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Nicolau S, Malhotra J, Kaler M, Magistrado-Coxen P, Iammarino MA, Reash NF, Frair EC, Wijeratne S, Kelly BJ, White P, Lowes LP, Waldrop MA, Flanigan KM. Increase in Full-Length Dystrophin by Exon Skipping in Duchenne Muscular Dystrophy Patients with Single Exon Duplications: An Open-label Study. J Neuromuscul Dis 2024; 11:679-685. [PMID: 38461513 DOI: 10.3233/jnd-230107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Single exon duplications account for disease in a minority of Duchenne muscular dystrophy patients. Exon skipping in these patients has the potential to be highly therapeutic through restoration of full-length dystrophin expression. We conducted a 48-week open label study of casimersen and golodirsen in 3 subjects with an exon 45 or 53 duplication. Two subjects (aged 18 and 23 years) were non-ambulatory at baseline. Upper limb, pulmonary, and cardiac function appeared stable in the 2 subjects in whom they could be evaluated. Dystrophin expression increased from 0.94 % ±0.59% (mean±SD) of normal to 5.1% ±2.9% by western blot. Percent dystrophin positive fibers also rose from 14% ±17% at baseline to 50% ±42% . Our results provide initial evidence that the use of exon-skipping drugs may increase dystrophin levels in patients with single-exon duplications.
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Affiliation(s)
- Stefan Nicolau
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Maryann Kaler
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Megan A Iammarino
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
| | - Natalie F Reash
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
| | - Emma C Frair
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
| | - Saranga Wijeratne
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Benjamin J Kelly
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Peter White
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Linda P Lowes
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
| | - Megan A Waldrop
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- >Department of Neurology>, The Ohio State University, Columbus, OH, USA
| | - Kevin M Flanigan
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- >Department of Neurology>, The Ohio State University, Columbus, OH, USA
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Gushchina LV, Bradley AJ, Vetter TA, Lay JW, Rohan NL, Frair EC, Wein N, Flanigan KM. Persistence of exon 2 skipping and dystrophin expression at 18 months after U7snRNA-mediated therapy in the Dup2 mouse model. Mol Ther Methods Clin Dev 2023; 31:101144. [PMID: 38027058 PMCID: PMC10679948 DOI: 10.1016/j.omtm.2023.101144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a progressive X-linked disease caused by mutations in the DMD gene that prevent the expression of a functional dystrophin protein. Exon duplications represent 6%-11% of mutations, and duplications of exon 2 (Dup2) are the most common (∼11%) of duplication mutations. An exon-skipping strategy for Dup2 mutations presents a large therapeutic window. Skipping one exon copy results in full-length dystrophin expression, whereas skipping of both copies (Del2) activates an internal ribosomal entry site (IRES) in exon 5, inducing the expression of a highly functional truncated dystrophin isoform. We have previously confirmed the therapeutic efficacy of AAV9.U7snRNA-mediated skipping in the Dup2 mouse model and showed the absence of off-target splicing effects and lack of toxicity in mice and nonhuman primates. Here, we report long-term dystrophin expression data following the treatment of 3-month-old Dup2 mice with the scAAV9.U7.ACCA vector. Significant exon 2 skipping and robust dystrophin expression in the muscles and hearts of treated mice persist at 18 months after treatment, along with the partial rescue of muscle function. These data extend our previous findings and show that scAAV9.U7.ACCA provides long-term protection by restoring the disrupted dystrophin reading frame in the context of exon 2 duplications.
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Affiliation(s)
- Liubov V. Gushchina
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Adrienne J. Bradley
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Tatyana A. Vetter
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Jacob W. Lay
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Natalie L. Rohan
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Emma C. Frair
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Nicolas Wein
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Kevin M. Flanigan
- The Center for Gene Therapy, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Department of Neurology, The Ohio State University, Columbus, OH, USA
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3
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Vihinen M. Systematic errors in annotations of truncations, loss-of-function and synonymous variants. Front Genet 2023; 14:1015017. [PMID: 36713076 PMCID: PMC9880313 DOI: 10.3389/fgene.2023.1015017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of variation, and synonymous variants that are not synonymous and lead to sequence changes or to missing protein.
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Abstract
Muscular dystrophies are a group of genetic disorders characterized by varying degrees of progressive muscle weakness and degeneration. They are clinically and genetically heterogeneous but share the common histological features of dystrophic muscle. There is currently no cure for muscular dystrophies, which is of particular concern for the more disabling and/or lethal forms of the disease. Through the years, several therapies have encouragingly been developed for muscular dystrophies and include genetic, cellular, and pharmacological approaches. In this chapter, we undertake a comprehensive exploration of muscular dystrophy therapeutics under current development. Our review includes antisense therapy, CRISPR, gene replacement, cell therapy, nonsense suppression, and disease-modifying small molecule compounds.
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Embree CM, Abu-Alhasan R, Singh G. Features and factors that dictate if terminating ribosomes cause or counteract nonsense-mediated mRNA decay. J Biol Chem 2022; 298:102592. [PMID: 36244451 PMCID: PMC9661723 DOI: 10.1016/j.jbc.2022.102592] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control pathway in eukaryotes that continuously monitors mRNA transcripts to ensure truncated polypeptides are not produced. The expression of many normal mRNAs that encode full-length polypeptides is also regulated by this pathway. Such transcript surveillance by NMD is intimately linked to translation termination. When a ribosome terminates translation at a normal termination codon, NMD is not activated, and mRNA can undergo repeated rounds of translation. On the other hand, when translation termination is deemed abnormal, such as that on a premature termination codon, it leads to a series of poorly understood events involving the NMD pathway, which destabilizes the transcript. In this review, we summarize our current understanding of how the NMD machinery interfaces with the translation termination factors to initiate NMD. We also discuss a variety of cis-acting sequence contexts and trans-acting factors that can cause readthrough, ribosome reinitiation, or ribosome frameshifting at stop codons predicted to induce NMD. These alternative outcomes can lead to the ribosome translating downstream of such stop codons and hence the transcript escaping NMD. NMD escape via these mechanisms can have wide-ranging implications on human health, from being exploited by viruses to hijack host cell systems to being harnessed as potential therapeutic possibilities to treat genetic diseases.
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Affiliation(s)
- Caleb M Embree
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Rabab Abu-Alhasan
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio USA.
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6
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Poyatos‐García J, Martí P, Liquori A, Muelas N, Pitarch I, Martinez‐Dolz L, Rodríguez B, Gonzalez‐Quereda L, Damiá M, Aller E, Selva‐Gimenez M, Vilchez R, Diaz‐Manera J, Alonso‐Pérez J, Barcena JE, Jauregui A, Gámez J, Aladrén JA, Fernández A, Montolio M, Azorin I, Hervas D, Casasús A, Nieto M, Gallano P, Sevilla T, Vilchez JJ. Dystrophinopathy Phenotypes and Modifying Factors in DMD Exon 45-55 Deletion. Ann Neurol 2022; 92:793-806. [PMID: 35897138 PMCID: PMC9825930 DOI: 10.1002/ana.26461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Duchenne muscular dystrophy (DMD) exon 45-55 deletion (del45-55) has been postulated as a model that could treat up to 60% of DMD patients, but the associated clinical variability and complications require clarification. We aimed to understand the phenotypes and potential modifying factors of this dystrophinopathy subset. METHODS This cross-sectional, multicenter cohort study applied clinical and functional evaluation. Next generation sequencing was employed to identify intronic breakpoints and their impact on the Dp140 promotor, intronic long noncoding RNA, and regulatory splicing sequences. DMD modifiers (SPP1, LTBP4, ACTN3) and concomitant mutations were also assessed. Haplotypes were built using DMD single nucleotide polymorphisms. Dystrophin expression was evaluated via immunostaining, Western blotting, reverse transcription polymerase chain reaction (PCR), and droplet digital PCR in 9 muscle biopsies. RESULTS The series comprised 57 subjects (23 index) expressing Becker phenotype (28%), isolated cardiopathy (19%), and asymptomatic features (53%). Cognitive impairment occurred in 90% of children. Patients were classified according to 10 distinct index-case breakpoints; 4 of them were recurrent due to founder events. A specific breakpoint (D5) was associated with severity, but no significant effect was appreciated due to the changes in intronic sequences. All biopsies showed dystrophin expression of >67% and traces of alternative del45-57 transcript that were not deemed pathogenically relevant. Only the LTBP4 haplotype appeared associated the presence of cardiopathy among the explored extragenic factors. INTERPRETATION We confirmed that del45-55 segregates a high proportion of benign phenotypes, severe cases, and isolated cardiac and cognitive presentations. Although some influence of the intronic breakpoint position and the LTBP4 modifier may exist, the pathomechanisms responsible for the phenotypic variability remain largely unresolved. ANN NEUROL 2022;92:793-806.
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Affiliation(s)
- Javier Poyatos‐García
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Pilar Martí
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Alessandro Liquori
- Hematology Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Cancer (CIBERONC); CB16/12/00284MadridSpain
| | - Nuria Muelas
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain
| | - Inmaculada Pitarch
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Neuropediatric DepartmentUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Luis Martinez‐Dolz
- Cardiology DepartmentUniversity and Polytechnic La Fe Hospital, IIS La FeValenciaSpain,Centre for Biomedical Network Research on Cardiovascular Diseases (CIBERCV)ValenciaSpain
| | - Benjamin Rodríguez
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Lidia Gonzalez‐Quereda
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Maria Damiá
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Neuropediatric DepartmentUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Elena Aller
- Genetics UnitUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Marta Selva‐Gimenez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Roger Vilchez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Jordi Diaz‐Manera
- Neuromuscular Disorders Unit, Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Hospital of Sant PauBarcelonaSpain,Autonomous University of BarcelonaBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U762, CB06/05/0030BarcelonaSpain
| | - Jorge Alonso‐Pérez
- Neuromuscular Disorders Unit, Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Hospital of Sant PauBarcelonaSpain,Autonomous University of BarcelonaBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U762, CB06/05/0030BarcelonaSpain
| | - José Eulalio Barcena
- Neuromuscular Section, Neurology ServiceCruces University HospitalBarakaldoSpain
| | - Amaia Jauregui
- Neuromuscular Section, Neurology ServiceCruces University HospitalBarakaldoSpain
| | - Josep Gámez
- Autonomous University of BarcelonaBarcelonaSpain,Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)GMA ClinicBarcelonaSpain
| | | | | | - Marisol Montolio
- Duchenne Parent Project SpainMadridSpain,Department of Cell Biology, Physiology, and Immunology, Faculty of BiologyBarcelonaSpain
| | - Inmaculada Azorin
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - David Hervas
- Department of Applied Statistics and Operations Research, and QualityPolytechnic University of ValenciaValenciaSpain
| | - Ana Casasús
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Marisa Nieto
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Pia Gallano
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Teresa Sevilla
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Department of MedicineUniversity of ValenciaValenciaSpain
| | - Juan Jesus Vilchez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Department of MedicineUniversity of ValenciaValenciaSpain
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Wein N, Vetter TA, Vulin A, Simmons TR, Frair EC, Bradley AJ, Gushchina LV, Almeida CF, Huang N, Lesman D, Rajakumar D, Weiss RB, Flanigan KM. Systemic delivery of an AAV9 exon-skipping vector significantly improves or prevents features of Duchenne muscular dystrophy in the Dup2 mouse. Mol Ther Methods Clin Dev 2022; 26:279-293. [PMID: 35949298 PMCID: PMC9356240 DOI: 10.1016/j.omtm.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022]
Abstract
Duchenne muscular dystrophy (DMD) is typically caused by mutations that disrupt the DMD reading frame, but nonsense mutations in the 5′ part of the gene induce utilization of an internal ribosomal entry site (IRES) in exon 5, driving expression of a highly functional N-truncated dystrophin. We have developed an AAV9 vector expressing U7 small nuclear RNAs targeting DMD exon 2 and have tested it in a mouse containing a duplication of exon 2, in which skipping of both exon 2 copies induces IRES-driven expression, and skipping of one copy leads to wild-type dystrophin expression. One-time intravascular injection either at postnatal days 0–1 or at 2 months results in efficient exon skipping and dystrophin expression, and significant protection from functional and pathologic deficits. Immunofluorescence quantification showed 33%–53% average dystrophin intensity and 55%–79% average dystrophin-positive fibers in mice treated in adulthood, with partial amelioration of DMD pathology and correction of DMD-associated alterations in gene expression. In mice treated neonatally, dystrophin immunofluorescence reached 49%–85% of normal intensity and 76%–99% dystrophin-positive fibers, with near-complete correction of dystrophic pathology, and these beneficial effects persisted for at least 6 months. Our results demonstrate the robustness, durability, and safety of exon 2 skipping using scAAV9.U7snRNA.ACCA, supporting its clinical use.
