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CRISPR/Cas9 Editing in Induced Pluripotent Stem Cells: A Way Forward for Treating Cystic Fibrosis?

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Abstract

Despite drastic improvements in the treatment of cystic fibrosis (CF), there are still no curative options and severe CF remains a terminal diagnosis. With the recent advances in state-of-the-art techniques such as induced pluripotent stem cells (iPSC), stem cell expansion, differentiation, and gene editing technologies, we now have the ability to expand patient-specific cells for therapeutic application. These autologous cells can be readily genetically edited and clonally expanded with the potential for differentiation into the desired mature cell types. Such techniques hold enormous potential for therapeutic application. This chapter aims to provide an overview of the current state of iPSCs, proximal lung stem cells and gene editing techniques focusing on their potential for clinical application in CF.

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References

  1. Davis PB. Cystic fibrosis since 1938. Am J Respir Crit Care Med. 2006;173(5):475–82.

    Article  PubMed  Google Scholar 

  2. Rosenfeld M, et al. An open-label extension study of ivacaftor in children with CF and a CFTR gating mutation initiating treatment at age 2-5years (KLIMB). J Cyst Fibros. 2019. in press.

    Google Scholar 

  3. McColley SA, et al. Lumacaftor/Ivacaftor reduces pulmonary exacerbations in patients irrespective of initial changes in FEV1. J Cyst Fibros. 2019;18(1):94–101.

    Article  CAS  PubMed  Google Scholar 

  4. Pike-Overzet K, van der Burg M, Wagemaker G, van Dongen JJ, Staal FJ. New insights and unresolved issues regarding insertional mutagenesis in X-linked SCID gene therapy. Mol Ther. 2007;15(11):1910–6.

    Article  CAS  PubMed  Google Scholar 

  5. Hu BY, et al. Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc Natl Acad Sci U S A. 2010;107(9):4335–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Ohno Y, et al. Distinct iPS cells show different cardiac differentiation efficiency. Stem Cells Int. 2013:659739.

    Google Scholar 

  7. Siller R, et al. Development of a rapid screen for the endodermal differentiation potential of human pluripotent stem cell lines. Sci Rep. 2016;6:37178.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Burrows CK, et al. Genetic variation, not cell type of origin, underlies the majority of identifiable regulatory differences in iPSCs. PLoS Genet. 2016;12(1):e1005793.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. DeBoever C, et al. Large-scale profiling reveals the influence of genetic variation on gene expression in human induced pluripotent stem cells. Cell Stem Cell. 2017;20(4):533–46. e537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Ortmann D, Vallier L. Variability of human pluripotent stem cell lines. Curr Opin Genet Dev. 2017;46:179–85.

    Article  CAS  PubMed  Google Scholar 

  11. Cahan P, Daley GQ. Origins and implications of pluripotent stem cell variability and heterogeneity. Nat Rev Mol Cell Biol. 2013;14(6):357–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Wang Y, et al. Genome editing of isogenic human induced pluripotent stem cells recapitulates long QT phenotype for drug testing. J Am Coll Cardiol. 2014;64(5):451–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Boucher RCKM, Yankaskas JR. Cystic fibrosis. In: Mason RJ, Martin T, King TEJ, Schraufnagel D, Murray JF, Nadel JA, editors. Murray and Nadel’s textbook of respiratory medicine. Philadelphia: Elsevier Saunders; 2010. p. 985–1022.

    Chapter  Google Scholar 

  14. Welsh MJ, Smith AE. Molecular mechanisms of CFTR chloride channel dysfunction in cystic fibrosis. Cell. 1993;73(7):1251–4.

    Article  CAS  PubMed  Google Scholar 

  15. Liou TG, et al. Survival effect of lung transplantation among patients with cystic fibrosis. JAMA. 2001;286(21):2683–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Liou TG, Adler FR, Cox DR, Cahill BC. Lung transplantation and survival in children with cystic fibrosis. N Engl J Med. 2007;357(21):2143–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Foundation CF. (2009) Cystic Fibrosis Foundation patient registry annual data report, 2009. Bethesda MD: Cystic Fibrosis Foundation; 2009.

    Google Scholar 

  18. Lopes-Pacheco M. CFTR modulators: shedding light on precision medicine for cystic fibrosis. Front Pharmacol. 2016;7:275.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Patterson GA, et al. Technique of successful clinical double-lung transplantation. Ann Thorac Surg. 1988;45(6):626–33.

    Article  CAS  PubMed  Google Scholar 

  20. Inci I, et al. Lung transplantation for cystic fibrosis: a single center experience of 100 consecutive cases. Eur J Cardiothorac Surg. 2012;41(2):435–40.

    Article  PubMed  Google Scholar 

  21. Meachery G, et al. Outcomes of lung transplantation for cystic fibrosis in a large UK cohort. Thorax. 2008;63(8):725–31.

    Article  CAS  PubMed  Google Scholar 

  22. Hofer M, et al. True survival benefit of lung transplantation for cystic fibrosis patients: the Zurich experience. J Heart Lung Transplant. 2009;28(4):334–9.

    Article  PubMed  Google Scholar 

  23. Aurora P, et al. The registry of the International Society for Heart and Lung Transplantation: thirteenth official pediatric lung and heart-lung transplantation report--2010. J Heart Lung Transplant. 2010;29(10):1129–41.

    Article  PubMed  Google Scholar 

  24. Christie JD, et al. The registry of the International Society for Heart and Lung Transplantation: twenty-seventh official adult lung and heart-lung transplant report--2010. J Heart Lung Transplant. 2010;29(10):1104–18.

