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Ma Y, Gui C, Shi M, Wei L, He J, Xie B, Zheng H, Lei X, Wei X, Cheng Z, Zhou X, Chen S, Luo J, Huang Y, Gui B. The cryptic complex rearrangements involving the DMD gene: etiologic clues about phenotypical differences revealed by optical genome mapping. Hum Genomics 2024; 18:103. [PMID: 39285482 PMCID: PMC11406873 DOI: 10.1186/s40246-024-00653-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/05/2024] [Indexed: 09/19/2024] Open
Abstract
BACKGROUND Deletion or duplication in the DMD gene is one of the most common causes of Duchenne and Becker muscular dystrophy (DMD/BMD). However, the pathogenicity of complex rearrangements involving DMD, especially segmental duplications with unknown breakpoints, is not well understood. This study aimed to evaluate the structure, pattern, and potential impact of rearrangements involving DMD duplication. METHODS Two families with DMD segmental duplications exhibiting phenotypical differences were recruited. Optical genome mapping (OGM) was used to explore the cryptic pattern of the rearrangements. Breakpoints were validated using long-range polymerase chain reaction combined with next-generation sequencing and Sanger sequencing. RESULTS A multi-copy duplication involving exons 64-79 of DMD was identified in Family A without obvious clinical symptoms. Family B exhibited typical DMD neuromuscular manifestations and presented a duplication involving exons 10-13 of DMD. The rearrangement in Family A involved complex in-cis tandem repeats shown by OGM but retained a complete copy (reading frame) of DMD inferred from breakpoint validation. A reversed insertion with a segmental repeat was identified in Family B by OGM, which was predicted to disrupt the normal structure and reading frame of DMD after confirming the breakpoints. CONCLUSIONS Validating breakpoint and rearrangement pattern is crucial for the functional annotation and pathogenic classification of genomic structural variations. OGM provides valuable insights into etiological analysis of DMD/BMD and enhances our understanding for cryptic effects of complex rearrangements.
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Affiliation(s)
- Yunting Ma
- The Second School of Medicine, Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Chunrong Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Meizhen Shi
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Lilin Wei
- Department of Obstetrics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Junfang He
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Guilin Medical University, No. 212, Renmin Road, Lingui District, Guilin, Guangxi Zhuang Autonomous Region, 541100, China
| | - Bobo Xie
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Haiyang Zheng
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Xiaoyun Lei
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Xianda Wei
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Zifeng Cheng
- The Second School of Medicine, Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Xu Zhou
- The Second School of Medicine, Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Shaoke Chen
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Jiefeng Luo
- The Second School of Medicine, Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
| | - Yan Huang
- The Second School of Medicine, Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
- Department of Obstetrics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
| | - Baoheng Gui
- The Second School of Medicine, Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, No. 166, Daxuedong Road, Xixiangtang District, Nanning, Guangxi Zhuang Autonomous Region, 530007, China.
