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Precision gene editing technology and applications in nephrology

Abstract

The expanding field of precision gene editing is empowering researchers to directly modify DNA. Gene editing is made possible using synonymous technologies: a DNA-binding platform to molecularly locate user-selected genomic sequences and an associated biochemical activity that serves as a functional editor. The advent of accessible DNA-targeting molecular systems, such as zinc-finger nucleases, transcription activator-like effectors (TALEs) and CRISPR–Cas9 gene editing systems, has unlocked the ability to target nearly any DNA sequence with nucleotide-level precision. Progress has also been made in harnessing endogenous DNA repair machineries, such as non-homologous end joining, homology-directed repair and microhomology-mediated end joining, to functionally manipulate genetic sequences. As understanding of how DNA damage results in deletions, insertions and modifications increases, the genome becomes more predictably mutable. DNA-binding platforms such as TALEs and CRISPR can also be used to make locus-specific epigenetic changes and to transcriptionally enhance or suppress genes. Although many challenges remain, the application of precision gene editing technology in the field of nephrology has enabled the generation of new animal models of disease as well as advances in the development of novel therapeutic approaches such as gene therapy and xenotransplantation.

Key points

  • Zinc-finger nucleases, transcription activator-like effector nucleases and CRISPR systems are powerful tools that are enabling new applications of genome engineering in diverse systems.

  • Targeted double-stranded breaks in DNA activate diverse repair processes, such as non-homologous end joining, homology-directed repair and microhomology-mediated end joining, which can be utilized to modify the nucleotide sequence of DNA.

  • Use of non-nuclease genomic tools enables the editing of single bases and locus-specific epigenetic targeting to modify gene expression.

  • Applications of precision gene editing in nephrology include the generation of animal models to investigate kidney development and disease mechanisms as well as the development of targeted gene therapies.

  • Genome editing in the kidney is challenging owing to anatomical barriers to gene delivery, limitations of vector size and immune responses against viral vectors, modified cells and editing proteins.

  • Despite these challenges, precision gene editing has great potential to accelerate basic science in nephrology and to advance clinical practice through the development of novel therapies for renal diseases.

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Fig. 1: Programmable DNA platforms that recognize double-stranded DNA.
Fig. 2: Cost and utilization of precision gene editing in scientific research.
Fig. 3: Utilization of DNA repair pathways for precision gene editing.
Fig. 4: Precision epigenetic modulation.

References

  1. 1.

    Kim, Y. G., Cha, J. & Chandrasegaran, S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl Acad. Sci. USA 93, 1156–1160 (1996).

    CAS  PubMed  Google Scholar 

  2. 2.

    Carroll, D. Genome engineering with zinc-finger nucleases. Genetics 188, 773–782 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Christian, M. et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186, 757–761 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Joung, J. K. & Sander, J. D. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 14, 49–55 (2013).

    CAS  PubMed  Google Scholar 

  5. 5.

    Doudna, J. A. & Charpentier, E. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).

    PubMed  Google Scholar 

  6. 6.

    Sternberg, S. H. & Doudna, J. A. Expanding the biologists toolkit with CRISPR-Cas9. Mol. Cell 58, 568–574 (2015).

    CAS  PubMed  Google Scholar 

  7. 7.

    Peng, Y. et al. Making designer mutants in model organisms. Development 141, 4042–4054 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Porteus, M. H. & Baltimore, D. Chimeric nucleases stimulate gene targeting in hu-man cells. Science 300, 763–763 (2003).

    Google Scholar 

  9. 9.

    Bibikova, M., Beumer, K., Trautman, J. K. & Carroll, D. Enhancing gene targeting with designed zinc finger nucleases. Science 300, 764–764 (2003).

    CAS  Google Scholar 

  10. 10.

    Wolfe, S. A., Nekludova, L. & Pabo, C. O. DNA recognition by Cys(2)His(2) zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29, 183–212 (2000).

    CAS  Google Scholar 

  11. 11.

    Pavletich, N. P. & Pabo, C. O. Zinc finger dna recognition - crystal-structure of a Zif268-DNA complex at 2.1-A. Science 252, 809–817 (1991).

    CAS  PubMed  Google Scholar 

  12. 12.

    Desjarlais, J. R. & Berg, J. M. Redesigning the DNA-binding specificity of a zinc finger protein - a data base-guided approach. Proteins 12, 101–104 (1992).

    CAS  PubMed  Google Scholar 

  13. 13.

    Segal, D. J., Dreier, B., Beerli, R. R. & Barbas, C. F. Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences. Proc. Natl Acad. Sci. USA 96, 2758–2763 (1999).

    CAS  PubMed  Google Scholar 

  14. 14.

    Beerli, R. R. & Barbas, C. F. Engineering polydactyl zinc-finger transcription factors. Nat. Biotechnol. 20, 135–141 (2002).

    CAS  PubMed  Google Scholar 

  15. 15.

    Kim, H. J., Lee, H. J., Kim, H., Cho, S. W. & Kim, J.-S. Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res. 19, 1279–1288 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Bhakta, M. S. et al. Highly active zinc-finger nucleases by extended modular assembly. Genome Res. 23, 530–538 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Gupta, A. et al. An optimized two-finger archive for ZFN-mediated gene targeting. Nat. Methods 9, 588–590 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Laoharawee, K. et al. Dose-dependent prevention of metabolic and neurologic disease in murine MPS II by ZFN-mediated in vivo genome editing. Mol. Ther. 26, 1127–1136 (2018).

    CAS  PubMed  Google Scholar 

  19. 19.

    Bibikova, M. et al. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol. Cell. Biol. 21, 289–297 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Bibikova, M., Golic, M., Golic, K. G. & Carroll, D. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161, 1169–1175 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Urnov, F. D. et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646–651 (2005).

    CAS  Google Scholar 

  22. 22.

    Doyon, Y. et al. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat. Biotechnol. 26, 702–708 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23.

    Miller, J. C. et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778–785 (2007).

    CAS  PubMed  Google Scholar 

  24. 24.

    Szczepek, M. et al. Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat. Biotechnol. 25, 786–793 (2007).

    CAS  PubMed  Google Scholar 

  25. 25.

    Doyon, Y. et al. Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. Nat. Methods 8, 74–79 (2011).

    CAS  PubMed  Google Scholar 

  26. 26.

    Cornu, T. I. et al. DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol. Ther. 16, 352–358 (2008).

    CAS  PubMed  Google Scholar 

  27. 27.

    Haendel, E.-M., Alwin, S. & Cathomen, T. Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity. Mol. Ther. 17, 104–111 (2009).

    CAS  Google Scholar 

  28. 28.

    Gabriel, R. et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol. 29, 816–823 (2011).

    CAS  PubMed  Google Scholar 

  29. 29.

    Boch, J. et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509–1512 (2009).

    CAS  PubMed  Google Scholar 

  30. 30.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Deng, D. et al. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science 335, 720–723 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Moscou, M. J. & Bogdanove, A. J. A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501 (2009).

    CAS  Google Scholar 

  33. 33.

    Bogdanove, A. J. & Voytas, D. F. TAL effectors: customizable proteins for DNA targeting. Science 333, 1843–1846 (2011).

    CAS  PubMed  Google Scholar 

  34. 34.

    Mussolino, C. et al. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res. 39, 9283–9293 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833–838 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Smith, C. et al. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell 15, 13–14 (2014).

    Google Scholar 

  37. 37.

    Hockemeyer, D. et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nat. Biotechnol. 29, 731–734 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Lamb, B. M., Mercer, A. C. & Barbas, C. F. Directed evolution of the TALE N-terminal domain for recognition of all 5′ bases. Nucleic Acids Res. 41, 9779–9785 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Deng, D. et al. Recognition of methylated DNA by TAL effectors. Cell Res. 22, 1502–1504 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Kim, Y. et al. A library of TAL effector nucleases spanning the human genome. Nat. Biotechnol. 31, 251–258 (2013).

    CAS  PubMed  Google Scholar 

  41. 41.

    Zhang, F. et al. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat. Biotechnol. 29, 149–153 (2011).

    PubMed  PubMed Central  Google Scholar 

  42. 42.

    Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. Nat. Biotechnol. 30, 460–465 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Heigwer, F. et al. E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Res. 41, e190 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Ma, A. C. et al. FusX: a rapid one-step transcription activator-like effector assembly system for genome science. Hum. Gene Ther. 27, 451–463 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 45.

    Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    CAS  Google Scholar 

  46. 46.

    Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I. & Koonin, E. V. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7 (2006).

    PubMed  PubMed Central  Google Scholar 

  47. 47.

    Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).

    CAS  Google Scholar 

  48. 48.

    Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467–477 (2011).

    CAS  PubMed  Google Scholar 

  49. 49.

    Sapranauskas, R. et al. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res. 39, 9275–9282 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Barrangou, R. & Marraffini, L. A. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol. Cell 54, 234–244 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Bolotin, A., Ouinquis, B., Sorokin, A. & Ehrlich, S. D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551–2561 (2005).

    CAS  PubMed  Google Scholar 

  52. 52.

    Mojica, F. J. M., Diez-Villasenor, C., Garcia-Martinez, J. & Soria, E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174–182 (2005).

    CAS  PubMed  Google Scholar 

  53. 53.

    Brouns, S. J. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. 54.

    Mojica, F. J. M., Diez-Villasenor, C., Garcia-Martinez, J. & Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733–740 (2009).

    CAS  PubMed  Google Scholar 

  55. 55.

    Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579–E2586 (2012).

    CAS  PubMed  Google Scholar 

  56. 56.

    Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62–67 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Wiedenheft, B., Sternberg, S. H. & Doudna, J. A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331–338 (2012).

    CAS  PubMed  Google Scholar 

  58. 58.

    Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014).

    PubMed  PubMed Central  Google Scholar 

  59. 59.

    Mali, P., Esvelt, K. M. & Church, G. M. Cas9 as a versatile tool for engineering biology. Nat. Methods 10, 957–963 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Cencic, R. et al. Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage. PLoS ONE 9, e109213 (2014).