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Affiliation(s)
- Nicolas Wein
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Tatyana A Vetter
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Adeline Vulin
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Tabatha R Simmons
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Emma C Frair
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Adrienne J Bradley
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Liubov V Gushchina
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Camila F Almeida
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Nianyuan Huang
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Daniel Lesman
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Dhanarajan Rajakumar
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Robert B Weiss
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kevin M Flanigan
- Center for Gene Therapy, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Neurology, The Ohio State University, Columbus, OH, USA
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8
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Functional analysis of variants in DMD exon/intron 10 predicted to affect splicing. J Hum Genet 2022; 67:495-501. [DOI: 10.1038/s10038-022-01035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/08/2022] [Accepted: 03/31/2022] [Indexed: 11/08/2022]
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9
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Zambon AA, Waldrop MA, Alles R, Weiss RB, Conroy S, Moore-Clingenpeel M, Previtali S, Flanigan KM. Phenotypic Spectrum of Dystrophinopathy Due to Duchenne Muscular Dystrophy Exon 2 Duplications. Neurology 2022; 98:e730-e738. [PMID: 34937785 PMCID: PMC8865888 DOI: 10.1212/wnl.0000000000013246] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES To describe the phenotypic spectrum of dystrophinopathy in a large cohort of individuals with DMD exon 2 duplications (Dup2), who may be particularly amenable to therapies directed at restoring expression of either full-length dystrophin or nearly full-length dystrophin through utilization of the DMD exon 5 internal ribosome entry site (IRES). METHODS In this retrospective observational study, we analyzed data from large genotype-phenotype databases (the United Dystrophinopathy Project [UDP] and the Italian DMD network) and classified participants into Duchenne muscular dystrophy (DMD), intermediate muscular dystrophy (IMD), or Becker muscular dystrophy (BMD) phenotypes. Log-rank tests for time-to-event variables were used to compare age at loss of ambulation (LOA) in participants with Dup2 vs controls without Dup2 in the UDP database and for comparisons between steroid-treated vs steroid-naive participants with Dup2. RESULTS Among 66 participants with Dup2 (UDP = 40, Italy = 26), 61% were classified as DMD, 9% as IMD, and 30% as BMD. Median age at last observation was 15.4 years (interquartile range 8.79-26.0) and 75% had been on corticosteroids for at least 6 months. Age at LOA differed significantly between participants with Dup2 DMD and historical controls without Dup2 DMD (p < 0.001). Valid spirometry was limited but suggested a delay in the typical age-related decline in forced vital capacity and 24 of 55 participants with adequate cardiac data had cardiomyopathy. DISCUSSION Some patients with Dup2 display a milder disease course than controls without Dup2 DMD, and prolonged ambulation with corticosteroids suggests the potential of IRES activation as a molecular mechanism. As Dup2-targeted therapies reach clinical applications, this information is critical to aid in the interpretation of the efficacy of new treatments.
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Affiliation(s)
- Alberto A Zambon
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Megan A Waldrop
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Roxane Alles
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Robert B Weiss
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Sara Conroy
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Melissa Moore-Clingenpeel
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Stefano Previtali
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Kevin M Flanigan
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City.
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10
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Triana-Fonseca P, Parada-Márquez JF, Silva-Aldana CT, Zambrano-Arenas D, Arias-Gomez LL, Morales-Fonseca N, Medina-Méndez E, Restrepo CM, Silgado-Guzmán DF, Fonseca-Mendoza DJ. Genetic Profile of the Dystrophin Gene Reveals New Mutations in Colombian Patients Affected with Muscular Dystrophinopathy. APPLICATION OF CLINICAL GENETICS 2021; 14:399-408. [PMID: 34629887 PMCID: PMC8493106 DOI: 10.2147/tacg.s317721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/31/2021] [Indexed: 11/23/2022]
Abstract
Background Duchenne and Becker muscular dystrophies (DMD/BMD) are the most common human dystrophinopathies with recessive X-linked inheritance. Dystrophin gene deletions and duplications are the most common mutations, followed by point mutations. The aim of this study is to characterize the mutational profile of the dystrophin gene in Colombian patients with DMD/BMD. Material and Methods Mutational profiling was determined in 69 affected patients using Sanger sequencing, next-generation sequencing (NGS) and/or multiplex ligation dependent-probes amplification (MLPA). Genetic variants were classified according to molecular consequence and new variants were determined through database and literature analysis. Results Mutational profile in affected patients revealed that large deletions/duplications analyzed by MLPA accounted for 72.5% of all genetic variations. By using Sanger sequencing or NGS, we identified point mutations in 15.9% and small deletions in 11.6% of the patients. New mutations were found, most of them were point mutations or small deletions (10.1%). Conclusion Our results described the genetic profile of the dystrophin gene in Colombian patients with DMD and contribute to efforts to identify molecular variants in Latin American populations. For our population, 18.8% of cases could be treated with FDA or MDA approved molecular therapies based on specific mutations. These data contribute to the establishment of appropriate genetic counseling and potential treatment.
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Affiliation(s)
| | | | - Claudia T Silva-Aldana
- Department of Molecular Diagnosis, Genética Molecular de Colombia SAS, Bogotá, DC, Colombia
| | | | | | | | - Esteban Medina-Méndez
- Department of Molecular Diagnosis, Genética Molecular de Colombia SAS, Bogotá, DC, Colombia
| | - Carlos M Restrepo
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, DC, Colombia
| | | | - Dora Janeth Fonseca-Mendoza
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, DC, Colombia
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11
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Wein N, Dunn DM, Waldrop MA, Gushchina LV, Frair EC, Weiss RB, Flanigan KM. Absence of Significant Off-Target Splicing Variation with a U7snRNA Vector Targeting DMD Exon 2 Duplications. Hum Gene Ther 2021; 32:1346-1359. [PMID: 34060935 DOI: 10.1089/hum.2020.315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Exon skipping therapies for Duchenne muscular dystrophy that restore an open reading frame can be induced by the use of noncoding U7 small nuclear RNA (U7snRNA) modified by an antisense exon-targeting sequence delivered by an adeno-associated virus (AAV) vector. We have developed an AAV vector (AAV9.U7-ACCA) containing four U7snRNAs targeting the splice donor and acceptor sites of dystrophin exon 2, resulting in highly efficient exclusion of DMD exon 2. We assessed the specificity of splice variation induced by AAV9.U7-ACCA delivery in the Dmd exon 2 duplication (Dup2) mouse model through an unbiased RNA-seq approach. Treatment-related effects on pre-mRNA splicing were quantified using local splicing variation (LSV) analysis. Filtering the transcriptome for differences in treatment-related splicing resulted in only 16 candidate off-target LSVs. Only a single candidate off-target LSV was found in both skeletal and cardiac muscle tissue and occurred at a known variable cassette exon. In contrast, four LSVs represented significant on-target correction of Dmd exon 2 splicing and transcriptome analysis showed correction of known dystrophin-deficient gene dysregulation. We conclude that the absence of off-target splicing induced by treatment with the U7-ACCA vector supports the continued clinical development of this approach.
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Affiliation(s)
- Nicolas Wein
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Megan A Waldrop
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Liubov V Gushchina
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Emma C Frair
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Kevin M Flanigan
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Neurology, The Ohio State University, Columbus, Ohio, USA
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12
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Gushchina LV, Frair EC, Rohan N, Bradley AJ, Simmons TR, Chavan HD, Chou HJ, Eggers M, Waldrop MA, Wein N, Flanigan KM. Lack of Toxicity in Nonhuman Primates Receiving Clinically Relevant Doses of an AAV9.U7snRNA Vector Designed to Induce DMD Exon 2 Skipping. Hum Gene Ther 2021; 32:882-894. [PMID: 33406986 PMCID: PMC10112461 DOI: 10.1089/hum.2020.286] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Therapeutic exon skipping as a treatment for Duchenne muscular dystrophy (DMD) has largely concentrated on the delivery of antisense oligomers to treat out-of-frame exon deletions. Here we report on the preclinical development of an adeno-associated virus (AAV)-encapsidated viral vector containing four copies of the noncoding U7 small nuclear RNA (U7snRNA), each targeted to either the splice donor or the splice acceptor sites of DMD exon 2. We have previously shown that delivery of this vector (scAAV9.U7.ACCA) to the Dup2 mouse model results in expression of full-length dystrophin from wild-type DMD mRNA, as well as an internal ribosome entry site (IRES)-driven isoform translated only in the absence of exon 2 (deletion exon 2 [Del2] mRNA). Here we present the data from a rigorous dose escalation toxicity study in nonhuman primates, encompassing two doses (3 × 1013 and 8 × 1013 vg/kg) and two time points (3 and 6 months postinjection). No evidence for significant toxicity was seen by biochemical, histopathologic, or clinical measures, providing evidence for safety that led to initiation of a first-in-human clinical trial.
