AAV-mediated FOXG1 gene editing in human Rett primary cells.
Adult
CRISPR-Cas Systems
Cell Transdifferentiation
Cells, Cultured
Cellular Reprogramming Techniques
/ methods
Child, Preschool
Dependovirus
/ genetics
Female
Fibroblasts
/ cytology
Forkhead Transcription Factors
/ genetics
Gene Editing
/ methods
Genetic Therapy
/ methods
Humans
Induced Pluripotent Stem Cells
/ cytology
Male
Nerve Tissue Proteins
/ genetics
Neurons
/ cytology
Rett Syndrome
/ genetics
Journal
European journal of human genetics : EJHG
ISSN: 1476-5438
Titre abrégé: Eur J Hum Genet
Pays: England
ID NLM: 9302235
Informations de publication
Date de publication:
10 2020
10 2020
Historique:
received:
07
06
2019
accepted:
24
04
2020
revised:
16
04
2020
pubmed:
17
6
2020
medline:
9
6
2021
entrez:
17
6
2020
Statut:
ppublish
Résumé
Variations in the Forkhead Box G1 (FOXG1) gene cause FOXG1 syndrome spectrum, including the congenital variant of Rett syndrome, characterized by early onset of regression, Rett-like and jerky movements, and cortical visual impairment. Due to the largely unknown pathophysiological mechanisms downstream the impairment of this transcriptional regulator, a specific treatment is not yet available. Since both haploinsufficiency and hyper-expression of FOXG1 cause diseases in humans, we reasoned that adding a gene under nonnative regulatory sequences would be a risky strategy as opposed to a genome editing approach where the mutated gene is reversed into wild-type. Here, we demonstrate that an adeno-associated viruses (AAVs)-coupled CRISPR/Cas9 system is able to target and correct FOXG1 variants in patient-derived fibroblasts, induced Pluripotent Stem Cells (iPSCs) and iPSC-derived neurons. Variant-specific single-guide RNAs (sgRNAs) and donor DNAs have been selected and cloned together with a mCherry/EGFP reporter system. Specific sgRNA recognition sequences were inserted upstream and downstream Cas9 CDS to allow self-cleavage and inactivation. We demonstrated that AAV serotypes vary in transduction efficiency depending on the target cell type, the best being AAV9 in fibroblasts and iPSC-derived neurons, and AAV2 in iPSCs. Next-generation sequencing (NGS) of mCherry
Identifiants
pubmed: 32541681
doi: 10.1038/s41431-020-0652-6
pii: 10.1038/s41431-020-0652-6
pmc: PMC7608362
doi:
Substances chimiques
FOXG1 protein, human
0
Forkhead Transcription Factors
0
Nerve Tissue Proteins
0
Types de publication
Case Reports
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1446-1458Références
Ariani F, Hayek G, Rondinella D, Artuso R, Mencarelli MA, Spanhol-Rosseto A, et al. FOXG1 is responsible for the congenital variant of Rett syndrome. Am J Hum Genet. 2008;83:89–93.
pubmed: 18571142
pmcid: 2443837
Papa FT, Mencarelli MA, Caselli R, Katzaki E, Sampieri K, Meloni I, et al. A 3 Mb deletion in 14q12 causes severe mental retardation, mild facial dysmorphisms and Rett-like features. Am J Med Genet A. 2008;146A:1994–8.
pubmed: 18627055
Rolando S. Rett syndrome: report of eight cases. Brain Dev. 1985;7:290–6.
pubmed: 4061760
Yeung A, Bruno D, Scheffer IE, Carranza D, Burgess T, Slater HR, et al. 4.45 Mb microduplication in chromosome band 14q12 including FOXG1 in a girl with refractory epilepsy and intellectual impairment. Eur J Med Genet. 2009;52:440–2.
pubmed: 19772934
Brunetti-Pierri N, Paciorkowski AR, Ciccone R, Della Mina E, Bonaglia MC, Borgatti R, et al. Duplications of FOXG1 in 14q12 are associated with developmental epilepsy, mental retardation, and severe speech impairment. Eur J Hum Genet. 2011;19:102–7.
pubmed: 20736978
Kortüm F, Das S, Flindt M, Morris-Rosendahl DJ, Stefanova I, Goldstein A, et al. The core FOXG1 syndrome phenotype consists of postnatal microcephaly, severe mental retardation, absent language, dyskinesia, and corpus callosum hypogenesis. J Med Genet. 2011;48:396–406.
pubmed: 21441262
pmcid: 5522617
De Filippis RD, Pancrazi L, Bjørgo K, Rosseto A, Kleefstra T, Grillo E, et al. Expanding the phenotype associated with FOXG1 mutations and in vivo FoxG1 chromatin-binding dynamics. Clin Genet. 2012;82:395–403.
pubmed: 22091895
Boggio EM, Pancrazi L, Lo Rizzo C, Mari F, Meloni I, Ariani F, et al. Visual impairment in FOXG1-mutated individuals and mice. Neuroscience. 2016;324:496–508.
