[1] M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J.A. Doudna, E. Charpentier, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science 337 (6096) (Aug. 2012) 816–821, https://doi.org/10.1126/ science.1225829.
[2] M. Behr, J. Zhou, B. Xu, H. Zhang, In vivo delivery of CRISPR-Cas9 therapeutics: Progress and challenges, Acta Pharm. Sin. B 11 (8) (Aug. 2021) 2150–2171, https://doi.org/10.1016/j.apsb.2021.05.020.
[3] B.H. Yip, Recent advance in CRISPR/Cas9 delivery strategies, Biomolecules 10 (6) (May 2020) 839, https://doi.org/10.3390/biom10060839.
[4] X. Xu, et al., Delivery of CRISPR/Cas9 for therapeutic genome editing, J. Gene Med. 21 (7) (2019), e3107, https://doi.org/10.1002/jgm.3107.
[5] K. Ishida, P. Gee, A. Hotta, Minimizing off-target mutagenesis risks caused by programmable nucleases, Int. J. Mol. Sci. 16 (10) (Oct. 2015) 24751–24771, https://doi.org/10.3390/ijms161024751.
[6] X. Liang, et al., Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection, J. Biotechnol. 208 (Aug. 2015) 44–53, https://doi.org/ 10.1016/j.jbiotec.2015.04.024.
[7] B. Li, et al., Engineering CRISPR-Cpf1 crRNAs and mRNAs to maximize genome editing efficiency, Nat. Biomed. Eng. 1 (5) (May 2017), https://doi.org/10.1038/ s41551-017-0066.
[8] A. Kagita, et al., Efficient ssODN-mediated targeting by avoiding cellular inhibitory RNAs through Precomplexed CRISPR-Cas9/sgRNA ribonucleoprotein, Stem Cell Rep. 16 (4) (Apr. 2021) 985–996, https://doi.org/10.1016/j. stemcr.2021.02.013.
[9] I.S. Ludwig, et al., Hepatitis C virus targets DC-SIGN and L-SIGN to escape lysosomal degradation, J. Virol. 78 (15) (Aug. 2004) 8322–8332, https://doi.org/ 10.1128/JVI.78.15.8322-8332.2004.
[10] J. Gao, K. Mese, O. Bunz, A. Ehrhardt, State-of-the-art human adenovirus vectorology for therapeutic approaches, FEBS Lett. 593 (24) (2019) 3609–3622, https://doi.org/10.1002/1873-3468.13691.
[11] R.J. Samulski, N. Muzyczka, AAV-mediated gene therapy for research and therapeutic purposes, Annu. Rev. Virol. 1 (1) (Nov. 2014) 427–451, https://doi. org/10.1146/annurev-virology-031413-085355.
[12] T.R. Flotte, Gene therapy Progress and prospects: recombinant adeno-associated virus (rAAV) vectors, Gene Ther. 11 (10) (May 2004) 805–810, https://doi.org/ 10.1038/sj.gt.3302233.
[13] V.W. Choi, D.M. McCarty, R. Jude Samulski, AAV hybrid serotypes: improved vectors for gene delivery, Curr. Gene Ther. 5 (3) (Jun. 2005) 299–310.
[14] Z. Wu, A. Asokan, R.J. Samulski, Adeno-associated virus serotypes: vector toolkit for human gene therapy, Mol. Ther. J. Am. Soc. Gene Ther. 14 (3) (Sep. 2006), https://doi.org/10.1016/j.ymthe.2006.05.009. Art. no. 3.
[15] G. Buchlis, et al., Factor IX expression in skeletal muscle of a severe hemophilia B patient 10 years after AAV-mediated gene transfer, Blood 119 (13) (Mar. 2012) 3038–3041, https://doi.org/10.1182/blood-2011-09-382317.
[16] D.Y. Richards, et al., AAV-mediated CRISPR/Cas9 gene editing in murine phenylketonuria, Mol. Ther. Methods Clin. Dev. 17 (Jun. 2020) 234–245, https:// doi.org/10.1016/j.omtm.2019.12.004.
[17] L. Wang, et al., A mutation-independent CRISPR-Cas9-mediated gene targeting approach to treat a murine model of ornithine transcarbamylase deficiency, Sci. Adv. 6 (7) (Feb. 2020) eaax5701, https://doi.org/10.1126/sciadv.aax5701.
[18] W. Duan, et al., The deletion of mutant SOD1 via CRISPR/Cas9/sgRNA prolongs survival in an amyotrophic lateral sclerosis mouse model, Gene Ther. 27 (3–4) (Apr. 2020) 157–169, https://doi.org/10.1038/s41434-019-0116-1.
[19] H. Zhao, et al., In vivo AAV-CRISPR/Cas9-mediated gene editing ameliorates atherosclerosis in familial hypercholesterolemia, Circulation 141 (1) (Jan. 2020) 67–79, https://doi.org/10.1161/CIRCULATIONAHA.119.042476.