    Article  PubMed  Google Scholar 

  25. Belperio JA, Weigt SS, Fishbein MC, Lynch JP 3rd. Chronic lung allograft rejection: mechanisms and therapy. Proc Am Thorac Soc. 2009;6(1):108–21.

    Article  CAS  PubMed  Google Scholar 

  26. Clancy JP, et al. CFTR modulator theratyping: current status, gaps and future directions. J Cyst Fibros. 2019;18(1):22–34.

    Article  CAS  PubMed  Google Scholar 

  27. Chaudary N. Triplet CFTR modulators: future prospects for treatment of cystic fibrosis. Ther Clin Risk Manag. 2018;14:2375–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Zomer-van Ommen DD, et al. Limited premature termination codon suppression by read-through agents in cystic fibrosis intestinal organoids. J Cyst Fibros. 2016;15(2):158–62.

    Article  CAS  PubMed  Google Scholar 

  29. De Boeck K, Amaral MD. Classification of CFTR mutation classes—Authors' reply. Lancet Respir Med. 2016;4(8):e39.

    Article  PubMed  Google Scholar 

  30. Verma IM. The reverse transcriptase. Biochim Biophys Acta. 1977;473(1):1–38.

    CAS  PubMed  Google Scholar 

  31. Cooney AL, McCray PB Jr, Sinn PL. Cystic fibrosis gene therapy: looking Back, looking forward. Genes (Basel). 2018;9(11):E538.

    Article  CAS  Google Scholar 

  32. Griesenbach U, Pytel KM, Alton EW. Cystic fibrosis gene therapy in the UK and elsewhere. Hum Gene Ther. 2015;26(5):266–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hanna E, Remuzat C, Auquier P, Toumi M. Gene therapies development: slow progress and promising prospect. J Mark Access Health Policy. 2017;5(1):1265293.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Hida K, et al. Common gene therapy viral vectors do not efficiently penetrate sputum from cystic fibrosis patients. PLoS One. 2011;6(5):e19919.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Wirth T, Parker N, Yla-Herttuala S. History of gene therapy. Gene. 2013;525(2):162–9.

    Article  CAS  PubMed  Google Scholar 

  36. Dudley DD, Chaudhuri J, Bassing CH, Alt FW. Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences. Adv Immunol. 2005;86:43–112.

    Article  CAS  PubMed  Google Scholar 

  37. Weiner BM, Kleckner N. Chromosome pairing via multiple interstitial interactions before and during meiosis in yeast. Cell. 1994;77(7):977–91.

    Article  CAS  PubMed  Google Scholar 

  38. Kauppi L, et al. Distinct properties of the XY pseudoautosomal region crucial for male meiosis. Science. 2011;331(6019):916–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Jang S, Sandler SJ, Harshey RM. Mu insertions are repaired by the double-strand break repair pathway of Escherichia coli. PLoS Genet. 2012;8(4):e1002642.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Stahl F. Meiotic recombination in yeast: coronation of the double-strand-break repair model. Cell. 1996;87(6):965–8.

    Article  CAS  PubMed  Google Scholar 

  41. Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW. The double-strand-break repair model for recombination. Cell. 1983;33(1):25–35.

    Article  CAS  PubMed  Google Scholar 

  42. Bzymek M, Thayer NH, Oh SD, Kleckner N, Hunter N. Double Holliday junctions are intermediates of DNA break repair. Nature. 2010;464(7290):937–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Baker MD, Birmingham EC. Evidence for biased Holliday junction cleavage and mismatch repair directed by junction cuts during double-strand-break repair in mammalian cells. Mol Cell Biol. 2001;21(10):3425–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Hastings PJ. Mechanism and control of recombination in fungi. Mutat Res. 1992;284(1):97–110.

    Article  CAS  PubMed  Google Scholar 

  45. Costantino L, et al. Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science. 2014;343(6166):88–91.

    Article  CAS  PubMed  Google Scholar 

  46. Anand RP, Lovett ST, Haber JE. Break-induced DNA replication. Cold Spring Harb Perspect Biol. 2013;5(12):a010397.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Smith CE, Llorente B, Symington LS. Template switching during break-induced replication. Nature. 2007;447(7140):102–5.

    Article  CAS  PubMed  Google Scholar 

  48. Malkova A, Ivanov EL, Haber JE. Double-strand break repair in the absence of RAD51 in yeast: a possible role for break-induced DNA replication. Proc Natl Acad Sci U S A. 1996;93(14):7131–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. McMahill MS, Sham CW, Bishop DK. Synthesis-dependent strand annealing in meiosis. PLoS Biol. 2007;5(11):e299.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  50. Adams MD, McVey M, Sekelsky JJ. Drosophila BLM in double-strand break repair by synthesis-dependent strand annealing. Science. 2003;299(5604):265–7.

    Article  CAS  PubMed  Google Scholar 

  51. Bibikova M, Golic M, Golic KG, Carroll D. Targeted chromosomal cleavage and mutagenesis in drosophila using zinc-finger nucleases. Genetics. 2002;161(3):1169–75.

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Rudin N, Sugarman E, Haber JE. Genetic and physical analysis of double-strand break repair and recombination in Saccharomyces cerevisiae. Genetics. 1989;122(3):519–34.

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Plessis A, Perrin A, Haber JE, Dujon B. Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus. Genetics. 1992;130(3):451–60.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Rouet P, Smih F, Jasin M. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol. 1994;14(12):8096–106.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Thomas KR, Folger KR, Capecchi MR. High frequency targeting of genes to specific sites in the mammalian genome. Cell. 1986;44(3):419–28.

