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Pickart AM, Martin AS, Gross BN, Dellefave-Castillo LM, McCallen LM, Nagaraj CB, Rippert AL, Schultz CP, Ulm EA, Armstrong N. Genetic counseling for the dystrophinopathies-Practice resource of the National Society of Genetic Counselors. J Genet Couns 2024. [PMID: 38682751 DOI: 10.1002/jgc4.1892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 05/01/2024]
Abstract
The dystrophinopathies encompass the phenotypically variable forms of muscular dystrophy caused by pathogenic variants in the DMD gene. The dystrophinopathies include the most common inherited muscular dystrophy among 46,XY individuals, Duchenne muscular dystrophy, as well as Becker muscular dystrophy and other less common phenotypic variants. With increased access to and utilization of genetic testing in the diagnostic and carrier setting, genetic counselors and clinicians in diverse specialty areas may care for individuals with and carriers of dystrophinopathy. This practice resource was developed as a tool for genetic counselors and other health care professionals to support counseling regarding dystrophinopathies, including diagnosis, health risks and management, psychosocial needs, reproductive options, clinical trials, and treatment. Genetic testing efforts have enabled genotype/phenotype correlation in the dystrophinopathies, but have also revealed unexpected findings, further complicating genetic counseling for this group of conditions. Additionally, the therapeutic landscape for dystrophinopathies has dramatically changed with several FDA-approved therapeutics, an expansive research pathway, and numerous clinical trials. Genotype-phenotype correlations are especially complex and genetic counselors' unique skill sets are useful in exploring and explaining this to families. Given the recent advances in diagnostic testing and therapeutics related to dystrophinopathies, this practice resource is a timely update for genetic counselors and other healthcare professionals involved in the diagnosis and care of individuals with dystrophinopathies.
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Affiliation(s)
- Angela M Pickart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ann S Martin
- Parent Project Muscular Dystrophy, Washington, District of Columbia, USA
| | - Brianna N Gross
- Department of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lisa M Dellefave-Castillo
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Leslie M McCallen
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Chinmayee B Nagaraj
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Alyssa L Rippert
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Elizabeth A Ulm
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Niki Armstrong
- Parent Project Muscular Dystrophy, Washington, District of Columbia, USA
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Zhong H, Sian V, Johari M, Katayama S, Oghabian A, Jonson PH, Hackman P, Savarese M, Udd B. Revealing myopathy spectrum: integrating transcriptional and clinical features of human skeletal muscles with varying health conditions. Commun Biol 2024; 7:438. [PMID: 38600180 PMCID: PMC11006663 DOI: 10.1038/s42003-024-06143-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
Myopathy refers to a large group of heterogeneous, rare muscle diseases. Bulk RNA-sequencing has been utilized for the diagnosis and research of these diseases for many years. However, the existing valuable sequencing data often lack integration and clinical interpretation. In this study, we integrated bulk RNA-sequencing data from 1221 human skeletal muscles (292 with myopathies, 929 controls) from both databases and our local samples. By applying a method similar to single-cell analysis, we revealed a general spectrum of muscle diseases, ranging from healthy to mild disease, moderate muscle wasting, and severe muscle disease. This spectrum was further partly validated in three specific myopathies (97 muscles) through clinical features including trinucleotide repeat expansion, magnetic resonance imaging fat fraction, pathology, and clinical severity scores. This spectrum helped us identify 234 genuinely healthy muscles as unprecedented controls, providing a new perspective for deciphering the hallmark genes and pathways among different myopathies. The newly identified featured genes of general myopathy, inclusion body myositis, and titinopathy were highly expressed in our local muscles, as validated by quantitative polymerase chain reaction.
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Affiliation(s)
- Huahua Zhong
- Department of Neurology, Huashan Rare Disease Center, Huashan Hospital, Fudan University, Shanghai, China.
| | - Veronica Sian
- Department of Precision Medicine, "Luigi Vanvitelli" University of Campania, Via L. De Crecchio 7, Naples, Italy
| | - Mridul Johari
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Shintaro Katayama
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ali Oghabian
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per Harald Jonson
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Peter Hackman
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Marco Savarese
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Tampere Neuromuscular Center, University Hospital, Tampere, Finland
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Chen Z, Wang G, Wang W, Wang X, Huang Y, Jia J, Gao Q, Xu H, Xu Y, Ma Z, He L, Cheng J, Li C. PDE9A polymorphism and association analysis with growth performance and gastrointestinal weight of Hu sheep. Gene 2024; 900:148137. [PMID: 38184018 DOI: 10.1016/j.gene.2024.148137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/26/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024]
Abstract
Phosphodiesterase 9A (PDE9A) plays a crucial role in activating the cGMP-dependent signaling pathway and may have important effects on the growth and development of the gastrointestinal tract in Hu sheep. In this study, we analyzed the single nucleotide polymorphisms of PDE9A in 988 Hu sheep and their correlation with growth performance, feed efficiency, and gastrointestinal development. Additionally, we examined the expression level of different PDE9A genotypes in the gastrointestinal tract of Hu sheep by using fluorescence quantitative PCR. The results revealed a moderate level of polymorphism (0.25 < PIC < 0.50) at the g.286248617 T > C mutation site located in the first intron of PDE9A in Hu sheep, with three genotypes: CC, CT, and TT. The weights of the omasum, colon, and cecum were significantly greater in the CC genotype than in the TT genotype (P < 0.05), and the expression level of PDE9A in the tissues of the rumen, ileum, cecum, and colon was notably lower in the CC genotype individuals (P < 0.05). These findings suggest that the polymorphism of PDE9A affects the weight of the stomach, colon, and cecum in Hu sheep through expression regulation. Overall, the results of this study suggest that the g.286248617 T > C mutation site in the first intron of PDE9A can serve as a potential molecular marker for breeding practices related to the gastrointestinal weight of Hu sheep.
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Affiliation(s)
- Zhanyu Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Guoxiu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiale Jia
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Qihao Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Haoyu Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yunfei Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Lijuan He
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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Gatto F, Benemei S, Piluso G, Bello L. The complex landscape of DMD mutations: moving towards personalized medicine. