Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Updated summary of genome editing technology in human cultured cells linked to human genetics studies

Abstract

Current deep-sequencing technology provides a mass of nucleotide variations associated with human genetic disorders to accelerate the identification of causative mutations. To understand the etiology of genetic disorders, reverse genetics in human cultured cells is a useful approach for modeling a disease in vitro. However, gene targeting in human cultured cells is difficult because of their low activity of homologous recombination. Engineered endonucleases enable enhancement of the local activation of DNA repair pathways at the human genome target site to rewrite the desired sequence, thereby efficiently generating disease-modeling cultured cell clones. These edited cells can be used to explore the molecular functions of a causative gene product to uncover the etiological mechanisms. The correction of mutations in patient cells using genome editing technology could contribute to the development of unique gene therapies. This technology can also be applied to screening causative mutations. Rare genetic disorders and non-exonic mutation-caused diseases remain frontier in the field of human genetics as it is difficult to validate whether the extracted nucleotide variants are mutation or polymorphism. When isogenic human cultured cells with a candidate variant reproduce the pathogenic phenotypes, it is confirmed that the variant is a causative mutation.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1

References

  1. 1.

    Deciphering Developmental Disorders, S. Large-scale discovery of novel genetic causes of developmental disorders. Nature. 2015;519:223–8.

    Article  CAS  Google Scholar 

  2. 2.

    Wright CF, Fitzgerald TW, Jones WD, Clayton S, McRae JF, van Kogelenberg M, et al. Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. Lancet. 2015;385:1305–14.

    PubMed  PubMed Central  Article  Google Scholar 

  3. 3.

    Sedivy JM, Vogelstein B, Liber HL, Hendrickson EA, Rosmarin AG. Gene targeting in human cells without isogenic DNA. Science. 1999;283:9.

    Article  Google Scholar 

  4. 4.

    Cornu TI, Mussolino C, Cathomen T. Refining strategies to translate genome editing to the clinic. Nat Med. 2017;23:415–23.

    CAS  PubMed  Article  Google Scholar 

  5. 5.

    Cox DB, Platt RJ, Zhang F. Therapeutic genome editing: prospects and challenges. Nat Med. 2015;21:121–31.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  6. 6.

    Maeder ML, Gersbach CA. Genome-editing technologies for gene and cell therapy. Mol Ther. 2016;24:430–46.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  7. 7.

    Bassett, A.R. Editing the genome of hiPSC with CRISPR/Cas9: disease models. Mamm Genome. 2017;28:348–364.

  8. 8.

    Yang L, Yang JL, Byrne S, Pan J, Church GM. CRISPR/Cas9-directed genome editing of cultured cells. Curr Protoc Mol Biol. 2014;107:31.

    PubMed  Google Scholar 

  9. 9.

    Urnov FD. Human genome editing as a tool to establish causality. Proc Natl Acad Sci USA. 2014;111:1233–4.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. 10.

    Merkle FT, Eggan K. Modeling human disease with pluripotent stem cells: from genome association to function. Cell Stem Cell. 2013;12:656–68.

    CAS  PubMed  Article  Google Scholar 

  11. 11.

    Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD. Genome editing with engineered zinc finger nucleases. Nat Rev Genet. 2010;11:636–46.

    CAS  PubMed  Article  Google Scholar 

  12. 12.

    Joung JK, Sander JD. TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol. 2013;14:49–55.

    CAS  PubMed  Article  Google Scholar 

  13. 13.

    Zhang F, Wen Y, Guo X. CRISPR/Cas9 for genome editing: progress, implications and challenges. Hum Mol Genet. 2014;23:R40–6.

    CAS  PubMed  Article  Google Scholar 

  14. 14.

    Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014;157:1262–78.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15.

    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.

    CAS  PubMed  Article  Google Scholar 

  16. 16.

    Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819–23.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  17. 17.

    Chang HHY, Pannunzio NR, Adachi N, Lieber MR. Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol. 2017;18:495–506.

    CAS  PubMed  Article  Google Scholar 

  18. 18.

    Renkawitz J, Lademann CA, Jentsch S. Mechanisms and principles of homology search during recombination. Nat Rev Mol Cell Biol. 2014;15:369–83.

