Base editing correction of hypertrophic cardiomyopathy in human cardiomyocytes and humanized mice.
Journal
Nature medicine
ISSN: 1546-170X
Titre abrégé: Nat Med
Pays: United States
ID NLM: 9502015
Informations de publication
Date de publication:
02 2023
02 2023
Historique:
received:
28
06
2022
accepted:
07
12
2022
pubmed:
17
2
2023
medline:
25
2
2023
entrez:
16
2
2023
Statut:
ppublish
Résumé
The most common form of genetic heart disease is hypertrophic cardiomyopathy (HCM), which is caused by variants in cardiac sarcomeric genes and leads to abnormal heart muscle thickening. Complications of HCM include heart failure, arrhythmia and sudden cardiac death. The dominant-negative c.1208G>A (p.R403Q) pathogenic variant (PV) in β-myosin (MYH7) is a common and well-studied PV that leads to increased cardiac contractility and HCM onset. In this study we identify an adenine base editor and single-guide RNA system that can efficiently correct this human PV with minimal bystander editing and off-target editing at selected sites. We show that delivery of base editing components rescues pathological manifestations of HCM in induced pluripotent stem cell cardiomyocytes derived from patients with HCM and in a humanized mouse model of HCM. Our findings demonstrate the potential of base editing to treat inherited cardiac diseases and prompt the further development of adenine base editor-based therapies to correct monogenic variants causing cardiac disease.
Identifiants
pubmed: 36797478
doi: 10.1038/s41591-022-02176-5
pii: 10.1038/s41591-022-02176-5
pmc: PMC10053064
mid: NIHMS1876621
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
401-411Subventions
Organisme : British Heart Foundation
ID : BBC/F/21/220106
Pays : United Kingdom
Organisme : NHLBI NIH HHS
ID : R01 HL157281
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL130253
Pays : United States
Organisme : NICHD NIH HHS
ID : U54 HD087351
Pays : United States
Organisme : American Heart Association-American Stroke Association
ID : 907611
Pays : United States
Organisme : NHLBI NIH HHS
ID : F30 HL163915
Pays : United States
Commentaires et corrections
Type : CommentIn
Type : CommentIn
Type : CommentIn
Type : CommentIn
Type : CommentIn
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Maron, B. J. Clinical course and management of hypertrophic cardiomyopathy. N. Engl. J. Med 379, 655–668 (2018).
pubmed: 30110588
doi: 10.1056/NEJMra1710575
Semsarian, C., Ingles, J., Maron, M. S. & Maron, B. J. New perspectives on the prevalence of hypertrophic cardiomyopathy. J. Am. Coll. Cardiol. 65, 1249–1254 (2015).
pubmed: 25814232
doi: 10.1016/j.jacc.2015.01.019
Trivedi, D. V., Adhikari, A. S., Sarkar, S. S., Ruppel, K. M. & Spudich, J. A. Hypertrophic cardiomyopathy and the myosin mesa: viewing an old disease in a new light. Biophys. Rev. 10, 27–48 (2018).
pubmed: 28717924
doi: 10.1007/s12551-017-0274-6
Geisterfer-Lowrance, A. A. et al. A molecular basis for familial hypertrophic cardiomyopathy: a beta cardiac myosin heavy chain gene missense mutation. Cell 62, 999–1006 (1990).
pubmed: 1975517
doi: 10.1016/0092-8674(90)90274-I
Tyska, M. J. et al. Single-molecule mechanics of R403Q cardiac myosin isolated from the mouse model of familial hypertrophic cardiomyopathy. Circ. Res. 86, 737–744 (2000).
pubmed: 10764406
doi: 10.1161/01.RES.86.7.737
Sarkar, S. S. et al. The hypertrophic cardiomyopathy mutations R403Q and R663H increase the number of myosin heads available to interact with actin. Sci. Adv. 6, eaax0069 (2020).
pubmed: 32284968
pmcid: 7124958
doi: 10.1126/sciadv.aax0069
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).
pubmed: 29160308
pmcid: 5726555
doi: 10.1038/nature24644
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).
pubmed: 27096365
pmcid: 4873371
doi: 10.1038/nature17946
Koblan, L. W. et al. In vivo base editing rescues Hutchinson-Gilford progeria syndrome in mice. Nature 589, 608–614 (2021).
pubmed: 33408413
pmcid: 7872200
doi: 10.1038/s41586-020-03086-7
Suh, S. et al. Restoration of visual function in adult mice with an inherited retinal disease via adenine base editing. Nat. Biomed. Eng. 5, 169–178 (2021).
pubmed: 33077938
doi: 10.1038/s41551-020-00632-6
Chemello, F. et al. Precise correction of Duchenne muscular dystrophy exon deletion mutations by base and prime editing. Sci. Adv. 7, eabg4910 (2021).
pubmed: 33931459
pmcid: 8087404
doi: 10.1126/sciadv.abg4910
Reichart, D. et al. Efficient in vivo genome editing prevents hypertrophic cardiomyopathy in mice. Nat. Med. (2022).
