Nature & Animals

The NIH Somatic Cell Genome Editing program

  • 1.

    High, K. A. & Roncarolo, M. G. Gene therapy. N. Engl. J. Med. 381, 455–464 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 2.

    Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229–236 (2020).

    ADS 
    CAS 
    Article 

    Google Scholar
     

  • 3.

    Pickar-Oliver, A. & Gersbach, C. A. The next generation of CRISPR–Cas technologies and applications. Nat. Rev. Mol. Cell Biol. 20, 490–507 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 4.

    Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 5.

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

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 6.

    Smith, J. et al. A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res. 34, e149 (2006).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 7.

    Miller, J. C. et al. A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 29, 143–148 (2011).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 8.

    Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012). This paper, together with reference 9, established the RNA-guided DNA cleavage activity of the Cas9 protein, providing the biochemical basis for CRISPR genome editing.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 9.

    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).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 10.

    Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013). This paper, together with references 11–14, established the genome editing of eukaryotic cells by CRISPR–Cas9.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 11.

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

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 12.

    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 
    PubMed Central 

    Google Scholar
     

  • 13.

    Hwang, W. Y. et al. Efficient genome editing in zebrafish using a CRISPR–Cas system. Nat. Biotechnol. 31, 227–229 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 14.

    Jinek, M. et al. RNA-programmed genome editing in human cells. eLife 2, e00471 (2013).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 15.

    Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR–Cas systems. Nat. Biotechnol. 31, 233–239 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 16.

    Makarova, K. S. et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 17.

    Rouet, P., Smih, F. & Jasin, M. Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc. Natl Acad. Sci. USA 91, 6064–6068 (1994).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 18.

    Yeh, C. D., Richardson, C. D. & Corn, J. E. Advances in genome editing through control of DNA repair pathways. Nat. Cell Biol. 21, 1468–1478 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 19.

    Naldini, L., Trono, D. & Verma, I. M. Lentiviral vectors, two decades later. Science 353, 1101–1102 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 20.

    Dominguez, A. A., Lim, W. A. & Qi, L. S. Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 17, 5–15 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 21.

    Rees, H. A. & Liu, D. R. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19, 770–788 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 22.

    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). CRISPR–Cas9 was fused to a DNA-editing enzyme that enabled targeted nucleotide editing at genome locations recognized by Cas9, while avoiding double-stranded DNA breaks.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 23.

    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).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 24.

    Mok, B. Y. et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583, 631–637 (2020). This study, along with references 99–104, describes the development of mitochondrial DNA genome editors.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 25.

    Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019). A CRISPR–Cas9-reverse transcriptase fusion protein, along with an extended guide-RNA template, introduced small sequence changes that include all possible transitions and transversions as well as insertions and deletions.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 26.

    Kearns, N. A. et al. Functional annotation of native enhancers with a Cas9–histone demethylase fusion. Nat. Methods 12, 401–403 (2015). This work, along with reference 27, showed that CRISPR–Cas9 can be fused to a histone-modifying enzyme to enable targeted epigenetic editing.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 27.

    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
     

  • 28.

    Maeder, M. L. & Gersbach, C. A. Genome-editing technologies for gene and cell therapy. Mol. Ther. 24, 430–446 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 29.

    Porteus, M. H. A new class of medicines through DNA editing. N. Engl. J. Med. 380, 947–959 (2019).

    CAS 

    Google Scholar
     

  • 30.

    Li, H. et al. In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature 475, 217–221 (2011).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 31.

    Amoasii, L. et al. Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy. Science 362, 86–91 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 32.

    Maeder, M. L. et al. Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10. Nat. Med. 25, 229–233 (2019). This paper described preclinical work for the treatment of inherited retinal disease using a somatic cell genome-editing approach that uses an AAV vector to deliver SauCas9 and guide RNAs to photoreceptor cells by subretinal injection.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 33.

    Moretti, A. et al. Somatic gene editing ameliorates skeletal and cardiac muscle failure in pig and human models of Duchenne muscular dystrophy. Nat. Med. 26, 207–214 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 34.

    Tebas, P. et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N. Engl. J. Med. 370, 901–910 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 35.

    Xu, L. et al. CRISPR-edited stem cells in a patient with HIV and acute lymphocytic leukemia. N. Engl. J. Med. 381, 1240–1247 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 36.