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Affiliation(s)
- Liubov V Gushchina
- The Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Emma C Frair
- The Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Natalie Rohan
- The Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Adrienne J Bradley
- The Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Tabatha R Simmons
- The Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Megan A Waldrop
- The Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Nicolas Wein
- The Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kevin M Flanigan
- The Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Neurology, The Ohio State University, Columbus, Ohio, USA
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13
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Pre-clinical dose-escalation studies establish a therapeutic range for U7snRNA-mediated DMD exon 2 skipping. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 21:325-340. [PMID: 33898631 PMCID: PMC8047432 DOI: 10.1016/j.omtm.2021.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/18/2021] [Indexed: 01/09/2023]
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked progressive disease characterized by loss of dystrophin protein that typically results from truncating mutations in the DMD gene. Current exon-skipping therapies have sought to treat deletion mutations that abolish an open reading frame (ORF) by skipping an adjacent exon, in order to restore an ORF that allows translation of an internally deleted yet partially functional protein, as is seen with many patients with the milder Becker muscular dystrophy (BMD) phenotype. In contrast to that approach, skipping of one copy of a duplicated exon would be expected to result in a full-length transcript and production of a wild-type protein. We have developed an adeno-associated virus (AAV)-based U7snRNA exon-skipping approach directed toward exon 2, duplications of which represent 10% of all DMD duplication mutations. Deletion of exon 2 results in utilization of an exon 5 internal ribosome entry site (IRES) that allows translation beginning in exon 6 of a highly protective dystrophin protein, providing a wide therapeutic window for treatment. Both intramuscular and systemic administration of this vector in the Dup2 mouse model results in robust dystrophin expression and correction of muscle physiologic defects, allowing dose escalation to establish a putative minimal efficacious dose for a human clinical trial.
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14
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Stephenson AA, Flanigan KM. Gene editing and modulation for Duchenne muscular dystrophy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:225-255. [PMID: 34175043 DOI: 10.1016/bs.pmbts.2021.01.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a progressive muscle disease caused by loss of dystrophin protein, encoded by the DMD gene. DMD manifests early in childhood as difficulty walking, progresses to loss of ambulation by the teens, and leads to death in early adulthood. Adeno-associated virus-vectorized gene therapies to restore dystrophin protein expression using gene replacement or antisense oligonucleotide-mediated pre-mRNA splicing modulation have emerged, making great strides in uncovering barriers to gene therapies for DMD and other genetic diseases. While this first-generation of DMD therapies are being evaluated in ongoing clinical trials, uncertainties regarding durability and therapeutic efficacy prompted the development of new experimental therapies for DMD that take advantage of somatic cell gene editing. These experimental therapies continue to advance toward clinic trials, but questions remain unanswered regarding safety and translatable efficacy. Here we review the advancements toward treatment of DMD using gene editing and modulation therapies, with an emphasis on those nearest to clinical applications.
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Affiliation(s)
- Anthony A Stephenson
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
| | - Kevin M Flanigan
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States; Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States; Department of Neurology, College of Medicine, The Ohio State University, Columbus, OH, United States.
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15
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Zimowski JG, Purzycka J, Pawelec M, Ozdarska K, Zaremba J. Small mutations in Duchenne/Becker muscular dystrophy in 164 unrelated Polish patients. J Appl Genet 2021; 62:289-295. [PMID: 33420945 DOI: 10.1007/s13353-020-00605-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/09/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
In the 164 patients with Duchenne/Becker muscular dystrophy, we found 142 different small mutations including 51 novel mutations not listed in the LOVD, the UMD-DMD, the ClinVar, and the HGMD databases. Among all mutations, nonsense mutations occurred in 45.7%, frameshift mutations in 32.9%, and splicing mutations in 19.5%. Small mutations were distributed throughout the whole dystrophin gene. Splicing mutations were twice more common in BMD patients than in DMD patients. Eighty-two percent of mothers of the males affected with DMD/BMD were found to be carriers of small mutations.
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Affiliation(s)
- Janusz G Zimowski
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland. .,, Warsaw, Poland.
| | - Joanna Purzycka
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Magdalena Pawelec
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Katarzyna Ozdarska
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Jacek Zaremba
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
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16
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Lim KRQ, Nguyen Q, Yokota T. Genotype-Phenotype Correlations in Duchenne and Becker Muscular Dystrophy Patients from the Canadian Neuromuscular Disease Registry. J Pers Med 2020; 10:E241. [PMID: 33238405 PMCID: PMC7712074 DOI: 10.3390/jpm10040241] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 02/07/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal neuromuscular disorder generally caused by out-of-frame mutations in the DMD gene. In contrast, in-frame mutations usually give rise to the milder Becker muscular dystrophy (BMD). However, this reading frame rule does not always hold true. Therefore, an understanding of the relationships between genotype and phenotype is important for informing diagnosis and disease management, as well as the development of genetic therapies. Here, we evaluated genotype-phenotype correlations in DMD and BMD patients enrolled in the Canadian Neuromuscular Disease Registry from 2012 to 2019. Data from 342 DMD and 60 BMD patients with genetic test results were analyzed. The majority of patients had deletions (71%), followed by small mutations (17%) and duplications (10%); 2% had negative results. Two deletion hotspots were identified, exons 3-20 and exons 45-55, harboring 86% of deletions. Exceptions to the reading frame rule were found in 13% of patients with deletions. Surprisingly, C-terminal domain mutations were associated with decreased wheelchair use and increased forced vital capacity. Dp116 and Dp71 mutations were also linked with decreased wheelchair use, while Dp140 mutations significantly predicted cardiomyopathy. Finally, we found that 12.3% and 7% of DMD patients in the registry could be treated with FDA-approved exon 51- and 53-skipping therapies, respectively.
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Affiliation(s)
- Kenji Rowel Q. Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada; (K.R.Q.L.); (Q.N.)
| | - Quynh Nguyen
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada; (K.R.Q.L.); (Q.N.)
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada; (K.R.Q.L.); (Q.N.)
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada, HM Toupin Neurological Science Research Chair, Edmonton, AB T6G2H7, Canada
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17
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EMQN best practice guidelines for genetic testing in dystrophinopathies. Eur J Hum Genet 2020; 28:1141-1159. [PMID: 32424326 PMCID: PMC7608854 DOI: 10.1038/s41431-020-0643-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 02/04/2023] Open
Abstract
Dystrophinopathies are X-linked diseases, including Duchenne muscular dystrophy and Becker muscular dystrophy, due to DMD gene variants. In recent years, the application of new genetic technologies and the availability of new personalised drugs have influenced diagnostic genetic testing for dystrophinopathies. Therefore, these European best practice guidelines for genetic testing in dystrophinopathies have been produced to update previous guidelines published in 2010.These guidelines summarise current recommended technologies and methodologies for analysis of the DMD gene, including testing for deletions and duplications of one or more exons, small variant detection and RNA analysis. Genetic testing strategies for diagnosis, carrier testing and prenatal diagnosis (including non-invasive prenatal diagnosis) are then outlined. Guidelines for sequence variant annotation and interpretation are provided, followed by recommendations for reporting results of all categories of testing. Finally, atypical findings (such as non-contiguous deletions and dual DMD variants), implications for personalised medicine and clinical trials and incidental findings (identification of DMD gene variants in patients where a clinical diagnosis of dystrophinopathy has not been considered or suspected) are discussed.
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18
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Torella A, Zanobio M, Zeuli R, del Vecchio Blanco F, Savarese M, Giugliano T, Garofalo A, Piluso G, Politano L, Nigro V. The position of nonsense mutations can predict the phenotype severity: A survey on the DMD gene. PLoS One 2020; 15:e0237803. [PMID: 32813700 PMCID: PMC7437896 DOI: 10.1371/journal.pone.0237803] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/03/2020] [Indexed: 12/23/2022] Open
Abstract
A nonsense mutation adds a premature stop signal that hinders any further translation of a protein-coding gene, usually resulting in a null allele. To investigate the possible exceptions, we used the DMD gene as an ideal model. First, because dystrophin absence causes Duchenne muscular dystrophy (DMD), while its reduction causes Becker muscular dystrophy (BMD). Second, the DMD gene is X-linked and there is no second allele that can interfere in males. Third, databases are accumulating reports on many mutations and phenotypic data. Finally, because DMD mutations may have important therapeutic implications. For our study, we analyzed large databases (LOVD, HGMD and ClinVar) and literature and revised critically all data, together with data from our internal patients. We totally collected 2593 patients. Positioning these mutations along the dystrophin transcript, we observed a nonrandom distribution of BMD-associated mutations within selected exons and concluded that the position can be predictive of the phenotype. Nonsense mutations always cause DMD when occurring at any point in fifty-one exons. In the remaining exons, we found milder BMD cases due to early 5’ nonsense mutations, if reinitiation can occur, or due to late 3’ nonsense when the shortened product retains functionality. In the central part of the gene, all mutations in some in-frame exons, such as in exons 25, 31, 37 and 38 cause BMD, while mutations in exons 30, 32, 34 and 36 cause DMD. This may have important implication in predicting the natural history and the efficacy of therapeutic use of drug-stimulated translational readthrough of premature termination codons, also considering the action of internal natural rescuers. More in general, our survey confirm that a nonsense mutation should be not necessarily classified as a null allele and this should be considered in genetic counselling.
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Affiliation(s)
- Annalaura Torella
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Mariateresa Zanobio
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Roberta Zeuli
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | | | - Marco Savarese
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Teresa Giugliano
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Arcomaria Garofalo
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Giulio Piluso
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Luisa Politano
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Vincenzo Nigro
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- * E-mail:
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19
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Gieron-Korthals M, Fernandez R. New Developments in Diagnosis, Treatment, and Management of Duchenne Muscular Dystrophy. Adv Pediatr 2020; 67:183-196. [PMID: 32591061 DOI: 10.1016/j.yapd.2020.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Maria Gieron-Korthals
- Department of Pediatrics, Division of Child Neurology, University of South Florida, Morsani College of Medicine, 17 Davis Boulevard, Suite 200, Tampa, FL 33606, USA.
| | - Raymond Fernandez
- Pediatric Neurology Associates, 4150 North Armenia Avenue, Suite 103, Tampa, FL 33607, USA; Muscular Dystrophy Association Care Center, Shriners Hospital for Children, Tampa, FL, USA
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20
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Kumar SH, Athimoolam K, Suraj M, Das Christu Das MS, Muralidharan A, Jeyam D, Ashokan J, Karthikeyan P, Krishna R, Khanna-Gupta A, Bremadesam Raman L. Comprehensive genetic analysis of 961 unrelated Duchenne Muscular Dystrophy patients: Focus on diagnosis, prevention and therapeutic possibilities. PLoS One 2020; 15:e0232654. [PMID: 32559196 PMCID: PMC7304910 DOI: 10.1371/journal.pone.0232654] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 04/19/2020] [Indexed: 02/06/2023] Open
Abstract
Recently DNA sequencing analysis has played a vital role in the unambiguous diagnosis of clinically suspected patients with Duchenne Muscular Dystrophy (DMD). DMD is a monogenic, X-linked, recessive, degenerative pediatric neuromuscular disorder affecting males, invariably leading to fatal cardiopulmonary failure. Early and precise diagnosis of the disease is an essential part of an effective disease management strategy as care guidelines and prevention through counseling need to be initiated at the earliest particularly since therapies are now available for a subset of patients. In this manuscript we report the DMD gene mutational profiles of 961 clinically suspected male DMD patients, 99% of whom were unrelated. We utilized a molecular diagnostic approach which is cost-effective for most patients and follows a systematic process that sequentially involves identification of hotspot deletions using mPCR, large deletions and duplications using MLPA and small insertions/ deletions and point mutations using an NGS muscular dystrophy gene panel. Pathogenic DMD gene mutations were identified in 84% of patients. Our data compared well with the frequencies and distribution of deletions and duplications reported in the DMD gene in other published studies. We also describe a number of rare in-frame mutations, which appeared to be enriched in the 5’ proximal hotspot region of the DMD gene. Furthermore, we identified a family with a rare non-contiguous deletion mutation in the DMD gene where three males were affected and two females were deemed carriers. A subset of patients with mutations in the DMD gene who are likely to benefit therapeutically from new FDA and EMA approved drugs were found in our cohort. Given that the burden of care for DMD patients invariably falls on the mothers, particularly in rural India, effective genetic counseling followed by carrier screening is crucial for prevention of this disorder. We analyzed the carrier status of consented female relatives of 463 probands to gauge the percentage of patients with familial disease. Our analysis revealed 43.7% of mothers with DMD gene mutations. Our comprehensive efforts, involving complete genetic testing coupled with compassionate genetic counseling provided to DMD patients and their families, are intended to improve the quality of life of DMD patients and to empower carrier females to make informed reproductive choices to impede the propagation of this deadly disease.
