Traditional gene therapy (gene replacement) has made a breakthrough in treating inherited diseases. Adeno-associated virus (AAV) has emerged as a highly promising vector with innate ability, boosting the development of gene replacement and gene targeting. With the recent advance of engineered nucleases that work efficiently in human cells, AAV mediated-genome editing with nucleases has raised hopes for in situ gene therapy of inherited and non-inherited diseases. Here, the applications of AAV-mediated genome editing are highlighted, and the prospect of AAV and nucleases that will render extension of such success in clinical gene therapy is discussed.
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References
1.
BallingerML, GoodeDL, Ray-CoquardI, et al.Monogenic and polygenic determinants of sarcoma risk: an international genetic study. Lancet Oncol, 2016; 17:1261–1271.
2.
FerreiraV, TwiskJ, KwikkersK, et al.Immune responses to intramuscular administration of alipogene tiparvovec (AAV1-LPL(S447X)) in a Phase II clinical trial of lipoprotein lipase deficiency gene therapy. Hum Gene Ther, 2014; 25:180–188.
3.
NathwaniAC, ReissUM, TuddenhamEG, et al.Long-term safety and efficacy of factor IX gene therapy in hemophilia B. N Engl J Med, 2014; 371:1994–2004.
4.
MacLarenRE, GroppeM, BarnardAR, et al.Retinal gene therapy in patients with choroideremia: initial findings from a Phase 1/2 clinical trial. Lancet, 2014; 383:1129–1137.
5.
PlegerST, ShanC, KsienzykJ, et al.Cardiac AAV9-S100A1 gene therapy rescues post-ischemic heart failure in a preclinical large animal model. Sci Transl Med, 2011; 3:92ra64.
6.
HeierJS, KheraniS, DesaiS, et al.Intravitreous injection of AAV2-sFLT01 in patients with advanced neovascular age-related macular degeneration: a Phase 1, open-label trial. Lancet, 2017; 390:50–61.
XieQ, BuW, BhatiaS, et al.The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy. Proc Natl Acad Sci U S A, 2002; 99:10405–10410.
9.
SonntagF, SchmidtK, KleinschmidtJA. A viral assembly factor promotes AAV2 capsid formation in the nucleolus. Proc Natl Acad Sci U S A, 2010; 107:10220–10225.
10.
HenckaertsE, DutheilN, ZeltnerN, et al.Site-specific integration of adeno-associated virus involves partial duplication of the target locus. Proc Natl Acad Sci U S A, 2009; 106:7571–7576.
11.
LamartinaS, CilibertoG, ToniattiC. Selective cleavage of AAVS1 substrates by the adeno-associated virus type 2 rep68 protein is dependent on topological and sequence constraints. J Virol, 2000; 74:8831–8842.
12.
SmithJR, MaguireS, DavisLA, et al.Robust, persistent transgene expression in human embryonic stem cells is achieved with AAVS1-targeted integration. Stem cells, 2008; 26:496–504.
RussellDW, HirataRK. Human gene targeting by viral vectors. Nat Genet, 1998; 18:325–330.
15.
YanezRJ, PorterAC. A chromosomal position effect on gene targeting in human cells. Nucleic Acids Res, 2002; 30:4892–4901.
16.
DeyleDR, LiLB, RenG, et al.The effects of polymorphisms on human gene targeting. Nucleic Acids Res, 2014; 42:3119–3124.
17.
InoueN, DongR, HirataRK, et al.Introduction of single base substitutions at homologous chromosomal sequences by adeno-associated virus vectors. Mol Ther, 2001; 3:526–530.
18.
DeyleDR, HansenRS, CorneaAM, et al.A genome-wide map of adeno-associated virus-mediated human gene targeting. Nat Struct Mol Biol, 2014; 21:969–975.
19.
HirataR, ChamberlainJ, DongR, et al.Targeted transgene insertion into human chromosomes by adeno-associated virus vectors. Nat Biotechnol, 2002; 20:735–738.
20.
MillerDG, WangPR, PetekLM, et al.Gene targeting in vivo by adeno-associated virus vectors. Nat Biotechnol, 2006; 24:1022–1026.