[20] J. Gao, T. Bergmann, W. Zhang, M. Schiwon, E. Ehrke-Schulz, A. Ehrhardt, Viral vector-based delivery of CRISPR/Cas9 and donor DNA for homology-directed repair in an in vitro model for canine hemophilia B, Mol. Ther. Nucleic Acids 14 (Mar. 2019) 364–376, https://doi.org/10.1016/j.omtn.2018.12.008.
[21] A.M. Monteys, S.A. Ebanks, M.S. Keiser, B.L. Davidson, CRISPR/Cas9 editing of the mutant huntingtin allele in vitro and in vivo, Mol. Ther. J. Am. Soc. Gene Ther. 25 (1) (Jan. 2017) 12–23, https://doi.org/10.1016/j.ymthe.2016.11.010.
[22] K.M. Nishiguchi, K. Fujita, F. Miya, S. Katayama, T. Nakazawa, Single AAV- mediated mutation replacement genome editing in limited number of photoreceptors restores vision in mice, Nat. Commun. 11 (1) (Jan. 2020) 482, https://doi.org/10.1038/s41467-019-14181-3.
[23] T. Koo, et al., CRISPR-LbCpf1 prevents choroidal neovascularization in a mouse model of age-related macular degeneration, Nat. Commun. 9 (1) (May 2018) 1855, https://doi.org/10.1038/s41467-018-04175-y.
[24] W. Yu, et al., Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice, Nat. Commun. 8 (1) (Mar. 2017) 14716, https://doi.org/ 10.1038/ncomms14716.
[25] X. Huang, et al., Genome editing abrogates angiogenesis in vivo, Nat. Commun. 8 (1) (Jul. 2017) 112, https://doi.org/10.1038/s41467-017-00140-3.
[26] G.-X. Ruan, E. Barry, D. Yu, M. Lukason, S.H. Cheng, A. Scaria, CRISPR/Cas9- mediated genome editing as a therapeutic approach for Leber congenital Amaurosis 10, Mol. Ther. J. Am. Soc. Gene Ther. 25 (2) (Feb. 2017) 331–341, https://doi.org/10.1016/j.ymthe.2016.12.006.
[27] M.L. Maeder, et al., Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10, Nat. Med. 25 (2) (Feb. 2019) 229–233, https://doi.org/10.1038/s41591-018-0327-9.
[28] N.E. Bengtsson, et al., Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy, Nat. Commun. 8 (1) (Feb. 2017) 14454, https://doi.org/10.1038/ ncomms14454.
[29] Y.-L. Min, et al., Correction of three prominent mutations in mouse and human models of Duchenne muscular dystrophy by single-cut genome editing, Mol. Ther. 28 (9) (Sep. 2020) 2044–2055, https://doi.org/10.1016/j.ymthe.2020.05.024.
[30] Y.-L. Min, et al., CRISPR-Cas9 corrects Duchenne muscular dystrophy exon 44 deletion mutations in mice and human cells, Sci. Adv. 5 (3) (Mar. 2019) eaav4324, https://doi.org/10.1126/sciadv.aav4324.
[31] Y. Zhang, et al., Enhanced CRISPR-Cas9 correction of Duchenne muscular dystrophy in mice by a self-complementary AAV delivery system, Sci. Adv. 6 (8) (Feb. 2020) eaay6812, https://doi.org/10.1126/sciadv.aay6812.
[32] L. Amoasii, et al., In vivo non-invasive monitoring of dystrophin correction in a new Duchenne muscular dystrophy reporter mouse, Nat. Commun. 10 (Oct. 2019) 4537, https://doi.org/10.1038/s41467-019-12335-x.
[33] M. Tabebordbar, et al., Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species, Cell 184 (19) (Sep. 2021) 4919–4938.e22, https://doi.org/10.1016/j.cell.2021.08.028.
[34] A. Philippidis, Editas Early Data for CRISPR Therapy EDIT-101 Shows Efficacy ‘Signals’ in Two Patients, GEN - Genetic Engineering and Biotechnology News, Sep. 29, 2021. https://www.genengnews.com/news/editas-early-data-for-crispr-therapy-edit-101-shows-efficacy-signals-in-two-patients/ (accessed Oct. 27, 2021).
[35] First CRISPR therapy dosed, Nat. Biotechnol., vol. 38, no. 4, pp. 382–382, Apr. 2020, doi: https://doi.org/10.1038/s41587-020-0493-4.
[36] L. Ou, et al., A highly efficacious PS gene editing system corrects metabolic and neurological complications of mucopolysaccharidosis type I, Mol. Ther. J. Am. Soc. Gene Ther. 28 (6) (Jun. 2020) 1442–1454, https://doi.org/10.1016/j. ymthe.2020.03.018.
[37] A.C. Nathwani, Gene therapy for hemophilia, Hematol. Am. Soc. Hematol. Educ. Program 2019 (1) (Dec. 2019) 1–8, https://doi.org/10.1182/ hematology.2019000007.
[38] W. Ding, et al., Zinc finger nucleases targeting the human papillomavirus E7 oncogene induce E7 disruption and a transformed phenotype in HPV16/18- positive cervical cancer cells, Clin. Cancer Res. (Oct. 2014), https://doi.org/ 10.1158/1078-0432.CCR-14-0250.