    CAS  PubMed  Article  Google Scholar 

  19. 19.

    Hayflick L, Moorhead PS. The serial cultivation of human diploid cell strains. Exp Cell Res. 1961;25:585–621.

    CAS  PubMed  Article  Google Scholar 

  20. 20.

    Howden SE, Maufort JP, Duffin BM, Elefanty AG, Stanley EG, Thomson JA. Simultaneous reprogramming and gene correction of patient fibroblasts. Stem Cell Rep. 2015;5:1109–18.

    CAS  Article  Google Scholar 

  21. 21.

    Scherer WF, Syverton JT, Gey GO. Studies on the propagation in vitro of poliomyelitis viruses. IV. Viral multiplication in a stable strain of human malignant epithelial cells (strain HeLa) derived from an epidermoid carcinoma of the cervix. J Exp Med. 1953;97:695–710.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. 22.

    Shay JW, Tomlinson G, Piatyszek MA, Gollahon LS. Spontaneous in vitro immortalization of breast epithelial cells from a patient with Li-Fraumeni syndrome. Mol Cell Biol. 1995;15:425–32.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  23. 23.

    Shay JW, Wright WE. Senescence and immortalization: role of telomeres and telomerase. Carcinogenesis. 2005;26:867–74.

    CAS  PubMed  Article  Google Scholar 

  24. 24.

    Fearon ER, Vogelstein B. A genetic model for colorectal tumorigenesis. Cell. 1990;61:759–67.

    CAS  PubMed  Article  Google Scholar 

  25. 25.

    Draviam VM, Xie S, Sorger PK. Chromosome segregation and genomic stability. Curr Opin Genet Dev. 2004;14:120–5.

    CAS  PubMed  Article  Google Scholar 

  26. 26.

    Cahill DP, Lengauer C, Yu J, Riggins GJ, Willson JK, Markowitz SD, et al. Mutations of mitotic checkpoint genes in human cancers. Nature. 1998;392:300–3.

    CAS  PubMed  Article  Google Scholar 

  27. 27.

    Funk LC, Zasadil LM, Weaver BA. Living in CIN: mitotic infidelity and its consequences for tumor promotion and suppression. Dev Cell. 2016;39:638–52.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  28. 28.

    Ponten J, Saksela E. Two established in vitro cell lines from human mesenchymal tumours. Int J Cancer. 1967;2:434–47.

    CAS  PubMed  Article  Google Scholar 

  29. 29.

    Strand M, Prolla TA, Liskay RM, Petes TD. Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature. 1993;365:274–6.

    CAS  PubMed  Article  Google Scholar 

  30. 30.

    Kinzler KW, Vogelstein B. Lessons from hereditary colorectal cancer. Cell. 1996;87:159–70.

    CAS  PubMed  Article  Google Scholar 

  31. 31.

    Bunz F, Dutriaux A, Lengauer C, Waldman T, Zhou S, Brown JP, et al. Requirement for p53 and p21 to sustain G2 arrest after DNA damage. Science. 1998;282:1497–501.

    CAS  PubMed  Article  Google Scholar 

  32. 32.

    Roschke AV, Stover K, Tonon G, Schaffer AA, Kirsch IR. Stable karyotypes in epithelial cancer cell lines despite high rates of ongoing structural and numerical chromosomal instability. Neoplasia. 2002;4:19–31.

    PubMed  PubMed Central  Article  Google Scholar 

  33. 33.

    Nigg EA, Raff JW. Centrioles, centrosomes, and cilia in health and disease. Cell. 2009;139:663–78.

    CAS  PubMed  Article  Google Scholar 

  34. 34.

    Speiseder, T., Hofmann-Sieber, H., Rodriguez, E., Schellenberg, A., Akyuz, N., Dierlamm, J. et al. Efficient transformation of primary human mesenchymal stromal cells by adenovirus early region 1 oncogenes. J Virol. 2017:91:e01782–16.

  35. 35.

    Matsumura T, Takesue M, Westerman KA, Okitsu T, Sakaguchi M, Fukazawa T, et al. Establishment of an immortalized human-liver endothelial cell line with SV40T and hTERT. Transplantation. 2004;77:1357–65.

    CAS  PubMed  Article  Google Scholar 

  36. 36.