    Stadtmauer, E. A. et al. CRISPR-engineered T cells in patients with refractory cancer. Science 367, eaba7365 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 37.

    Qasim, W. et al. Molecular remission of infant B-ALL after infusion of universal TALEN gene-edited CAR T cells. Sci. Transl. Med. 9, eaaj2013 (2017).


    Google Scholar
     

  • 38.

    Chew, W. L. et al. A multifunctional AAV–CRISPR–Cas9 and its host response. Nat. Methods 13, 868–874 (2016). This study, along with references 39–47 and 142, described host immune responses to genome editors or their delivery vectors.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 39.

    Wang, D. et al. Adenovirus-mediated somatic genome editing of Pten by CRISPR/Cas9 in mouse liver in spite of Cas9-specific immune responses. Hum. Gene Ther. 26, 432–442 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 40.

    Nelson, C. E. et al. Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nat. Med. 25, 427–432 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 41.

    Wang, L. et al. Meganuclease targeting of PCSK9 in macaque liver leads to stable reduction in serum cholesterol. Nat. Biotechnol. 36, 717–725 (2018).

    CAS 

    Google Scholar
     

  • 42.

    Sedic, M. et al. Safety evaluation of lipid nanoparticle-formulated modified mRNA in the Sprague-Dawley rat and cynomolgus monkey. Vet. Pathol. 55, 341–354 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 43.

    Moreno, A. M. et al. Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy. Nat. Biomed. Eng. 3, 806–816 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 44.

    Charlesworth, C. T. et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat. Med. 25, 249–254 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 45.

    Wagner, D. L. et al. High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population. Nat. Med. 25, 242–248 (2019).

    CAS 

    Google Scholar
     

  • 46.

    Ferdosi, S. R. et al. Multifunctional CRISPR–Cas9 with engineered immunosilenced human T cell epitopes. Nat. Commun. 10, 1842 (2019).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 47.

    Li, A. et al. AAV-CRISPR gene editing is negated by pre-existing immunity to Cas9. Mol. Ther. 28, 1432–1441 (2020).

    CAS 

    Google Scholar
     

  • 48.

    Canver, M. C. et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527, 192–197 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 49.

    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). This study, along with reference 50, demonstrated the feasibility of achieving therapeutically meaningful levels of genome editing in affected tissues in a mouse model of muscular dystrophy.

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 50.

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

    ADS 
    CAS 

    Google Scholar
     

  • 51.

    Amoasii, L. et al. Single-cut genome editing restores dystrophin expression in a new mouse model of muscular dystrophy. Sci. Transl. Med. 9, eaan8081 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 52.

    Liu, Z. et al. Highly efficient RNA-guided base editing in rabbit. Nat. Commun. 9, 2717 (2018).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 53.

    Zafra, M. P. et al. Optimized base editors enable efficient editing in cells, organoids and mice. Nat. Biotechnol. 36, 888–893 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 54.

    Villiger, L. et al. Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nat. Med. 24, 1519–1525 (2018).

    CAS 

    Google Scholar
     

  • 55.

    Li, Q. et al. CRISPR–Cas9-mediated base-editing screening in mice identifies DND1 amino acids that are critical for primordial germ cell development. Nat. Cell Biol. 20, 1315–1325 (2018).

    CAS 

    Google Scholar
     

  • 56.

    Yeh, W.-H., Chiang, H., Rees, H. A., Edge, A. S. B. & Liu, D. R. In vivo base editing of post-mitotic sensory cells. Nat. Commun. 9, 2184 (2018).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 57.

    Zeng, Y. et al. Correction of the Marfan syndrome pathogenic FBN1 mutation by base editing in human cells and heterozygous embryos. Mol. Ther. 26, 2631–2637 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 58.

    Ryu, S.-M. et al. Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy. Nat. Biotechnol. 36, 536–539 (2018).

    CAS 

    Google Scholar
     

  • 59.

    Levy, J. M. et al. Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses. Nat. Biomed. Eng. 4, 97–110 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 60.

    Yeh, W.-H. et al. In vivo base editing restores sensory transduction and transiently improves auditory function in a mouse model of recessive deafness. Sci. Transl. Med. 12, eaay9101 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 61.