[39] Z. Hu, et al., TALEN-mediated targeting of HPV oncogenes ameliorates HPV- related cervical malignancy, J. Clin. Invest. 125 (1) (Jan. 2015) 425–436, https:// doi.org/10.1172/JCI78206.
[40] Z. Hu, et al., Disruption of HPV16-E7 by CRISPR/Cas system induces apoptosis and growth inhibition in HPV16 positive human cervical Cancer cells, Biomed. Res. Int. Jul. 2014 (2014), e612823, https://doi.org/10.1155/2014/612823.
[41] A. Mullard, Gene-editing pipeline takes off, Nat. Rev. Drug Discov. 19 (6) (May 2020) 367–372, https://doi.org/10.1038/d41573-020-00096-y.
[42] D. Yin, et al., Targeting herpes simplex virus with CRISPR-Cas9 cures herpetic stromal keratitis in mice, Nat. Biotechnol. 39 (5) (May 2021) 567–577, https:// doi.org/10.1038/s41587-020-00781-8.
[43] J.D. Gillmore, et al., CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis, N. Engl. J. Med. 385 (6) (Aug. 2021), https://doi.org/10.1056/ NEJMoa2107454. Art. no. 6.
[44] C.S. Manno, et al., Successful transduction of liver in hemophilia by AAV-factor IX and limitations imposed by the host immune response, Nat. Med. 12 (3) (Mar. 2006) 342–347, https://doi.org/10.1038/nm1358.
[45] S. Boutin, et al., Prevalence of serum IgG and neutralizing factors against adeno- associated virus (AAV) types 1, 2, 5, 6, 8, and 9 in the healthy population: implications for gene therapy using AAV vectors, Hum. Gene Ther. 21 (6) (Jun. 2010) 704–712, https://doi.org/10.1089/hum.2009.182.
[46] A. Li, et al., AAV-CRISPR gene editing is negated by pre-existing immunity to Cas9, Mol. Ther. 28 (6) (Jun. 2020) 1432–1441, https://doi.org/10.1016/j. ymthe.2020.04.017.
[47] K. Erles, P. Sebo¨kova`, J.R. Schlehofer, Update on the prevalence of serum antibodies (IgG and IgM) to adeno-associated virus (AAV), J. Med. Virol. 59 (3) (Nov. 1999) 406–411, https://doi.org/10.1002/(sici)1096-9071(199911)59: 3<406::aid-jmv22>3.0.co;2-n.
[48] F. Mingozzi, K.A. High, Immune responses to AAV vectors: overcoming barriers to successful gene therapy, Blood 122 (1) (Jul. 2013) 23–36, https://doi.org/ 10.1182/blood-2013-01-306647.
[49] M.A. Bartel, J.R. Weinstein, D.V. Schaffer, Directed evolution of novel adeno- associated viruses for therapeutic gene delivery, Gene Ther. 19 (6) (Jun. 2012) 694–700, https://doi.org/10.1038/gt.2012.20.
[50] I. Ates, T. Rathbone, C. Stuart, P.H. Bridges, R.N. Cottle, Delivery approaches for therapeutic genome editing and challenges, Genes 11 (10) (Sep. 2020) 1113, https://doi.org/10.3390/genes11101113.
[51] V. Monteilhet, et al., A 10 patient case report on the impact of plasmapheresis upon neutralizing factors against adeno-associated virus (AAV) types 1, 2, 6, and 8, Mol. Ther. J. Am. Soc. Gene Ther. 19 (11) (Nov. 2011) 2084–2091, https://doi. org/10.1038/mt.2011.108.
[52] C. Hinderer, et al., Severe toxicity in nonhuman Primates and piglets following High-dose intravenous Administration of an Adeno-Associated Virus Vector Expressing Human SMN, Hum. Gene Ther. 29 (3) (Mar. 2018) 285–298, https:// doi.org/10.1089/hum.2018.015.
[53] Audentes press release. https://www.joshuafrase.org/get-involved/recensus-stud y.php, 2020 (accessed Oct. 01, 2021).
[54] Audentes press release, Astellas Gene Therapies Therapeutics. https://www.astell as.com/system/files/news/2021-09/20210901_en.pdf, 2021 (accessed Oct. 01,2021).
[55] C.E. Nelson, et al., Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy, Nat. Med. 25 (3) (Mar. 2019) 427–432, https:// doi.org/10.1038/s41591-019-0344-3.
[56] K.S. Hanlon, et al., High levels of AAV vector integration into CRISPR-induced DNA breaks, Nat. Commun. 10 (1) (Sep. 2019) 4439, https://doi.org/10.1038/ s41467-019-12449-2.
[57] A. Li, et al., A self-deleting AAV-CRISPR system for in vivo genome editing, Mol. Ther. Methods Clin. Dev. 12 (Mar. 2019) 111–122, https://doi.org/10.1016/j. omtm.2018.11.009.
[58] Z. Wu, H. Yang, P. Colosi, Effect of genome size on AAV vector packaging, Mol. Ther. J. Am. Soc. Gene Ther. 18 (1) (Jan. 2010) 80–86, https://doi.org/10.1038/ mt.2009.255.