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Wijekoon N, Gonawala L, Ratnayake P, Liyanage R, Amaratunga D, Hathout Y, Steinbusch HWM, Dalal A, Hoffman EP, de Silva KRD. Title-molecular diagnostics of dystrophinopathies in Sri Lanka towards phenotype predictions: an insight from a South Asian resource limited setting. Eur J Med Res 2024; 29:37. [PMID: 38195599 PMCID: PMC10775540 DOI: 10.1186/s40001-023-01600-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The phenotype of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) patients is determined by the type of DMD gene variation, its location, effect on reading frame, and its size. The primary objective of this investigation was to determine the frequency and distribution of DMD gene variants (deletions/duplications) in Sri Lanka through the utilization of a combined approach involving multiplex polymerase chain reaction (mPCR) followed by Multiplex Ligation Dependent Probe Amplification (MLPA) and compare to the international literature. The current consensus is that MLPA is a labor efficient yet expensive technique for identifying deletions and duplications in the DMD gene. METHODOLOGY Genetic analysis was performed in a cohort of 236 clinically suspected pediatric and adult myopathy patients in Sri Lanka, using mPCR and MLPA. A comparative analysis was conducted between our findings and literature data. RESULTS In the entire patient cohort (n = 236), mPCR solely was able to identify deletions in the DMD gene in 131/236 patients (DMD-120, BMD-11). In the same cohort, MLPA confirmed deletions in 149/236 patients [DMD-138, BMD -11]. These findings suggest that mPCR has a detection rate of 95% (131/138) among all patients who received a diagnosis. The distal and proximal deletion hotspots for DMD were exons 45-55 and 6-15. Exon 45-60 identified as a novel in-frame variation hotspot. Exon 45-59 was a hotspot for BMD deletions. Comparisons with the international literature show significant variations observed in deletion and duplication frequencies in DMD gene across different populations. CONCLUSION DMD gene deletions and duplications are concentrated in exons 45-55 and 2-20 respectively, which match global variation hotspots. Disparities in deletion and duplication frequencies were observed when comparing our data to other Asian and Western populations. Identified a 95% deletion detection rate for mPCR, making it a viable initial molecular diagnostic approach for low-resource countries where MLPA could be used to evaluate negative mPCR cases and cases with ambiguous mutation borders. Our findings may have important implications in the early identification of DMD with limited resources in Sri Lanka and to develop tailored molecular diagnostic algorithms that are regional and population specific and easily implemented in resource limited settings.
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Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | | | - Roshan Liyanage
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - Harry W M Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Eric P Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - K Ranil D de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka.
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands.
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, 10390, Sri Lanka.
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Wijekoon N, Gonawala L, Ratnayake P, Amaratunga D, Hathout Y, Mohan C, Steinbusch HWM, Dalal A, Hoffman EP, de Silva KRD. Duchenne Muscular Dystrophy from Brain to Muscle: The Role of Brain Dystrophin Isoforms in Motor Functions. J Clin Med 2023; 12:5637. [PMID: 37685704 PMCID: PMC10488491 DOI: 10.3390/jcm12175637] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Brain function and its effect on motor performance in Duchenne muscular dystrophy (DMD) is an emerging concept. The present study explored how cumulative dystrophin isoform loss, age, and a corticosteroid treatment affect DMD motor outcomes. A total of 133 genetically confirmed DMD patients from Sri Lanka were divided into two groups based on whether their shorter dystrophin isoforms (Dp140, Dp116, and Dp71) were affected: Group 1, containing patients with Dp140, Dp116, and Dp71 affected (n = 98), and Group 2, containing unaffected patients (n = 35). A subset of 52 patients (Group 1, n = 38; Group 2, n = 14) was followed for up to three follow-ups performed in an average of 28-month intervals. The effect of the cumulative loss of shorter dystrophin isoforms on the natural history of DMD was analyzed. A total of 74/133 (56%) patients encountered developmental delays, with 66/74 (89%) being in Group 1 and 8/74 (11%) being in Group 2 (p < 0.001). Motor developmental delays were predominant. The hip and knee muscular strength, according to the Medical Research Council (MRC) scale and the North Star Ambulatory Assessment (NSAA) activities, "standing on one leg R", "standing on one leg L", and "walk", declined rapidly in Group 1 (p < 0.001 In the follow-up analysis, Group 1 patients became wheelchair-bound at a younger age than those of Group 2 (p = 0.004). DMD motor dysfunction is linked to DMD mutations that affect shorter dystrophin isoforms. When stratifying individuals for clinical trials, considering the DMD mutation site and its impact on a shorter dystrophin isoform is crucial.
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Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (N.W.); (L.G.)
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200 Maastricht, The Netherlands;
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (N.W.); (L.G.)
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200 Maastricht, The Netherlands;
| | | | | | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA; (Y.H.); (E.P.H.)
| | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, TX 77204, USA;
| | - Harry W. M. Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200 Maastricht, The Netherlands;
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India;
| | - Eric P. Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA; (Y.H.); (E.P.H.)
| | - K. Ranil D. de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (N.W.); (L.G.)