    Lundberg AS, Hahn WG, Gupta P, Weinberg RA. Genes involved in senescence and immortalization. Curr Opin Cell Biol. 2000;12:705–9.

    CAS  PubMed  Article  Google Scholar 

  37. 37.

    Dubridge RB, Tang P, Hsia HC, Leong PM, Miller JH, Calos MP. Analysis of mutation in human-cells by using an Epstein-Barr-Virus shuttle system. Mol Cell Biol. 1987;7:379–87.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  38. 38.

    Jiang XR, Jimenez G, Chang E, Frolkis M, Kusler B, Sage M, et al. Telomerase expression in human somatic cells does not induce changes associated with a transformed phenotype. Nat Genet. 1999;21:111–4.

    CAS  PubMed  Article  Google Scholar 

  39. 39.

    Miyamoto T, Hosoba K, Ochiai H, Royba E, Izumi H, Sakuma T, et al The microtubule-depolymerizing activity of a mitotic kinesin protein KIF2A drives primary cilia disassembly coupled with cell proliferation. Cell Rep. 2015;S2211-1247:00004–2.

    Google Scholar 

  40. 40.

    Katoh Y, Michisaka S, Nozaki S, Funabashi T, Hirano T, Takei R, et al. Practical method for targeted disruption of cilia-related genes by using CRISPR/Cas9-mediated, homology-independent knock-in system. Mol Biol Cell. 2017;28:898–906.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  41. 41.

    Muffat J, Li Y, Jaenisch R. CNS disease models with human pluripotent stem cells in the CRISPR age. Curr Opin Cell Biol. 2016;43:96–103.

    CAS  PubMed  Article  Google Scholar 

  42. 42.

    Parekh U, Yusupova M, Mali P. Genome engineering in human pluripotent stem cells. Curr Opin Chem Eng. 2017;15:56–67.

    Article  Google Scholar 

  43. 43.

    Thomson JA, Itskovitz-Eldor J, Shapiro SS, Waknitz MA, Swiergiel JJ, Marshall VS, et al. Embryonic stem cell lines derived from human blastocysts. Science. 1998;282:1145–7.

    CAS  PubMed  Article  Google Scholar 

  44. 44.

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

    CAS  PubMed  Article  Google Scholar 

  45. 45.

    Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007;131:861–72.

    CAS  PubMed  Article  Google Scholar 

  46. 46.

    Watanabe K, Ueno M, Kamiya D, Nishiyama A, Matsumura M, Wataya T, et al. A ROCK inhibitor permits survival of dissociated human embryonic stem cells. Nat Biotechnol. 2007;25:681–6.

    CAS  PubMed  Article  Google Scholar 

  47. 47.

    Ohgushi M, Matsumura M, Eiraku M, Murakami K, Aramaki T, Nishiyama A, et al. Molecular pathway and cell state responsible for dissociation-induced apoptosis in human pluripotent stem cells. Cell Stem Cell. 2010;7:225–39.

    CAS  PubMed  Article  Google Scholar 

  48. 48.

    Hockemeyer D, Soldner F, Beard C, Gao Q, Mitalipova M, DeKelver RC, et al. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol. 2009;27:851–7.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. 49.

    Liu GH, Suzuki K, Qu J, Sancho-Martinez I, Yi F, Li M, et al. Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs. Cell Stem Cell. 2011;8:688–94.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  50. 50.

    Soldner F, Laganiere J, Cheng AW, Hockemeyer D, Gao Q, Alagappan R, et al. Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell. 2011;146:318–31.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. 51.

    Wang G, Yang L, Grishin D, Rios X, Ye LY, Hu Y, et al. Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies. Nat Protoc. 2017;12:88–103.

    CAS  PubMed  Article  Google Scholar 

  52. 52.

    Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013;8:2281–308.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  53. 53.

    Yost S, de Wolf B, Hanks S, Zachariou A, Marcozzi C, Clarke M, et al. Biallelic TRIP13 mutations predispose to Wilms tumor and chromosome missegregation. Nat Genet. 2017;49:1148–51.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  54. 54.

    Liu Z, Hui Y, Shi L, Chen Z, Xu X, Chi L, et al. Efficient CRISPR/Cas9-mediated versatile, predictable, and donor-free gene knockout in human pluripotent stem cells. Stem Cell Rep. 2016;7:496–507.

