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Dwianingsih EK, Iskandar K, Hapsara S, Ping Liu C, Malueka RG, Gunadi, Matsuo M, Lai PS. Mutation spectrum analysis of DMD gene in Indonesian Duchenne and Becker muscular dystrophy patients. F1000Res 2023; 11:148. [PMID: 38009102 PMCID: PMC10668572 DOI: 10.12688/f1000research.73476.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 11/28/2023] Open
Abstract
Background Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are allelic disorders caused by mutations in the DMD gene. The full mutation spectrum of the DMD gene in Indonesian patients is currently unknown. Mutation-specific therapies are currently being developed, such as exon skipping or stop codon read-through therapy. This study was conducted with the aim of identifying the mutation spectrum of the DMD gene in Indonesia to guide future development and application of feasible therapeutic strategies. Methods This study is a cross sectional study that enrolled 43 male patients with a clinical suspicion of DMD or BMD. Multiplex ligation-dependent probe amplification (MLPA) reaction was performed to screen for the common mutations in the DMD gene. Results Out of 43 subjects, deletions accounted for 69.77% (n=30) cases, while duplications were found in 11.63% (n=5) cases. One novel duplication spanning exons 2 to 62 was identified. Deletion mutations clustered around the distal (66.67%) and proximal (26.67%) hot spot regions of the DMD gene while duplication mutations were observed solely at the proximal region. Two false positive cases of single exon deletion detected through MLPA were attributed to sequence mutations affecting primer ligation sites, confirming the need to validate all single exon deletions when using this screening method. Analysis of available maternal DNA samples showed that the rate of de novo mutations (48.15%) appears higher than expected in this population. Out of 31 patients who were classified as DMD based on clinical and genotype characterizations, 60.47% (n=26) of cases were suitable for exon skipping therapy. Conclusion This is the first comprehensive study showing the feasibility of implementing the MLPA method for routine screening of DMD patients in Indonesia. This is also the first study showing the potential applicability of exon skipping therapy in the majority of DMD cases in the country.
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Affiliation(s)
- Ery Kus Dwianingsih
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Department of Anatomical Pathology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Kristy Iskandar
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Academic Hospital, Universitas Gadjah Mada, Yogyakarta, 55291, Indonesia
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Sunartini Hapsara
- Academic Hospital, Universitas Gadjah Mada, Yogyakarta, 55291, Indonesia
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Chun Ping Liu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Rusdy Ghazali Malueka
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Department of Neurology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Gunadi
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobegakuin University, Kobe, 651-2180, Japan
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
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Viggiano E, Picillo E, Passamano L, Onore ME, Piluso G, Scutifero M, Torella A, Nigro V, Politano L. Spectrum of Genetic Variants in the Dystrophin Gene: A Single Centre Retrospective Analysis of 750 Duchenne and Becker Patients from Southern Italy. Genes (Basel) 2023; 14:214. [PMID: 36672955 PMCID: PMC9859256 DOI: 10.3390/genes14010214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/29/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Dystrophinopathies are X-linked recessive muscle disorders caused by mutations in the dystrophin (DMD) gene that include deletions, duplications, and point mutations. Correct diagnosis is important for providing adequate patient care and family planning, especially at this time when mutation-specific therapies are available. We report a large single-centre study on the spectrum of DMD gene variants observed in 750 patients analyzed for suspected Duchenne (DMD) or Becker (BMD) muscular dystrophy, over the past 30 years, at the Cardiomyology and Medical Genetics of the University of Campania. We found 534 (71.21%) large deletions, 73 (9.73%) large duplications, and 112 (14.93%) point mutations, of which 44 (5.9%) were small ins/del causing frame-shifts, 57 (7.6%) nonsense mutations, 8 (1.1%) splice site and 3 (0.4%) intronic mutations, and 31 (4.13%) non mutations. Moreover, we report the prevalence of the different types of mutations in patients with DMD and BMD according to their decade of birth, from 1930 to 2020, and correlate the data to the different techniques used over the years. In the most recent decades, we observed an apparent increase in the prevalence of point mutations, probably due to the use of Next-Generation Sequencing (NGS). In conclusion, in southern Italy, deletions are the most frequent variation observed in DMD and BMD patients followed by point mutations and duplications, as elsewhere in the world. NGS was useful to identify point mutations in cases of strong suspicion of DMD/BMD negative on deletions/duplications analyses. In the era of personalized medicine and availability of new causative therapies, a collective effort is necessary to enable DMD and BMD patients to have timely genetic diagnoses and avoid late implementation of standard of care and late initiation of appropriate treatment.
