major via transplantation of autologous hematopoietic stem cells transduced ex vivo with a lentiviral β-AT87Q-globin vector. Blood 126, abstr. 202 (2015).
159. Kanter, J. et al. Initial results from study Hgb-206: a phase 1 study evaluating gene therapy by transplantation of autologous CD34+ stem cells transduced ex vivo with the lentiglobin BB305 lentiviral vector in subjects with severe sickle cell disease. Blood 126, abstr. 3233 (2015).