21.
OdomGL, GregorevicP, AllenJM, et al.Gene therapy of mdx mice with large truncated dystrophins generated by recombination using rAAV6. Mol Ther, 2011; 19:36–45.
22.
LisowskiL, LauA, WangZ, et al.Ribosomal DNA integrating rAAV-rDNA vectors allow for stable transgene expression. Mol Ther, 2012; 20:1912–1923.
23.
WangZ, LisowskiL, FinegoldMJ, et al.AAV vectors containing rDNA homology display increased chromosomal integration and transgene persistence. Mol Ther, 2012; 20:1902–1911.
24.
KarnanS, OtaA, KonishiY, et al.Improved methods of AAV-mediated gene targeting for human cell lines using ribosome-skipping 2A peptide. Nucleic Acids Res, 2016; 44:e54.
25.
FattahFJ, LichterNF, FattahKR, et al.Ku70, an essential gene, modulates the frequency of rAAV-mediated gene targeting in human somatic cells. Proc Natl Acad Sci U S A, 2008; 105:8703–8708.
26.
PaulkNK, LozaLM, FinegoldMJ, et al.AAV-mediated gene targeting is significantly enhanced by transient inhibition of nonhomologous end joining or the proteasome in vivo. Hum Gene Ther, 2012; 23:658–665.
27.
SmithLJ, Ul-HasanT, CarvainesSK, et al.Gene transfer properties and structural modeling of human stem cell-derived AAV. Mol Ther, 2014; 22:1625–1634.
28.
SmithLJ, WrightJ, ClarkG, et al.Stem cell-derived clade F AAVs mediate high-efficiency homologous recombination-based genome editing. Proc Natl Acad Sci U S A, 2018; 115:E7379–E7388.
29.
ChamberlainJR, SchwarzeU, WangPR, et al.Gene targeting in stem cells from individuals with osteogenesis imperfecta. Science, 2004; 303:1198–1201.
30.
PaulkNK, WursthornK, WangZ, et al.Adeno-associated virus gene repair corrects a mouse model of hereditary tyrosinemia in vivo. Hepatology, 2010; 51:1200–1208.
31.
PetekLM, FleckmanP, MillerDG. Efficient KRT14 targeting and functional characterization of transplanted human keratinocytes for the treatment of epidermolysis bullosa simplex. Mol Ther, 2010; 18:1624–1632.
32.
LiLB, ChangKH, WangPR, et al.Trisomy correction in Down syndrome induced pluripotent stem cells. Cell Stem Cell, 2012; 11:615–619.
33.
BarzelA, PaulkNK, ShiY, et al.Promoterless gene targeting without nucleases ameliorates haemophilia B in mice. Nature, 2015; 517:360–364.
34.
WangJ, ExlineCM, DeClercqJJ, et al.Homology-driven genome editing in hematopoietic stem and progenitor cells using ZFN mRNA and AAV6 donors. Nat Biotechnol, 2015; 33:1256–1263.
35.
LandauDJ, BrooksED, Perez-PineraP, et al.In vivo zinc finger nuclease-mediated targeted integration of a glucose-6-phosphatase transgene promotes survival in mice with glycogen storage disease type IA. Mol Ther, 2016; 24:697–706.
36.
AnguelaXM, SharmaR, DoyonY, et al.Robust ZFN-mediated genome editing in adult hemophilic mice. Blood, 2013; 122:3283–3287.
37.
LiH, HaurigotV, DoyonY, et al.In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature, 2011; 475:217–221.
38.
WeberND, StoneD, SedlakRH, et al.AAV-mediated delivery of zinc finger nucleases targeting hepatitis B virus inhibits active replication. PLoS One, 2014; 9:e97579.
39.
GuptaA, MengX, ZhuLJ, et al.Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res, 2011; 39:381–392.
40.
SanderJD, RamirezCL, LinderSJ, et al.In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acids Res, 2013; 41:e181.
41.
MussolinoC, AlzubiJ, FineEJ, et al.TALENs facilitate targeted genome editing in human cells with high specificity and low cytotoxicity. Nucleic Acids Res, 2014; 42:6762–6773.
42.
ChapdelaineP, GerardC, SanchezN, et al.Development of an AAV9 coding for a 3XFLAG-TALEfrat#8-VP64 able to increase in vivo the human frataxin in YG8R mice. Gene Ther, 2016; 23:606–614.
43.
SenisE, FatourosC, GrosseS, et al.CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox. Biotechnol J, 2014; 9:1402–1412.
44.
SwiechL, HeidenreichM, BanerjeeA, et al.In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat Biotechnol, 2015; 33:102–106.
45.
NishiyamaJ, MikuniT, YasudaR. Virus-mediated genome editing via homology-directed repair in mitotic and postmitotic cells in mammalian brain. Neuron, 2017; 96:755–768.e5.
46.
WuZ, YangH, ColosiP. Effect of genome size on AAV vector packaging. Mol Ther, 2010; 18:80–86.
47.
RanFA, CongL, YanWX, et al.In vivo genome editing using Staphylococcus aureus Cas9. Nature, 2015; 520:186–191.
48.
FriedlandAE, BaralR, SinghalP, et al.Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biol, 2015; 16:257.
49.
GeX, XiH, YangF, et al.CRISPR/Cas9-AAV mediated knock-in at NRL locus in human embryonic stem cells. Mol Ther Nucleic Acids, 2016; 5:e393.
50.
BakRO, PorteusMH. CRISPR-mediated integration of large gene cassettes using AAV donor vectors. Cell Rep, 2017; 20:750–756.
51.
GwiazdaKS, GrierAE, SahniJ, et al.High efficiency CRISPR/Cas9-mediated gene editing in primary human T-cells using mutant adenoviral E4orf6/E1b55k “helper” proteins. Mol Ther, 2016; 24:1570–1580.
52.
SuzukiK, TsunekawaY, Hernandez-BenitezR, et al.In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature, 2016; 540:144–149.
53.
YaoX, WangX, HuX, et al.Homology-mediated end joining-based targeted integration using CRISPR/Cas9. Cell Res, 2017; 27:801–814.
54.
LongC, AmoasiiL, MireaultAA, et al.Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy. Science, 2016; 351:400–403.
55.
NelsonCE, HakimCH, Ousterout DGRM, et al.In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science, 2016; 351:403–407.
56.
TabebordbarM, ZhuK, ChengJKW, et al.In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science, 2016; 351:407–411.
57.
BengtssonNE, HallJK, OdomGL, et al.Muscle-specific CRISPR/Cas9 dystrophin gene editing ameliorates pathophysiology in a mouse model for Duchenne muscular dystrophy. Nat Commun, 2017; 8:14454.
58.
KooT, Lu-NguyenNB, MalerbaA, et al.Functional rescue of dystrophin deficiency in mice caused by frameshift mutations using Campylobacter jejuni Cas9. Mol Ther, 2018; 26:1529–1538.
59.
KemaladewiDU, MainoE, HyattE, et al.Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism. Nat Med, 2017; 23:984–989.
60.
YangY, WangL, BellP, et al.A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice. Nat Biotechnol, 2016; 34:334–338.
61.
MonteysAM, EbanksSA, KeiserMS, et al.CRISPR/Cas9 editing of the mutant huntingtin allele in vitro and in vivo. Mol Ther, 2017; 25:12–23.
62.
RuanGX, BarryE, YuD, et al.CRISPR/Cas9-mediated genome editing as a therapeutic approach for Leber congenital amaurosis 10. Mol Ther, 2017; 25:331–341.
63.
YuW, MookherjeeS, ChaitankarV, et al.Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice. Nat Commun, 2017; 8:14716.
64.
HuangX, ZhouG, WuW, et al.Genome editing abrogates angiogenesis in vivo. Nat Commun, 2017; 8:112.
65.
GyorgyB, LoovC, ZaborowskiMP, et al.CRISPR/Cas9 mediated disruption of the Swedish APP allele as a therapeutic approach for early-onset Alzheimer's disease. Mol Ther Nucleic Acids, 2018; 11:429–440.
