Precise therapeutic gene correction by a simple nuclease-induced double-stranded break.

Alleles CRISPR-Associated Protein 9 / metabolism CRISPR-Associated Proteins / metabolism Cells, Cultured Connectin / genetics DNA Breaks, Double-Stranded DNA End-Joining Repair / genetics Frameshift Mutation / genetics Hermanski-Pudlak Syndrome / genetics Humans Muscular Dystrophies, Limb-Girdle / genetics Myoblasts / cytology Poly (ADP-Ribose) Polymerase-1 / antagonists & inhibitors Poly(ADP-ribose) Polymerase Inhibitors / pharmacology Repetitive Sequences, Nucleic Acid / genetics

Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
04 2019
Historique:
received: 28 05 2018
accepted: 22 02 2019
pubmed: 5 4 2019
medline: 18 12 2019
entrez: 5 4 2019
Statut: ppublish

Résumé

Current programmable nuclease-based methods (for example, CRISPR-Cas9) for the precise correction of a disease-causing genetic mutation harness the homology-directed repair pathway. However, this repair process requires the co-delivery of an exogenous DNA donor to recode the sequence and can be inefficient in many cell types. Here we show that disease-causing frameshift mutations that result from microduplications can be efficiently reverted to the wild-type sequence simply by generating a DNA double-stranded break near the centre of the duplication. We demonstrate this in patient-derived cell lines for two diseases: limb-girdle muscular dystrophy type 2G (LGMD2G)

Identifiants

DOI: 10.1038/s41586-019-1076-8 PMID: 30944467 PMC: PMC6483862
pubmed: 30944467
doi: 10.1038/s41586-019-1076-8
pii: 10.1038/s41586-019-1076-8
pmc: PMC6483862
mid: NIHMS1522514
doi:

Substances chimiques

CRISPR-Associated Proteins 0
Connectin 0
Poly(ADP-ribose) Polymerase Inhibitors 0
TCAP protein, human 0
PARP1 protein, human EC 2.4.2.30
Poly (ADP-Ribose) Polymerase-1 EC 2.4.2.30
CRISPR-Associated Protein 9 EC 3.1.-
Cas9 endonuclease Streptococcus pyogenes EC 3.1.-

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

561-565

Subventions

Organisme : NHLBI NIH HHS
ID : R01 HL093766
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001453
Pays : United States
Organisme : NHLBI NIH HHS
ID : F31 HL147482
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS088689
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI117839
Pays : United States
Organisme : NICHD NIH HHS
ID : U54 HD060848
Pays : United States
Organisme : NHLBI NIH HHS
ID : P01 HL131471
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK098252
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM115911
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG007910
Pays : United States