    PubMed  PubMed Central  Google Scholar 

  61. 61.

    Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569–573 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Belhaj, K., Chaparro-Garcia, A., Kamoun, S. & Nekrasov, V. Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9, 39 (2013).

    PubMed  PubMed Central  Google Scholar 

  63. 63.

    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).

    CAS  PubMed  Google Scholar 

  64. 64.

    Dickinson, D. J., Ward, J. D., Reiner, D. J. & Goldstein, B. Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat. Methods 10, 1028–1034 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Cradick, T. J., Fine, E. J., Antico, C. J. & Bao, G. CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res. 41, 9584–9592 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66.

    Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. 67.

    Cho, S. W., Lee, J., Carroll, D., Kim, J.-S. & Lee, J. Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9-sgRNA ribonucleoproteins. Genetics 195, 1177–1180 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68.

    Gratz, S. J. et al. Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194, 1029–1035 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. 69.

    Fu, Y. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 31, 822–826 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. 70.

    Hsu, P. D. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827–832 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. 71.

    Cho, S. W. et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 24, 132–141 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. 72.

    Tsai, S. Q. & Joung, J. K. Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases. Nat. Rev. Genet. 17, 300–312 (2016).

    CAS  Google Scholar 

  73. 73.

    Peng, R. X., Lin, G. G. & Li, J. M. Potential pitfalls of CRISPR/Cas9-mediated genome editing. FEBS J. 283, 1218–1231 (2016).

    CAS  PubMed  Google Scholar 

  74. 74.

    Duan, J. Z. et al. Genome-wide identification of CRISPR/Cas9 off-targets in human genome. Cell Res. 24, 1009–1012 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. 75.

    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).

    CAS  PubMed  Google Scholar 

  76. 76.

    Frock, R. L. et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat. Biotechnol. 33, 179–186 (2015).

    CAS  PubMed  Google Scholar 

  77. 77.

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. 78.

    Guilinger, J. P., Thompson, D. B. & Liu, D. R. Fusion of catalytically inactive Cas9 to Fokl nuclease improves the specificity of genome modification. Nat. Biotechnol. 32, 577–582 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. 79.

    Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. 80.

    Tsai, S. Q. et al. Dimeric CRISPR RNA-guided Fokl nucleases for highly specific genome editing. Nat. Biotechnol. 32, 569–576 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. 81.

    Ran, F. A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380–1389 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. 82.

    Slaymaker, I. M. et al. Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84–88 (2016).

    CAS  Google Scholar 

  83. 83.

    Kleinstiver, B. P. et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84.

    Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163, 759–771 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. 85.

    Kim, D. et al. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat. Biotechnol. 34, 863–868 (2016).

    CAS  Google Scholar 

  86. 86.

    East-Seletsky, A., O’Connell, M. R., Burstein, D., Knott, G. J. & Doudna, J. A. RNA targeting by functionally orthogonal type VI-A CRISPR-Cas enzymes. Mol. Cell 66, 373–383 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. 87.

    East-Seletsky, A. et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538, 270–273 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88.

    Yin, P. et al. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature 504, 168–171 (2013).

    CAS  PubMed  Google Scholar 

  89. 89.

    Kim, Y., Kweon, J. & Kim, J.-S. TALENs and ZFNs are associated with different mutation signatures. Nat. Methods 10, 185–185 (2013).

    PubMed  Google Scholar 

  90. 90.

    Xiao, A. et al. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res. 41, e141 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. 91.

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. 92.

    Chu, V. T. et al. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. 33, 543–548 (2015).

    CAS  Google Scholar 

  93. 93.

    Maruyama, T. et al. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat. Biotechnol. 33, 538–542 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94.

    Sakuma, T., Nakade, S., Sakane, Y., Suzuki, K. T. & Yamamoto, T. MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems. Nat. Protoc. 11, 118–133 (2016).

    CAS  PubMed  Google Scholar 

  95. 95.

    Hoeijmakers, J. H. J. Genome maintenance mechanisms for preventing cancer. Nature 411, 366–374 (2001).

    CAS  Google Scholar 

  96. 96.

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. 97.

    Auer, T. O., Duroure, K., De Cian, A., Concordet, J.-P. & Del Bene, F. Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res. 24, 142–153 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. 98.

    Greene, E. C. DNA sequence alignment during homologous recombination. J. Biol. Chem. 291, 11572–11580 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 99.

    Qi, Z. et al. DNA sequence alignment by microhomology sampling during homologous recombination. Cell 160, 856–869 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. 100.

    Zu, Y. et al. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat. Methods 10, 329–331 (2013).

    CAS  PubMed  Google Scholar 

  101. 101.

    Radecke, S., Radecke, F., Cathomen, T. & Schwarz, K. Zinc-finger nuclease-induced gene repair with oligodeoxynucleotides: wanted and unwanted target locus modifications. Mol. Ther. 18, 743–753 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. 102.

    Sakuma, T. & Yamamoto, T. Magic wands of CRISPR-lots of choices for gene knock-in. Cell Biol. Toxicol. 33, 501–505 (2017).

    PubMed  Google Scholar 

  103. 103.