[59] D.-J.J. Truong, et al., Development of an intein-mediated split–Cas9 system for gene therapy, Nucleic Acids Res. 43 (13) (Jul. 2015) 6450–6458, https://doi.org/ 10.1093/nar/gkv601.
[60] B. Zetche, S.E. Volz, F. Zhang, A Split Cas9 architecture for inducible genome editing and transcription modulation, Nat. Biotechnol. 33 (2) (Feb. 2015) 139–142, https://doi.org/10.1038/nbt.3149.
[61] F.A. Ran, et al., In vivo genome editing using Staphylococcus aureus Cas9, Nature 520 (7546) (Apr. 2015) 186–191, https://doi.org/10.1038/nature14299.
[62] E. Kim, et al., In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni, Nat. Commun. 8 (1) (Feb. 2017), https://doi.org/10.1038/ ncomms14500. Art. no. 1.
[63] J. Strecker, et al., Engineering of CRISPR-Cas12b for human genome editing, Nat. Commun. 10 (1) (Jan. 2019) 212, https://doi.org/10.1038/s41467-018-08224-4.
[64] R.G. Crystal, Adenovirus: the first effective in vivo gene delivery vector, Hum. Gene Ther. 25 (1) (Jan. 2014) 3–11, https://doi.org/10.1089/hum.2013.2527.
[65] M.S. Jones, et al., New adenovirus species found in a patient presenting with gastroenteritis, J. Virol. 81 (11) (Jun. 2007) 5978–5984, https://doi.org/ 10.1128/JVI.02650-06.
[66] K. Aoki, et al., Epidemic keratoconjunctivitis due to the novel hexon-chimeric- intermediate 22,37/H8 human adenovirus, J. Clin. Microbiol. 46 (10) (Oct. 2008) 3259–3269, https://doi.org/10.1128/JCM.02354-07.
[67] C.J. Stephens, E.J. Lauron, E. Kashentseva, Z.H. Lu, W.M. Yokoyama, D.T. Curiel, Long-term correction of hemophilia B using adenoviral delivery of CRISPR/Cas9, J. Control. Release Off. J. Control. Release Soc. 298 (Mar. 2019) 128–141, https://doi.org/10.1016/j.jconrel.2019.02.009.
[68] C.S. Lee, et al., Adenovirus-mediated gene delivery: potential applications for gene and cell-based therapies in the new era of personalized medicine, Genes Dis. 4 (2) (Apr. 2017) 43–63, https://doi.org/10.1016/j.gendis.2017.04.001.
[69] L.E. Ailles, L. Naldini, HIV-1-derived lentiviral vectors, Curr. Top. Microbiol. Immunol. 261 (2002) 31–52, https://doi.org/10.1007/978-3-642-56114-6_2.
[70] E.M. Poeschla, Non-primate lentiviral vectors, Curr. Opin. Mol. Ther. 5 (5) (Oct. 2003) 529–540.
[71] S. Kubo, K. Mitani, A new hybrid system capable of efficient lentiviral vector production and stable gene transfer mediated by a single helper-dependent adenoviral vector, J. Virol. 77 (5) (Mar. 2003) 2964–2971, https://doi.org/ 10.1128/JVI.77.5.2964-2971.2003.
[72] E. Abordo-Adesida, et al., Stability of lentiviral vector-mediated transgene expression in the brain in the presence of systemic antivector immune responses, Hum. Gene Ther. 16 (6) (Jun. 2005) 741–751, https://doi.org/10.1089/ hum.2005.16.741.
[73] S. Hacein-Bey-Abina, et al., LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1, Science 302 (5644) (Oct. 2003) 415–419, https://doi.org/10.1126/science.1088547.
[74] E. Haapaniemi, S. Botla, J. Persson, B. Schmierer, J. Taipale, CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response, Nat. Med. 24 (7) (Jul. 2018) 927–930, https://doi.org/10.1038/s41591-018-0049-z.
[75] Y. Fu, et al., High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells, Nat. Biotechnol. 31 (9) (Sep. 2013) 822–826, https:// doi.org/10.1038/nbt.2623.
[76] P.I. Ortinski, B. O’Donovan, X. Dong, B. Kantor, Integrase-deficient lentiviral vector as an all-in-one platform for highly efficient CRISPR/Cas9-mediated gene editing, Mol. Ther. Methods Clin. Dev. 5 (Jun. 2017) 153–164, https://doi.org/ 10.1016/j.omtm.2017.04.002.
[77] N. Uchida, et al., Cas9 protein delivery non-integrating lentiviral vectors for gene correction in sickle cell disease, Mol. Ther. - Methods Clin. Dev. 21 (Jun. 2021) 121–132, https://doi.org/10.1016/j.omtm.2021.02.022.
[78] H.I. Segall, E. Yoo, R.E. Sutton, Characterization and detection of artificial replication-competent lentivirus of altered host range, Mol. Ther. 8 (1) (Jul. 2003) 118–129, https://doi.org/10.1016/S1525-0016(03)00134-5.