Références

Moreira, E. S. et al. Limb-girdle muscular dystrophy type 2G is caused by mutations in the gene encoding the sarcomeric protein telethonin. Nat. Genet. 24, 163–166 (2000).
pubmed: 10655062 doi: 10.1038/72822
El-Chemaly, S. & Young, L. R. Hermansky–Pudlak syndrome. Clin. Chest Med. 37, 505–511 (2016).
pubmed: 27514596 pmcid: 4987498 doi: 10.1016/j.ccm.2016.04.012
Sfeir, A. & Symington, L. S. Microhomology-mediated end joining: a back-up survival mechanism or dedicated pathway? Trends Biochem. Sci. 40, 701–714 (2015).
pubmed: 26439531 pmcid: 4638128 doi: 10.1016/j.tibs.2015.08.006
Bae, S., Kweon, J., Kim, H. S. & Kim, J.-S. Microhomology-based choice of Cas9 nuclease target sites. Nat. Methods 11, 705–706 (2014).
pubmed: 24972169 doi: 10.1038/nmeth.3015
Kim, S.-I. et al. Microhomology-assisted scarless genome editing in human iPSCs. Nat. Commun. 9, 939 (2018).
pubmed: 29507284 pmcid: 5838097 doi: 10.1038/s41467-018-03044-y
Hisano, Y. et al. Precise in-frame integration of exogenous DNA mediated by CRISPR/Cas9 system in zebrafish. Sci. Rep. 5, 8841 (2015).
pubmed: 25740433 pmcid: 4350073 doi: 10.1038/srep08841
Sakuma, T., Nakade, S., Sakane, Y., Suzuki, K. T. & Yamamoto, T. MMEJ-assisted gene knock-in using TALENs and CRISPR–Cas9 with the PITCh systems. Nat. Protoc. 11, 118–133 (2016).
pubmed: 26678082 doi: 10.1038/nprot.2015.140
Bertz, M., Wilmanns, M. & Rief, M. The titin-telethonin complex is a directed, superstable molecular bond in the muscle Z-disk. Proc. Natl Acad. Sci. USA 106, 13307–13310 (2009).
pubmed: 19622741 doi: 10.1073/pnas.0902312106 pmcid: 2726412
Nigro, V. & Savarese, M. Genetic basis of limb-girdle muscular dystrophies: the 2014 update. Acta Myol. 33, 1–12 (2014).
pubmed: 24843229 pmcid: 4021627
Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nat. Biotechnol. 36, 765–771 (2018).
pubmed: 30010673 pmcid: 6390938 doi: 10.1038/nbt.4192
Caron, L. et al. A human pluripotent stem cell model of facioscapulohumeral muscular dystrophy-affected skeletal muscles. Stem Cells Transl. Med. 5, 1145–1161 (2016).
pubmed: 27217344 pmcid: 4996435 doi: 10.5966/sctm.2015-0224
Oh, J. et al. Positional cloning of a gene for Hermansky–Pudlak syndrome, a disorder of cytoplasmic organelles. Nat. Genet. 14, 300–306 (1996).
pubmed: 8896559 doi: 10.1038/ng1196-300
Richmond, B. et al. Melanocytes derived from patients with Hermansky–Pudlak syndrome types 1, 2, and 3 have distinct defects in cargo trafficking. J. Invest. Dermatol. 124, 420–427 (2005).
pubmed: 15675963 pmcid: 1635963 doi: 10.1111/j.0022-202X.2004.23585.x
Brantly, M. et al. Pulmonary function and high-resolution CT findings in patients with an inherited form of pulmonary fibrosis, Hermansky–Pudlak syndrome, due to mutations in HPS-1. Chest 117, 129–136 (2000).
pubmed: 10631210 doi: 10.1378/chest.117.1.129
Bolukbasi, M. F. et al. Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing. Nat. Commun. 9, 4856 (2018).
pubmed: 30451839 pmcid: 6242970 doi: 10.1038/s41467-018-07310-x
Sharma, S. et al. Homology and enzymatic requirements of microhomology-dependent alternative end joining. Cell Death Dis. 6, e1697 (2015).
pubmed: 25789972 pmcid: 4385936 doi: 10.1038/cddis.2015.58
Wang, M. et al. PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways. Nucleic Acids Res. 34, 6170–6182 (2006).
pubmed: 17088286 pmcid: 1693894 doi: 10.1093/nar/gkl840
Dutta, A. et al. Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex. Nucleic Acids Res. 45, 2585–2599 (2017).
pubmed: 27994036
Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR–Cas system. Cell 163, 759–771 (2015).
pubmed: 26422227 pmcid: 4638220 doi: 10.1016/j.cell.2015.09.038
Landrum, M. J. et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 46, D1062–D1067 (2018).
pubmed: 29165669 doi: 10.1093/nar/gkx1153
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).
pubmed: 27535533 pmcid: 5018207 doi: 10.1038/nature19057
Komor, A. C., Badran, A. H. & Liu, D. R. CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell 168, 20–36 (2017).
pubmed: 27866654 doi: 10.1016/j.cell.2016.10.044
Kim, E. et al. In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nat. Commun. 8, 14500 (2017).
pubmed: 28220790 pmcid: 5473640 doi: 10.1038/ncomms14500
Edraki, A. et al. A compact, high-accuracy Cas9 with a dinucleotide PAM for in vivo genome editing. Mol. Cell 73, 714–726 (2019).
pubmed: 30581144 doi: 10.1016/j.molcel.2018.12.003
Kleinstiver, B. P. et al. Engineered CRISPR–Cas9 nucleases with altered PAM specificities. Nature 523, 481–485 (2015).
pubmed: 26098369 pmcid: 4540238 doi: 10.1038/nature14592
Bolukbasi, M. F. et al. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat. Methods 12, 1150–1156 (2015).
pubmed: 26480473 pmcid: 4679368 doi: 10.1038/nmeth.3624
Hu, J. H. et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 556, 57–63 (2018).
pubmed: 29512652 pmcid: 5951633 doi: 10.1038/nature26155
van Overbeek, M. et al. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Mol. Cell 63, 633–646 (2016).
pubmed: 27499295 doi: 10.1016/j.molcel.2016.06.037
Suzuki, K. et al. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540, 144–149 (2016).
pubmed: 27851729 pmcid: 5331785 doi: 10.1038/nature20565
Shen, M. W. et al. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature 563, 646–651 (2018).
pubmed: 30405244 pmcid: 6517069 doi: 10.1038/s41586-018-0686-x
Rittié, L. & Fisher, G. J. Isolation and culture of skin fibroblasts. Methods Mol. Med. 117, 83–98 (2005).
pubmed: 16118447
Stadler, G. et al. Establishment of clonal myogenic cell lines from severely affected dystrophic muscles — CDK4 maintains the myogenic population. Skelet. Muscle 1, 12 (2011).
pubmed: 21798090 pmcid: 3156635 doi: 10.1186/2044-5040-1-12
Kearns, N. A. et al. Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development 141, 219–223 (2014).
pubmed: 24346702 pmcid: 3865759 doi: 10.1242/dev.103341
Brinkman, E. K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 42, e168 (2014).
pubmed: 25300484 pmcid: 4267669 doi: 10.1093/nar/gku936
Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2014).
pubmed: 24142950 doi: 10.1093/bioinformatics/btt593
Blankenberg, D. et al. Manipulation of FASTQ data with Galaxy. Bioinformatics 26, 1783–1785 (2010).
pubmed: 20562416 pmcid: 2894519 doi: 10.1093/bioinformatics/btq281
Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568–576 (2012).
pubmed: 22300766 pmcid: 3290792 doi: 10.1101/gr.129684.111
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
pubmed: 29750242 pmcid: 6137996 doi: 10.1093/bioinformatics/bty191
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
pubmed: 21221095 pmcid: 3346182 doi: 10.1038/nbt.1754
1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).
doi: 10.1038/nature15393
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943 pmcid: 2723002
Tan, A., Abecasis, G. R. & Kang, H. M. Unified representation of genetic variants. Bioinformatics 31, 2202–2204 (2015).
pubmed: 25701572 pmcid: 4481842 doi: 10.1093/bioinformatics/btv112
Obenchain, V. et al. VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. Bioinformatics 30, 2076–2078 (2014).
pubmed: 24681907 pmcid: 4080743 doi: 10.1093/bioinformatics/btu168
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
pubmed: 9862982 pmcid: 148217 doi: 10.1093/nar/27.2.573
Li, H. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28, 1838–1844 (2012).
pubmed: 22569178 pmcid: 3389770 doi: 10.1093/bioinformatics/bts280
Wu, Y. et al. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat. Med. https://doi.org/10.1038/s41591-019-0401-y (2019).
pubmed: 30911135 pmcid: 6512986 doi: 10.1038/s41591-019-0401-y
Liu, P. et al. Enhanced Cas12a editing in mammalian cells and zebrafish. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz184 (2019).
pubmed: 30892626 pmcid: 6486634 doi: 10.1093/nar/gkz184