    Richardson, C. D. et al. CRISPR-Cas9 genome editing in human cells works via the Fanconi anemia pathway. Preprint at bioRxiv https://doi.org/10.1101/136028 (2017).

  104. 104.

    Danner, E. et al. Control of gene editing by manipulation of DNA repair mechanisms. Mamm. Genome 28, 262–274 (2017).

    CAS  Google Scholar 

  105. 105.

    Bothmer, A. et al. Characterization of the interplay between DNA repair and CRISPR/Cas9-induced DNA lesions at an endogenous locus. Nat. Commun. 8, 13905 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. 106.

    Chen, F. et al. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat. Methods 8, 753–755 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. 107.

    Kostyrko, K. & Mermod, N. Assays for DNA double-strand break repair by microhomology-based end-joining repair mechanisms. Nucleic Acids Res. 44, e56 (2016).

    PubMed  Google Scholar 

  108. 108.

    Ahrabi, S. et al. A role for human homologous recombination factors in suppressing microhomology-mediated end joining. Nucleic Acids Res. 44, 5743–5757 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. 109.

    McVey, M. & Lee, S. E. MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings. Trends Genet. 24, 529–538 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. 110.

    Lu, G. Q. et al. Ligase I and ligase III mediate the DNA double-strand break ligation in alternative end-joining. Proc. Natl Acad. Sci. USA 113, 1256–1260 (2016).

    CAS  PubMed  Google Scholar 

  111. 111.

    Nakamae, K. et al. Establishment of expanded and streamlined pipeline of PITCh knock-in - a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO. Bioengineered 8, 302–308 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. 112.

    Aida, T. et al. Gene cassette knock-in in mammalian cells and zygotes by enhanced MMEJ. BMC Genomics 17, 979 (2016).

    Google Scholar 

  113. 113.

    Yao, X. et al. Homology-mediated end joining-based targeted integration using CRISPR/Cas9. Cell Res. 27, 801–814 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. 114.

    Bennardo, N., Cheng, A., Huang, N. & Stark, J. M. Alternative-NHEJ Is a mechanistically distinct pathway of mammalian chromosome break repair. PLoS Genet. 4, e1000110 (2008).

    PubMed  PubMed Central  Google Scholar 

  115. 115.

    Yang, L. H. et al. Corrigendum: engineering and optimising deaminase fusions for genome editing. Nat. Commun. 8, 16169 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. 116.

    Gaudelli, N. M. et al. Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. 117.

    Zong, Y. et al. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat. Biotechnol. 35, 438–440 (2017).

    CAS  PubMed  Google Scholar 

  118. 118.

    Zhang, Y. H. et al. Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system. Nat. Commun. 8, 118 (2017).

    PubMed  PubMed Central  Google Scholar 

  119. 119.

    Li, Z. et al. APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL. Leukemia 31, 2057–2064 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. 120.

    Kouno, T. et al. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity. Nat. Commun. 8, 15024 (2017).

    PubMed  PubMed Central  Google Scholar 

  121. 121.

    Kim, Y. B. et al. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat. Biotechnol. 35, 371–376 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. 122.

    Brachova, P., Alvarez, N. S., Van Voorhis, B. J. & Christenson, L. K. Cytidine deaminase Apobec3a induction in fallopian epithelium after exposure to follicular fluid. Gynecol. Oncol. 145, 577–583 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. 123.

    Billon, P. et al. CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons. Mol. Cell 67, 1068–1079 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. 124.

    Yang, L. H. et al. Engineering and optimising deaminase fusions for genome editing. Nat. Commun. 7, 13330 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  125. 125.

    Kungulovski, G. & Jeltsch, A. Epigenome editing: state of the art, concepts, and perspectives. Trends Genet. 32, 101–113 (2016).

    CAS  PubMed  Google Scholar 

  126. 126.

    Smith, A. E. & Ford, K. G. Specific targeting of cytosine methylation to DNA sequences in vivo. Nucleic Acids Res. 35, 740–754 (2007).

    CAS  PubMed  Google Scholar 

  127. 127.

    Thakore, P. I., Black, J. B., Hilton, I. B. & Gersbach, C. A. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat. Methods 13, 127–137 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. 128.

    Xu, X. X. et al. A CRISPR-based approach for targeted DNA demethylation. Cell Discov. 2, 16009 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. 129.

    Carvin, C. D., Parr, R. D. & Kladde, M. P. Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins. Nucleic Acids Res. 31, 6493–6501 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  130. 130.

    Maeder, M. L. et al. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat. Biotechnol. 31, 1137–1142 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  131. 131.

    Liu, Y. D. et al. Zinc finger protein 618 regulates the function of UHRF2 (ubiquitin-like with PHD and ring finger domains 2) as a specific 5-hydroxymethylcytosine reader. J. Biol. Chem. 291, 13679–13688 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. 132.

    Vojta, A. et al. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res. 44, 5615–5628 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  133. 133.

    Sterner, D. E. & Berger, S. L. Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev. 64, 435–459 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  134. 134.