    Article  CAS  PubMed  Google Scholar 

  56. Thomas KR, Capecchi MR. Site-directed mutagenesis by gene targeting in mouse embryo-derived stem cells. Cell. 1987;51(3):503–12.

    Article  CAS  PubMed  Google Scholar 

  57. Mansour SL, Thomas KR, Capecchi MR. Disruption of the proto-oncogene int-2 in mouse embryo-derived stem cells: a general strategy for targeting mutations to non-selectable genes. Nature. 1988;336(6197):348–52.

    Article  CAS  PubMed  Google Scholar 

  58. Capecchi MR. Altering the genome by homologous recombination. Science. 1989;244(4910):1288–92.

    Article  CAS  PubMed  Google Scholar 

  59. Durai S, et al. Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res. 2005;33(18):5978–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Mani M, Kandavelou K, Dy FJ, Durai S, Chandrasegaran S. Design, engineering, and characterization of zinc finger nucleases. Biochem Biophys Res Commun. 2005;335(2):447–57.

    Article  CAS  PubMed  Google Scholar 

  61. Sander JD, et al. Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol. 2011;29(8):697–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Hockemeyer D, et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol. 2011;29(8):731–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Cermak T, et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011;39(12):e82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Huang P, et al. Heritable gene targeting in zebrafish using customized TALENs. Nat Biotechnol. 2011;29(8):699–700.

    Article  PubMed  CAS  Google Scholar 

  65. Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science. 2010;329(5997):1355–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Wiedenheft B, et al. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure. 2009;17(6):904–12.

    Article  CAS  PubMed  Google Scholar 

  67. Bibikova M, et al. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol. 2001;21(1):289–97.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Bibikova M, Beumer K, Trautman JK, Carroll D. Enhancing gene targeting with designed zinc finger nucleases. Science. 2003;300(5620):764.

    Article  CAS  PubMed  Google Scholar 

  69. Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A. 1996;93(3):1156–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Urnov FD, et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature. 2005;435(7042):646–51.

    Article  CAS  PubMed  Google Scholar 

  71. Miller JC, et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol. 2007;25(7):778–85.

    Article  CAS  PubMed  Google Scholar 

  72. Moscou MJ, Bogdanove AJ. A simple cipher governs DNA recognition by TAL effectors. Science. 2009;326(5959):1501.

    Article  CAS  PubMed  Google Scholar 

  73. Boch J, et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science. 2009;326(5959):1509–12.

    Article  CAS  PubMed  Google Scholar 

  74. Christian M, et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics. 2010;186(2):757–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. La Russa MF, Qi LS. The new state of the art: CRISPR for gene activation and repression. Mol Cell Biol. 2015;35(22):3800–9.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  76. Sternberg SH, Doudna JA. Expanding the Biologist's toolkit with CRISPR-Cas9. Mol Cell. 2015;58(4):568–74.

    Article  CAS  PubMed  Google Scholar 

  77. Wiles MV, Qin W, Cheng AW, Wang H. CRISPR-Cas9-mediated genome editing and guide RNA design. Mamm Genome. 2015;26(9–10):501–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213):1258096.

    Article  PubMed  CAS  Google Scholar 

  79. Ma Y, Zhang L, Huang X. Genome modification by CRISPR/Cas9. FEBS J. 2014;281(23):5186–93.

    Article  CAS  PubMed  Google Scholar 

  80. Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol. 2014;32(4):347–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Jiang F, Zhou K, Ma L, Gressel S, Doudna JA. STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition. Science. 2015;348(6242):1477–81.

    Article  CAS  PubMed  Google Scholar 

  82. Ramakrishna S, et al. Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA. Genome Res. 2014;24(6):1020–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Qi LS, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152(5):1173–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Chang CW, et al. Modeling human severe combined immunodeficiency and correction by CRISPR/Cas9-enhanced gene targeting. Cell Rep. 2015;12(10):1668–77.

    Article  CAS  PubMed  Google Scholar 

  85. Menon T, et al. Lymphoid regeneration from gene-corrected SCID-X1 subject-derived iPSCs. Cell Stem Cell. 2015;16(4):367–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Park CY, et al. Functional correction of large factor VIII gene chromosomal inversions in Hemophilia a patient-derived iPSCs using CRISPR-Cas9. Cell Stem Cell. 2015;17(2):213–20.

    Article  CAS  PubMed  Google Scholar 

  87. 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. 2015;11(5):774–87.

    Article  CAS  Google Scholar 

  88. Long C, et al. Prevention of muscular dystrophy in mice by CRISPR/Cas9-mediated editing of germline DNA. Science. 2014;345(6201):1184–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Yoshimi K, Kaneko T, Voigt B, Mashimo T. Allele-specific genome editing and correction of disease-associated phenotypes in rats using the CRISPR-Cas platform. Nat Commun. 2014;5:4240.