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Affiliation(s)
- Emanuela Viggiano
- Department of Prevention, Hygiene and Public Health Service, ASL Roma 2, 00157 Rome, Italy
| | - Esther Picillo
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Luigia Passamano
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Maria Elena Onore
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Giulio Piluso
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Marianna Scutifero
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Annalaura Torella
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Vincenzo Nigro
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Luisa Politano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
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Ulm EA, Nagaraj CB, Tian C, Smolarek TA. Identification of Biallelic dystrophin gene variants during maternal carrier testing for Becker muscular dystrophy and review of the DMD exon 49-51 deletion phenotype. Mol Genet Genomic Med 2022; 11:e2088. [PMID: 36424846 PMCID: PMC9834199 DOI: 10.1002/mgg3.2088] [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: 08/15/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Dystrophinopathies are X-linked recessive conditions caused by pathogenic variants in the dystrophin (DMD) gene. In a family that included two boys with Becker muscular dystrophy (BMD) due to a DMD deletion of exons 45-47, maternal carrier testing unexpectedly identified biallelic DMD deletions of exons 45-47 and 49-51. METHODS The patient's mild phenotype in the setting of biallelic DMD variants prompted further investigation of the exon 49-51 deletion in particular, via literature review and retrospective chart review of patients who have been evaluated in our institution's comprehensive neuromuscular center and/or diagnosed in our clinical genetic testing laboratory. RESULTS To our knowledge, this is only the fifth case of confirmed biallelic DMD variants in a female. In males, the DMD exon 49-51 deletion appears to result in a mild BMD phenotype with low or normal creatine kinase levels. This deletion comprised 19% (4/21) of dystrophinopathies diagnosed by chromosomal microarray (CMA) in males during the past ten years in our clinical laboratory. Most individuals identified by chart review were diagnosed through CMA, despite the fact that microarray was genome-wide and not DMD-specific. This case raised important genetic counseling issues. CONCLUSION The DMD exon 49-51 deletion appears to cause a variable but generally mild BMD phenotype. Its relatively frequent detection by CMA suggests it may be underdiagnosed.
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Affiliation(s)
- Elizabeth A. Ulm
- Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Chinmayee B. Nagaraj
- Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA,Division of NeurologyCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Cuixia Tian
- Division of NeurologyCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA,Department of PediatricsUniversity of Cincinnati School of MedicineCincinnatiOhioUSA
| | - Teresa A. Smolarek
- Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA,Department of PediatricsUniversity of Cincinnati School of MedicineCincinnatiOhioUSA
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Tomar S, Moorthy V, Sethi R, Chai J, Low PS, Hong STK, Lai PS. Mutational spectrum of dystrophinopathies in Singapore: Insights for genetic diagnosis and precision therapy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:230-244. [DOI: 10.1002/ajmg.c.31704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Vikaesh Moorthy
- Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Josiah Chai
- Department of Neurology, National Neuroscience Institute Singapore
| | - Poh Sim Low
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Stacey Tay Kiat Hong
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
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Aartsma-Rus A, Hegde M, Ben-Omran T, Buccella F, Ferlini A, Gallano P, Howell RR, Leturcq F, Martin AS, Potulska-Chromik A, Saute JA, Schmidt WM, Sejersen T, Tuffery-Giraud S, Uyguner ZO, Witcomb LA, Yau S, Nelson SF. Evidence-Based Consensus and Systematic Review on Reducing the Time to Diagnosis of Duchenne Muscular Dystrophy. J Pediatr 2019; 204:305-313.e14. [PMID: 30579468 DOI: 10.1016/j.jpeds.2018.10.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/27/2018] [Accepted: 10/24/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine/School of Biological Sciences, Georgia Institute of Technology/Perkin Elmer Genetics, Atlanta, GA
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | | | | | - Pia Gallano
- U705 CIBERER, Servei de Genetica, Hospital de Sant Pau, Barcelona, Spain
| | | | - France Leturcq
- Department of Genetics and Molecular Biology, Hospitalier Universitaire Paris Centre, Cochin Hospital, Paris, France
| | - Ann S Martin
- Parent Project Muscular Dystrophy, Hackensack, NJ
| | | | - Jonas A Saute
- Medical Genetics and Neurology Services, Hospital de Clinicas de Porto Alegre/Internal Medicine Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Wolfgang M Schmidt
- Neuromuscular Research Department, Medical University of Vienna, Vienna, Austria
| | - Thomas Sejersen
- Department of Women's and Children's Health, Karolinska Institute/Astrid Lindgrens Barnsjukhus, Karolinska University Hospital, Stockholm, Sweden
| | - Sylvie Tuffery-Giraud
- Laboratory of Rare Genetic Diseases (LGMR), University of Montpellier, Montpellier, France
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | | | - Shu Yau
- Viapath Analytics, Guy's Hospital, London, United Kingdom
| | - Stanley F Nelson
- Department of Human Genetics, University of California, Los Angeles, CA.