[79] S. Nooraei, et al., Virus-like particles: preparation, immunogenicity and their roles as nanovaccines and drug nanocarriers, J. Nanobiotechnology 19 (1) (Feb. 2021) 59, https://doi.org/10.1186/s12951-021-00806-7.
[80] Y.H. Chung, H. Cai, N.F. Steinmetz, Viral nanoparticles for drug delivery, imaging, immunotherapy, and theranostic applications, Adv. Drug Deliv. Rev. 156 (2020) 214–235, https://doi.org/10.1016/j.addr.2020.06.024.
[81] B. Donaldson, Z. Lateef, G.F. Walker, S.L. Young, V.K. Ward, Virus-like particle vaccines: immunology and formulation for clinical translation, Expert Rev. Vaccines 17 (9) (Sep. 2018) 833–849, https://doi.org/10.1080/14760584.2018.1516552.
[82] J.G. Choi, et al., Lentivirus pre-packed with Cas9 protein for safer gene editing, Gene Ther. 23 (7) (Jul. 2016) 627–633, https://doi.org/10.1038/gt.2016.27.
[83] C. Montagna, et al., VSV-G-enveloped vesicles for traceless delivery of CRISPR- Cas9, Mol. Ther. Nucleic Acids 12 (Jul. 2018) 453–462, https://doi.org/10.1016/ j.omtn.2018.05.010.
[84] P.E. Mangeot, et al., Genome editing in primary cells and in vivo using viral- derived Nanoblades loaded with Cas9-sgRNA ribonucleoproteins, Nat. Commun. 10 (1) (Jan. 2019) 45, https://doi.org/10.1038/s41467-018-07845-z.
[85] L.A. Campbell, L.M. Coke, C.T. Richie, L.V. Fortuno, A.Y. Park, B.K. Harvey, Gesicle-mediated delivery of CRISPR/Cas9 ribonucleoprotein complex for inactivating the HIV provirus, Mol. Ther. J. Am. Soc. Gene Ther. 27 (1) (Jan. 2019) 151–163, https://doi.org/10.1016/j.ymthe.2018.10.002.
[86] P. Gee, et al., Extracellular nanovesicles for packaging of CRISPR-Cas9 protein and sgRNA to induce therapeutic exon skipping, Nat. Commun. 11 (1) (Mar. 2020) 1334, https://doi.org/10.1038/s41467-020-14957-y.
[87] F. Heitz, M.C. Morris, G. Divita, Twenty years of cell-penetrating peptides: from molecular mechanisms to therapeutics, Br. J. Pharmacol. 157 (2) (May 2009) 195–206, https://doi.org/10.1111/j.1476-5381.2009.00057.x.
[88] G. Guidotti, L. Brambilla, D. Rossi, Cell-penetrating peptides: from basic research to clinics, Trends Pharmacol. Sci. 38 (4) (Apr. 2017) 406–424, https://doi.org/ 10.1016/j.tips.2017.01.003.
[89] O. Gustafsson, et al., Efficient Peptide-Mediated In Vitro Delivery of Cas9 RNP, Pharmaceutics 13 (6) (Jun. 2021), https://doi.org/10.3390/ pharmaceutics13060878. Art. no. 6.
[90] Y.J. Kim, H. Lee, H. Cha, J.H. Park, Non-viral gene disruption by CRISPR/Cas9 delivery using cell-permeable and protein-stabilizing 30Kc19 protein, Biotechnol. Bioprocess Eng. 25 (5) (Sep. 2020) 724–733, https://doi.org/10.1007/s12257-020-0068-8.
[91] B.T. Staahl, et al., Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes, Nat. Biotechnol. 35 (5) (May 2017) 431–434, https://doi.org/10.1038/nbt.3806.
[92] I. Maggio, et al., Integrating gene delivery and gene-editing technologies by adenoviral vector transfer of optimized CRISPR-Cas9 components, Gene Ther. 27 (5) (May 2020) 209–225, https://doi.org/10.1038/s41434-019-0119-y.
[93] J. Habault, J.-L. Poyet, Recent advances in cell penetrating peptide-based anticancer therapies, Molecules 24 (5) (Mar. 2019) 927, https://doi.org/ 10.3390/molecules24050927.
[94] K. Lee, et al., Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair, Nat. Biomed. Eng. 1 (2017) 889–901, https://doi.org/10.1038/s41551-017-0137-2.
[95] S. Abbasi, et al., Co-encapsulation of Cas9 mRNA and guide RNA in polyplex micelles enables genome editing in mouse brain, J. Control. Release 332 (Apr. 2021) 260–268, https://doi.org/10.1016/j.jconrel.2021.02.026.
[96] E.E. Walsh, et al., Safety and immunogenicity of two RNA-based Covid-19 vaccine candidates, N. Engl. J. Med. 383 (25) (Dec. 2020) 2439–2450, https://doi.org/ 10.1056/NEJMoa2027906.
[97] M.J. Mulligan, et al., Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults, Nature 586 (7830) (Oct. 2020) 589–593, https://doi.org/10.1038/ s41586-020-2639-4.