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Affiliation(s)
- Shalini H. Kumar
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Kalpana Athimoolam
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Manikandan Suraj
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Mary Shoba Das Christu Das
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Aparna Muralidharan
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Divya Jeyam
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Jaicy Ashokan
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Priya Karthikeyan
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Ragav Krishna
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Arati Khanna-Gupta
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
| | - Lakshmi Bremadesam Raman
- Molecular Diagnostics, Counseling, Care and Research Centre (MDCRC), Royal CareSuper Speciality Hospital, Neelambur, Coimbatore, Tamil Nadu, India
- * E-mail:
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21
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Saylam E, Aravindhan A, Stefans V, Veerapandiyan A. Pseudometabolic Presentation of Dystrophinopathy in a Family Due to a Rare Nonsense Mutation. J Clin Neuromuscul Dis 2020; 21:245-246. [PMID: 32453103 DOI: 10.1097/cnd.0000000000000286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Ezgi Saylam
- Division of Neurology, Department of Pediatrics, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Akilandeswari Aravindhan
- Division of Neurology, Department of Pediatrics, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Vikki Stefans
- Departments of Pediatrics and Physical Medicine and Rehabilitation, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Aravindhan Veerapandiyan
- Division of Neurology, Department of Pediatrics, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR
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22
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Stepniak-Konieczna E, Konieczny P, Cywoniuk P, Dluzewska J, Sobczak K. AON-induced splice-switching and DMPK pre-mRNA degradation as potential therapeutic approaches for Myotonic Dystrophy type 1. Nucleic Acids Res 2020; 48:2531-2543. [PMID: 31965181 PMCID: PMC7049696 DOI: 10.1093/nar/gkaa007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/28/2019] [Accepted: 01/03/2020] [Indexed: 01/04/2023] Open
Abstract
Expansion of an unstable CTG repeat in the 3′UTR of the DMPK gene causes Myotonic Dystrophy type 1 (DM1). CUG-expanded DMPK transcripts (CUGexp) sequester Muscleblind-like (MBNL) alternative splicing regulators in ribonuclear inclusions (foci), leading to abnormalities in RNA processing and splicing. To alleviate the burden of CUGexp, we tested therapeutic approach utilizing antisense oligonucleotides (AONs)-mediated DMPK splice-switching and degradation of mutated pre-mRNA. Experimental design involved: (i) skipping of selected constitutive exons to induce frameshifting and decay of toxic mRNAs by an RNA surveillance mechanism, and (ii) exclusion of the alternative exon 15 (e15) carrying CUGexp from DMPK mRNA. While first strategy failed to stimulate DMPK mRNA decay, exclusion of e15 enhanced DMPK nuclear export but triggered accumulation of potentially harmful spliced out pre-mRNA fragment containing CUGexp. Neutralization of this fragment with antisense gapmers complementary to intronic sequences preceding e15 failed to diminish DM1-specific spliceopathy due to AONs’ chemistry-related toxicity. However, intronic gapmers alone reduced the level of DMPK mRNA and mitigated DM1-related cellular phenotypes including spliceopathy and nuclear foci. Thus, a combination of the correct chemistry and experimental approach should be carefully considered to design a safe AON-based therapeutic strategy for DM1.
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Affiliation(s)
- Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Patryk Konieczny
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Julia Dluzewska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
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23
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Berger J, Li M, Berger S, Meilak M, Rientjes J, Currie PD. Effect of Ataluren on dystrophin mutations. J Cell Mol Med 2020; 24:6680-6689. [PMID: 32343037 PMCID: PMC7299694 DOI: 10.1111/jcmm.15319] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 01/09/2023] Open
Abstract
Duchenne muscular dystrophy is a severe muscle wasting disease caused by mutations in the dystrophin gene (dmd). Ataluren has been approved by the European Medicines Agency for treatment of Duchenne muscular dystrophy. Ataluren has been reported to promote ribosomal read‐through of premature stop codons, leading to restoration of full‐length dystrophin protein. However, the mechanism of Ataluren action has not been fully described. To evaluate the efficacy of Ataluren on all three premature stop codons featuring different termination strengths (UAA > UAG > UGA), novel dystrophin‐deficient zebrafish were generated. Pathological assessment of the muscle by birefringence quantification, a tool to directly measure muscle integrity, did not reveal a significant effect of Ataluren on any of the analysed dystrophin‐deficient mutants at 3 days after fertilization. Functional analysis of the musculature at 6 days after fertilization by direct measurement of the generated force revealed a significant improvement by Ataluren only for the UAA‐carrying mutant dmdta222a. Interestingly however, all other analysed dystrophin‐deficient mutants were not affected by Ataluren, including the dmdpc3 and dmdpc2 mutants that harbour weaker premature stop codons UAG and UGA, respectively. These in vivo results contradict reported in vitro data on Ataluren efficacy, suggesting that Ataluren might not promote read‐through of premature stop codons. In addition, Ataluren had no effect on dystrophin transcript levels, but mild adverse effects on wild‐type larvae were identified. Further assessment of N‐terminally truncated dystrophin opened the possibility of Ataluren promoting alternative translation codons within dystrophin, thereby potentially shifting the patient cohort applicable for Ataluren.
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Affiliation(s)
- Joachim Berger
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic, Australia.,Victoria Node, EMBL Australia, Clayton, Vic, Australia
| | - Mei Li
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic, Australia.,Victoria Node, EMBL Australia, Clayton, Vic, Australia
| | - Silke Berger
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic, Australia.,Victoria Node, EMBL Australia, Clayton, Vic, Australia
| | - Michelle Meilak
- Monash Genome Modification Platform, Monash University, Clayton, Vic, Australia
| | - Jeanette Rientjes
- Monash Genome Modification Platform, Monash University, Clayton, Vic, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Vic, Australia.,Victoria Node, EMBL Australia, Clayton, Vic, Australia
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24
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Ikeda T, Fujinaka H, Goto K, Nakajima T, Ozawa T. Becker muscular dystrophy caused by exon 2-truncating mutation of DMD. Hum Genome Var 2019; 6:52. [PMID: 31754439 PMCID: PMC6859157 DOI: 10.1038/s41439-019-0083-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/09/2022] Open
Abstract
Nonsense and frameshift mutations of the dystrophin (DMD) gene usually cause severe Duchenne muscular dystrophy (DMD). Interestingly, however, premature stop codons in exons 1 and 2 result in relatively mild Becker muscular dystrophy (BMD). Herein, we report the clinical course of a patient with a very mild phenotype of BMD caused by a frameshift mutation, NM_004006.2: c.40_41del GA/p.(Glu14ArgfsX17), in exon 2 of the DMD gene.
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Affiliation(s)
- Tetsuhiko Ikeda
- Department of Neurology, National Hospital Organization Niigata National Hospital, Kashiwazaki, Niigata Japan.,2Department of Neurology, Brain Research Institute, Niigata University, Niigata, Niigata Japan
| | - Hidehiko Fujinaka
- Department of Pediatrics, National Hospital Organization Niigata National Hospital, Kashiwazaki, Niigata Japan.,Department of Clinical Research, National Hospital Organization Niigata National Hospital, Kashiwazaki, Niigata Japan
| | - Kiyoe Goto
- Deprtment of Genetic Counseling, National Hospital Organization Niigata National Hospital, Kashiwazaki, Niigata Japan
| | - Takashi Nakajima
- Department of Neurology, National Hospital Organization Niigata National Hospital, Kashiwazaki, Niigata Japan
| | - Tetsuo Ozawa
- Department of Internal Medicine, National Hospital Organization Niigata National Hospital, Kashiwazaki, Niigata Japan
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25
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Oleaga-Quintas C, Deswarte C, Moncada-Vélez M, Metin A, Krishna Rao I, Kanık-Yüksek S, Nieto-Patlán A, Guérin A, Gülhan B, Murthy S, Özkaya-Parlakay A, Abel L, Martínez-Barricarte R, Pérez de Diego R, Boisson-Dupuis S, Kong XF, Casanova JL, Bustamante J. A purely quantitative form of partial recessive IFN-γR2 deficiency caused by mutations of the initiation or second codon. Hum Mol Genet 2019; 27:3919-3935. [PMID: 31222290 DOI: 10.1093/hmg/ddy275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/17/2018] [Accepted: 07/17/2018] [Indexed: 02/07/2023] Open
Abstract
Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by clinical disease caused by weakly virulent mycobacteria, such as environmental mycobacteria and Bacillus Calmette-Guérin vaccines, in otherwise healthy individuals. All known genetic etiologies disrupt interferon (IFN)-γ immunity. Germline bi-allelic mutations of IFNGR2 can underlie partial or complete forms of IFN-γ receptor 2 (IFN-γR2) deficiency. Patients with partial IFN-γR2 deficiency express a dysfunctional molecule on the cell surface. We studied three patients with MSMD from two unrelated kindreds from Turkey (P1, P2) and India (P3), by whole-exome sequencing. P1 and P2 are homozygous for a mutation of the initiation codon(c.1A>G) of IFNGR2, whereas P3 is homozygous for a mutation of the second codon (c.4delC). Overexpressed mutant alleles produce small amounts of full-length IFN-γR2 resulting in an impaired, but not abolished, response to IFN-γ. Moreover, SV40-fibroblasts of P1 and P2 responded weakly to IFN-γ, and Epstein Barr virus-transformed B cells had a barely detectable response to IFN-γ. Studies in patients' primary T cells and monocyte-derived macrophages yielded similar results. The residual expression of IFN-γR2 protein of normal molecular weight and function is due to the initiation of translation between the second and ninth non-AUG codons. We thus describe mutations of the first and second codons of IFNGR2, which define a new form of partial recessive IFN-γR2 deficiency. Residual levels of IFN-γ signaling were very low, accounting for the more severe clinical phenotype of these patients with residual expression levels of normally functional surface receptors than of patients with partial recessive IFN-γR2 deficiency due to surface-expressed dysfunctional receptors, whose residual levels of IFN-γ signaling were higher.