    Zeng, J. et al. Therapeutic base editing of human hematopoietic stem cells. Nat. Med. 26, 535–541 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 62.

    Song, C.-Q. et al. Adenine base editing in an adult mouse model of tyrosinaemia. Nat. Biomed. Eng. 4, 125–130 (2020).

    CAS 

    Google Scholar
     

  • 63.

    Sürün, D. et al. Efficient generation and correction of mutations in human iPS cells utilizing mRNAs of CRISPR base editors and prime editors. Genes (Basel) 11, 511 (2020).


    Google Scholar
     

  • 64.

    Kim, D., Luk, K., Wolfe, S. A. & Kim, J.-S. Evaluating and enhancing target specificity of gene-editing nucleases and deaminases. Annu. Rev. Biochem. 88, 191–220 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 65.

    Gabriel, R. et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol. 29, 816 (2011). This study, along with references 133–140 and 143, established empirical methods for genome-wide profiling of off-target modifications.

    CAS 

    Google Scholar
     

  • 66.

    Khvorova, A. & Watts, J. K. The chemical evolution of oligonucleotide therapies of clinical utility. Nat. Biotechnol. 35, 238–248 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 67.

    Perry, M. E., Valdes, K. M., Wilder, E., Austin, C. P. & Brooks, P. J. Genome editing to ‘re-write’ wrongs. Nat. Rev. Drug Discov. 17, 689–690 (2018).

    CAS 

    Google Scholar
     

  • 68.

    Esvelt, K. M. et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10, 1116–1121 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 69.

    Hou, Z. et al. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc. Natl Acad. Sci. USA 110, 15644–15649 (2013).

    ADS 
    CAS 

    Google Scholar
     

  • 70.

    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
     

  • 71.

    Ran, F. A. et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520, 186–191 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 72.

    Kim, E. et al. In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nat. Commun. 8, 14500 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 73.

    Agudelo, D. et al. Versatile and robust genome editing with Streptococcus thermophilus CRISPR1–Cas9. Genome Res. 30, 107–117 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 74.

    Edraki, A. et al. A compact, high-accuracy Cas9 with a dinucleotide PAM for in vivo genome editing. Mol. Cell 73, 714–726.e4 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 75.

    Hirano, H. et al. Structure and engineering of Francisella novicida Cas9. Cell 164, 950–961 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 76.

    Harrington, L. B. et al. A thermostable Cas9 with increased lifetime in human plasma. Nat. Commun. 8, 1424 (2017).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 77.

    Chatterjee, P., Jakimo, N. & Jacobson, J. M. Minimal PAM specificity of a highly similar SpCas9 ortholog. Sci. Adv. 4, eaau0766 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 78.

    Chatterjee, P. et al. A Cas9 with PAM recognition for adenine dinucleotides. Nat. Commun. 11, 2474 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 79.

    Hu, Z. et al. A compact Cas9 ortholog from Staphylococcus auricularis (SauriCas9) expands the DNA targeting scope. PLoS Biol. 18, e3000686 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 80.

    Burstein, D. et al. New CRISPR–Cas systems from uncultivated microbes. Nature 542, 237–241 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 81.

    Gupta, A., Bahal, R., Gupta, M., Glazer, P. M. & Saltzman, W. M. Nanotechnology for delivery of peptide nucleic acids (PNAs). J. Control. Release 240, 302–311 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 82.

    Yan, W. X. et al. Functionally diverse type V CRISPR–Cas systems. Science 363, 88–91 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 83.

    Liu, J.-J. et al. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 566, 218–223 (2019); correction 568, E8–E10 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 84.

    Dolan, A. E. et al. Introducing a spectrum of long-range genomic deletions in human embryonic stem cells using type I CRISPR–Cas. Mol. Cell 74, 936–950.e5 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 85.

    Strecker, J. et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science 365, 48–53 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 86.

    Klompe, S. E., Vo, P. L. H., Halpin-Healy, T. S. & Sternberg, S. H. Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration. Nature 571, 219–225 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 87.

    Pausch, P. et al. CRISPR–CasΦ from huge phages is a hypercompact genome editor. Science 369, 333–337 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 88.