    Seto, E. & Yoshida, M. Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb. Perspect. Biol. 6, a018713 (2014).

    Google Scholar 

  135. 135.

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. 136.

    Kwon, D. Y., Zhao, Y. T., Lamonica, J. M. & Zhou, Z. Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC. Nat. Commun. 8, 15315 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  137. 137.

    Looman, C., Abrink, M., Mark, C. & Hellman, L. KRAB zinc finger proteins: an analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution. Mol. Biol. Evol. 19, 2118–2130 (2002).

    CAS  PubMed  Google Scholar 

  138. 138.

    Krishna, S. S., Majumdar, I. & Grishin, N. V. Structural classification of zinc fingers. Nucleic Acids Res. 31, 532–550 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  139. 139.

    Guilliere, F. et al. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold. PLoS ONE 8, e52908 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  140. 140.

    Erkes, A., Reschke, M., Boch, J. & Grau, J. Evolution of transcription activator-like effectors in Xanthomonas oryzae. Genome Biol. Evol. 9, 1599–1615 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  141. 141.

    Chavez, A. et al. Highly efficient Cas9-mediated transcriptional programming. Nat. Methods 12, 326–328 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  142. 142.

    Thakore, P. I. et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12, 1143–1149 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  143. 143.

    Shen, F., Triezenberg, S. J., Hensley, P., Porter, D. & Knutson, J. R. Transcriptional activation domain of the herpesvirus protein VP16 becomes conformationally constrained upon interaction with basal transcription factors. J. Biol. Chem. 271, 4827–4837 (1996).

    CAS  PubMed  Google Scholar 

  144. 144.

    Graslund, T., Li, X. L., Magnenat, L., Popkov, M. & Barbas, C. F. Exploring strategies for the design of artificial transcription factors. J. Biol. Chem. 280, 3707–3714 (2005).

    PubMed  Google Scholar 

  145. 145.

    Hofherr, A. et al. Efficient genome editing of differentiated renal epithelial cells. Pflugers Arch. 469, 303–311 (2017).

    CAS  PubMed  Google Scholar 

  146. 146.

    Freedman, B. S. et al. Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nat. Commun. 6, 8715 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  147. 147.

    Ben, J., Elworthy, S., Ng, A. S., van Eeden, F. & Ingham, P. W. Targeted mutation of the talpid3 gene in zebrafish reveals its conserved requirement for ciliogenesis and Hedgehog signalling across the vertebrates. Development 138, 4969–4978 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  148. 148.

    Jiang, D. et al. CRISPR/Cas9-induced disruption of wt1a and wt1b reveals their different roles in kidney and gonad development in Nile tilapia. Dev. Biol. 428, 63–73 (2017).

    CAS  PubMed  Google Scholar 

  149. 149.

    Jaffe, K. M. et al. c21orf59/kurly controls both cilia motility and polarization. Cell Rep. 14, 1841–1849 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  150. 150.

    Marusugi, K. et al. Functional validation of tensin2 SH2-PTB domain by CRISPR/Cas9-mediated genome editing. J. Vet. Med. Sci. 78, 1413–1420 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  151. 151.

    Brophy, P. D. et al. A gene implicated in activation of retinoic acid receptor targets is a novel renal agenesis gene in humans. Genetics 207, 215–228 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  152. 152.

    Wang, X. et al. Generation and phenotypic characterization of Pde1a mutant mice. PLoS ONE 12, e0181087 (2017).

    PubMed  PubMed Central  Google Scholar 

  153. 153.

    Ye, H. et al. Modulation of polycystic kidney disease severity by phosphodiesterase 1 and 3 subfamilies. J. Am. Soc. Nephrol. 27, 1312–1320 (2016).

    CAS  PubMed  Google Scholar 

  154. 154.

    Chen, C. C., Geurts, A. M., Jacob, H. J., Fan, F. & Roman, R. J. Heterozygous knockout of transforming growth factor-beta1 protects Dahl S rats against high salt-induced renal injury. Physiol. Genomics 45, 110–118 (2013).

    CAS  Google Scholar 

  155. 155.

    Mattson, D. L. et al. Genetic mutation of recombination activating gene 1 in Dahl salt-sensitive rats attenuates hypertension and renal damage. Am. J. Physiol. Regul. Integr. Comp. Physiol. 304, R407–R414 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  156. 156.

    Zhou, X. et al. Heterozygous disruption of renal outer medullary potassium channel in rats is associated with reduced blood pressure. Hypertension 62, 288–294 (2013).

    CAS  PubMed  Google Scholar 

  157. 157.

    He, J. et al. PKD1 mono-allelic knockout is sufficient to trigger renal cystogenesis in a mini-pig model. Int. J. Biol. Sci. 11, 361–369 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  158. 158.

    De Tomasi, L. et al. Mutations in GREB1L cause bilateral kidney agenesis in humans and mice. Am. J. Hum. Genet. 101, 803–814 (2017).

    PubMed  PubMed Central  Google Scholar 

  159. 159.

    Sanna-Cherchi, S. et al. Exome-wide association study identifies GREB1L mutations in congenital kidney malformations. Am. J. Hum. Genet. 101, 789–802 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  160. 160.