    Article  CAS  PubMed  Google Scholar 

  90. Wu Y, et al. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell. 2013;13(6):659–62.

    Article  CAS  PubMed  Google Scholar 

  91. Schwank G, et al. Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell. 2013;13(6):653–8.

    Article  CAS  PubMed  Google Scholar 

  92. Duda K, et al. High-efficiency genome editing via 2A-coupled co-expression of fluorescent proteins and zinc finger nucleases or CRISPR/Cas9 nickase pairs. Nucleic Acids Res. 2014;42(10):e84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Li S, et al. Human induced pluripotent stem cell NEUROG2 dual knockin reporter lines generated by the CRISPR/Cas9 system. Stem Cells Dev. 2015;24(24):2925–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Khair L, Baker RE, Linehan EK, Schrader CE, Stavnezer J. Nbs1 ChIP-Seq identifies off-target DNA double-Strand breaks induced by AID in activated splenic B cells. PLoS Genet. 2015;11(8):e1005438.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  95. Rojas-Fernandez A, et al. Rapid generation of endogenously driven transcriptional reporters in cells through CRISPR/Cas9. Sci Rep. 2015;5:9811.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Krentz NA, Nian C, Lynn FC. TALEN/CRISPR-mediated eGFP knock-in add-on at the OCT4 locus does not impact differentiation of human embryonic stem cells towards endoderm. PLoS One. 2014;9(12):e114275.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  97. Jinek M, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Gilbert LA, et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell. 2014;159(3):647–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Agrotis A, Ketteler R. A new age in functional genomics using CRISPR/Cas9 in arrayed library screening. Front Genet. 2015;6:300.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  100. Chen S, et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 2015;160(6):1246–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Konermann S, et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature. 2015;517(7536):583–8.

    Article  CAS  PubMed  Google Scholar 

  102. Sanjana NE, Shalem O, Zhang F. Improved vectors and genome-wide libraries for CRISPR screening. Nat Methods. 2014;11(8):783–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Kampmann M, Bassik MC, Weissman JS. Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps. Nat Protoc. 2014;9(8):1825–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Zhou Y, et al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature. 2014;509(7501):487–91.

    Article  CAS  PubMed  Google Scholar 

  105. 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(3):267–73.

    Article  CAS  PubMed  Google Scholar 

  106. Shalem O, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343(6166):84–7.

    Article  CAS  PubMed  Google Scholar 

  107. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014;343(6166):80–4.

    Article  CAS  PubMed  Google Scholar 

  108. Vanoli F, et al. CRISPR-Cas9-guided oncogenic chromosomal translocations with conditional fusion protein expression in human mesenchymal cells. Proc Natl Acad Sci U S A. 2017;114(14):3696–701.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Lei Y, et al. Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein. Nat Commun. 2017;8:16026.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Liu XS, et al. Editing DNA methylation in the mammalian genome. Cell. 2016;167(1):233–47. e217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Huang YH, et al. DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A. Genome Biol. 2017;18(1):176.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  112. Saunderson EA, et al. Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors. Nat Commun. 2017;8(1):1450.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  113. Anton T, Bultmann S. Site-specific recruitment of epigenetic factors with a modular CRISPR/Cas system. Nucleus. 2017;8(3):279–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Koo T, Lee J, Kim JS. Measuring and reducing off-target activities of programmable nucleases including CRISPR-Cas9. Mol Cells. 2015;38(6):475–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Kim D, et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods. 2015;12(3):237–43.

    Article  CAS  PubMed  Google Scholar 

  116. Tsai SQ, et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015;33(2):187–97.

    Article  CAS  PubMed  Google Scholar 

  117. Cradick TJ, Qiu P, Lee CM, Fine EJ, Bao G. COSMID: a web-based tool for identifying and validating CRISPR/Cas off-target sites. Mol Ther Nucleic Acids. 2014;3:e214.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Suzuki K, et al. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014;15(1):31–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Veres A, et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell. 2014;15(1):27–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Hruscha A, et al. Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development. 2013;140(24):4982–7.

    Article  CAS  PubMed  Google Scholar 

  121. Cho SW, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2014;24(1):132–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol. 2014;32(3):279–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Dahlman JE, et al. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nat Biotechnol. 2015;33(11):1159–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Ran FA, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013;154(6):1380–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Chen X, et al. In trans paired nicking triggers seamless genome editing without double-stranded DNA cutting. Nat Commun. 2017;8(1):657.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  126. Gaudelli NM, et al. Programmable base editing of a∗T to G∗C in genomic DNA without DNA cleavage. Nature. 2017;551(7681):464–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Cox DBT, et al. RNA editing with CRISPR-Cas13. Science. 2017;358(6366):1019–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126(4):663–76.

    Article  CAS  PubMed  Google Scholar 

  129. Lake BB, et al. Context-dependent enhancement of induced pluripotent stem cell reprogramming by silencing puma. Stem Cells. 2012;30(5):888–97.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Li W, et al. Identification of Oct4-activating compounds that enhance reprogramming efficiency. Proc Natl Acad Sci U S A. 2012;109(51):20853–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Takahashi K, Okita K, Nakagawa M, Yamanaka S. Induction of pluripotent stem cells from fibroblast cultures. Nat Protoc. 2007;2(12):3081–9.

    Article  CAS  PubMed  Google Scholar 

  132. Takahashi K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007;131(5):861–72.

    Article  CAS  PubMed  Google Scholar 

  133. Byrne JA, Nguyen HN, Reijo Pera RA. Enhanced generation of induced pluripotent stem cells from a subpopulation of human fibroblasts. PLoS One. 2009;4(9):e7118.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  134. He X, et al. Human fibroblast reprogramming to pluripotent stem cells regulated by the miR19a/b-PTEN axis. PLoS One. 2014;9(4):e95213.

    Article  PubMed  PubMed Central  Google Scholar 

  135. Zhou T, et al. Generation of human induced pluripotent stem cells from urine samples. Nat Protoc. 2012;7(12):2080–9.

    Article  CAS  PubMed  Google Scholar 

  136. Yu J, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007;318(5858):1917–20.

    Article  CAS  PubMed  Google Scholar 

  137. Nakagawa M, et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat Biotechnol. 2008;26(1):101–6.

    Article  CAS  PubMed  Google Scholar 

  138. Lai WH, et al. ROCK inhibition facilitates the generation of human-induced pluripotent stem cells in a defined, feeder-, and serum-free system. Cell Reprogram. 2010;12(6):641–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Novak A, et al. Enhanced reprogramming and cardiac differentiation of human keratinocytes derived from plucked hair follicles, using a single excisable lentivirus. Cell Reprogram. 2010;12(6):665–78.