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Liang Y, Chen S, Zhu J, Zhou X, Yang C, Yao L, Zhang C. Dystrophin hydrophobic regions in the pathogenesis of Duchenne and Becker muscular dystrophies. Bosn J Basic Med Sci 2015; 15:42-9. [PMID: 26042512 DOI: 10.17305/bjbms.2015.300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 01/16/2023] Open
Abstract
The aim of our study was to determine the role of dystrophin hydrophobic regions in the pathogenesis of Duchenne (DMD) and Becker (BMD) muscular dystrophies, by the Kyte-Doolittle scale mean hydrophobicity profile and 3D molecular models. A total of 1038 cases diagnosed with DMD or BMD with the in-frame mutation were collected in our hospital and the Leiden DMD information database in the period 2002-2013. Correlation between clinical types and genotypes were determined on the basis of these two sources. In addition, the Kyte-Doolittle scale mean hydrophobicity of dystrophin was analyzed using BioEdit software and the models of the hydrophobic domains of dystrophin were constructed. The presence of four hydrophobic regions is confirmed. They include the calponin homology CH2 domain on the actin-binding domain (ABD), spectrin-type repeat 16, hinge III and the EF Hand domain. The severe symptoms of DMD usually develop as a result of the mutational disruption in the hydrophobic regions I, II and IV of dystrophin - those that bind associated proteins of the dystrophin-glycoprotein complex (DGC). On the other hand, when the hydrophobic region III is deleted, the connection of the ordered repeat domains of the central rod domain remains intact, resulting in the less severe clinical presentation. We conclude that mutational changes in the structure of hydrophobic regions of dystrophin play an important role in the pathogenesis of DMD.
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Affiliation(s)
- Yingyin Liang
- Department of Neurology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province.
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Comparison of mutation profiles in the Duchenne muscular dystrophy gene among populations: implications for potential molecular therapies. Int J Mol Sci 2015; 16:5334-46. [PMID: 25761239 PMCID: PMC4394478 DOI: 10.3390/ijms16035334] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/17/2015] [Accepted: 02/27/2015] [Indexed: 11/16/2022] Open
Abstract
Novel therapeutic approaches are emerging to restore dystrophin function in Duchenne Muscular Dystrophy (DMD), a severe neuromuscular disease characterized by progressive muscle wasting and weakness. Some of the molecular therapies, such as exon skipping, stop codon read-through and internal ribosome entry site-mediated translation rely on the type and location of mutations. Hence, their potential applicability worldwide depends on mutation frequencies within populations. In view of this, we compared the mutation profiles of the populations represented in the DMD Leiden Open-source Variation Database with original data from Mexican patients (n = 162) with clinical diagnosis of the disease. Our data confirm that applicability of exon 51 is high in most populations, but also show that differences in theoretical applicability of exon skipping may exist among populations; Mexico has the highest frequency of potential candidates for the skipping of exons 44 and 46, which is different from other populations (p < 0.001). To our knowledge, this is the first comprehensive comparison of theoretical applicability of exon skipping targets among specific populations.
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