    Johnson, B. G. et al. Uromodulin p. Cys147Trp mutation drives kidney disease by activating ER stress and apoptosis. J. Clin. Invest. 127, 3954–3969 (2017).

    PubMed  PubMed Central  Google Scholar 

  161. 161.

    Yang, L. H. et al. Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science 350, 1101–1104 (2015).

    CAS  PubMed  Google Scholar 

  162. 162.

    Niu, D. et al. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 357, 1303–1307 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  163. 163.

    Petersen, B. & Niemann, H. Molecular scissors and their application in genetically modified farm animals. Transgenic Res. 24, 381–396 (2015).

    CAS  Google Scholar 

  164. 164.

    Long, C. et al. Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy. Science 351, 400–403 (2016).

    CAS  PubMed  Google Scholar 

  165. 165.

    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).

    CAS  Google Scholar 

  166. 166.

    Tabebordbar, M. et al. In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science 351, 407–411 (2016).

    CAS  Google Scholar 

  167. 167.

    Cirak, S. et al. Exon skipping and dystrophin restoration in patients with Duchenne muscular dystrophy after systemic phosphorodiamidate morpholino oligomer treatment: an open-label, phase 2, dose-escalation study. Lancet 378, 595–605 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  168. 168.

    Hildebrandt, F. Decade in review–genetics of kidney diseases: genetic dissection of kidney disorders. Nat. Rev. Nephrol. 11, 635–636 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  169. 169.

    Samulski, R. J. & Muzyczka, N. AAV-mediated gene therapy for research and therapeutic purposes. Annu. Rev. Virol. 1, 427–451 (2014).

    PubMed  Google Scholar 

  170. 170.

    Hwang, M. et al. TGF-beta1 siRNA suppresses the tubulointerstitial fibrosis in the kidney of ureteral obstruction. Exp. Mol. Pathol. 81, 48–54 (2006).

    CAS  PubMed  Google Scholar 

  171. 171.

    Zincarelli, C., Soltys, S., Rengo, G. & Rabinowitz, J. E. Analysis of AAV serotypes 1–9 mediated gene expression and tropism in mice after systemic injection. Mol. Ther. 16, 1073–1080 (2008).

    CAS  PubMed  Google Scholar 

  172. 172.

    Hillestad, M. L., Guenzel, A. J., Nath, K. A. & Barry, M. A. A. Vector-host system to fingerprint virus tropism. Hum. Gene Ther. 23, 1116–1126 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  173. 173.

    Chung, D. C. et al. Adeno-associated virus-mediated gene transfer to renal tubule cells via a retrograde ureteral approach. Nephron Extra 1, 217–223 (2011).

    PubMed  PubMed Central  Google Scholar 

  174. 174.

    Ellis, B. L., Hirsch, M. L., Porter, S. N., Samulski, R. J. & Porteus, M. H. Zinc-finger nuclease-mediated gene correction using single AAV vector transduction and enhancement by Food and Drug Administration-approved drugs. Gene Ther. 20, 35–42 (2013).

    CAS  PubMed  Google Scholar 

  175. 175.

    Yang, J. et al. Targeting of macrophage activity by adenovirus-mediated intragraft overexpression of TNFRp55-Ig, IL-12p40, and vIL-10 ameliorates adenovirus-mediated chronic graft injury, whereas stimulation of macrophages by overexpression of IFN-gamma accelerates chronic graft injury in a rat renal allograft model. J. Am. Soc. Nephrol. 14, 214–225 (2003).

    CAS  PubMed  Google Scholar 

  176. 176.

    Brunetti-Pierri, N. & Ng, P. Gene therapy with helper-dependent adenoviral vectors: lessons from studies in large animal models. Virus Genes 53, 684–691 (2017).

    CAS  PubMed  Google Scholar 

  177. 177.

    Yang, Y. P., Su, Q. & Wilson, J. M. Role of viral antigens in destructive cellular immune responses to adenovirus vector-transduced cells in mouse lungs. J. Virol. 70, 7209–7212 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  178. 178.

    Raper, S. E. et al. Fatal systemic inflammatory response syndrome in a ornithine transcarbamylase deficient patient following adenoviral gene transfer. Mol. Genet. Metab. 80, 148–158 (2003).

    CAS  Google Scholar 

  179. 179.

    Jooss, K., Yang, Y., Fisher, K. J. & Wilson, J. M. Transduction of dendritic cells by DNA viral vectors directs the immune response to transgene products in muscle fibers. J. Virol. 72, 4212–4223 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  180. 180.

    Chirmule, N. et al. Immune responses to adenovirus and adeno-associated virus in humans. Gene Ther. 6, 1574–1583 (1999).

    CAS  PubMed  Google Scholar 

  181. 181.

    Ertl, H. C. J. & High, K. A. Impact of AAV capsid-specific T-cell responses on design and outcome of clinical gene transfer trials with recombinant adeno-associated viral vectors: an evolving controversy. Hum. Gene Ther. 28, 328–337 (2017).

    CAS  PubMed  Google Scholar 

  182. 182.