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200 Maastricht, The Netherlands;
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana 10390, Sri Lanka
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Wijekoon N, Gonawala L, Ratnayake P, Sirisena D, Gunasekara H, Dissanayake A, Senanayake S, Keshavaraj A, Hathout Y, Steinbusch HW, Mohan C, Dalal A, Hoffman E, D de Silva K. Gene therapy for selected neuromuscular and trinucleotide repeat disorders - An insight to subsume South Asia for multicenter clinical trials. IBRO Neurosci Rep 2023; 14:146-153. [PMID: 36819775 PMCID: PMC9931913 DOI: 10.1016/j.ibneur.2023.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Background In this article, the authors discuss how they utilized the genetic mutation data in Sri Lankan Duchenne muscular dystrophy (DMD), Spinal muscular atrophy (SMA), Spinocerebellar ataxia (SCA) and Huntington's disease (HD) patients and compare the available literature from South Asian countries to identifying potential candidates for available gene therapy for DMD, SMA, SCA and HD patients. Methods Rare disease patients (n = 623) with the characteristic clinical findings suspected of HD, SCA, SMA and Muscular Dystrophy were genetically confirmed using Multiplex Ligation Dependent Probe Amplification (MLPA), and single plex PCR. A survey was conducted in the "Wiley database on Gene Therapy Trials Worldwide" to identify DMD, SMA, SCA, and HD gene therapy clinical trials performed worldwide up to April 2021. In order to identify candidates for gene therapy in other neighboring countries we compared our findings with available literature from India and Pakistan which has utilized the same molecular diagnostic protocol to our study. Results From the overall cohort of 623 rare disease patients with the characteristic clinical findings suspected of HD, SCA, SMA and Muscular Dystrophy, n = 343 (55%) [Muscular Dystrophy- 65%; (DMD-139, Becker Muscular Dystrophy -BMD-11), SCA type 1-3-53% (SCA1-61,SCA2- 23, SCA3- 39), HD- 52% (45) and SMA- 34% (22)] patients were positive for molecular diagnostics by MLPA and single plex PCR. A total of 147 patients in Sri Lanka amenable to available gene therapy; [DMD-83, SMA-15 and HD-49] were identified. A comparison of Sri Lankan finding with available literature from India and Pakistan identified a total of 1257 patients [DMD-1076, SMA- 57, and HD-124] from these three South Asian Countries as amenable for existing gene therapy trials. DMD, SMA, and HD gene therapy clinical trials (113 studies) performed worldwide up to April 2021 were concentrated mostly (99%) in High Income Countries (HIC) and Upper Middle-Income Countries (UMIC). However, studies on the potential use of anti-sense oligonucleotides (ASO) for treatment of SCAs have yet to reach clinical trials. Conclusion Most genetic therapies for neurodegenerative and neuromuscular disorders have been evaluated for efficacy primarily in Western populations. No multicenter gene therapy clinical trial sites for DMD, SMA and HD in the South Asian region, leading to lack of knowledge on the safety and efficacy of such personalized therapies in other populations, including South Asians. By fostering collaboration between researchers, clinicians, patient advocacy groups, government and industry in gene therapy initiatives for the inherited-diseases community in the developing world would link the Global North and Global South and breathe life into the motto "Together we can make a difference".
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Key Words
- BMD, Becker muscular dystrophy
- Bio Bank
- DMD, Duchenne muscular dystrophy
- Developing Countries
- Duchenne Muscular Dystrophy
- EMA, European Medical Agency
- EMQN, European Molecular Quality Genetics Network
- FDA, U. S. Food and Drug Administration
- HD, Huntington’s disease
- HIC, High Income Countries
- Huntington’s Disease
- Indian Sub-continent
- MLPA, Multiplex Ligation Dependent Probe Amplification
- Neurogenetic Disorders
- SCA, Spinocerebellar ataxia
- SMA, Spinal muscular atrophy
- Spinal Muscular Atrophy
- Spinocerebellar Ataxia
- UMIC, Upper Middle Income Countries
- WTO, World Trade Organization
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Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands
| | | | | | | | | | | | | | - Yetrib Hathout
- Pharmaceutical Sciences Department, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Harry W.M. Steinbusch
- School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands,Dept. of Brain & Cognitive Sciences, Daegu Gyeungbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, TX, USA
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, India
| | - Eric Hoffman
- Pharmaceutical Sciences Department, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - K.Ranil D de Silva
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,EURON - European Graduate School of Neuroscience, the Netherlands,Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka,Corresponding author at: Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.