    Article  CAS  PubMed  Google Scholar 

  140. Somers A, et al. Generation of transgene-free lung disease-specific human induced pluripotent stem cells using a single excisable lentiviral stem cell cassette. Stem Cells. 2010;28(10):1728–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Firth AL, et al. Generation of multiciliated cells in functional airway epithelia from human induced pluripotent stem cells. Proc Natl Acad Sci U S A. 2014;111(17):E1723–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Merling RK, et al. Transgene-free iPSCs generated from small volume peripheral blood nonmobilized CD34+ cells. Blood. 2013;121(14):e98–107.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Anokye-Danso F, et al. Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell. 2011;8(4):376–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Sohn YD, et al. Induction of pluripotency in bone marrow mononuclear cells via polyketal nanoparticle-mediated delivery of mature microRNAs. Biomaterials. 2013;34(17):4235–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Fusaki N, Ban H, Nishiyama A, Saeki K, Hasegawa M. Efficient induction of transgene-free human pluripotent stem cells using a vector based on Sendai virus, an RNA virus that does not integrate into the host genome. Proc Jpn Acad Ser B Phys Biol Sci. 2009;85(8):348–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Nishimura K, et al. Development of defective and persistent Sendai virus vector: a unique gene delivery/expression system ideal for cell reprogramming. J Biol Chem. 2011;286(6):4760–71.

    Article  CAS  PubMed  Google Scholar 

  147. Macarthur CC, et al. Generation of human-induced pluripotent stem cells by a nonintegrating RNA Sendai virus vector in feeder-free or xeno-free conditions. Stem Cells Int. 2012;2012:564612.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. Trokovic R, et al. Small molecule inhibitors promote efficient generation of induced pluripotent stem cells from human skeletal myoblasts. Stem Cells Dev. 2013;22(1):114–23.

    Article  CAS  PubMed  Google Scholar 

  149. Ono M, et al. Generation of induced pluripotent stem cells from human nasal epithelial cells using a Sendai virus vector. PLoS One. 2012;7(8):e42855.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Miere C, Devito L, Ilic D. Sendai virus-based reprogramming of Mesenchymal stromal/stem cells from umbilical cord Wharton's jelly into induced pluripotent stem cells. Methods Mol Biol. 2015;1357:33–44.

    Article  CAS  Google Scholar 

  151. Fujie Y, et al. New type of Sendai virus vector provides transgene-free iPS cells derived from chimpanzee blood. PLoS One. 2014;9(12):e113052.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  152. Yu J, et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science. 2009;324(5928):797–801.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Hu K, et al. Efficient generation of transgene-free induced pluripotent stem cells from normal and neoplastic bone marrow and cord blood mononuclear cells. Blood. 2011;117(14):e109–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Su RJ, et al. Efficient generation of integration-free ips cells from human adult peripheral blood using BCL-XL together with Yamanaka factors. PLoS One. 2013;8(5):e64496.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Meng X, et al. Efficient reprogramming of human cord blood CD34+ cells into induced pluripotent stem cells with OCT4 and SOX2 alone. Mol Ther. 2012;20(2):408–16.

    Article  CAS  PubMed  Google Scholar 

  156. Okita K, et al. An efficient nonviral method to generate integration-free human-induced pluripotent stem cells from cord blood and peripheral blood cells. Stem Cells. 2013;31(3):458–66.

    Article  CAS  PubMed  Google Scholar 

  157. Warren L, Ni Y, Wang J, Guo X. Feeder-free derivation of human induced pluripotent stem cells with messenger RNA. Sci Rep. 2012;2:657.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  158. Warren L, et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 2010;7(5):618–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Yusa K, Rad R, Takeda J, Bradley A. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon. Nat Methods. 2009;6(5):363–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Tsukiyama T, et al. Simple and efficient method for generation of induced pluripotent stem cells using piggyBac transposition of doxycycline-inducible factors and an EOS reporter system. Genes Cells. 2011;16(7):815–25.

    Article  CAS  PubMed  Google Scholar 

  161. Li G, Chunxu Y, Guisheng L. Efficient p53 gene targeting by homologous recombination in rat-induced pluripotent stem cells. Cell Prolif. 2013;46(1):1–9.

    Article  PubMed  CAS  Google Scholar 

  162. Talluri TR, et al. Derivation and characterization of bovine induced pluripotent stem cells by transposon-mediated reprogramming. Cell Reprogram. 2015;17(2):131–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Davis RP, et al. Generation of induced pluripotent stem cells from human foetal fibroblasts using the sleeping beauty transposon gene delivery system. Differentiation. 2013;86(1-2):30–7.

    Article  CAS  PubMed  Google Scholar 

  164. Narsinh KH, et al. Generation of adult human induced pluripotent stem cells using nonviral minicircle DNA vectors. Nat Protoc. 2011;6(1):78–88.

    Article  CAS  PubMed  Google Scholar 

  165. Diecke S, Lisowski L, Kooreman NG, Wu JC. Second generation codon optimized minicircle (CoMiC) for nonviral reprogramming of human adult fibroblasts. Methods Mol Biol. 2014;1181:1–13.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  166. Yu P, et al. Nonviral minicircle generation of induced pluripotent stem cells compatible with production of chimeric chickens. Cell Reprogram. 2014;16(5):366–78.