    Mitani, K., Graham, F. L., Caskey, C. T. & Kochanek, S. Rescue, propagation, and partial-purification of a helper virus-dependent adenovirus vector. Proc. Natl Acad. Sci. USA 92, 3854–3858 (1995).

    CAS  PubMed  Google Scholar 

  183. 183.

    Fisher, K. J., Choi, H., Burda, J., Chen, S. J. & Wilson, J. M. Recombinant adenovirus deleted of all viral genes for gene therapy of cystic fibrosis. Virology 217, 11–22 (1996).

    CAS  PubMed  Google Scholar 

  184. 184.

    Morral, N. et al. High doses of a helper-dependent adenoviral vector yield supraphysiological levels of alpha(1)-antitrypsin with negligible toxicity. Hum. Gene Ther. 9, 2709–2716 (1998).

    CAS  PubMed  Google Scholar 

  185. 185.

    Morral, N. et al. Administration of helper-dependent adenoviral vectors and sequential delivery of different vector serotype for long-term liver-directed gene transfer in baboons. Proc. Natl Acad. Sci. USA 96, 12816–12821 (1999).

    CAS  PubMed  Google Scholar 

  186. 186.

    Charlesworth, C. T. et al. Identification of pre-existing adaptive immunity to Cas9 proteins in humans. Preprint at bioRxiv https://doi.org/10.1101/243345 (2018).

  187. 187.

    US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT00923390 (2018).

  188. 188.

    US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT03432364 (2018).

  189. 189.

    US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT02695160 (2018).

  190. 190.

    Hotta, A. & Yamanaka, S. in Annual Review of Genetics Vol. 49 (ed. Bassler, B. L.) 47–70 (Annual Reviews, 2015).

  191. 191.

    US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/NCT03041324 (2018).

  192. 192.

    Ahn, J. D. et al. Transcription factor decoy for AP-1 reduces mesangial cell proliferation and extracellular matrix production in vitro and in vivo. Gene Ther. 11, 916–923 (2004).

    CAS  PubMed  Google Scholar 

  193. 193.

    Isaka, Y. et al. Gene therapy by skeletal muscle expression of decorin prevents fibrotic disease in rat kidney. Nat. Med. 2, 418–423 (1996).

    CAS  PubMed  Google Scholar 

  194. 194.

    Higuchi, N. et al. Hydrodynamics-based delivery of the viral interleukin-10 gene suppresses experimental crescentic glomerulonephritis in Wistar-Kyoto rats. Gene Ther. 10, 1297–1310 (2003).

    CAS  PubMed  Google Scholar 

  195. 195.

    Ka, S. M. et al. Decoy receptor 3 inhibits renal mononuclear leukocyte infiltration and apoptosis and prevents progression of IgA nephropathy in mice. Am. J. Physiol. Renal Physiol. 301, F1218–F1230 (2011).

    CAS  PubMed  Google Scholar 

  196. 196.

    Choi, Y. K. et al. Suppression of glomerulosclerosis by adenovirus-mediated IL-10 expression in the kidney. Gene Ther. 10, 559–568 (2003).

    CAS  PubMed  Google Scholar 

  197. 197.

    Chao, J. & Chao, L. Experimental kallikrein gene therapy in hypertension, cardiovascular and renal diseases. Pharmacol. Res. 35, 517–522 (1997).

    CAS  PubMed  Google Scholar 

  198. 198.

    Yang, C. C., Hsu, S. P., Chen, K. H. & Chien, C. T. Effect of adenoviral catalase gene transfer on renal ischemia/reperfusion injury in rats. Chin. J. Physiol. 58, 420–430 (2015).

    CAS  PubMed  Google Scholar 

  199. 199.

    Ravichandran, K., Ozkok, A., Wang, Q., Mullick, A. E. & Edelstein, C. L. Antisense-mediated angiotensinogen inhibition slows polycystic kidney disease in mice with a targeted mutation in Pkd2. Am. J. Physiol. Renal Physiol. 308, F349–357 (2015).

    CAS  PubMed  Google Scholar 

  200. 200.

    Zheng, X. et al. Attenuating ischemia-reperfusion injury in kidney transplantation by perfusing donor organs with siRNA cocktail solution. Transplantation 100, 743–752 (2016).

    CAS  PubMed  Google Scholar 

  201. 201.

    Ding, Z. et al. Adenovirus-mediated anti-sense ERK2 gene therapy inhibits tubular epithelial-mesenchymal transition and ameliorates renal allograft fibrosis. Transpl. Immunol. 25, 34–41 (2011).

    CAS  PubMed  Google Scholar 

  202. 202.

    Nakamura, H. et al. Introduction of DNA enzyme for Egr-1 into tubulointerstitial fibroblasts by electroporation reduced interstitial alpha-smooth muscle actin expression and fibrosis in unilateral ureteral obstruction (UUO) rats. Gene Ther. 9, 495–502 (2002).

    CAS  PubMed  Google Scholar 

  203. 203.

    Terada, Y. et al. Gene transfer of Smad7 using electroporation of adenovirus prevents renal fibrosis in post-obstructed kidney. Kidney Int. 61, S94–S98 (2002).