    CAS  Article  Google Scholar 

  55. 55.

    Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, et al. Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nat Med. 2014;20:616–23.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  56. 56.

    Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, et al. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet. 2015;47:469–78.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  57. 57.

    Horii T, Tamura D, Morita S, Kimura M, Hatada I. Generation of an ICF syndrome model by efficient genome editing of human induced pluripotent stem cells using the CRISPR system. Int J Mol Sci. 2013;14:19774–81.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  58. 58.

    Wen Z, Nguyen HN, Guo Z, Lalli MA, Wang X, Su Y, et al. Synaptic dysregulation in a human iPS cell model of mental disorders. Nature. 2014;515:414–8.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  59. 59.

    Li Y, Wang H, Muffat J, Cheng AW, Orlando DA, Loven J, et al. Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons. Cell Stem Cell. 2013;13:446–58.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  60. 60.

    Economides AN, Frendewey D, Yang P, Dominguez MG, Dore AT, Lobov IB, et al. Conditionals by inversion provide a universal method for the generation of conditional alleles. Proc Natl Acad Sci USA. 2013;110:E3179–88.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  61. 61.

    Andersson-Rolf A, Mustata RC, Merenda A, Kim J, Perera S, Grego T, et al. One-step generation of conditional and reversible gene knockouts. Nat Methods. 2017;14:287–9.

    CAS  PubMed  Article  Google Scholar 

  62. 62.

    Li H, Bielas SL, Zaki MS, Ismail S, Farfara D, Um K, et al. Biallelic mutations in citron kinase link mitotic cytokinesis to human primary microcephaly. Am J Hum Genet. 2016;99:501–10.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  63. 63.

    Chang CW, Lai YS, Westin E, Khodadadi-Jamayran A, Pawlik KM, Lamb LS Jr., et al. Modeling human severe combined immunodeficiency and correction by CRISPR/Cas9-enhanced gene targeting. Cell Rep. 2015;12:1668–77.

    CAS  PubMed  Article  Google Scholar 

  64. 64.

    Pardo B, Gomez-Gonzalez B, Aguilera A. DNA repair in mammalian cells: DNA double-strand break repair: how to fix a broken relationship. Cell Mol Life Sci. 2009;66:1039–56.

    CAS  PubMed  Article  Google Scholar 

  65. 65.

    Heidenreich M, Zhang F. Applications of CRISPR-Cas systems in neuroscience. Nat Rev Neurosci. 2016;17:36–44.

    CAS  PubMed  Article  Google Scholar 

  66. 66.

    Maresca M, Lin VG, Guo N, Yang Y. Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Res. 2013;23:539–46.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  67. 67.

    Royba E, Miyamoto T, Akutsu S, Hosoba K, Tauchi H, Kudo Y, et al. Evaluation of ATM heterozygous mutations underlying individual differences in radiosensitivity using genome editing in human cultured cells. Sci Rep. 2017;7:5996.

    PubMed  PubMed Central  Article  Google Scholar 

  68. 68.

    Suzuki K, Tsunekawa Y, Hernandez-Benitez R, Wu J, Zhu J, Kim EJ, et al. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature. 2016;540:144–9.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  69. 69.

    Gibson G. Rare and common variants: twenty arguments. Nat Rev Genet 2012;13:135–45.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  70. 70.

    Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, et al. 10 Years of GWAS discovery: biology, function, and translation. Am J Hum Genet. 2017;101:5–22.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. 71.

    Chen F, Pruett-Miller SM, Huang Y, Gjoka M, Duda K, Taunton J, et al. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Methods. 2011;8:753–5.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  72. 72.

    Li HL, Gee P, Ishida K, Hotta A. Efficient genomic correction methods in human iPS cells using CRISPR-Cas9 system. Methods. 2016;101:27–35.

    CAS  PubMed  Article  Google Scholar 

  73. 73.

    Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, et al. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 2013;41:9049–61.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  74. 74.

    Yoshimi K, Kunihiro Y, Kaneko T, Nagahora H, Voigt B, Mashimo T. ssODN-mediated knock-in with CRISPR-Cas for large genomic regions in zygotes. Nat Commun. 2016;7:10431.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  75. 75.

    Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell. 2013;153:910–8.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  76. 76.

    Armstrong GA, Liao M, You Z, Lissouba A, Chen BE, Drapeau P. Homology directed knockin of point mutations in the zebrafish tardbp and fus genes in ALS Using the CRISPR/Cas9 system. PLoS ONE. 2016;11:e0150188.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  77. 77.

    Li C, Ding L, Sun CW, Wu LC, Zhou D, Pawlik KM, et al. Novel HDAd/EBV reprogramming vector and highly efficient Ad/CRISPR-Cas sickle cell disease gene correction. Sci Rep. 2016;6:30422.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  78. 78.

    Niu X, He W, Song B, Ou Z, Fan D, Chen Y, et al. Combining single strand oligodeoxynucleotides and CRISPR/Cas9 to correct gene mutations in beta-thalassemia-induced pluripotent stem cells. J Biol Chem. 2016;291:16576–85.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  79. 79.

    Miyaoka Y, Chan AH, Judge LM, Yoo J, Huang M, Nguyen TD, et al. Isolation of single-base genome-edited human iPS cells without antibiotic selection. Nat Methods. 2014;11:291–3.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  80. 80.

    Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152:1173–83.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  81. 81.

    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.

    CAS  PubMed  Article  Google Scholar 

  82. 82.

    Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013;154:442–51.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  83. 83.

    Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013;155:1479–91.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  84. 84.

    Ma H, Naseri A, Reyes-Gutierrez P, Wolfe SA, Zhang S, Pederson T. Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci USA. 2015;112:3002–7.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  85. 85.

    Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, et al. Editing DNA methylation in the mammalian genome. Cell. 2016;167:233–47 e217.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  86. 86.

    Morita S, Noguchi H, Horii T, Nakabayashi K, Kimura M, Okamura K, et al. Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions. Nat Biotechnol. 2016;34:1060–5.

    CAS  PubMed  Article  Google Scholar 

  87. 87.

    Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M. et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science. 2016:353:aaf8729.

  88. 88.

    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.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  89. 89.

    Ma Y, Zhang J, Yin W, Zhang Z, Song Y, Chang X. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nat Methods. 2016;13:1029–35.

    CAS  PubMed  Article  Google Scholar 

  90. 90.

    Paquet D, Kwart D, Chen A, Sproul A, Jacob S, Teo S, et al. Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9. Nature. 2016;533:125–9.

    CAS  PubMed  Article  Google Scholar 

  91. 91.

    Kwart D, Paquet D, Teo S, Tessier-Lavigne M. Precise and efficient scarless genome editing in stem cells using CORRECT. Nat Protoc. 2017;12:329–54.

    CAS  PubMed  Article  Google Scholar 

  92. 92.

    Ochiai H, Miyamoto T, Kanai A, Hosoba K, Sakuma T, Kudo Y, et al. TALEN-mediated single-base-pair editing identification of an intergenic mutation upstream of BUB1B as causative of PCS (MVA) syndrome. Proc Natl Acad Sci USA. 2014;111:1461–6.

    CAS  PubMed  Article  Google Scholar 

  93. 93.

    Kajii T, Kawai T, Takumi T, Misu H, Mabuchi O, Takahashi Y, et al. Mosaic variegated aneuploidy with multiple congenital abnormalities: homozygosity for total premature chromatid separation trait. Am J Med Genet. 1998;78:245–9.

    CAS  PubMed  Article  Google Scholar 

  94. 94.

    Matsuura S, Ito E, Tauchi H, Komatsu K, Ikeuchi T, Kajii T. Chromosomal instability syndrome of total premature chromatid separation with mosaic variegated aneuploidy is defective in mitotic-spindle checkpoint. Am J Hum Genet. 2000;67:483–6.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  95. 95.

    Hanks S, Coleman K, Reid S, Plaja A, Firth H, Fitzpatrick D, et al. Constitutional aneuploidy and cancer predisposition caused by biallelic mutations in BUB1B. Nat Genet. 2004;36:1159–61.

    CAS  PubMed  Article  Google Scholar 

  96. 96.