66.
SongCQ, WangD, JiangT, et al.In vivo genome editing partially restores alpha1-antitrypsin in a murine model of AAT deficiency. Hum Gene Ther, 2018; 29:853–860.
67.
McCulloughKT, BoyeSL, FajardoD, et al.Somatic gene editing of GUCY2D by AAV-CRISPR/Cas9 alters retinal structure and function in mouse and macaque. Hum Gene Ther, 2018 Oct 25 [Epub ahead of print]; DOI: 10.1089/hum.2018.193.
68.
DeverDP, BakRO, ReinischA, et al.CRISPR/Cas9 beta-globin gene targeting in human haematopoietic stem cells. Nature, 2016; 539:384–389.
69.
KimE, KooT, ParkSW, et al.In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nat Commun, 2017; 8:14500.
70.
YinC, ZhangT, QuX, et al.In vivo excision of HIV-1 provirus by saCas9 and multiplex single-guide RNAs in animal models. Mol Ther, 2017; 25:1168–1186.
71.
LiH, ShengC, LiuH, et al.Inhibition of HBV expression in HBV transgenic mice using AAV-delivered CRISPR-SaCas9. Front Immunol, 2018; 9:2080.
72.
GaudelliNM, KomorAC, ReesHA, et al.Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature, 2017; 551:464–471.
73.
KimYB, KomorAC, LevyJM, et al.Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat Biotechnol, 2017; 35:371–376.
74.
LoganGJ, DaneAP, HallwirthCV, et al.Identification of liver-specific enhancer-promoter activity in the 3′ untranslated region of the wild-type AAV2 genome. Nat Genet, 2017; 49:1267–1273.
75.
LaiY, YueY, LiuM, et al.Efficient in vivo gene expression by trans-splicing adeno-associated viral vectors. Nat Biotechnol, 2005; 23:1435–1439.
76.
TruongDJ, KühnerK, KühnR, et al.Development of an intein-mediated split-Cas9 system for gene therapy. Nucleic Acids Res, 2015; 43:6450–6458.
77.
VilligerL, Grisch-ChanHM, LindsayH, et al.Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nat Med, 2018; 24:1519–1525.
78.
AsokanA, ConwayJC, PhillipsJL, et al.Reengineering a receptor footprint of adeno-associated virus enables selective and systemic gene transfer to muscle. Nat Biotechnol, 2010; 28:79–82.
79.
MurlidharanG, SakamotoK, RaoL, et al.CNS-restricted transduction and CRISPR/Cas9-mediated gene deletion with an engineered AAV vector. Mol Ther Nucleic Acids, 2016; 5:e338.
80.
LandeggerLD, PanB, AskewC, et al.A synthetic AAV vector enables safe and efficient gene transfer to the mammalian inner ear. Nat Biotechnol, 2017; 35:280–284.
81.
ChanKY, JangMJ, YooBB, et al.Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat Neurosci, 2017; 20:1172–1179.
82.
MorenoAM, PalmerN, AlemanF, et al.Exploring protein orthogonality in immune space: a case study with AAV and Cas9 orthologs. bioRxiv, 2018 Jan 10 [Epub ahead of print]; DOI: 10.1101/245985.
83.
Di MeoI, MarchetS, LampertiC, et al.AAV9-based gene therapy partially ameliorates the clinical phenotype of a mouse model of Leigh syndrome. Gene Ther, 2017; 24:661–667.
84.
LaoharaweeK, Podetz-PedersenKM, NguyenTT, et al.Prevention of neurocognitive deficiency in mucopolysaccharidosis type II mice by central nervous system-directed, AAV9-mediated iduronate sulfatase gene transfer. Hum Gene Ther, 2017; 28:626–638.
85.
MorabitoG, GiannelliSG, OrdazzoG, et al.AAV-PHP.B-mediated global-scale expression in the mouse nervous system enables GBA1 gene therapy for wide protection from synucleinopathy. Mol Ther, 2017; 25:2727–2742.