    Sakata, R. C. et al. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. Nat. Biotechnol. 38, 865–869 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 89.

    Grünewald, J. et al. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nat. Biotechnol. 38, 861–864 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 90.

    Zhang, X. et al. Dual base editor catalyzes both cytosine and adenine base conversions in human cells. Nat. Biotechnol. 38, 856–860 (2020).

    CAS 

    Google Scholar
     

  • 91.

    Kurt, I. C. et al. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nat. Biotechnol. 39, 41–46 (2021).

    CAS 

    Google Scholar
     

  • 92.

    Zhao, D. et al. Glycosylase base editors enable C-to-A and C-to-G base changes. Nat. Biotechnol. 39, 35–40 (2021).

    CAS 

    Google Scholar
     

  • 93.

    Holtzman, L. & Gersbach, C. A. Editing the epigenome: reshaping the genomic landscape. Annu. Rev. Genomics Hum. Genet. 19, 43–71 (2018).

    CAS 

    Google Scholar
     

  • 94.

    Zeitler, B. et al. Allele-selective transcriptional repression of mutant HTT for the treatment of Huntington’s disease. Nat. Med. 25, 1131–1142 (2019).

    CAS 

    Google Scholar
     

  • 95.

    Black, J. B. & Gersbach, C. A. Synthetic transcription factors for cell fate reprogramming. Curr. Opin. Genet. Dev. 52, 13–21 (2018).

    CAS 

    Google Scholar
     

  • 96.

    Economos, N. G. et al. Peptide nucleic acids and gene editing: perspectives on structure and repair. Molecules 25, 735 (2020).

    CAS 

    Google Scholar
     

  • 97.

    McNeer, N. A. et al. Nanoparticles that deliver triplex-forming peptide nucleic acid molecules correct F508del CFTR in airway epithelium. Nat. Commun. 6, 6952 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 98.

    Bahal, R. et al. In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery. Nat. Commun. 7, 13304 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 99.

    Gammage, P. A., Moraes, C. T. & Minczuk, M. Mitochondrial genome engineering: the revolution may not be CRISPR-ized. Trends Genet. 34, 101–110 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 100.

    Minczuk, M., Kolasinska-Zwierz, P., Murphy, M. P. & Papworth, M. A. Construction and testing of engineered zinc-finger proteins for sequence-specific modification of mtDNA. Nat. Protoc. 5, 342–356 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 101.

    Gammage, P. A. et al. Genome editing in mitochondria corrects a pathogenic mtDNA mutation in vivo. Nat. Med. 24, 1691–1695 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 102.

    Bacman, S. R. et al. MitoTALEN reduces mutant mtDNA load and restores tRNAAla levels in a mouse model of heteroplasmic mtDNA mutation. Nat. Med. 24, 1696–1700 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 103.

    Hashimoto, M. et al. MitoTALEN: a general approach to reduce mutant mtDNA loads and restore oxidative phosphorylation function in mitochondrial diseases. Mol. Ther. 23, 1592–1599 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 104.

    Campbell, J. M. et al. Engineering targeted deletions in the mitochondrial genome. Preprint at https://doi.org/10.1101/287342 (2018).

  • 105.

    Yin, H., Kauffman, K. J. & Anderson, D. G. Delivery technologies for genome editing. Nat. Rev. Drug Discov. 16, 387–399 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 106.

    Wang, D., Zhang, F. & Gao, G. CRISPR-based therapeutic genome editing: strategies and in vivo delivery by AAV vectors. Cell 181, 136–150 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 107.

    van Haasteren, J., Li, J., Scheideler, O. J., Murthy, N. & Schaffer, D. V. The delivery challenge: fulfilling the promise of therapeutic genome editing. Nat. Biotechnol. 38, 845–855 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 108.

    Finn, J. D. et al. A single administration of CRISPR/Cas9 lipid nanoparticles achieves robust and persistent in vivo genome editing. Cell Rep. 22, 2227–2235 (2018). Nonviral, systemic, lipid nanoparticle-based delivery of mRNA-encoded Cas9 and sgRNAs provided therapeutically relevant levels of genome editing in the liver in mice.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 109.