[98] D. Chatzikleanthous, D.T. O’Hagan, R. Adamo, Lipid-based nanoparticles for delivery of vaccine adjuvants and antigens: toward multicomponent vaccines, Mol. Pharm. 18 (8) (Aug. 2021) 2867–2888, https://doi.org/10.1021/acs. molpharmaceut.1c00447.
[99] P.R. Cullis, M.J. Hope, Lipid nanoparticle Systems for Enabling Gene Therapies, Mol. Ther. J. Am. Soc. Gene Ther. 25 (7) (Jul. 2017) 1467–1475, https://doi.org/ 10.1016/j.ymthe.2017.03.013.
[100] M. Qiu, et al., Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single- guide RNA achieves liver-specific in vivo genome editing of Angptl3, Proc. Natl. Acad. Sci. 118 (10) (Mar. 2021), https://doi.org/10.1073/pnas.2020401118.
[101] J.D. Finn, et al., A single administration of CRISPR/Cas9 lipid nanoparticles achieves robust and persistent in vivo genome editing, Cell Rep. 22 (9) (Feb. 2018) 2227–2235, https://doi.org/10.1016/j.celrep.2018.02.014.
[102] T. Wei, Q. Cheng, Y.-L. Min, E.N. Olson, D.J. Siegwart, Systemic nanoparticle delivery of CRISPR-Cas9 ribonucleoproteins for effective tissue specific genome editing, Nat. Commun. 11 (1) (Jun. 2020) 3232, https://doi.org/10.1038/ s41467-020-17029-3.
[103] Y. Suzuki, et al., Lipid nanoparticles loaded with ribonucleoprotein- oligonucleotide complexes synthesized using a microfluidic device exhibit robust genome editing and hepatitis B virus inhibition, J. Control. Release Off. J. Control. Release Soc. 330 (Feb. 2021) 61–71, https://doi.org/10.1016/j. jconrel.2020.12.013.
[104] Q. Cheng, T. Wei, L. Farbiak, L.T. Johnson, S.A. Dilliard, D.J. Siegwart, Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR–Cas gene editing, Nat. Nanotechnol. 15 (4) (Apr. 2020) 313–320, https:// doi.org/10.1038/s41565-020-0669-6.
[105] T.-C. Ho, et al., Scaffold-mediated CRISPR-Cas9 delivery system for acute myeloid leukemia therapy, Sci. Adv. 7 (21) (May 2021) eabg3217, https://doi.org/ 10.1126/sciadv.abg3217.
[106] J.D. Gillmore, et al., CRISPR-Cas9 in vivo gene editing for transthyretin amyloidosis, N. Engl. J. Med. 385 (6) (Aug. 2021) 493–502, https://doi.org/ 10.1056/NEJMoa2107454.
[107] E. Kenjo, et al., Low immunogenicity of LNP allows repeated administrations of CRISPR-Cas9 mRNA into skeletal muscle in mice, Nat. Commun. 12 (1) (Dec. 2021) 7101, https://doi.org/10.1038/s41467-021-26714-w.
[108] H. Xu, et al., Targeted disruption of HLA genes via CRISPR-Cas9 generates iPSCs with enhanced immune compatibility, Cell Stem Cell 24 (4) (Apr. 2019) 566–578. e7, https://doi.org/10.1016/j.stem.2019.02.005.
[109] E.A. Stadtmauer, et al., CRISPR-engineered T cells in patients with refractory cancer, Science 367 (6481) (Feb. 2020), https://doi.org/10.1126/science. aba7365 eaba7365.
[110] L. Xu, et al., CRISPR-edited stem cells in a patient with HIV and acute lymphocytic leukemia, N. Engl. J. Med. (Sep. 2019), https://doi.org/10.1056/ NEJMoa1817426.
[111] Y. Shinmyo, S. Tanaka, S. Tsunoda, K. Hosomichi, A. Tajima, H. Kawasaki, CRISPR/Cas9-mediated gene knockout in the mouse brain using in utero electroporation, Sci. Rep. 6 (1) (Feb. 2016) 20611, https://doi.org/10.1038/ srep20611.
[112] C.A. Lino, J.C. Harper, J.P. Carney, J.A. Timlin, Delivering CRISPR: a review of the challenges and approaches, Drug Deliv. 25 (1) (May 2018) 1234–1257, https://doi.org/10.1080/10717544.2018.1474964.
[113] P. Gu, et al., Genetically blocking HPD via CRISPR-Cas9 protects against lethal liver injury in a pig model of tyrosinemia type I, Mol. Ther. - Methods Clin. Dev. 21 (Jun. 2021) 530–547, https://doi.org/10.1016/j.omtm.2021.04.002.
[114] S.Z. Mirjalili Mohanna, et al., Germline CRISPR/Cas9-mediated gene editing prevents vision loss in a novel mouse model of Aniridia, Mol. Ther. - Methods Clin. Dev 17 (Jun. 2020) 478–490, https://doi.org/10.1016/j. omtm.2020.03.002.