    Matsuura S, Matsumoto Y, Morishima K, Izumi H, Matsumoto H, Ito E, et al. Monoallelic BUB1B mutations and defective mitotic-spindle checkpoint in seven families with premature chromatid separation (PCS) syndrome. Am J Med Genet A. 2006;140:358–67.

    PubMed  Article  CAS  Google Scholar 

  97. 97.

    Yusa K, Rashid ST, Strick-Marchand H, Varela I, Liu PQ, Paschon DE, et al. Targeted gene correction of alpha1-antitrypsin deficiency in induced pluripotent stem cells. Nature. 2011;478:391–4.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. 98.

    Yusa K. Seamless genome editing in human pluripotent stem cells using custom endonuclease-based gene targeting and the piggyBac transposon. Nat Protoc. 2013;8:2061–78.

    CAS  PubMed  Article  Google Scholar 

  99. 99.

    Imamura K, Sahara N, Kanaan NM, Tsukita K, Kondo T, Kutoku Y, et al. Calcium dysregulation contributes to neurodegeneration in FTLD patient iPSC-derived neurons. Sci Rep. 2016;6:34904.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  100. 100.

    Maetzel D, Sarkar S, Wang H, Abi-Mosleh L, Xu P, Cheng AW, et al. Genetic and chemical correction of cholesterol accumulation and impaired autophagy in hepatic and neural cells derived from Niemann-Pick Type C patient-specific iPS cells. Stem Cell Rep. 2014;2:866–80.

    CAS  Article  Google Scholar 

  101. 101.

    Young CS, Hicks MR, Ermolova NV, Nakano H, Jan M, Younesi S, et al. A single CRISPR-Cas9 deletion strategy that targets the majority of DMD patients restores dystrophin function in hiPSC-derived muscle cells. Cell Stem Cell. 2016;18:533–40.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  102. 102.

    Tebas P, Stein D, Tang WW, Frank I, Wang SQ, Lee G, et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med. 2014;370:901–10.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  103. 103.

    Nakade S, Tsubota T, Sakane Y, Kume S, Sakamoto N, Obara M, et al. Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9. Nat Commun. 2014;5:5560.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  104. 104.

    Sakuma T, Nakade S, Sakane Y, Suzuki KT, Yamamoto T. MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems. Nat Protoc. 2016;11:118–33.

    CAS  PubMed  Article  Google Scholar 

  105. 105.

    Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol. 2015;33:538–42.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  106. 106.

    Chu VT, Weber T, Wefers B, Wurst W, Sander S, Rajewsky K, et al. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol. 2015;33:543–8.

    CAS  PubMed  Article  Google Scholar 

  107. 107.

    Yu C, Liu Y, Ma T, Liu K, Xu S, Zhang Y, et al. Small molecules enhance CRISPR genome editing in pluripotent stem cells. Cell Stem Cell. 2015;16:142–7.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  108. 108.

    Song J, Yang D, Xu J, Zhu T, Chen YE, Zhang J. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency. Nat Commun. 2016;7:10548.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  109. 109.

    Gutschner T, Haemmerle M, Genovese G, Draetta GF, Chin L. Post-translational regulation of Cas9 during G1 enhances homology-directed repair. Cell Rep. 2016;14:1555–66.

    CAS  PubMed  Article  Google Scholar 

  110. 110.

    Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163:759–71.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

Download references

Acknowledgements

This work was supported by AMED-PRIME from the Japan Agency for Medical Research and Development, AMED (to TM); Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan (to TM and SM); Grant-in-Aid for Scientific Research from the Ministry of Health, Labor and Welfare (to SM); the Center of World Intelligence Projects for Nuclear S&T and Human Resource Development from the Japan Science and Technology Agency (to S.M.); research grants from the Naito Foundation (to SM and TM); the Mochida Memorial Foundation for Medical and Pharmaceutical Research (to TM); Ono Medical Research Foundation (to TM); and Takeda Science Foundation (to TM).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Tatsuo Miyamoto.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Miyamoto, T., Akutsu, S. & Matsuura, S. Updated summary of genome editing technology in human cultured cells linked to human genetics studies. J Hum Genet 63, 133–143 (2018). https://doi.org/10.1038/s10038-017-0349-z

Download citation

Further reading

Search

Quick links