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Affiliation(s)
- Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,Department of Immunology, School of Medicine, Complutense University, Madrid, Spain
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France
| | - Marcela Moncada-Vélez
- Primary Immunodeficiencies Group, School of Medicine, University of Antioquia UdeA, Medellin, Colombia
| | - Ayse Metin
- Infectious Diseases Unit, Ankara Hematology Oncology Children's Training and Research Hospital, Ankara, Turkey
| | | | - Saliha Kanık-Yüksek
- Infectious Diseases Unit, Ankara Hematology Oncology Children's Training and Research Hospital, Ankara, Turkey
| | - Alejandro Nieto-Patlán
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France
| | - Antoine Guérin
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France
| | - Belgin Gülhan
- Infectious Diseases Unit, Ankara Hematology Oncology Children's Training and Research Hospital, Ankara, Turkey
| | - Savita Murthy
- Department of Pediatrics, St John's Medical College, Bangalore, India
| | - Aslınur Özkaya-Parlakay
- Infectious Diseases Unit, Ankara Hematology Oncology Children's Training and Research Hospital, Ankara, Turkey
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA
| | - Rubén Martínez-Barricarte
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA
| | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases IdiPAZ Institute for Health Research, La Paz University Hospital, Madrid, Spain
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA
| | - Xiao-Fei Kong
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA.,Howard Hughes Medical Institute, New York, USA.,Pediatric Hematology-Immunology Unit, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, the Rockefeller University, New York, USA.,Center for the Study of Primary Immunodeficiencies, AP-HP, Necker Hospital for Sick Children, Paris, France
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26
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Molecular and Histopathological Characterization of Patients Presenting with the Duchenne Muscular Dystrophy Phenotype in a Tertiary Care Center in Southern India. Indian Pediatr 2019. [DOI: 10.1007/s13312-019-1553-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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27
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Multiple Exon Skipping in the Duchenne Muscular Dystrophy Hot Spots: Prospects and Challenges. J Pers Med 2018; 8:jpm8040041. [PMID: 30544634 PMCID: PMC6313462 DOI: 10.3390/jpm8040041] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/24/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD), a fatal X-linked recessive disorder, is caused mostly by frame-disrupting, out-of-frame deletions in the dystrophin (DMD) gene. Antisense oligonucleotide-mediated exon skipping is a promising therapy for DMD. Exon skipping aims to convert out-of-frame mRNA to in-frame mRNA and induce the production of internally-deleted dystrophin as seen in the less severe Becker muscular dystrophy. Currently, multiple exon skipping has gained special interest as a new therapeutic modality for this approach. Previous retrospective database studies represented a potential therapeutic application of multiple exon skipping. Since then, public DMD databases have become more useful with an increase in patient registration and advances in molecular diagnosis. Here, we provide an update on DMD genotype-phenotype associations using a global DMD database and further provide the rationale for multiple exon skipping development, particularly for exons 45–55 skipping and an emerging therapeutic concept, exons 3–9 skipping. Importantly, this review highlights the potential of multiple exon skipping for enabling the production of functionally-corrected dystrophin and for treating symptomatic patients not only with out-of-frame deletions but also those with in-frame deletions. We will also discuss prospects and challenges in multiple exon skipping therapy, referring to recent progress in antisense chemistry and design, as well as disease models.
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28
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Wein N, Vulin A, Findlay AR, Gumienny F, Huang N, Wilton SD, Flanigan KM. Efficient Skipping of Single Exon Duplications in DMD Patient-Derived Cell Lines Using an Antisense Oligonucleotide Approach. J Neuromuscul Dis 2018; 4:199-207. [PMID: 28869484 DOI: 10.3233/jnd-170233] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Exon skipping strategies in Duchenne muscular dystrophy (DMD) have largely been directed toward altering splicing of exons flanking out-of-frame deletions, with the goal of restoring an open mRNA reading frame that leads to production of an internally deleted but partially functional dystrophin protein. OBJECTIVE We sought to apply exon skipping to duplication mutations, assuming that the inherently limited efficiency of antisense oligonucleotide-induced exon skipping would more frequently skip a single copy of a duplicated exon, rather than both and result in significant amounts of wild-type DMD mRNA. METHODS We tested this hypothesis in fibroblast cell lines derived from patients with a variety of single or multiple exon duplications that have been modified to allow transdifferentiation into a myogenic lineage. RESULTS Using a variety of 2'O-methyl antisense oligonucleotides, significant skipping was induced for each duplication leading to a wild-type transcript as a major mRNA product. CONCLUSIONS This study provides another proof of concept for the feasibility of therapeutic skipping in patients carrying exon duplications in order to express wild-type, full-length mRNA, although careful evaluation of the skipping efficiency should be performed as some exons are easier to skip than others. Such a personalized strategy is expected to be highly beneficial for this subset of DMD patients, compared to inducing expression of an internally-deleted dystrophin.
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Affiliation(s)
- Nicolas Wein
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Adeline Vulin
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Andrew R Findlay
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Felecia Gumienny
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Nianyuan Huang
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Steve D Wilton
- Perron Institute for Neurological and Translational Science, Center for Comparative Genomics, Murdoch University, Perth, Australia
| | - Kevin M Flanigan
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Neurology, The Ohio State University, Columbus, OH, USA
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29
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Cain JT, Kim DI, Quast M, Shivega WG, Patrick RJ, Moser C, Reuter S, Perez M, Myers A, Weimer JM, Roux KJ, Landsverk M. Nonsense pathogenic variants in exon 1 of PHOX2B lead to translational reinitiation in congenital central hypoventilation syndrome. Am J Med Genet A 2017; 173:1200-1207. [PMID: 28371199 DOI: 10.1002/ajmg.a.38162] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/15/2016] [Accepted: 01/09/2017] [Indexed: 11/06/2022]
Abstract
Pathogenic variants in PHOX2B lead to congenital central hypoventilation syndrome (CCHS), a rare disorder of the nervous system characterized by autonomic dysregulation and hypoventilation typically presenting in the neonatal period, although a milder late-onset (LO) presentation has been reported. More than 90% of cases are caused by polyalanine repeat mutations (PARMs) in the C-terminus of the protein; however non-polyalanine repeat mutations (NPARMs) have been reported. Most NPARMs are located in exon 3 of PHOX2B and result in a more severe clinical presentation including Hirschsprung disease (HSCR) and/or peripheral neuroblastic tumors (PNTs). A previously reported nonsense pathogenic variant in exon 1 of a patient with LO-CCHS and no HSCR or PNTs leads to translational reinitiation at a downstream AUG codon producing an N-terminally truncated protein. Here we report additional individuals with nonsense pathogenic variants in exon 1 of PHOX2B. In vitro analyses were used to determine if these and other reported nonsense variants in PHOX2B exon 1 produced N-terminally truncated proteins. We found that all tested nonsense variants in PHOX2B exon 1 produced a truncated protein of the same size. This truncated protein localized to the nucleus and transactivated a target promoter. These data suggest that nonsense pathogenic variants in the first exon of PHOX2B likely escape nonsense mediated decay (NMD) and produce N-terminally truncated proteins functionally distinct from those produced by the more common PARMs.
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Affiliation(s)
- Jacob T Cain
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Dae I Kim
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Megan Quast
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Winnie G Shivega
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Ryan J Patrick
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Chuanpit Moser
- Section of Pediatric Pulmonology, Sanford School of Medicine at the University of South Dakota, Sioux Falls, South Dakota
| | - Suzanne Reuter
- Section of Neonatal-Perinatal Medicine, Sanford School of Medicine at the University of South Dakota, Sioux Falls, South Dakota
| | - Myrza Perez
- Department of Pediatric Pulmonology, Kaiser Permanente, Roseville, California
| | - Angela Myers
- Department of Pediatrics, Sanford School of Medicine at the University of South Dakota, Sioux Falls, South Dakota
| | - Jill M Weimer
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota.,Department of Pediatrics, Sanford School of Medicine at the University of South Dakota, Sioux Falls, South Dakota
| | - Kyle J Roux
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota.,Department of Pediatrics, Sanford School of Medicine at the University of South Dakota, Sioux Falls, South Dakota
| | - Megan Landsverk
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota.,Department of Pediatrics, Sanford School of Medicine at the University of South Dakota, Sioux Falls, South Dakota
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30
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The sensitivity of exome sequencing in identifying pathogenic mutations for LGMD in the United States. J Hum Genet 2016; 62:243-252. [PMID: 27708273 PMCID: PMC5266644 DOI: 10.1038/jhg.2016.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 01/12/2023]
Abstract
The current study characterizes a cohort of limb-girdle muscular dystrophy (LGMD) in the United States using whole exome sequencing. Fifty-five families affected by LGMD were recruited using an institutionally-approved protocol. Exome sequencing was performed on probands and selected parental samples. Pathogenic mutations and co-segregation patterns were confirmed by Sanger sequencing. Twenty-two families (40%) had novel and previously reported pathogenic mutations, primarily in LGMD genes, but also in genes for Duchenne muscular dystrophy, facioscapulohumeral muscular dystrophy, congenital myopathy, myofibrillar myopathy, inclusion body myopathy, and Pompe disease. One family was diagnosed via clinical testing. Dominant mutations were identified in COL6A1, COL6A3, FLNC, LMNA, RYR1, SMCHD1, and VCP, recessive mutations in ANO5, CAPN3, GAA, LAMA2, SGCA, and SGCG, and X-linked mutations in DMD. A previously reported variant in DMD was confirmed to be benign. Exome sequencing is a powerful diagnostic tool for LGMD. Despite careful phenotypic screening, pathogenic mutations were found in other muscle disease genes, largely accounting for the increased sensitivity of exome sequencing. Our experience suggests that broad sequencing panels are useful for these analyses due to the phenotypic overlap of many neuromuscular conditions. The confirmation of a benign DMD variant illustrates the potential of exome sequencing to help determine pathogenicity.
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31
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Brinkmeyer-Langford C, Balog-Alvarez C, Cai JJ, Davis BW, Kornegay JN. Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy. BMC Genomics 2016; 17:665. [PMID: 27549615 PMCID: PMC4994242 DOI: 10.1186/s12864-016-2948-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 07/18/2016] [Indexed: 12/17/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) causes progressive muscle degeneration, cardiomyopathy and respiratory failure in approximately 1/5,000 boys. Golden Retriever muscular dystrophy (GRMD) resembles DMD both clinically and pathologically. Like DMD, GRMD exhibits remarkable phenotypic variation among affected dogs, suggesting the influence of modifiers. Understanding the role(s) of genetic modifiers of GRMD may identify genes and pathways that also modify phenotypes in DMD and reveal novel therapies. Therefore, our objective in this study was to identify genetic modifiers that affect discrete GRMD phenotypes. Results We performed a linear mixed-model (LMM) analysis using 16 variably-affected dogs from our GRMD colony (8 dystrophic, 8 non-dystrophic). All of these dogs were either full or half-siblings, and phenotyped for 19 objective, quantitative biomarkers at ages 6 and 12 months. Each biomarker was individually assessed. Gene expression profiles of 59 possible candidate genes were generated for two muscle types: the cranial tibialis and medial head of the gastrocnemius. SNPs significantly associated with GRMD biomarkers were identified on multiple chromosomes (including the X chromosome). Gene expression levels for candidate genes located near these SNPs correlated with biomarker values, suggesting possible roles as GRMD modifiers. Conclusions The results of this study enhance our understanding of GRMD pathology and represent a first step toward the characterization of GRMD modifiers that may be relevant to DMD pathology. Such modifiers are likely to be useful for DMD treatment development based on their relationships to GRMD phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2948-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Cynthia Balog-Alvarez
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Brian W Davis
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joe N Kornegay
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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32
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Todeschini A, Gualandi F, Trabanelli C, Armaroli A, Ravani A, Fanin M, Rota S, Bello L, Ferlini A, Pegoraro E, Padovani A, Filosto M. Becker muscular dystrophy due to an intronic splicing mutation inducing a dual dystrophin transcript. Neuromuscul Disord 2016; 26:662-665. [PMID: 27616544 DOI: 10.1016/j.nmd.2016.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 07/24/2016] [Accepted: 08/12/2016] [Indexed: 11/15/2022]
Abstract
We describe a 29-year-old patient who complained of left thigh muscle weakness since he was 23 and of moderate proximal weakness of both lower limbs with difficulty in climbing stairs and running since he was 27. Mild weakness of iliopsoas and quadriceps muscles and muscle atrophy of both the distal forearm and thigh were observed upon clinical examination. He harboured a novel c.1150-3C>G substitution in the DMD gene, affecting the intron 10 acceptor splice site and causing exon 11 skipping and an out-of-frame transcript. However, protein of normal molecular weight but in reduced amounts was observed on Western Blot analysis. Reverse transcription analysis on muscle RNA showed production, via alternative splicing, of a transcript missing exon 11 as well as a low abundant full-length transcript which is enough to avoid the severe Duchenne phenotype. Our study showed that a reduced amount of full length dystrophin leads to a mild form of Becker muscular dystrophy. These results confirm earlier findings that low amounts of dystrophin can be associated with a milder phenotype, which is promising for therapies aiming at dystrophin restoration.