[115] I. Lentacker, I. De Cock, R. Deckers, S.C. De Smedt, C.T.W. Moonen, Understanding ultrasound induced sonoporation: definitions and underlying mechanisms, Adv. Drug Deliv. Rev. 72 (Jun. 2014) 49–64, https://doi.org/ 10.1016/j.addr.2013.11.008.
[116] J.-Y. Ryu, et al., Ultrasound-activated particles as CRISPR/Cas9 delivery system for androgenic alopecia therapy, Biomaterials 232 (Feb. 2020), 119736, https:// doi.org/10.1016/j.biomaterials.2019.119736.
[117] J. Cai, S. Huang, Y. Yi, S. Bao, Ultrasound microbubble-mediated CRISPR/Cas9 knockout of C-erbB-2 in HEC-1A cells, J. Int. Med. Res. 47 (5) (May 2019) 2199–2206, https://doi.org/10.1177/0300060519840890.
[118] E. Bianconi, et al., An estimation of the number of cells in the human body, Ann. Hum. Biol. 40 (6) (Dec. 2013) 463–471, https://doi.org/10.3109/03014460.2013.807878.
[119] C.T. Charlesworth, et al., Identification of preexisting adaptive immunity to Cas9 proteins in humans, Nat. Med. 25 (2) (Feb. 2019) 249–254, https://doi.org/ 10.1038/s41591-018-0326-x.
[120] D.L. Wagner, et al., High prevalence of streptococcus pyogenes Cas9-reactive T cells within the adult human population, Nat. Med. 25 (2) (Feb. 2019) 242–248, https://doi.org/10.1038/s41591-018-0204-6.
[121] W.L. Chew, et al., A multi-functional AAV-CRISPR-Cas9 and its host response, Nat. Methods 13 (10) (Oct. 2016) 868–874, https://doi.org/10.1038/ nmeth.3993.
[122] S.R. Ferdosi, et al., Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes, Nat. Commun. 10 (1) (Apr. 2019) 1842, https://doi.org/10.1038/s41467-019-09693-x.
[123] D. Wilbie, J. Walther, E. Mastrobattista, Delivery aspects of CRISPR/Cas for in vivo genome editing, Acc. Chem. Res. 52 (6) (Jun. 2019) 1555–1564, https://doi. org/10.1021/acs.accounts.9b00106.
[124] S. Perrin, Preclinical research: make mouse studies work, Nature 507 (7493) (Mar. 2014) 423–425, https://doi.org/10.1038/507423a.
[125] L. Koch, A primate view of gene expression, Nat. Rev. Genet. 21 (3) (Mar. 2020) 135, https://doi.org/10.1038/s41576-020-0217-0.
[126] M. Shrivastav, L.P. De Haro, J.A. Nickoloff, Regulation of DNA double-strand break repair pathway choice, Cell Res. 18 (1) (Jan. 2008), https://doi.org/ 10.1038/cr.2007.111. Art. no. 1.
[127] P. Katsonis, et al., Single nucleotide variations: Biological impact and theoretical interpretation, Protein Sci. Publ. Protein Soc 23 (12) (Dec. 2014), https://doi.org/ 10.1002/pro.2552. Art. no. 12.
[128] I.I. Suvorova, N.V. Katolikova, V.A. Pospelov, Chapter four - new insights into cell cycle regulation and dna damage response in embryonic stem cells, in: K.W. Jeon (Ed.), International Review of Cell and Molecular Biology vol. 299, Academic Press, 2012, pp. 161–198, https://doi.org/10.1016/B978-0-12-394310-1.00004-7.
[129] Z. Mao, M. Bozzella, A. Seluanov, V. Gorbunova, DNA repair by nonhomologous end joining and homologous recombination during cell cycle in human cells, Cell Cycle Georget. Tex 7 (18) (Sep. 2008), https://doi.org/10.4161/cc.7.18.6679. Art. no. 18.
[130] W.-D. Heyer, K.T. Ehmsen, J. Liu, Regulation of homologous recombination in eukaryotes, Annu. Rev. Genet. 44 (2010) 113–139, https://doi.org/10.1146/ annurev-genet-051710-150955.
[131] T. Maruyama, S.K. Dougan, M. Truttmann, A.M. Bilate, J.R. Ingram, H.L. Ploegh, Inhibition of non-homologous end joining increases the efficiency of CRISPR/ Cas9-mediated precise [TM: inserted] genome editing, Nat. Biotechnol. 33 (5) (May 2015), https://doi.org/10.1038/nbt.3190. Art. no. 5.
[132] D. Yang, M.A. Scavuzzo, J. Chmielowiec, R. Sharp, A. Bajic, M. Borowiak, Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases, Sci. Rep. 6 (1) (Feb. 2016) 21264, https://doi.org/10.1038/srep21264.
[133] L. Farbiak, et al., All-in-one dendrimer-based lipid nanoparticles enable precise HDR-mediated gene editing in vivo, Adv. Mater. Deerfield Beach Fla 33 (30) (Jul. 2021), https://doi.org/10.1002/adma.202006619. Art. no. 30.
[134] M. Charpentier, et al., CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair, Nat. Commun. 9 (1) (Mar. 2018) 1133, https://doi. org/10.1038/s41467-018-03475-7.