Koblan, L. W. et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat. Biotechnol. 36, 843–846 (2018).
pubmed: 29813047
pmcid: 6126947
doi: 10.1038/nbt.4172
Richter, M. F. et al. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat. Biotechnol. 38, 883–891 (2020).
pubmed: 32433547
pmcid: 7357821
doi: 10.1038/s41587-020-0453-z
Walton, R. T., Christie, K. A., Whittaker, M. N. & Kleinstiver, B. P. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science 368, 290–296 (2020).
pubmed: 32217751
pmcid: 7297043
doi: 10.1126/science.aba8853
Nishimasu, H. et al. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 361, 1259–1262 (2018).
pubmed: 30166441
pmcid: 6368452
doi: 10.1126/science.aas9129
Kleinstiver, B. P. et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495 (2016).
pubmed: 26735016
pmcid: 4851738
doi: 10.1038/nature16526
Marian, A. J. & Braunwald, E. Hypertrophic cardiomyopathy: genetics, pathogenesis, clinical manifestations, diagnosis, and therapy. Circ. Res 121, 749–770 (2017).
pubmed: 28912181
pmcid: 5654557
doi: 10.1161/CIRCRESAHA.117.311059
Concordet, J. P. & Haeussler, M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic. Acid. Res. 46, W242–W245 (2018).
pubmed: 29762716
pmcid: 6030908
doi: 10.1093/nar/gky354
Pua, C. J. et al. Genetic studies of hypertrophic cardiomyopathy in Singaporeans identify variants in TNNI3 and TNNT2 that are common in Chinese patients. Circ. Genom. Precis. Med. 13, 424–434 (2020).
pubmed: 32815737
pmcid: 7676617
doi: 10.1161/CIRCGEN.119.002823
Toepfer, C. N. et al. Myosin sequestration regulates sarcomere function, cardiomyocyte energetics, and metabolism, informing the pathogenesis of hypertrophic cardiomyopathy. Circulation 141, 828–842 (2020).
pubmed: 31983222
pmcid: 7077965
doi: 10.1161/CIRCULATIONAHA.119.042339
Cohn, R. et al. A contraction stress model of hypertrophic cardiomyopathy due to sarcomere mutations. Stem Cell Rep. 12, 71–83 (2019).
doi: 10.1016/j.stemcr.2018.11.015
Vakrou, S. & Abraham, M. R. Hypertrophic cardiomyopathy: a heart in need of an energy bar? Front. Physiol. 5, 309 (2014).
pubmed: 25191275
pmcid: 4137386
doi: 10.3389/fphys.2014.00309
Lyons, G. E., Schiaffino, S., Sassoon, D., Barton, P. & Buckingham, M. Developmental regulation of myosin gene expression in mouse cardiac muscle. J. Cell Biol. 111, 2427–2436 (1990).
pubmed: 2277065
doi: 10.1083/jcb.111.6.2427
Geisterfer-Lowrance, A. A. et al. A mouse model of familial hypertrophic cardiomyopathy. Science 272, 731–734 (1996).
pubmed: 8614836
doi: 10.1126/science.272.5262.731
Ma, S. et al. Efficient correction of a hypertrophic cardiomyopathy mutation by ABEmax-NG. Circ. Res. 129, 895–908 (2021).
pubmed: 34525843
doi: 10.1161/CIRCRESAHA.120.318674
Ishikawa, K., Weber, T. & Hajjar, R. J. Human cardiac gene therapy. Circ. Res. 123, 601–613 (2018).
pubmed: 30355138
pmcid: 6390977
doi: 10.1161/CIRCRESAHA.118.311587
Zettler, J., Schutz, V. & Mootz, H. D. The naturally split Npu DnaE intein exhibits an extraordinarily high rate in the protein trans-splicing reaction. FEBS Lett. 583, 909–914 (2009).
pubmed: 19302791
doi: 10.1016/j.febslet.2009.02.003
Prasad, K. M., Xu, Y., Yang, Z., Acton, S. T. & French, B. A. Robust cardiomyocyte-specific gene expression following systemic injection of AAV: in vivo gene delivery follows a Poisson distribution. Gene Ther. 18, 43–52 (2011).