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Affiliation(s)
- Alice Todeschini
- Center for Neuromuscular Diseases and Neuropathies, Unit of Neurology, ASST "Spedali Civili", University of Brescia, Brescia, Italy
| | - Francesca Gualandi
- Department of Medical Sciences, Logistic Unit of Medical Genetics, University- Hospital of Ferrara, Italy
| | - Cecilia Trabanelli
- Department of Medical Sciences, Logistic Unit of Medical Genetics, University- Hospital of Ferrara, Italy
| | - Annarita Armaroli
- Department of Medical Sciences, Logistic Unit of Medical Genetics, University- Hospital of Ferrara, Italy
| | - Anna Ravani
- Department of Medical Sciences, Logistic Unit of Medical Genetics, University- Hospital of Ferrara, Italy
| | - Marina Fanin
- Department of Neurosciences, University of Padua, Padua
| | - Silvia Rota
- Center for Neuromuscular Diseases and Neuropathies, Unit of Neurology, ASST "Spedali Civili", University of Brescia, Brescia, Italy
| | - Luca Bello
- Department of Neurosciences, University of Padua, Padua
| | - Alessandra Ferlini
- Department of Medical Sciences, Logistic Unit of Medical Genetics, University- Hospital of Ferrara, Italy; Dubowitz Neuromuscular Centre, Developmental Neuroscience Programme, UCL Institute of Child Health, London, UK
| | | | - Alessandro Padovani
- Center for Neuromuscular Diseases and Neuropathies, Unit of Neurology, ASST "Spedali Civili", University of Brescia, Brescia, Italy
| | - Massimiliano Filosto
- Center for Neuromuscular Diseases and Neuropathies, Unit of Neurology, ASST "Spedali Civili", University of Brescia, Brescia, Italy.
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Toh ZYC, Thandar Aung-Htut M, Pinniger G, Adams AM, Krishnaswarmy S, Wong BL, Fletcher S, Wilton SD. Deletion of Dystrophin In-Frame Exon 5 Leads to a Severe Phenotype: Guidance for Exon Skipping Strategies. PLoS One 2016; 11:e0145620. [PMID: 26745801 PMCID: PMC4706350 DOI: 10.1371/journal.pone.0145620] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 12/07/2015] [Indexed: 12/03/2022] Open
Abstract
Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels) manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes.
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Affiliation(s)
- Zhi Yon Charles Toh
- Western Australian Neuroscience Research Institute, Perth, Australia
- University of Western Australia, Perth, Australia
| | | | - Gavin Pinniger
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, Australia
| | - Abbie M. Adams
- Western Australian Neuroscience Research Institute, Perth, Australia
- University of Western Australia, Perth, Australia
- Centre for Comparative Genomics, Murdoch University, Perth, Australia
| | | | - Brenda L. Wong
- Department of Paediatrics, Department of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sue Fletcher
- Western Australian Neuroscience Research Institute, Perth, Australia
- University of Western Australia, Perth, Australia
- Centre for Comparative Genomics, Murdoch University, Perth, Australia
| | - Steve D. Wilton
- Western Australian Neuroscience Research Institute, Perth, Australia
- University of Western Australia, Perth, Australia
- Centre for Comparative Genomics, Murdoch University, Perth, Australia
- * E-mail:
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Massouridès E, Polentes J, Mangeot PE, Mournetas V, Nectoux J, Deburgrave N, Nusbaum P, Leturcq F, Popplewell L, Dickson G, Wein N, Flanigan KM, Peschanski M, Chelly J, Pinset C. Dp412e: a novel human embryonic dystrophin isoform induced by BMP4 in early differentiated cells. Skelet Muscle 2015; 5:40. [PMID: 26568816 PMCID: PMC4644319 DOI: 10.1186/s13395-015-0062-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/21/2015] [Indexed: 01/09/2023] Open
Abstract
Background Duchenne muscular dystrophy (DMD) is a devastating X-linked recessive genetic myopathy. DMD physiopathology is still not fully understood and a prenatal onset is suspected but difficult to address. Methods The bone morphogenetic protein 4 (BMP4) is a critical signaling molecule involved in mesoderm commitment. Human induced pluripotent stem cells (hiPSCs) from DMD and healthy individuals and human embryonic stem cells (hESCs) treated with BMP4 allowed us to model the early steps of myogenesis in normal and DMD contexts. Results Unexpectedly, 72h following BMP4 treatment, a new long DMD transcript was detected in all tested hiPSCs and hESCs, at levels similar to that found in adult skeletal muscle. This novel transcript named “Dp412e” has a specific untranslated first exon which is conserved only in a sub-group of anthropoids including human. The corresponding novel dystrophin protein of 412-kiloDalton (kDa), characterized by an N-terminal-truncated actin-binding domain, was detected in normal BMP4-treated hiPSCs/hESCs and in embryoid bodies. Finally, using a phosphorodiamidate morpholino oligomer (PMO) targeting the DMD exon 53, we demonstrated the feasibility of exon skipping validation with this BMP4-inducible hiPSCs model. Conclusions In this study, the use of hiPSCs to analyze early phases of human development in normal and DMD contexts has led to the discovery of an embryonic 412 kDa dystrophin isoform. Deciphering the regulation process(es) and the function(s) associated to this new isoform can contribute to a better understanding of the DMD physiopathology and potential developmental defects. Moreover, the simple and robust BMP4-inducible model highlighted here, providing large amount of a long DMD transcript and the corresponding protein in only 3 days, is already well-adapted to high-throughput and high-content screening approaches. Therefore, availability of this powerful cell platform can accelerate the development, validation and improvement of DMD genetic therapies. Electronic supplementary material The online version of this article (doi:10.1186/s13395-015-0062-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jérôme Polentes
- I-STEM, CECS, Génopôle-Campus 1, 5 rue Henri Desbruères, 91030 Evry, Cedex France
| | - Philippe-Emmanuel Mangeot
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France ; Inserm, U1111, Lyon, France ; CNRS, UMR5308, Lyon, France ; Ecole Normale Supérieure de Lyon, Lyon, France ; Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
| | | | - Juliette Nectoux
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Nathalie Deburgrave
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Patrick Nusbaum
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - France Leturcq
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Linda Popplewell
- School of Biological Sciences, Royal Holloway-University of London, Surrey, TW20 0EX UK
| | - George Dickson
- School of Biological Sciences, Royal Holloway-University of London, Surrey, TW20 0EX UK
| | - Nicolas Wein
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205 USA
| | - Kevin M Flanigan
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205 USA
| | - Marc Peschanski
- UEVE U861, 91030 Evry, France ; Inserm U861, 91030 Evry, France
| | - Jamel Chelly
- IGBMC-CNRS UMR7104/Inserm U964, 67404 Illkirch, Cedex France
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Chu L, Li J, Liu Y, Cheng CHK. Gonadotropin Signaling in Zebrafish Ovary and Testis Development: Insights From Gene Knockout Study. Mol Endocrinol 2015; 29:1743-58. [PMID: 26452104 DOI: 10.1210/me.2015-1126] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Using the transcription activator-like effectors nucleases-mediated gene knockout technology, we have previously demonstrated that LH signaling is required for oocyte maturation and ovulation but is dispensable for testis development in zebrafish. Here, we have further established the fshb and fshr knockout zebrafish lines. In females, fshb mutant is subfertile, whereas fshr mutant is infertile. Folliculogenesis is partially affected in the fshb mutant but is completely arrested at the primary growth stage in the fshr mutant. In males, fshb and fshr mutant are fertile. The fertilization rate and histological structure of the testis is not affected. However, double knockout of fshb;lhb or fshr;lhr leads to all infertile male offspring. The key steroid hormones and steroidogenic genes are dramatically decreased in double knockout mutant (fshb;lhb and fshr;lhr) but not in single knockout mutant (fshb, lhb, fshr, and lhr) males. Furthermore, we have also demonstrated the constitutive activities of both FSH receptor (FSHR) and LH receptor in zebrafish and the compensatory role of LH by cross-reacting with FSHR in the fshb;lhr double mutant, thus explaining the phenotypic discrepancy observed among the ligand/receptor mutant lines. Taken together, our data established the following models on the roles of gonadotropin signaling in zebrafish gonad development. In females, FSH signaling is mainly responsible for promoting follicular growth, whereas LH signaling is mainly responsible for stimulating oocyte maturation and ovulation. In males, the functions of FSH and LH signaling overlap, and only disruption of both FSH and LH signaling could lead to the infertile phenotype. In the absence of FSH, LH could play a compensatory role by cross-reacting with FSHR in both male and female.