86.
RinconMY, de VinF, DuqueSI, et al.Widespread transduction of astrocytes and neurons in the mouse central nervous system after systemic delivery of a self-complementary AAV-PHP.B vector. Gene Ther, 2018; 25:83–92.
87.
BalazsAB, ChenJ, HongCM, et al.Antibody-based protection against HIV infection by vectored immunoprophylaxis. Nature, 2011; 481:81–84.
88.
GardnerMR, KattenhornLM, KondurHR, et al.AAV-expressed eCD4-Ig provides durable protection from multiple SHIV challenges. Nature, 2015; 519:87–91.
89.
RuoziG, BortolottiF, FalcioneA, et al.AAV-mediated in vivo functional selection of tissue-protective factors against ischaemia. Nat Commun. 2015; 6:7388.
90.
WangZ, ZhuT, QiaoC, et al.Adeno-associated virus serotype 8 efficiently delivers genes to muscle and heart. Nat Biotechnol, 2005; 23:321–328.
91.
GeorgeLA, SullivanSK, GiermaszA, et al.Hemophilia B gene therapy with a high-specific-activity factor IX variant. N Engl J Med, 2017; 377:2215–2227.
92.
LisowskiL, DaneAP, ChuK, et al.Selection and evaluation of clinically relevant AAV variants in a xenograft liver model. Nature, 2014; 506:382–386.
93.
NaultJC, DattaS, ImbeaudS, et al.Adeno-associated virus type 2 as an oncogenic virus in human hepatocellular carcinoma. Mol Cell Oncol, 2016; 3:e1095271.
94.
RezvaniM, Espanol-SunerR, MalatoY, et al.In vivo hepatic reprogramming of myofibroblasts with AAV vectors as a therapeutic strategy for liver fibrosis. Cell Stem Cell, 2016; 18:809–816.
95.
ChenC, AkerstromV, BausJ, et al.Comparative analysis of the transduction efficiency of five adeno associated virus serotypes and VSV-G pseudotype lentiviral vector in lung cancer cells. J Virol, 2013; 10:86.
96.
HayesM, CurleyGF, MastersonC, et al.Pulmonary overexpression of inhibitor kappaBalpha decreases the severity of ventilator-induced lung injury in a rat model. Br J Anaesth, 2014; 113:1046–1054.
97.
LimberisMP, VandenbergheLH, ZhangL, et al.Transduction efficiencies of novel AAV vectors in mouse airway epithelium in vivo and human ciliated airway epithelium in vitro. Mol Ther, 2009; 17:294–301.
98.
LimberisMP, WilsonJM. Adeno-associated virus serotype 9 vectors transduce murine alveolar and nasal epithelia and can be readministered. Proc Natl Acad Sci U S A, 2006; 103:12993–12998.
99.
WileyLA, BurnightE, KaalbergEE, et al.Assessment of adeno-associated virus serotype tropism in human retinal explants. Hum Gene Ther, 2018; 29:424–436.
100.
MendellJR, SahenkZ, MalikV, et al.A Phase 1/2a follistatin gene therapy trial for Becker muscular dystrophy. Mol Ther, 2015; 23:192–201.
101.
ZetscheB, GootenbergJS, AbudayyehOO, et al.Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell, 2015; 163:759–771.
102.
SampsonTR, SarojSD, LlewellynAC, et al.A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature, 2013; 497:254–257.
103.
TuM, LinL, ChengY, et al.A “new lease of life”: FnCpf1 possesses DNA cleavage activity for genome editing in human cells. Nucleic Acids Res, 2017; 45:11295–11304.
104.
EsveltKM, MaliP, BraffJL, et al.Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods, 2013; 10:1116–1121.
105.
CongL, RanFA, CoxD, et al.Multiplex genome engineering using CRISPR/Cas systems. Science, 2013; 339:819–823.
106.
GarneauJE, DupuisME, VillionM, et al.The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature, 2010; 468:67–71.
107.
GasiunasG, BarrangouR, HorvathP, et al.Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A, 2012; 109:E2579–2586.