pubmed: 20703310
doi: 10.1038/gt.2010.105
Mendell, J.R. et al. Current Clinical Applications of In Vivo Gene Therapy with AAVs. Mol. Ther. 29, 464–488 (2021).
pubmed: 33309881
doi: 10.1016/j.ymthe.2020.12.007
Teekakirikul, P. et al. Cardiac fibrosis in mice with hypertrophic cardiomyopathy is mediated by non-myocyte proliferation and requires Tgf-beta. J. Clin. Invest. 120, 3520–3529 (2010).
pubmed: 20811150
pmcid: 2947222
doi: 10.1172/JCI42028
Pinto, A. R. et al. Revisiting cardiac cellular composition. Circ. Res. 118, 400–409 (2016).
pubmed: 26635390
doi: 10.1161/CIRCRESAHA.115.307778
Jiang, J., Wakimoto, H., Seidman, J. G. & Seidman, C. E. Allele-specific silencing of mutant Myh6 transcripts in mice suppresses hypertrophic cardiomyopathy. Science 342, 111–114 (2013).
pubmed: 24092743
pmcid: 4100553
doi: 10.1126/science.1236921
Pare, J. A., Fraser, R. G., Pirozynski, W. J., Shanks, J. A. & Stubington, D. Hereditary cardiovascular dysplasia. A form of familial cardiomyopathy. Am. J. Med. 31, 37–62 (1961).
pubmed: 13732753
doi: 10.1016/0002-9343(61)90222-4
Fananapazir, L. & Epstein, N. D. Genotype-phenotype correlations in hypertrophic cardiomyopathy. Insights provided by comparisons of kindreds with distinct and identical beta-myosin heavy chain gene mutations. Circulation 89, 22–32 (1994).
pubmed: 8281650
doi: 10.1161/01.CIR.89.1.22
Ho, C. Y. et al. Genotype and lifetime burden of disease in hypertrophic cardiomyopathy: Insights from the Sarcomeric Human Cardiomyopathy Registry (SHaRe). Circulation 138, 1387–1398 (2018).
pubmed: 30297972
pmcid: 6170149
doi: 10.1161/CIRCULATIONAHA.117.033200
Carroll, K. J. et al. A mouse model for adult cardiac-specific gene deletion with CRISPR/Cas9. Proc. Natl Acad. Sci. USA 113, 338–343 (2016).
pubmed: 26719419
doi: 10.1073/pnas.1523918113
Maron, B. J., Yeates, L. & Semsarian, C. Clinical challenges of genotype positive (+)-phenotype negative (-) family members in hypertrophic cardiomyopathy. Am. J. Cardiol. 107, 604–608 (2011).
pubmed: 21185001
doi: 10.1016/j.amjcard.2010.10.022
Green, E. M. et al. A small-molecule inhibitor of sarcomere contractility suppresses hypertrophic cardiomyopathy in mice. Science 351, 617–621 (2016).
pubmed: 26912705
pmcid: 4784435
doi: 10.1126/science.aad3456
Stern, J. A. et al. A small molecule inhibitor of sarcomere contractility acutely relieves left ventricular outflow tract obstruction in feline hypertrophic cardiomyopathy. PLoS ONE 11, e0168407 (2016).
pubmed: 27973580
pmcid: 5156432
doi: 10.1371/journal.pone.0168407
Ladage, D., Ishikawa, K., Tilemann, L., Muller-Ehmsen, J. & Kawase, Y. Percutaneous methods of vector delivery in preclinical models. Gene Ther. 19, 637–641 (2012).
pubmed: 22418064
doi: 10.1038/gt.2012.14
Cheng, Q. et al. Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR-Cas gene editing. Nat. Nanotechnol. 15, 313–320 (2020).
pubmed: 32251383
pmcid: 7735425
doi: 10.1038/s41565-020-0669-6
Banskota, S. et al. Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins. Cell 185, 250–265 e216 (2022).
pubmed: 35021064
pmcid: 8809250
doi: 10.1016/j.cell.2021.12.021
Tabebordbar, M. et al. Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species. Cell 184, 4919–4938 e4922 (2021).
pubmed: 34506722
pmcid: 9344975
doi: 10.1016/j.cell.2021.08.028
Weinmann, J. et al. Identification of a myotropic AAV by massively parallel in vivo evaluation of barcoded capsid variants. Nat. Commun. 11, 5432 (2020).