    Article  CAS  PubMed  Google Scholar 

  167. Park H, et al. Increased genomic integrity of an improved protein-based mouse induced pluripotent stem cell method compared with current viral-induced strategies. Stem Cells Transl Med. 2014;3(5):599–609.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Fink KD, et al. Intrastriatal transplantation of adenovirus-generated induced pluripotent stem cells for treating neuropathological and functional deficits in a rodent model of Huntington's disease. Stem Cells Transl Med. 2014;3(5):620–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Fink KD, et al. Survival and differentiation of adenovirus-generated induced pluripotent stem cells transplanted into the rat striatum. Cell Transplant. 2014;23(11):1407–23.

    Article  PubMed  Google Scholar 

  170. Diecke S, et al. Novel codon-optimized mini-intronic plasmid for efficient, inexpensive, and xeno-free induction of pluripotency. Sci Rep. 2015;5:8081.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Thomson JA, et al. Embryonic stem cell lines derived from human blastocysts. Science. 1998;282(5391):1145–7.

    Article  CAS  PubMed  Google Scholar 

  172. Cichutek K. Lessons learned from gene therapy concerning and the use of integrating vectors and the possible risk of insertional oncogenesis. Dev Biol (Basel). 2006;123:29–34; discussion 55-73

    CAS  Google Scholar 

  173. Kang EM, Tisdale JF. The leukemogenic risk of integrating retroviral vectors in hematopoietic stem cell gene therapy applications. Curr Hematol Rep. 2004;3(4):274–81.

    PubMed  Google Scholar 

  174. Woods NB, et al. Lentiviral vector transduction of NOD/SCID repopulating cells results in multiple vector integrations per transduced cell: risk of insertional mutagenesis. Blood. 2003;101(4):1284–9.

    Article  CAS  PubMed  Google Scholar 

  175. Li HL, et al. Precise correction of the dystrophin gene in duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9. Stem cell Reports. 2015;4(1):143–54.

    Article  CAS  PubMed  Google Scholar 

  176. Matano M, et al. Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids. Nat Med. 2015;21(3):256–62.

    Article  CAS  PubMed  Google Scholar 

  177. Bikard D, et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 2013;41(15):7429–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Gilbert LA, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013;154(2):442–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Maeder ML, et al. CRISPR RNA-guided activation of endogenous human genes. Nat Methods. 2013;10(10):977–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Zalatan JG, et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell. 2015;160(1-2):339–50.

    Article  CAS  PubMed  Google Scholar 

  181. Inui M, et al. Rapid generation of mouse models with defined point mutations by the CRISPR/Cas9 system. Sci Rep. 2014;4:5396.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Wang H, et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell. 2013;153(4):910–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Fujii W, Kawasaki K, Sugiura K, Naito K. Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease. Nucleic Acids Res. 2013;41(20):e187.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Fujii W, Onuma A, Sugiura K, Naito K. Efficient generation of genome-modified mice via offset-nicking by CRISPR/Cas system. Biochem Biophys Res Commun. 2014;445(4):791–4.

    Article  CAS  PubMed  Google Scholar 

  185. Ni W, et al. Efficient gene knockout in goats using CRISPR/Cas9 system. PLoS One. 2014;9(9):e106718.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  186. Whitworth KM, et al. Use of the CRISPR/Cas9 system to produce genetically engineered pigs from in vitro-derived oocytes and embryos. Biol Reprod. 2014;91(3):78.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  187. Chen Y, et al. Functional disruption of the dystrophin gene in rhesus monkey using CRISPR/Cas9. Hum Mol Genet. 2015;24(13):3764–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Harel I, Valenzano DR, Brunet A. Efficient genome engineering approaches for the short-lived African turquoise killifish. Nat Protoc. 2016;11(10):2010–28.

    Article  CAS  PubMed  Google Scholar 

  189. Oishi I, Yoshii K, Miyahara D, Kagami H, Tagami T. Targeted mutagenesis in chicken using CRISPR/Cas9 system. Sci Rep. 2016;6:23980.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  190. Yin H, et al. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol. 2014;32(6):551–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Yin H, et al. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol. 2016;34(3):328–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Blasco RB, et al. Simple and rapid in vivo generation of chromosomal rearrangements using CRISPR/Cas9 technology. Cell Rep. 2014;9(4):1219–27.

    Article  CAS  PubMed  Google Scholar 

  193. Tabebordbar M, et al. In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science. 2016;351(6271):407–11.

    Article  CAS  PubMed  Google Scholar 

  194. Ren Q, et al. A dual-reporter system for real-time monitoring and high-throughput CRISPR/Cas9 library screening of the hepatitis C virus. Sci Rep. 2015;5:8865.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Gonzalez F, et al. An iCRISPR platform for rapid, multiplexable, and inducible genome editing in human pluripotent stem cells. Cell Stem Cell. 2014;15(2):215–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Polstein LR, Gersbach CA. A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat Chem Biol. 2015;11(3):198–200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Zhen S, et al. Harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated Cas9 system to disrupt the hepatitis B virus. Gene Ther. 2015;22(5):404–12.

    Article  CAS  PubMed  Google Scholar 

  198. Hu W, et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci U S A. 2014;111(31):11461–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. DeWitt MA, et al. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci Transl Med. 2016;8(360):360ra134.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  200. Chen B, et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013;155(7):1479–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Ma H, et al. Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci U S A. 2015;112(10):3002–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Fujita T, Fujii H. Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Biochem Biophys Res Commun. 2013;439(1):132–6.