[135] I.F. Khan, R.K. Hirata, D.W. Russell, AAV-mediated gene targeting methods for human cells, Nat. Protoc. 6 (4) (Apr. 2011), https://doi.org/10.1038/ nprot.2011.301. Art. no. 4.
[136] F. Chen, et al., High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases, Nat. Methods 8 (9) (Sep. 2011) 753–755, https://doi.org/ 10.1038/nmeth.1653.
[137] N.K. Paulk, et al., Bioengineered AAV Capsids with Combined High Human Liver Transduction In Vivo and Unique Humoral Seroreactivity, Mol. Ther. 26 (1) (Jan. 2018), https://doi.org/10.1016/j.ymthe.2017.09.021. Art. no. 1.
[138] K. Suzuki, et al., In vivo genome editing via CRISPR/Cas9 mediated homology- independent targeted integration, Nature 1–18 (Dec. 2016) 144–149, https://doi. org/10.1038/nature20565.
[139] S.Q. Tsai, J.K. Joung, Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases, Nat. Rev. Genet. 17 (5) (May 2016) 300–312, https:// doi.org/10.1038/nrg.2016.28.
[140] A.C. Komor, Y.B. Kim, M.S. Packer, J.A. Zuris, D.R. Liu, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature 533 (7603) (May 2016), https://doi.org/10.1038/nature17946. Art. no. 7603.
[141] N.M. Gaudelli, et al., Programmable base editing of a•T to G•C in genomic DNA without DNA cleavage, Nature 551 (7681) (Nov. 2017) 464–471, https://doi.org/ 10.1038/nature24644.
[142] M. Rosello, et al., Precise base editing for the in vivo study of developmental signaling and human pathologies in zebrafish, eLife 10 (Feb. 2021), e65552, https://doi.org/10.7554/eLife.65552.
[143] L. Xu, et al., Efficient precise in vivo base editing in adult dystrophic mice, Nat. Commun. 12 (1) (Jun. 2021) 3719, https://doi.org/10.1038/s41467-021-23996- y.
[144] L. Villiger, et al., In vivo cytidine base editing of hepatocytes without detectable off-target mutations in RNA and DNA, Nat. Biomed. Eng. 5 (2) (Feb. 2021) 179–189, https://doi.org/10.1038/s41551-020-00671-z.
[145] Y.K. Jeong, et al., Adenine base editor engineering reduces editing of bystander cytosines, Nat. Biotechnol. (Jul. 2021) 1–8, https://doi.org/10.1038/s41587- 021-00943-2.
[146] J. Tan, F. Zhang, D. Karcher, R. Bock, Engineering of high-precision base editors for site-specific single nucleotide replacement, Nat. Commun. 10 (1) (Jan. 2019) 439, https://doi.org/10.1038/s41467-018-08034-8.
[147] Y. Liu, et al., A Cas-embedding strategy for minimizing off-target effects of DNA base editors, Nat. Commun. 11 (1) (Nov. 2020) 6073, https://doi.org/10.1038/ s41467-020-19690-0.
[148] E. Zuo, et al., A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects, Nat. Methods 17 (6) (Jun. 2020), https://doi.org/10.1038/s41592-020-0832-x. Art. no. 6.
[149] D. Kim, D. Kim, G. Lee, S.-I. Cho, J.-S. Kim, Genome-wide target specificity of CRISPR RNA-guided adenine base editors, Nat. Biotechnol. 37 (4) (Apr. 2019) 430–435, https://doi.org/10.1038/s41587-019-0050-1.
[150] D. Kim, B.-C. Kang, J.-S. Kim, Identifying genome-wide off-target sites of CRISPR RNA–guided nucleases and deaminases with Digenome-seq, Nat. Protoc. 16 (2) (Feb. 2021) 1170–1192, https://doi.org/10.1038/s41596-020-00453-6.
[151] P. Liang, et al., Genome-wide profiling of adenine base editor specificity by EndoV-seq, Nat. Commun. 10 (1) (Jan. 2019) 67, https://doi.org/10.1038/ s41467-018-07988-z.
[152] Z. Lei, et al., Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors, Nat. Methods 18 (6) (Jun. 2021) 643–651, https://doi.org/10.1038/s41592-021-01172-w.
[153] E. Zuo, et al., Cytosine base editor generates substantial off-target single- nucleotide variants in mouse embryos, Science 364 (6437) (Apr. 2019), https:// doi.org/10.1126/science.aav9973. Art. no. 6437.
[154] Y. Yu, et al., Cytosine base editors with minimized unguided DNA and RNA off- target events and high on-target activity, Nat. Commun. 11 (1) (Apr. 2020) 2052, https://doi.org/10.1038/s41467-020-15887-5.
[155] S. Jin, et al., Cytosine, but not adenine, base editors induce genome-wide off- target mutations in rice, Science 364 (6437) (Apr. 2019), https://doi.org/ 10.1126/science.aaw7166. Art. no. 6437.
[156] T. Rothgangl, In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels, Nat. Biotechnol. (2021), https://doi.org/10.1038/s41587-021- 00933-4.