pubmed: 33116134
pmcid: 7595228
doi: 10.1038/s41467-020-19230-w
Lompre, A. M. et al. Species- and age-dependent changes in the relative amounts of cardiac myosin isoenzymes in mammals. Dev. Biol. 84, 286–290 (1981).
pubmed: 20737866
doi: 10.1016/0012-1606(81)90396-1
Desai, M. Y. et al. Study design and rationale of VALOR-HCM: evaluation of mavacamten in adults with symptomatic obstructive hypertrophic cardiomyopathy who are eligible for septal reduction therapy. Am. Heart J. 239, 80–89 (2021).
pubmed: 34038706
doi: 10.1016/j.ahj.2021.05.007
Saberi, S. et al. Mavacamten favorably impacts cardiac structure in obstructive hypertrophic cardiomyopathy: EXPLORER-HCM Cardiac Magnetic Resonance Substudy Analysis. Circulation 143, 606–608 (2021).
pubmed: 33190524
doi: 10.1161/CIRCULATIONAHA.120.052359
Keam, S.J. Mavacamten: First Approval. Drugs 82, 1127–1135 (2022).
pubmed: 35802255
pmcid: 9338109
doi: 10.1007/s40265-022-01739-7
Ho, C. Y. et al. Evaluation of mavacamten in symptomatic patients with nonobstructive hypertrophic cardiomyopathy. J. Am. Coll. Cardiol. 75, 2649–2660 (2020).
pubmed: 32466879
doi: 10.1016/j.jacc.2020.03.064
Murphy, E. & Steenbergen, C. Gender-based differences in mechanisms of protection in myocardial ischemia-reperfusion injury. Cardiovasc. Res. 75, 478–486 (2007).
pubmed: 17466956
doi: 10.1016/j.cardiores.2007.03.025
Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).
pubmed: 24157548
pmcid: 3969860
doi: 10.1038/nprot.2013.143
Huang, T. P. et al. Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nat. Biotechnol. 37, 626–631 (2019).
pubmed: 31110355
pmcid: 6551276
doi: 10.1038/s41587-019-0134-y
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).
pubmed: 31937940
pmcid: 6980783
doi: 10.1038/s41551-019-0501-5
Burridge, P. W. et al. Chemically defined generation of human cardiomyocytes. Nat. Method. 11, 855–860 (2014).
doi: 10.1038/nmeth.2999
Correia, C. et al. Distinct carbon sources affect structural and functional maturation of cardiomyocytes derived from human pluripotent stem cells. Sci. Rep. 7, 8590 (2017).
pubmed: 28819274
pmcid: 5561128
doi: 10.1038/s41598-017-08713-4
Kluesner, M. G. et al. EditR: a method to quantify base editing from Sanger sequencing. CRISPR J. 1, 239–250 (2018).
pubmed: 31021262
pmcid: 6694769
doi: 10.1089/crispr.2018.0014
Atmanli, A. et al. Cardiac myoediting attenuates cardiac abnormalities in human and mouse models of Duchenne muscular dystrophy. Circ. Res. 129, 602–616 (2021).
pubmed: 34372664
pmcid: 8416801
doi: 10.1161/CIRCRESAHA.121.319579
Kijlstra, J. D. et al. Integrated analysis of contractile kinetics, force generation, and electrical activity in single human stem cell-derived cardiomyocytes. Stem Cell Rep. 5, 1226–1238 (2015).
doi: 10.1016/j.stemcr.2015.10.017
Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).
pubmed: 26780180
pmcid: 4744125
doi: 10.1038/nbt.3437
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
pubmed: 30809026
pmcid: 6533916
doi: 10.1038/s41587-019-0032-3
Miura, H., Quadros, R. M., Gurumurthy, C. B. & Ohtsuka, M. Easi-CRISPR for creating knock-in and conditional knockout mouse models using long ssDNA donors. Nat. Protoc. 13, 195–215 (2018).
pubmed: 29266098
doi: 10.1038/nprot.2017.153
Creed, H. A. & Tong, C. W. Preparation and identification of cardiac myofibrils from whole heart samples. Methods Mol. Biol. 2319, 15–24 (2021).
pubmed: 34331238
doi: 10.1007/978-1-0716-1480-8_2
Cui, M. & Olson, E. N. Protocol for single-nucleus transcriptomics of diploid and tetraploid cardiomyocytes in murine hearts. STAR Protoc. 1, 100049 (2020).
pubmed: 33111095
pmcid: 7580205
doi: 10.1016/j.xpro.2020.100049
Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).
pubmed: 30944313
pmcid: 6447622
doi: 10.1038/s41467-019-09234-6