    PubMed  Google Scholar 

  204. 204.

    Lan, H. Y. et al. Inhibition of renal fibrosis by gene transfer of inducible Smad7 using ultrasound-microbubble system in rat UUO model. J. Am. Soc. Nephrol. 14, 1535–1548 (2003).

    CAS  PubMed  Google Scholar 

  205. 205.

    Liu, X., Shen, W., Yang, Y. & Liu, G. Therapeutic implications of mesenchymal stem cells transfected with hepatocyte growth factor transplanted in rat kidney with unilateral ureteral obstruction. J. Pediatr. Surg. 46, 537–545 (2011).

    PubMed  Google Scholar 

  206. 206.

    Qiao, X. et al. Intermedin is upregulated and attenuates renal fibrosis by inhibition of oxidative stress in rats with unilateral ureteral obstruction. Nephrology (Carlton) 20, 820–831 (2015).

    CAS  Google Scholar 

  207. 207.

    Ozbek, E. et al. Role of mesenchymal stem cells transfected with vascular endothelial growth factor in maintaining renal structure and function in rats with unilateral ureteral obstruction. Exp. Clin. Transplant 13, 262–272 (2015).

    PubMed  Google Scholar 

  208. 208.

    Ren, Y. et al. CTGF siRNA ameliorates tubular cell apoptosis and tubulointerstitial fibrosis in obstructed mouse kidneys in a Sirt1-independent manner. Drug Des. Devel. Ther. 9, 4155–4171 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  209. 209.

    Bolar, N. A. et al. Heterozygous loss-of-function SEC61A1 mutations cause autosomal-dominant tubulo-interstitial and glomerulocystic kidney disease with anemia. Am. J. Hum. Genet. 99, 174–187 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  210. 210.

    Huang, Y. H. et al. DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A. Genome Biol. 18, 176 (2017).

    PubMed  PubMed Central  Google Scholar 

  211. 211.

    Jin, C. et al. HV1 acts as a sodium sensor and promotes superoxide production in medullary thick ascending limb of Dahl salt-sensitive rats. Hypertension 64, 541–550 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  212. 212.

    Endres, B. T. et al. Mutation of Plekha7 attenuates salt-sensitive hypertension in the rat. Proc. Natl Acad. Sci. USA 111, 12817–12822 (2014).

    CAS  PubMed  Google Scholar 

  213. 213.

    Mullins, L. J. et al. Mineralocorticoid excess or glucocorticoid insufficiency: renal and metabolic phenotypes in a rat Hsd11b2 knockout model. Hypertension 66, 667–673 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  214. 214.

    Cowley, A. W. Jr et al. Evidence of the importance of Nox4 in production of hypertension in Dahl salt-sensitive rats. Hypertension 67, 440–450 (2016).

    CAS  PubMed  Google Scholar 

  215. 215.

    Anderson, B. R. et al. In vivo modeling implicates APOL1 in nephropathy: evidence for dominant negative effects and epistasis under anemic stress. PLoS Genet. 11, e1005349 (2015).

    PubMed  PubMed Central  Google Scholar 

  216. 216.

    Yoshino, H. et al. microRNA-210-3p depletion by CRISPR/Cas9 promoted tumorigenesis through revival of TWIST1 in renal cell carcinoma. Oncotarget 8, 20881–20894 (2017).

    PubMed  PubMed Central  Google Scholar 

  217. 217.

    Yang, L. et al. Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science 350, 1101–1104 (2015).

    CAS  PubMed  Google Scholar 

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Acknowledgements

The authors have received research funding from the Mayo Foundation and the US National Institutes of Health (grants GM63904 and P30DK084567 (S.C.E.) and P30DK090728 (C.R.S., P.C.H. and S.C.E.)).

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Z.W.J., W.A.C.G., M.A.B., P.C.H. and C.R.S. researched the data for the article. Z.W.J., J.M.C., M.A.B., P.C.H., C.R.S. and S.C.E. made substantial contributions to discussions of the content. Z.W.J., G.M.G., W.A.C.G., M.A.B., P.C.H. and C.R.S. wrote the article and Z.W.J., J.M.C., G.M.G., M.A.B., P.C.H., C.R.S. and S.C.E. reviewed and edited the manuscript before submission.

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Glossary

Programmable DNA nucleases

A DNA-binding platform that can be customized to bind to a specific DNA sequence and introduce a DSB in this targeted manner.

Transposon elements

DNA sequences that can be translocated within the genome by transposase proteins.

CpG site

A cytosine residue directly followed by a guanine residue in a DNA strand. Cytosine residues in CpG sites can be directly methylated by DNA methyltransferase.

Morpholino oligomers

Synthetic modified oligomers that are capable of sterically inhibiting translation of specific RNAs in a targetable manner.

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WareJoncas, Z., Campbell, J.M., Martínez-Gálvez, G. et al. Precision gene editing technology and applications in nephrology. Nat Rev Nephrol 14, 663–677 (2018). https://doi.org/10.1038/s41581-018-0047-x

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