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Affiliation(s)
- Lianhe Chu
- School of Biomedical Sciences (L.C., J.L., Y.L., C.H.K.C.), The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; and The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; and College of Life Sciences (J.L.), Northwest Normal University, Lanzhou 730070, China
| | - Jianzhen Li
- School of Biomedical Sciences (L.C., J.L., Y.L., C.H.K.C.), The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; and The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; and College of Life Sciences (J.L.), Northwest Normal University, Lanzhou 730070, China
| | - Yun Liu
- School of Biomedical Sciences (L.C., J.L., Y.L., C.H.K.C.), The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; and The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; and College of Life Sciences (J.L.), Northwest Normal University, Lanzhou 730070, China
| | - Christopher H K Cheng
- School of Biomedical Sciences (L.C., J.L., Y.L., C.H.K.C.), The Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; and The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China; and College of Life Sciences (J.L.), Northwest Normal University, Lanzhou 730070, China
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Moey C, Topper S, Karn M, Johnson AK, Das S, Vidaurre J, Shoubridge C. Reinitiation of mRNA translation in a patient with X-linked infantile spasms with a protein-truncating variant in ARX. Eur J Hum Genet 2015; 24:681-9. [PMID: 26306640 DOI: 10.1038/ejhg.2015.176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/30/2015] [Accepted: 07/03/2015] [Indexed: 12/30/2022] Open
Abstract
Mutations in the Aristaless-related homeobox gene (ARX) lead to a range of X-linked intellectual disability phenotypes, with truncating variants generally resulting in severe X-linked lissencephaly with ambiguous genitalia (XLAG), and polyalanine expansions and missense variants resulting in infantile spasms. We report two male patients with early-onset infantile spasms in whom a novel c.34G>T (p.(E12*)) variant was identified in the ARX gene. A similar variant c.81C>G (p.(Y27*)), has previously been described in two affected cousins with early-onset infantile spasms, leading to reinitiation of ARX mRNA translation resulting in an N-terminal truncated protein. We show that the novel c.34G>T (p.(E12*)) variant also reinitiated mRNA translation at the next AUG codon (c.121-123 (p.M41)), producing the same N-terminally truncated protein. The production of both of these truncated proteins was demonstrated to be at markedly reduced levels using in vitro cell assays. Using luciferase reporter assays, we demonstrate that transcriptional repression capacity of ARX was diminished by both the loss of the N-terminal corepressor octapeptide domain, as a consequence of truncation, and the marked reduction in mutant protein expression. Our study indicates that premature termination mutations very early in ARX lead to reinitiation of translation to produce N-terminally truncated protein at markedly reduced levels of expression. We conclude that even low levels of N-terminally truncated ARX is sufficient to improve the patient's phenotype compared with the severe phenotype of XLAG that includes malformations of the brain and genitalia normally seen in complete loss-of-function mutations in ARX.
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Affiliation(s)
- Ching Moey
- Department of Paediatrics, School of Peadiatrics and Reproductive Health, University of Adelaide, Adelaide, SA, Australia.,Robinson Research Institute, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Scott Topper
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Mary Karn
- Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Jorge Vidaurre
- Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Cheryl Shoubridge
- Department of Paediatrics, School of Peadiatrics and Reproductive Health, University of Adelaide, Adelaide, SA, Australia.,Robinson Research Institute, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia
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DMD Mutations in 576 Dystrophinopathy Families: A Step Forward in Genotype-Phenotype Correlations. PLoS One 2015; 10:e0135189. [PMID: 26284620 PMCID: PMC4540588 DOI: 10.1371/journal.pone.0135189] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/17/2015] [Indexed: 11/19/2022] Open
Abstract
Recent advances in molecular therapies for Duchenne muscular dystrophy (DMD) require precise genetic diagnosis because most therapeutic strategies are mutation-specific. To understand more about the genotype-phenotype correlations of the DMD gene we performed a comprehensive analysis of the DMD mutational spectrum in a large series of families. Here we provide the clinical, pathological and genetic features of 576 dystrophinopathy patients. DMD gene analysis was performed using the MLPA technique and whole gene sequencing in blood DNA and muscle cDNA. The impact of the DNA variants on mRNA splicing and protein functionality was evaluated by in silico analysis using computational algorithms. DMD mutations were detected in 576 unrelated dystrophinopathy families by combining the analysis of exonic copies and the analysis of small mutations. We found that 471 of these mutations were large intragenic rearrangements. Of these, 406 (70.5%) were exonic deletions, 64 (11.1%) were exonic duplications, and one was a deletion/duplication complex rearrangement (0.2%). Small mutations were identified in 105 cases (18.2%), most being nonsense/frameshift types (75.2%). Mutations in splice sites, however, were relatively frequent (20%). In total, 276 mutations were identified, 85 of which have not been previously described. The diagnostic algorithm used proved to be accurate for the molecular diagnosis of dystrophinopathies. The reading frame rule was fulfilled in 90.4% of DMD patients and in 82.4% of Becker muscular dystrophy patients (BMD), with significant differences between the mutation types. We found that 58% of DMD patients would be included in single exon-exon skipping trials, 63% from strategies directed against multiexon-skipping exons 45 to 55, and 14% from PTC therapy. A detailed analysis of missense mutations provided valuable information about their impact on the protein structure.
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38
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Vulin A, Wein N, Simmons TR, Rutherford AM, Findlay AR, Yurkoski JA, Kaminoh Y, Flanigan KM. The first exon duplication mouse model of Duchenne muscular dystrophy: A tool for therapeutic development. Neuromuscul Disord 2015; 25:827-34. [PMID: 26365037 DOI: 10.1016/j.nmd.2015.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 12/27/2022]
Abstract
Exon duplication mutations account for up to 11% of all cases of Duchenne muscular dystrophy (DMD), and a duplication of exon 2 is the most common duplication in patients. For use as a platform for testing of duplication-specific therapies, we developed a mouse model that carries a Dmd exon 2 duplication. By using homologous recombination we duplicated exon 2 within intron 2 at a location consistent with a human duplication hotspot. mRNA analysis confirms the inclusion of a duplicated exon 2 in mouse muscle. Dystrophin expression is essentially absent by immunofluorescent and immunoblot analysis, although some muscle specimens show very low-level trace dystrophin expression. Phenotypically, the mouse shows similarities to mdx, the standard laboratory model of DMD. In skeletal muscle, areas of necrosis and phagocytosis are seen at 3 weeks, with central nucleation prominent by four weeks, recapitulating the "crisis" period in mdx. Marked diaphragm fibrosis is noted by 6 months, and remains unchanged at 12 months. Our results show that the Dup2 mouse is both pathologically (in degree and distribution) and physiologically similar to mdx. As it recapitulates the most common single exon duplication found in DMD patients, this new model will be a useful tool to assess the potential of duplicated exon skipping.
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Affiliation(s)
- Adeline Vulin
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Nicolas Wein
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Tabatha R Simmons
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Andrea M Rutherford
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Andrew R Findlay
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Jacqueline A Yurkoski
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Yuuki Kaminoh
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Kevin M Flanigan
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA; Department of Neurology, The Ohio State University, Columbus, OH, USA.
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39
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Brookes E, Laurent B, Õunap K, Carroll R, Moeschler JB, Field M, Schwartz CE, Gecz J, Shi Y. Mutations in the intellectual disability gene KDM5C reduce protein stability and demethylase activity. Hum Mol Genet 2015; 24:2861-72. [PMID: 25666439 DOI: 10.1093/hmg/ddv046] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/02/2015] [Indexed: 01/03/2023] Open
Abstract
Mutations in KDM5C are an important cause of X-linked intellectual disability in males. KDM5C encodes a histone demethylase, suggesting that alterations in chromatin landscape may contribute to disease. We used primary patient cells and biochemical approaches to investigate the effects of patient mutations on KDM5C expression, stability and catalytic activity. We report and characterize a novel nonsense mutation, c.3223delG (p.V1075Yfs*2), which leads to loss of KDM5C protein. We also characterize two KDM5C missense mutations, c.1439C>T (p.P480L) and c.1204G>T (p.D402Y) that are compatible with protein production, but compromise stability and enzymatic activity. Finally, we demonstrate that a c.2T>C mutation in the translation initiation codon of KDM5C results in translation re-start and production of a N-terminally truncated protein (p.M1_E165del) that is unstable and lacks detectable demethylase activity. Patient fibroblasts do not show global changes in histone methylation but we identify several up-regulated genes, suggesting local changes in chromatin conformation and gene expression. This thorough examination of KDM5C patient mutations demonstrates the utility of examining the molecular consequences of patient mutations on several levels, ranging from enzyme production to catalytic activity, when assessing the functional outcomes of intellectual disability mutations.
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Affiliation(s)
- Emily Brookes
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA, Division of Newborn Medicine, Boston Children's Hospital, MA 02115, USA
| | - Benoit Laurent
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA, Division of Newborn Medicine, Boston Children's Hospital, MA 02115, USA
| | - Katrin Õunap
- Department of Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia, Department of Pediatrics, University of Tartu, Tartu, Estonia
| | - Renee Carroll
- School of Paediatrics and Reproductive Health and Robinson Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - John B Moeschler
- Department of Pediatrics, Geisel School of Medicine, Lebanon, NH 03756, USA
| | | | - Charles E Schwartz
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Jozef Gecz
- School of Paediatrics and Reproductive Health and Robinson Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA, Division of Newborn Medicine, Boston Children's Hospital, MA 02115, USA,
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40
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Lamandé SR, North KN. Activating internal ribosome entry to treat Duchenne muscular dystrophy. Nat Med 2014; 20:987-8. [PMID: 25198047 DOI: 10.1038/nm.3677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mutations in the DMD gene, encoding dystrophin, cause the most common forms of muscular dystrophy. A new study shows that forcing translation of DMD from an internal ribosome entry site can alleviate Duchenne muscular dystrophy symptoms in a mouse model.
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Affiliation(s)
- Shireen R Lamandé
- Murdoch Childrens Research Institute and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Kathryn N North
- Murdoch Childrens Research Institute and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
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41
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Wein N, Vulin A, Falzarano MS, Szigyarto CAK, Maiti B, Findlay A, Heller KN, Uhlén M, Bakthavachalu B, Messina S, Vita G, Passarelli C, Brioschi S, Bovolenta M, Neri M, Gualandi F, Wilton SD, Rodino-Klapac LR, Yang L, Dunn DM, Schoenberg DR, Weiss RB, Howard MT, Ferlini A, Flanigan KM. Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. Nat Med 2014; 20:992-1000. [PMID: 25108525 PMCID: PMC4165597 DOI: 10.1038/nm.3628] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/05/2014] [Indexed: 12/26/2022]
Abstract
Most mutations that truncate the reading frame of the DMD gene cause loss of dystrophin expression and lead to Duchenne muscular dystrophy. However, amelioration of disease severity can result from alternate translation initiation beginning in DMD exon 6 that leads to expression of a highly functional N-truncated dystrophin. This novel isoform results from usage of an internal ribosome entry site (IRES) within exon 5 that is glucocorticoid-inducible. IRES activity is confirmed in patient muscle by both peptide sequencing and ribosome profiling. Generation of a truncated reading frame upstream of the IRES by exon skipping leads to synthesis of a functional N-truncated isoform in both patient-derived cell lines and in a new DMD mouse model, where expression protects muscle from contraction-induced injury and corrects muscle force to the same level as control mice. These results support a novel therapeutic approach for patients with mutations within the 5’ exons of DMD.