pubmed: 27001178
Martynoga B, Morrison H, Price DJ, Mason JO. Foxg1 is required for specification of ventral telencephalon and region-specific regulation of dorsal telencephalic precursor proliferation and apoptosis. Dev Biol. 2005;283:113–27.
pubmed: 15893304
Patriarchi T, Amabile S, Frullanti E, Landucci E, Lo Rizzo C, Ariani F, et al. Imbalance of excitatory/inhibitory synaptic protein expression in iPSC-derived neurons from FOXG1(+/−) patients and in foxg1(+/−) mice. Eur J Hum Genet. 2016;24:871–80.
pubmed: 26443267
Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, et al. FOXG1-dependent dysregulation of GABA/glutamate neuron differentiation in autism spectrum disorders. Cell. 2015;162:375–90.
pubmed: 26186191
pmcid: 4519016
Shen Q, Wang Y, Dimos JT, Fasano CA, Phoenix TN, Lemischka IR, et al. The timing of cortical neurogenesis is encoded within lineages of individual progenitor cells. Nat Neurosci. 2006;9:743–51.
pubmed: 16680166
Nishiyama J, Mikuni T, Yasuda R. Virus-mediated genome editing via homology-directed repair in mitotic and postmitotic cells in mammalian brain. Neuron. 2017;96:755–68.e5.
pubmed: 29056297
pmcid: 5691606
Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346:1258096.
pubmed: 25430774
Sinnett SE, Hector RD, Gadalla KKE, Heindel C, Chen D, Zaric V, et al. Improved MECP2 gene therapy extends the survival of MeCP2-null mice without apparent toxicity after intracisternal delivery. Mol Ther Methods Clin Dev. 2017;5:106–15.
pubmed: 28497072
pmcid: 5424572
Gadalla KKE, Vudhironarit T, Hector RD, Sinnett S, Bahey NG, Bailey MES, et al. Development of a novel AAV gene therapy cassette with improved safety features and efficacy in a mouse model of Rett syndrome. Mol Ther Methods Clin Dev. 2017;5:180–90.
pubmed: 28497075
pmcid: 5423329
Gadalla KKE, Bailey MES, Spike RC, Ross PD, Woodard KT, Kalburgi SN, et al. Improved survival and reduced phenotypic severity following AAV9/MECP2 gene transfer to neonatal and juvenile male Mecp2 knockout mice. Mol Ther. 2013;21:18–30.
pubmed: 23011033
Li C, Guan X, Du T, Jin W, Wu B, Liu Y, et al. Inhibition of HIV-1 infection of primary CD4+ T-cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9. J Gen Virol. 2015;96:2381–93.
pubmed: 25854553
Xie N, Gong H, Suhl JA, Chopra P, Wang T, Warren ST. Reactivation of FMR1 by CRISPR/Cas9-mediated deletion of the expanded CGG-repeat of the fragile X chromosome. PLoS ONE. 2016;11:e0165499.
pubmed: 27768763
pmcid: 5074572
Zhang Y, Long C, Li H, McAnally JR, Baskin KK, Shelton JM, et al. CRISPR-Cpf1 correction of muscular dystrophy mutations in human cardiomyocytes and mice. Sci Adv. 2017;3:e1602814.
pubmed: 28439558
pmcid: 5389745
Young CS, Hicks MR, Ermolova NV, Nakano H, Jan M, Younesi S, et al. A single CRISPR-Cas9 deletion strategy that targets the majority of DMD patients restores dystrophin function in hiPSC-derived muscle cells. Cell Stem Cell. 2016;18:533–40.
pubmed: 26877224
pmcid: 4826286
Saraiva J, Nobre RJ, Pereira de Almeida L. Gene therapy for the CNS using AAVs: the impact of systemic delivery by AAV9. J Control Release. 2016;241:94–109.
pubmed: 27637390
Hagberg B. Clinical manifestations and stages of Rett syndrome. Ment Retard Dev Disabil Res Rev. 2002;8:61–5.
pubmed: 12112728
Vangipuram M, Ting D, Kim S, Diaz R, Schüle B. Skin punch biopsy explant culture for derivation of primary human fibroblasts. J Vis Exp. 2013;77:e3779.
Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126:663–76.
pubmed: 16904174
Landucci E, Brindisi M, Bianciardi L, Catania LM, Daga S, Croci S, et al. iPSC-derived neurons profiling reveals GABAergic circuit disruption and acetylated α-tubulin defect which improves after iHDAC6 treatment in Rett syndrome. Exp Cell Res. 2018;368:225–35.
pubmed: 29730163
Auricchio A, O’Connor E, Hildinger M, Wilson JM. A single-step affinity column for purification of serotype-5 based adeno-associated viral vectors. Mol Ther. 2001;4:372–4.
pubmed: 11592841
Niccheri F, Pecori R, Conticello S. An efficient method to enrich for knock-out and knock-in cellular clones using the CRISPR/Cas9 system. Cell Mol Life Sci. 2017;74:3413–23.
pubmed: 28421278
pmcid: 5544813
Swiech L, Heidenreich M, Banerjee A, Habib N, Li Y, Trombetta J, et al. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat Biotechnol. 2015;33:102–6.