Auteurs

Sukanya Iyer (S)

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.

Sneha Suresh (S)

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.

Dongsheng Guo (D)

Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.
Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA.

Katelyn Daman (K)

Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.
Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA.

Jennifer C J Chen (JCJ)

Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.
Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA.
Office of the Vice-Principal (Research), Queen's University, Kingston, Ontario, Canada.

Pengpeng Liu (P)

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.

Marina Zieger (M)

Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.

Kevin Luk (K)

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.

Benjamin P Roscoe (BP)

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
COGEN Therapeutics, Cambridge, MA, USA.

Christian Mueller (C)

Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.

Oliver D King (OD)

Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.
Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA.

Charles P Emerson (CP)

Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA. charles.emersonjr@umassmed.edu.
Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA. charles.emersonjr@umassmed.edu.
Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA. charles.emersonjr@umassmed.edu.

Scot A Wolfe (SA)

Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA. scot.wolfe@umassmed.edu.
Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA. scot.wolfe@umassmed.edu.
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. scot.wolfe@umassmed.edu.

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Classifications MeSH

Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Allèles › Precise therapeutic gene correction by a...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines associées aux CRISPR › Protéine-9 associée à CRISPR › Precise therapeutic gene correction by a...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines associées aux CRISPR › Precise therapeutic gene correction by a...
Recherchemedicale.com › Cellules › Cellules cultivées › Precise therapeutic gene correction by a...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines contractiles › Protéines du muscle › Connectine › Precise therapeutic gene correction by a...
Recherchemedicale.com › Phénomènes génétiques › Altération de l'ADN › Cassures de l'ADN › Cassures double-brin de l'ADN › Precise therapeutic gene correction by a...
Recherchemedicale.com › Phénomènes génétiques › Réparation de l'ADN › Réparation de l'ADN par jonction d'extrémités › Precise therapeutic gene correction by a...
Recherchemedicale.com › Phénomènes génétiques › Variation génétique › Mutation › Mutation avec décalage du cadre de lecture › Precise therapeutic gene correction by a...
Recherchemedicale.com › Maladies métaboliques et nutritionnelles › Maladies métaboliques › Erreurs innées du métabolisme › Aminoacidopathies congénitales › Albinisme › Albinisme oculocutané › Syndrome d'Hermanski-Pudlak › Precise therapeutic gene correction by a...
Recherchemedicale.com › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Precise therapeutic gene correction by a...
Recherchemedicale.com › Malformations et maladies congénitales, héréditaires et néonatales › Maladies génétiques congénitales › Dystrophies musculaires › Dystrophies musculaires des ceintures › Precise therapeutic gene correction by a...
Recherchemedicale.com › Cellules › Cellules souches › Myoblastes › Precise therapeutic gene correction by a...
Recherchemedicale.com › Enzymes et coenzymes › Enzymes › Transferases › Glycosyltransferase › Pentosyltransferases › ADP ribose transferases › Poly(ADP-ribose) polymerases › Poly (ADP-Ribose) polymerase-1 › Precise therapeutic gene correction by a...
Recherchemedicale.com › Actions chimiques et utilisations › Actions pharmacologiques › Utilisations thérapeutiques › Antinéoplasiques › Inhibiteurs de poly(ADP-ribose) polymérases › Precise therapeutic gene correction by a...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Séquences répétées d'acides nucléiques › Precise therapeutic gene correction by a...