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Fu X, Shi Y, Ma J, Zhang K, Wang G, Li G, Xiao L, Wang H. Advances of multiplex ligation-dependent probe amplification technology in molecular diagnostics. Biotechniques 2022; 73:205-213. [PMID: 36309987 DOI: 10.2144/btn-2022-0017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Multiplex ligation-dependent probe amplification (MLPA) is a multiplex copy number analysis tool which is routinely used to detect large mutations in genetic diseases. With continuous modifications, MLPA has been extended for the detection of DNA methylation variation, single nucleotide polymorphisms, chromosome abnormalities and other forms of genomic variation. The combination with other techniques has even enlarged the application of MLPA in molecular diagnostics of various human diseases. In this review, the principle of MLPA-based techniques as well as their main and latest applications in clinical detection are described. It is believed that with improved automation, increased multiplexing, lower cost and the combination with other technologies, MLPA will play an increasingly important role in molecular diagnosis of human disease.
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Affiliation(s)
- Xiaoni Fu
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yinmin Shi
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jiying Ma
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Kaiqian Zhang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Guowei Wang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Gang Li
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Lei Xiao
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Huijuan Wang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
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Ghori FF, Wahid M. Induced pluripotent stem cells derived cardiomyocytes from Duchenne Muscular Dystrophy patients in vitro. Pak J Med Sci 2021; 37:1376-1381. [PMID: 34475915 PMCID: PMC8377888 DOI: 10.12669/pjms.37.5.3104] [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: 06/22/2020] [Revised: 07/27/2020] [Accepted: 04/30/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE This study aimed at the in vitro generation of DMD-cardiomyocytes from patient-specific induced pluripotent stem cells derived from a Pakistani patient for future work on DMD in vitro disease modeling and drug testing for efficacy and toxicity. METHODS This in vitro experimental study was carried out from December 2018 to January 2019 at Stem Cells and Regenerative Medicine Lab (SCRML) at Dow Research Institute of Biotechnology and Biomedical Sciences (DRIBBS), Dow University of Health Sciences (DUHS) Urine derived DMD-iPSCs were used which had been generated previously from a Pakistani DMD patient who had been selected through non-random purposive sampling. These were differentiated towards cardiomyocytes using Cardiomyocytes Differentiation media having specified growth factors and then the molecular characterization of the differentiated cells was done using immunofluorescence. RESULTS Pakistani patient's DMD-Cardiomyocytes were generated and their identity was confirmed by positive immunofluorescence for the expression of cardiac markers NKX2-5 and TNNT-2. CONCLUSION This study aimed for in vitro generation of DMD cardiomyocytes for future application in disease modeling, new drug testing for efficacy and toxicity, as well as for drug-testing for tailored personalized therapy. To the best of our knowledge, this was the first time DMD-Cardiomyocytes were generated from Pakistani DMD patients using their own induced pluripotent stem cells.