    Wei, T., Cheng, Q., Min, Y.-L., Olson, E. N. & Siegwart, D. J. Systemic nanoparticle delivery of CRISPR–Cas9 ribonucleoproteins for effective tissue specific genome editing. Nat. Commun. 11, 3232 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 110.

    Yin, H. et al. Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Nat. Biotechnol. 35, 1179–1187 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 111.

    Krishnamurthy, S. et al. Engineered amphiphilic peptides enable delivery of proteins and CRISPR-associated nucleases to airway epithelia. Nat. Commun. 10, 4906 (2019).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 112.

    Chen, G. et al. A biodegradable nanocapsule delivers a Cas9 ribonucleoprotein complex for in vivo genome editing. Nat. Nanotechnol. 14, 974–980 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 113.

    Staahl, B. T. et al. Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes. Nat. Biotechnol. 35, 431–434 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 114.

    Yin, H. et al. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat. Biotechnol. 34, 328–333 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 115.

    Moon, S. B., Kim, D. Y., Ko, J.-H., Kim, J.-S. & Kim, Y.-S. Improving CRISPR genome editing by engineering guide RNAs. Trends Biotechnol. 37, 870–881 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 116.

    Wu, W. et al. Efficient in vivo gene editing using ribonucleoproteins in skin stem cells of recessive dystrophic epidermolysis bullosa mouse model. Proc. Natl Acad. Sci. USA 114, 1660–1665 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 117.

    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 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 118.

    Certo, M. T. et al. Tracking genome engineering outcome at individual DNA breakpoints. Nat. Methods 8, 671–676 (2011).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 119.

    Iwano, S. et al. Single-cell bioluminescence imaging of deep tissue in freely moving animals. Science 359, 935–939 (2018).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 120.

    Penheiter, A. R., Russell, S. J. & Carlson, S. K. The sodium iodide symporter (NIS) as an imaging reporter for gene, viral, and cell-based therapies. Curr. Gene Ther. 12, 33–47 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 121.

    Minn, I. et al. Imaging CAR T cell therapy with PSMA-targeted positron emission tomography. Sci. Adv. 5, eaaw5096 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 122.

    Bulte, J. W. M. Superparamagnetic iron oxides as MPI tracers: A primer and review of early applications. Adv. Drug Deliv. Rev. 138, 293–301 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 123.

    Pumphrey, A. L. et al. Cardiac chemical exchange saturation transfer MR imaging tracking of cell survival or rejection in mouse models of cell therapy. Radiology 282, 131–138 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 124.

    Huang, J., Lee, C. C. I., Sutcliffe, J. L., Cherry, S. R. & Tarantal, A. F. Radiolabeling rhesus monkey CD34+ hematopoietic and mesenchymal stem cells with 64Cu-pyruvaldehyde-bis(N4-methylthiosemicarbazone) for microPET imaging. Mol. Imaging 7, 1–11 (2008).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 125.

    Tarantal, A. F. et al. Radiolabeling and in vivo imaging of transplanted renal lineages differentiated from human embryonic stem cells in fetal rhesus monkeys. Mol. Imaging Biol. 14, 197–204 (2012).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 126.

    Tarantal, A. F., Lee, C. C. I., Kukis, D. L. & Cherry, S. R. Radiolabeling human peripheral blood stem cells for positron emission tomography (PET) imaging in young rhesus monkeys. PLoS ONE 8, e77148 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 127.

    Tarantal, A. F., Lee, C. C. I., Martinez, M. L., Asokan, A. & Samulski, R. J. Systemic and persistent muscle gene expression in rhesus monkeys with a liver de-targeted adeno-associated virus vector. Hum. Gene Ther. 28, 385–391 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 128.

    Bulte, J. W. M. et al. Quantitative “hot spot” imaging of transplanted stem cells using superparamagnetic tracers and magnetic particle imaging (MPI). Tomography 1, 91–97 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 129.

    Tarantal, A. F., Lee, C. C. I., Jimenez, D. F. & Cherry, S. R. Fetal gene transfer using lentiviral vectors: in vivo detection of gene expression by microPET and optical imaging in fetal and infant monkeys. Hum. Gene Ther. 17, 1254–1261 (2006).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 130.

    Tarantal, A. F. & Lee, C. C. I. Long-term luciferase expression monitored by bioluminescence imaging after adeno-associated virus-mediated fetal gene delivery in rhesus monkeys (Macaca mulatta). Hum. Gene Ther. 21, 143–148 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 131.

    Meier, S. et al. Non-invasive detection of adeno-associated viral gene transfer using a genetically encoded CEST-MRI reporter gene in the murine heart. Sci. Rep. 8, 4638 (2018).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 132.

    Nyström, N. N. et al. Longitudinal visualization of viable cancer cell intratumoral distribution in mouse models using Oatp1a1-enhanced magnetic resonance imaging. Invest. Radiol. 54, 302–311 (2019).


    Google Scholar
     

  • 133.

    Crosetto, N. et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat. Methods 10, 361–365 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 134.

    Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR–Cas nucleases. Nat. Biotechnol. 33, 187–197 (2015).

    CAS 

    Google Scholar
     

  • 135.

    Kim, D. et al. Digenome-seq: genome-wide profiling of CRISPR–Cas9 off-target effects in human cells. Nat. Methods 12, 237–243, 1, 243 (2015).

    CAS 

    Google Scholar
     

  • 136.

    Tsai, S. Q. et al. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets. Nat. Methods 14, 607–614 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 137.

    Cameron, P. et al. Mapping the genomic landscape of CRISPR–Cas9 cleavage. Nat. Methods 14, 600–606 (2017).

    CAS 

    Google Scholar
     

  • 138.

    Lazzarotto, C. R. et al. Defining CRISPR–Cas9 genome-wide nuclease activities with CIRCLE-seq. Nat. Protoc. 13, 2615–2642 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 139.

    Wienert, B. et al. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Science 364, 286–289 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 140.

    Schmid-Burgk, J. L. et al. Highly parallel profiling of Cas9 variant specificity. Mol. Cell 78, 794–800.e8 (2020).

    CAS 

    Google Scholar
     

  • 141.

    Cheng, Y. & Tsai, S. Q. Illuminating the genome-wide activity of genome editors for safe and effective therapeutics. Genome Biol. 19, 226 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 142.

    Simhadri, V. L. et al. Prevalence of pre-existing antibodies to CRISPR-associated nuclease Cas9 in the USA population. Mol. Ther. Methods Clin. Dev. 10, 105–112 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 143.

    Lazzarotto, C. R. et al. CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity. Nat. Biotechnol. 38, 1317–1327 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 144.

    Truskey, G. A. Development and application of human skeletal muscle microphysiological systems. Lab Chip 18, 3061–3073 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 145.

    Wang, J. et al. Engineered skeletal muscles for disease modeling and drug discovery. Biomaterials 221, 119416 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 146.

    Freedman, L. P., Cockburn, I. M. & Simcoe, T. S. The economics of reproducibility in preclinical research. PLoS Biol. 13, e1002165 (2015).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 147.

    Plant, A. L., Locascio, L. E., May, W. E. & Gallagher, P. D. Improved reproducibility by assuring confidence in measurements in biomedical research. Nat. Methods 11, 895–898 (2014).

    CAS 

    Google Scholar
     

  • 148.

    Plant, A. L. et al. How measurement science can improve confidence in research results. PLoS Biol. 16, e2004299 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 149.

    The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636–640 (2004).

    ADS 

    Google Scholar
     

  • 150.

    Brown, J. B. & Celniker, S. E. Lessons from modENCODE. Annu. Rev. Genomics Hum. Genet. 16, 31–53 (2015).

    CAS 

    Google Scholar
     

  • 151.

    Stunnenberg, H. G. & Hirst, M. The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery. Cell 167, 1145–1149 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 152.

    Dekker, J. et al. The 4D nucleome project. Nature 549, 219–226 (2017).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 153.

    Warren, C. R., Jaquish, C. E. & Cowan, C. A. The NextGen Genetic Association Studies Consortium: a foray into in vitro population genetics. Cell Stem Cell 20, 431–433 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 154.

    HuBMAP Consortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature 574, 187–192 (2019).

    ADS 
    CAS 

    Google Scholar
     

  • 155.

    Collins, F. & Galas, D. A new five-year plan for the U.S. Human Genome Project. Science 262, 43–46 (1993).

    ADS 
    CAS 

    Google Scholar
     


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