pubmed: 25326897
Li X-L, Li G-H, Fu J, Fu Y-W, Zhang L, Chen W, et al. Highly efficient genome editing via CRISPR-Cas9 in human pluripotent stem cells is achieved by transient BCL-XL overexpression. Nucleic Acids Res. 2018;46:10195–215.
pubmed: 30239926
pmcid: 6212847
Tornabene P, Tiberi P, Minopoli R, Manfredi A, Mutarelli M. et al. Triple vectors expand AAV transfer capacity in the retina. Mol Ther. 2018;26:524–41.
pubmed: 29292161
Doria M, Ferrara A, Auricchio A. AAV2/8 vectors purified from culture medium with a simple and rapid protocol transduce murine liver, muscle, and retina efficiently. Hum Gene Ther Methods. 2013;24:392–98.
pubmed: 24116943
pmcid: 3869536
Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015;33:187–97.
pubmed: 25513782
Casini A, Olivieri M, Petris G, Montagna C, Reginato G, Maule G, et al. A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nat Biotechnol. 2018;36:265–71.
pubmed: 29431739
pmcid: 6066108
Naso MF, Tomkowicz B, Perry WL, Strohl WR. Adeno-associated virus (AAV) as a vector for gene therapy. BioDrugs. 2017;31:317–34.
pubmed: 28669112
pmcid: 5548848
Weinberg MS, Samulski RJ, McCown TJ. Adeno-associated virus (AAV) gene therapy for neurological disease. Neuropharmacology. 2013;69:82–8.
pubmed: 22465202
Park J, Lim K, Kim SJ, et al. Cas-analyzer: an online tool for assessing genome editing results using NGS data. Bioinformatics. 2017;33:286–8.
Florian C, Bahi-Buisson N, Bienvenu T. FOXG1-related disorders: from clinical description to molecular genetics. Mol Syndromol. 2012;2:153–63.
pubmed: 22670136
Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, et al. CAGE-defined promoter regions of the genes implicated in Rett syndrome. BMC Genom. 2014;15:1177.
Voets O, Tielen F, Elstak E, Benschop J, Grimbergen M, Stallen J, et al. Highly efficient gene inactivation by adenoviral CRISPR/Cas9 in human primary cells. Lewin AS, curatore. PLoS ONE. 2017;12:e0182974.
pubmed: 28800587
pmcid: 5553774
Martufi M, Good RB, Rapiteanu R, Schmidt T, Patili E, Tvermosegaard K, et al. Single-step, high-efficiency CRISPR-Cas9 genome editing in primary human disease-derived fibroblasts. CRISPR J. 2019;2:31–40.
pubmed: 31021235
pmcid: 6636881
Lin S, Staahl BT, Alla RK, Doudna JA. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife. 2014;3:e04766.
pubmed: 25497837
pmcid: 4383097
Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, et al. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc Natl Acad Sci USA. 2015;112:10437–42.
pubmed: 26216948
Manuel MN, Martynoga B, Molinek MD, Quinn JC, Kroemmer C, Mason JO, et al. The transcription factor Foxg1 regulates telencephalic progenitor proliferation cell autonomously, in part by controlling Pax6 expression levels. Neural Dev. 2011;6:9.
pubmed: 21418559
pmcid: 3068069
Bell CL, Gurda BL, Van Vliet K, Agbandje-McKenna M, Wilson JM. Identification of the galactose binding domain of the adeno-associated virus serotype 9 capsid. J Virol. 2012;86:7326–33.
pubmed: 22514350
pmcid: 3416318
Zhang H, Yang B, Mu X, Ahmed SS, Su Q, He R, et al. Several rAAV vectors efficiently cross the blood-brain barrier and transduce neurons and astrocytes in the neonatal mouse central nervous system. Mol Ther. 2011;19:1440–8.
pubmed: 21610699
pmcid: 3149178
Mendell JR, Al-Zaidy S, Shell R, Arnold WD, Rodino-Klapac LR, Prior TW, et al. Single-dose gene-replacement therapy for spinal muscular atrophy. N Engl J Med. 2017;377:1713–22
pubmed: 29091557
Robinson L, Guy J, McKay L, Brockett E, Spike RC, Selfridge J, et al. Morphological and functional reversal of phenotypes in a mouse model of Rett syndrome. Brain. 2012;135:2699–710.
pubmed: 22525157
pmcid: 3437019
Buning H, Srivastava A. Capsid modifications for targeting and improving the efficacy of AAV vectors. Mol Ther Methods Clin Dev. 2019;12:248–65.
pubmed: 30815511
pmcid: 6378346
Ruan GX, Barry E, Yu D, Lukason M, Cheng SH, Scaria A. CRISPR/Cas9-mediated genome editing as a therapeutic approach for leber congenital amaurosis 10. Mol Ther. 2017;25:331–41.
pubmed: 28109959
pmcid: 5368591
Zhang X-H, Tee LY, Wang X-G, Huang Q-S, Yang S-H. Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol Ther Nucleic Acids. 2015;4:e264.
pubmed: 26575098
pmcid: 4877446