    Article  CAS  PubMed  Google Scholar 

  203. Hilton IB, et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015;33(5):510–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Kearns NA, et al. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat Methods. 2015;12(5):401–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  205. 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(7603):420–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. East-Seletsky A, et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. 2016;538(7624):270–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Gantz VM, Bier E. Genome editing. The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science. 2015;348(6233):442–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  208. Liang P, et al. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell. 2015;6(5):363–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Salomonis N, et al. Integrated genomic analysis of diverse induced pluripotent stem cells from the progenitor cell biology consortium. Stem Cell Reports. 2016;7(1):110–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Baghbaderani BA, et al. cGMP-manufactured human induced pluripotent stem cells are available for pre-clinical and clinical applications. Stem Cell Reports. 2015;5(4):647–59.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  211. Wang J, et al. Generation of clinical-grade human induced pluripotent stem cells in Xeno-free conditions. Stem Cell Res Ther. 2015;6:223.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  212. Vugler A, et al. Elucidating the phenomenon of HESC-derived RPE: anatomy of cell genesis, expansion and retinal transplantation. Exp Neurol. 2008;214(2):347–61.

    Article  CAS  PubMed  Google Scholar 

  213. Schwartz SD, et al. Embryonic stem cell trials for macular degeneration: a preliminary report. Lancet. 2012;379(9817):713–20.

    Article  CAS  PubMed  Google Scholar 

  214. Schwartz SD, et al. Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt's macular dystrophy: follow-up of two open-label phase 1/2 studies. Lancet. 2015;385(9967):509–16.

    Article  PubMed  Google Scholar 

  215. D'Amour KA, et al. Efficient differentiation of human embryonic stem cells to definitive endoderm. Nat Biotechnol. 2005;23(12):1534–41.

    Article  CAS  PubMed  Google Scholar 

  216. Green MD, et al. Generation of anterior foregut endoderm from human embryonic and induced pluripotent stem cells. Nat Biotechnol. 2011;29(3):267–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Hawkins F, et al. Prospective isolation of NKX2-1-expressing human lung progenitors derived from pluripotent stem cells. J Clin Invest. 2017;127(6):2277–94.

    Article  PubMed  PubMed Central  Google Scholar 

  218. Du X, et al. Barriers for deriving transgene-free pig iPS cells with Episomal vectors. Stem Cells. 2015;33(11):3228–38.

    Article  PubMed  PubMed Central  Google Scholar 

  219. Telugu BP, Ezashi T, Roberts RM. Porcine induced pluripotent stem cells analogous to naive and primed embryonic stem cells of the mouse. Int J Dev Biol. 2010;54(11–12):1703–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  220. Lei L, et al. Monitoring bovine fetal fibroblast reprogramming utilizing a bovine NANOG promoter-driven EGFP reporter system. Mol Reprod Dev. 2013;80(3):193–203.

    Article  CAS  PubMed  Google Scholar 

  221. Afanassieff M, Tapponnier Y, Savatier P. Generation of induced pluripotent stem cells in rabbits. Methods Mol Biol. 2016;1357:149–72.

    Article  CAS  PubMed  Google Scholar 

  222. Maherali N, Hochedlinger K. Guidelines and techniques for the generation of induced pluripotent stem cells. Cell Stem Cell. 2008;3(6):595–605.

    Article  CAS  PubMed  Google Scholar 

  223. Wunderlich S, et al. Induction of pluripotent stem cells from a cynomolgus monkey using a polycistronic simian immunodeficiency virus-based vector, differentiation toward functional cardiomyocytes, and generation of stably expressing reporter lines. Cell Reprogram. 2012;14(6):471–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Breton A, et al. Derivation and characterization of induced pluripotent stem cells from equine fibroblasts. Stem Cells Dev. 2013;22(4):611–21.

    Article  CAS  PubMed  Google Scholar 

  225. German SD, et al. Ovine induced pluripotent stem cells are resistant to reprogramming after nuclear transfer. Cell Reprogram. 2015;17(1):19–27.

    Article  CAS  PubMed  Google Scholar 

  226. Navara CS, et al. Derivation of induced pluripotent stem cells from the baboon: a nonhuman primate model for preclinical testing of stem cell therapies. Cell Reprogram. 2013;15(6):495–502.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Easley CA, et al. Human amniotic epithelial cells are reprogrammed more efficiently by induced pluripotency than adult fibroblasts. Cell Reprogram. 2012;14(3):193–203.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  228. Goh PA, Verma PJ. Generation of induced pluripotent stem cells from mouse adipose tissue. Methods Mol Biol. 2014;1194:253–70.

    Article  PubMed  CAS  Google Scholar 

  229. Heng BC, et al. mRNA transfection-based, feeder-free, induced pluripotent stem cells derived from adipose tissue of a 50-year-old patient. Metab Eng. 2013;18:9–24.

    Article  CAS  PubMed  Google Scholar 

  230. Hu K, Slukvin I. Generation of transgene-free iPSC lines from human normal and neoplastic blood cells using episomal vectors. Methods Mol Biol. 2013;997:163–76.

    Article  CAS  PubMed  Google Scholar 

  231. Sun X, et al. Disease phenotype of a ferret CFTR-knockout model of cystic fibrosis. J Clin Invest. 2010;120(9):3149–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  232. Welsh MJ, Rogers CS, Stoltz DA, Meyerholz DK, Prather RS. Development of a porcine model of cystic fibrosis. Trans Am Clin Climatol Assoc. 2009;120:149–62.

    PubMed  PubMed Central  Google Scholar 

  233. Rogers CS, et al. Disruption of the CFTR gene produces a model of cystic fibrosis in newborn pigs. Science. 2008;321(5897):1837–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  234. Wilke M, et al. Mouse models of cystic fibrosis: phenotypic analysis and research applications. J Cyst Fibros. 2011;10(Suppl 2):S152–71.