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Affiliation(s)
- Nicolas Wein
- 1] The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA. [2]
| | - Adeline Vulin
- 1] The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA. [2]
| | - Maria S Falzarano
- Section of Microbiology and Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Christina Al-Khalili Szigyarto
- Department of Proteomics and Nanobiotechnology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Baijayanta Maiti
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew Findlay
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Kristin N Heller
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Mathias Uhlén
- Department of Proteomics and Nanobiotechnology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Baskar Bakthavachalu
- 1] Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA. [2] Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sonia Messina
- Department of Neuroscience, University of Messina and Centro Clinico Nemo Sud, Messina, Italy
| | - Giuseppe Vita
- Department of Neuroscience, University of Messina and Centro Clinico Nemo Sud, Messina, Italy
| | | | | | | | | | - Francesca Gualandi
- Section of Microbiology and Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Steve D Wilton
- Centre for Comparative Genomics, Murdoch University, Perth, Western Australia, Australia
| | - Louise R Rodino-Klapac
- 1] The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA. [2] Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Lin Yang
- Division of Biomedical Informatics, Department of Computer Science, University of Kentucky Lexington, Kentucky, USA
| | - Diane M Dunn
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Daniel R Schoenberg
- 1] Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA. [2] Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Robert B Weiss
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Michael T Howard
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Alessandra Ferlini
- Section of Microbiology and Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Kevin M Flanigan
- 1] The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA. [2] Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA. [3] Department of Neurology, The Ohio State University, Columbus, Ohio, USA
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López-Hernández LB, Gómez-Díaz B, Bahena-Martínez E, Neri-Gómez T, Camacho-Molina A, Ruano-Calderón LA, García S, Coral-Vázquez RM. A novel noncontiguous duplication in the DMD gene escapes the 'reading-frame rule'. J Genet 2014; 93:225-9. [PMID: 24840845 DOI: 10.1007/s12041-014-0345-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Luz Berenice López-Hernández
- Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Subdireccion de Ensenanza e Investigacion, Centro Medico Nacional 20 de Noviembre, Mexico, C. P. 03100, D.F., Mexico.
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Targeted exon skipping to correct exon duplications in the dystrophin gene. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e155. [PMID: 24643206 PMCID: PMC3982197 DOI: 10.1038/mtna.2014.8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/24/2014] [Indexed: 01/16/2023]
Abstract
Duchenne muscular dystrophy is a severe muscle-wasting disease caused by mutations in the dystrophin gene that ablate functional protein expression. Although exonic deletions are the most common Duchenne muscular dystrophy lesion, duplications account for 10-15% of reported disease-causing mutations, and exon 2 is the most commonly duplicated exon. Here, we describe the in vitro evaluation of phosphorodiamidate morpholino oligomers coupled to a cell-penetrating peptide and 2'-O-methyl phosphorothioate oligonucleotides, using three distinct strategies to reframe the dystrophin transcript in patient cells carrying an exon 2 duplication. Differences in exon-skipping efficiencies in vitro were observed between oligomer analogues of the same sequence, with the phosphorodiamidate morpholino oligomer coupled to a cell-penetrating peptide proving the most effective. Differences in exon 2 excision efficiency between normal and exon 2 duplication cells, were apparent, indicating that exon context influences oligomer-induced splice switching. Skipping of a single copy of exon 2 was induced in the cells carrying an exon 2 duplication, the simplest strategy to restore the reading frame and generate a normal dystrophin transcript. In contrast, multiexon skipping of exons 2-7 to generate a Becker muscular dystrophy-like dystrophin transcript was more challenging and could only be induced efficiently with the phosphorodiamidate morpholino oligomer chemistry.
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Brinkmeyer-Langford C, Kornegay JN. Comparative Genomics of X-linked Muscular Dystrophies: The Golden Retriever Model. Curr Genomics 2014; 14:330-42. [PMID: 24403852 PMCID: PMC3763684 DOI: 10.2174/13892029113149990004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/16/2013] [Accepted: 07/19/2013] [Indexed: 12/30/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a devastating disease that dramatically decreases the lifespan and abilities of affected young people. The primary molecular cause of the disease is the absence of functional dystrophin protein, which is critical to proper muscle function. Those with DMD vary in disease presentation and dystrophin mutation; the same causal mutation may be associated with drastically different levels of disease severity. Also contributing to this variation are the influences of additional modifying genes and/or changes in functional elements governing such modifiers. This genetic heterogeneity complicates the efficacy of treatment methods and to date medical interventions are limited to treating symptoms. Animal models of DMD have been instrumental in teasing out the intricacies of DMD disease and hold great promise for advancing knowledge of its variable presentation and treatment. This review addresses the utility of comparative genomics in elucidating the complex background behind phenotypic variation in a canine model of DMD, Golden Retriever muscular dystrophy (GRMD). This knowledge can be exploited in the development of improved, more personalized treatments for DMD patients, such as therapies that can be tailor-matched to the disease course and genomic background of individual patients.
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Affiliation(s)
- Candice Brinkmeyer-Langford
- Texas A&M University College of Veterinary Medicine, Dept. of Veterinary Integrative Biosciences - Mailstop 4458, College Station, Texas, U.S.A. 77843-4458
| | - Joe N Kornegay
- Texas A&M University College of Veterinary Medicine, Dept. of Veterinary Integrative Biosciences - Mailstop 4458, College Station, Texas, U.S.A. 77843-4458
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45
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Juan-Mateu J, González-Quereda L, Rodríguez MJ, Verdura E, Lázaro K, Jou C, Nascimento A, Jiménez-Mallebrera C, Colomer J, Monges S, Lubieniecki F, Foncuberta ME, Pascual-Pascual SI, Molano J, Baiget M, Gallano P. Interplay between DMD point mutations and splicing signals in Dystrophinopathy phenotypes. PLoS One 2013; 8:e59916. [PMID: 23536893 PMCID: PMC3607557 DOI: 10.1371/journal.pone.0059916] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/19/2013] [Indexed: 12/12/2022] Open
Abstract
DMD nonsense and frameshift mutations lead to severe Duchenne muscular dystrophy while in-frame mutations lead to milder Becker muscular dystrophy. Exceptions are found in 10% of cases and the production of alternatively spliced transcripts is considered a key modifier of disease severity. Several exonic mutations have been shown to induce exon-skipping, while splice site mutations result in exon-skipping or activation of cryptic splice sites. However, factors determining the splicing pathway are still unclear. Point mutations provide valuable information regarding the regulation of pre-mRNA splicing and elements defining exon identity in the DMD gene. Here we provide a comprehensive analysis of 98 point mutations related to clinical phenotype and their effect on muscle mRNA and dystrophin expression. Aberrant splicing was found in 27 mutations due to alteration of splice sites or splicing regulatory elements. Bioinformatics analysis was performed to test the ability of the available algorithms to predict consequences on mRNA and to investigate the major factors that determine the splicing pathway in mutations affecting splicing signals. Our findings suggest that the splicing pathway is highly dependent on the interplay between splice site strength and density of regulatory elements.
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Affiliation(s)
- Jonàs Juan-Mateu
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Lidia González-Quereda
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Maria José Rodríguez
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Edgard Verdura
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Kira Lázaro
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Cristina Jou
- Servei d'Anatomia Patològica Hospital Sant Joan de Déu, Barcelona, Spain
| | - Andrés Nascimento
- Unitat de Patologia Neuromuscular, Servei de Neurologia, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Jaume Colomer
- Unitat de Patologia Neuromuscular, Servei de Neurologia, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Soledad Monges
- Servicio de Neuropediatría, Hospital Nacional Pediátrico Garrahan, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Servicio de Patología, Hospital Nacional Pediátrico Garrahan, Buenos Aires, Argentina
| | | | | | - Jesús Molano
- Unidad de Genética Molecular and CIBERER U753, Hospital Universitario Materno Infantil La Paz, Madrid, Spain
| | - Montserrat Baiget
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Pia Gallano
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
- * E-mail:
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46
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Cai X, Jin S, Liu X, Fan L, Lu Q, Wang J, Shen W, Gong S, Qiu L, Xiang D. Molecular genetic analysis of ABO blood group variations reveals 29 novel ABO subgroup alleles. Transfusion 2013; 53:2910-6. [PMID: 23521133 DOI: 10.1111/trf.12168] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 01/02/2013] [Accepted: 01/23/2013] [Indexed: 11/28/2022]
Abstract
BACKGROUND Identifying genetic variants of the ABO gene may reveal new biologic mechanisms underlying variant phenotypes of the ABO blood group. We report the molecular genetic analysis of 322 apparently unrelated ABO subgroup individuals in an estimated 2.1 million donors. STUDY DESIGN AND METHODS We performed phenotype investigations by serology studies, analyzed the DNA sequence of the ABO gene by direct sequencing or sequencing after cloning, and evaluated promoter activity by reporter assays. RESULTS In 62 rare ABO alleles, we identified 29 novel ABO subgroup alleles in 43 apparently unrelated subgroup individuals and their four available pedigrees. Of these alleles, one was a deletion-mutation allele, four were hybrid alleles, and 24 were point-mutation alleles. Most of the point mutations were detected in Exons 6 to 7, while several others were also detected in Exons 1 to 5 or splicing regions. One ABO promoter mutation, -35 to -18 del, was found and verified to reduce promoter activity, as determined by dual luciferase assays. Two mutations, 7G>T and 52C>T, carrying the premature terminal codons E3X and R18X in the 5'-region, were found to be associated with the very weak ABO subgroups "Ael" and "Bel." CONCLUSION Twenty-nine ABO subgroup alleles were newly linked to different kinds of ABO variations. We provide the first evidence that promoter abnormality is involved in the formation of weak ABO phenotypes. We also described the first naturally occurring ABO alleles with premature terminal codons in the 5'-region that led to Ael and Bel phenotypes.
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Affiliation(s)
- Xiaohong Cai
- Blood Group Reference Laboratory, Shanghai Institute of Blood Transfusion, Shanghai Blood Center; Blood Transfusion Department, Ruijin Hospital, Medical School of Shanghai Jiao Tong University, Shanghai, China; Blood Group Laboratory, Tanggu Blood Center, Tianjin, China
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Flanigan KM, Wein N, Gurvich OL, Howard MT, Weiss RB. Becker muscular dystrophy with widespread muscle hypertrophy and a non-sense mutation of exon 2. Neuromuscul Disord 2013; 23:192. [PMID: 23369578 DOI: 10.1016/j.nmd.2012.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 11/23/2012] [Indexed: 11/26/2022]
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48
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Response. Neuromuscul Disord 2013; 23:193. [PMID: 23357682 DOI: 10.1016/j.nmd.2012.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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49
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The medical genetics of dystrophinopathies: Molecular genetic diagnosis and its impact on clinical practice. Neuromuscul Disord 2013; 23:4-14. [DOI: 10.1016/j.nmd.2012.09.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 08/23/2012] [Accepted: 09/04/2012] [Indexed: 01/01/2023]
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50
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Witting N, Duno M, Vissing J. Becker muscular dystrophy with widespread muscle hypertrophy and a non-sense mutation of exon 2. Neuromuscul Disord 2012; 23:25-8. [PMID: 22939275 DOI: 10.1016/j.nmd.2012.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 06/21/2012] [Accepted: 07/09/2012] [Indexed: 10/28/2022]
Abstract
Becker muscular dystrophy features progressive proximal weakness, wasting and often focal hypertrophy. We present a patient with pain and cramps from adolescence. Widespread muscle hypertrophy, preserved muscle strength and a 10-20-fold raised CPK were noted. Muscle biopsy was dystrophic, and Western blot showed a 95% reduction of dystrophin levels. Genetic analyses revealed a non-sense mutation in exon 2 of the dystrophin gene. This mutation is predicted to result in a Duchenne phenotype, but resulted in a mild Becker muscular dystrophy with widespread muscle hypertrophy. We suggest that this unusual phenotype is caused by translation re-initiation downstream from the mutation site.
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Affiliation(s)
- N Witting
- Neuromuscular Research Unit and Department of Neurology 2082, University of Copenhagen, Rigshospitalet, Blegdamsvej, DK-2100 Copenhagen, Denmark.
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