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Affiliation(s)
- Fareeha Faizan Ghori
- Fareeha Faizan Ghori, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan
| | - Mohsin Wahid
- Mohsin Wahid, Department of Pathology, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan. Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan
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Ghori FF, Wahid M. Induced pluripotent stem cells from urine of Duchenne muscular dystrophy patients. Pediatr Int 2021; 63:1038-1047. [PMID: 33599058 DOI: 10.1111/ped.14655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/23/2021] [Accepted: 02/08/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The most common muscular dystrophy, Duchenne muscular dystrophy (DMD), is a lethal, X-linked disorder with no widespread cure. Worldwide, in vitro studies involving new, mutation-specific cures and regenerative therapies are employing disease-specific patient-specific cells. However, these may not be completely relevant for Pakistani children because of the human genome diversities and geographic variation in mutation type and frequency. Therefore, this study aimed to generate DMD induced pluripotent stem cells (iPSCs) from the urine of Pakistani children with DMD, to serve as a precious source of differentiated cells, such as Pakistani DMD-cardiomyocytes, for future disease-modelling, drug testing, and gene therapy. METHODS Urine-derived cells (UDCs) isolated from mid-stream urine underwent molecular characterization and cellular reprogramming towards iPSCs using the episomal vector system followed by molecular profiling of the iPSCs. RESULTS Colonies of elongated and spindle-shaped or rounded rice-grain like UDCs were spotted 4-7 days after plating and expanded rapidly with a second passage at 2-3 weeks. Multicolor flow cytometry confirmed the expression of mesenchymal stem-cell markers. The reprogramed iPSCs consisted of colonies of round, tightly-packed cells with large nuclei that were positively fluorescent for the pluripotency markers octamer binding transcription factor-4 (OCT-4), tumour resistance antigen 1-60 (TRA-1-60), and stage specific embryonic 4 antigen (SSEA-4), but not for the negative pluripotency marker SSEA-1. To the best of our knowledge, this was the first time DMD-iPSCs have been generated for Pakistani children. CONCLUSION This integration-free, feeder-free, efficient, and reproducible reprogramming method employed UDCs. Urine is a low-cost, non-invasive, painless, and repeatable source of rapidly expandable cells from children and morbid individuals for obtaining autologous cells for drug-assays and disease-modelling, suitable for DMD and other debilitating diseases.
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Affiliation(s)
- Fareeha Faizan Ghori
- Stem Cells and Regenerative Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan
| | - Mohsin Wahid
- Stem Cells and Regenerative Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan.,Department of Pathology, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
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Zehravi M, Wahid M, Ashraf J, Fatima T. Whole-Exome Sequencing Identifies Small Mutations in Pakistani Muscular Dystrophy Patients. Genet Test Mol Biomarkers 2021; 25:218-226. [PMID: 33734897 DOI: 10.1089/gtmb.2020.0246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Muscular dystrophies are a heterogeneous group of inherited disorders that cannot be diagnosed clinically due to overlapping clinical phenotypes. Whole-exome sequencing is considered as the diagnostic strategy of choice in these cases. In this study we aimed to determine the mutational spectrum of multiplex ligation-dependent probe amplification (MLPA)-negative muscular dystrophy patients in Pakistan using whole-exome sequencing. Subsequently the mutations identified via WES were used to screen additional dystrophinopathy patients by Sanger sequencing. Materials and Methods: DNA extracted from the peripheral blood of three MLPA-negative muscular dystrophy patients was sent for whole-exome sequencing. The identified variants in these 3 patients were then checked in 18 dystrophinopathy patients using Sanger sequencing. Results: Four missense variants and one nonsense variant in the Duchenne muscular dystrophy (DMD) gene were detected. WES diagnosed a DMD patient carrying a nonsense variant c.4375C>T (rs398123953) who can benefit from Ataluren therapy. The other two patients carried missense variant (c.572G>T) in the YARS2 gene (rs11539445) labeling them as patients of MLASA (myopathy, lactic acidosis, and sideroblastic anemia). The identified missense and nonsense variants in the DMD gene were detected in 18 clinically diagnosed dystrophinopathy patients using Sanger sequencing. Three missense variants were detected in our cohort of 18 dystrophinopathy patients. One missense variant c.3406A>T (rs3827462) and a nonsense variant c.4375C>T (rs398123953) were not detected in our cohort of 18 dystrophinopathy patients. Conclusions: Whole-exome sequencing identified a nonsense variant in Pakistani muscular dystrophy patients, which is amenable to treatment by Ataluren and a missense variant in YARS2 gene responsible for causing MLASA.
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Affiliation(s)
- Mehwish Zehravi
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan
| | - Mohsin Wahid
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan.,Department of Pathology, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Junaid Ashraf
- Department of Neurosurgery, Dow University of Health Sciences, Karachi, Pakistan
| | - Tehseen Fatima
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan.,Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
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Zehravi M, Wahid M, Ashraf J. Episomal reprogramming of Duchenne muscular dystrophy patients derived CD3 + T cells towards induced pluripotent stem cells. Pak J Med Sci 2021; 37:432-438. [PMID: 33679927 PMCID: PMC7931302 DOI: 10.12669/pjms.37.2.3388] [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] [Indexed: 11/15/2022] Open
Abstract
Objective To derive Duchenne muscular dystrophy patient specific induced pluripotent stem cells (iPSCs) from CD3+T cells of DMD patients using episomal reprogramming and characterization of these DMD-iPSCs using immunofluorescence to confirm their pluripotent state. Methods DMD patients were selected based upon their clinical history and examination. Peripheral blood mononuclear cells were isolated from peripheral blood of DMD patients (n=3) by density gradient centrifugation and were used to generate DMD patient specific T cells (DMD-T cells) using rhIL-2, plate bound anti CD3 antibody and T cell specific media along with specific culture conditions that promote T cell expansion. CD3+ T cells were characterized by flow cytometry and reprogrammed using episomal plasmid to generate DMD-iPSCs. These DMD-iPSCs were characterized using immunofluorescence. The study was carried out at Dow Research Institute of Biotechnology and Biomedical Sciences during August 2017- July 2018 for a period of approximately 12 months. Results The peripheral blood mononuclear cells (PBMNC) derived T cells appeared as suspended cell clumps morphologically were positive for the expression of CD3 and negative for CD31. The DMD patient specific iPSCs appeared as round, compact and flat colonies with well-defined edges morphologically and were positive for the expression of pluripotency markers OCT4, SSEA-4 and TRA-1-81 on immunofluorescence. Conclusion CD3+ T cell derived DMD-iPSCs were obtained under feeder free and xeno-free culture conditions using episomal reprogramming.
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Affiliation(s)
- Mehwish Zehravi
- Mehwish Zehravi, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan
| | - Mohsin Wahid
- Mohsin Wahid, Dow Research Institute of Biotechnology & Biomedical Sciences and Department of Pathology, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Junaid Ashraf
- Junaid Ashraf (Rtd) Department of Neurosurgery, Dow University of Health Sciences, Karachi, Pakistan
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Sheikh O, Yokota T. Advances in Genetic Characterization and Genotype-Phenotype Correlation of Duchenne and Becker Muscular Dystrophy in the Personalized Medicine Era. J Pers Med 2020; 10:E111. [PMID: 32899151 PMCID: PMC7565713 DOI: 10.3390/jpm10030111] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Currently, Duchenne muscular dystrophy (DMD) and the related condition Becker muscular dystrophy (BMD) can be usually diagnosed using physical examination and genetic testing. While BMD features partially functional dystrophin protein due to in-frame mutations, DMD largely features no dystrophin production because of out-of-frame mutations. However, BMD can feature a range of phenotypes from mild to borderline DMD, indicating a complex genotype-phenotype relationship. Despite two mutational hot spots in dystrophin, mutations can arise across the gene. The use of multiplex ligation amplification (MLPA) can easily assess the copy number of all exons, while next-generation sequencing (NGS) can uncover novel or confirm hard-to-detect mutations. Exon-skipping therapy, which targets specific regions of the dystrophin gene based on a patient's mutation, is an especially prominent example of personalized medicine for DMD. To maximize the benefit of exon-skipping therapies, accurate genetic diagnosis and characterization including genotype-phenotype correlation studies are becoming increasingly important. In this article, we present the recent progress in the collection of mutational data and optimization of exon-skipping therapy for DMD/BMD.
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Affiliation(s)
- Omar Sheikh
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, Edmonton, AB T6G 2H7, Canada;
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, Edmonton, AB T6G 2H7, Canada;
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB T6G 2H7, Canada
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