    Article  CAS  PubMed  Google Scholar 

  235. Fisher JT, Zhang Y, Engelhardt JF. Comparative biology of cystic fibrosis animal models. Methods Mol Biol. 2011;742:311–34.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  236. Tipirneni KE, et al. Characterization of primary rat nasal epithelial cultures in CFTR knockout rats as a model for CF sinus disease. Laryngoscope. 2017;127(11):E384–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  237. Fulcher ML, Gabriel S, Burns KA, Yankaskas JR, Randell SH. Well-differentiated human airway epithelial cell cultures. Methods Mol Med. 2005;107:183–206.

    CAS  PubMed  Google Scholar 

  238. Reynolds SD, et al. Airway progenitor clone formation is enhanced by Y-27632-dependent changes in the Transcriptome. Am J Respir Cell Mol Biol. 2016;55(3):323–36.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  239. Martinovich KM, et al. Conditionally reprogrammed primary airway epithelial cells maintain morphology, lineage and disease specific functional characteristics. Sci Rep. 2017;7(1):17971.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  240. Mou H, et al. Dual SMAD Signaling inhibition enables Long-term expansion of diverse epithelial basal cells. Cell Stem Cell. 2016;19(2):217–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  241. Porotto M, et al. Authentic Modeling of human respiratory virus infection in human pluripotent stem cell-derived lung Organoids. MBio. 2019;10(3):e00723-19.

    Article  PubMed  PubMed Central  Google Scholar 

  242. McCauley KB, Hawkins F, Kotton DN. Derivation of epithelial-only airway Organoids from human pluripotent stem cells. Curr Protoc Stem Cell Biol. 2018;45(1):e51.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  243. Dye BR, et al. In vitro generation of human pluripotent stem cell derived lung organoids. Elife. 2015;4:E05098.

    Google Scholar 

  244. Farinha CM, et al. Increased efficacy of VX-809 in different cellular systems results from an early stabilization effect of F508del-CFTR. Pharmacol Res Perspect. 2015;3(4):e00152.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  245. Fulcher ML, et al. Novel human bronchial epithelial cell lines for cystic fibrosis research. Am J Physiol Lung Cell Mol Physiol. 2009;296(1):L82–91.

    Article  CAS  PubMed  Google Scholar 

  246. McCauley KB, et al. Efficient derivation of functional human airway epithelium from pluripotent stem cells via temporal regulation of Wnt Signaling. Cell Stem Cell. 2017;20(6):844–57. e846

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  247. Mou H, et al. Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs. Cell Stem Cell. 2012;10(4):385–97.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  248. Firth AL, et al. Functional gene correction for cystic fibrosis in lung epithelial cells generated from patient iPSCs. Cell Rep. 2015;12(9):1385–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  249. Ghosh M, Ahmad S, White CW, Reynolds SD. Transplantation of airway epithelial stem/progenitor cells: a future for cell-based therapy. Am J Respir Cell Mol Biol. 2017;56(1):1–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  250. Nichane M, et al. Isolation and 3D expansion of multipotent Sox9(+) mouse lung progenitors. Nat Methods. 2017;14(12):1205–12.

    Article  CAS  PubMed  Google Scholar 

  251. Miller AJ, et al. In vitro induction and in vivo engraftment of lung bud tip progenitor cells derived from human pluripotent stem cells. Stem Cell Reports. 2018;10(1):101–19.

    Article  CAS  PubMed  Google Scholar 

  252. Crespo A, et al. Hydrodynamic liver gene transfer mechanism involves transient sinusoidal blood stasis and massive hepatocyte endocytic vesicles. Gene Ther. 2005;12(11):927–35.

    Article  CAS  PubMed  Google Scholar 

  253. Khorsandi SE, et al. Minimally invasive and selective hydrodynamic gene therapy of liver segments in the pig and human. Cancer Gene Ther. 2008;15(4):225–30.

    Article  CAS  PubMed  Google Scholar 

  254. Wang M, et al. Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles. Proc Natl Acad Sci U S A. 2016;113(11):2868–73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  255. Dye BR, et al. In vitro generation of human pluripotent stem cell derived lung organoids. Elife. 2015;4. E05098.

    Google Scholar 

  256. Ma H, et al. Correction of a pathogenic gene mutation in human embryos. Nature. 2017;548(7668):413–9.

    Article  CAS  PubMed  Google Scholar 

  257. Liang P, et al. Correction of beta-thalassemia mutant by base editor in human embryos. Protein Cell. 2017;8(11):811–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  258. Dzau VJ, McNutt M, Bai C. Wake-up call from Hong Kong. Science. 2018;362(6420):1215.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We would like to thank our graphical artist, Cameron Quon of the Eli and Edythe Broad Center for Regenerative Medicine for his assistance in generating Fig. 9.2 for this chapter. A.L.R. is supported by grants from the Cystic Fibrosis Foundation Therapeutics (FIRTH15XX0 and FIRTH17XX0), American Lung Association (RG-514617), UPenn Orphan Disease Grant (MBDR-17-107-CF), NIH:NHLBI 5R01HL139828 and the Hastings Foundation.

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Quiroz, E.J., Ryan (Firth), A.L. (2019). CRISPR/Cas9 Editing in Induced Pluripotent Stem Cells: A Way Forward for Treating Cystic Fibrosis?. In: Burgess, J., Heijink, I. (eds) Stem Cell-Based Therapy for Lung Disease. Springer, Cham. https://doi.org/10.1007/978-3-030-29403-8_9

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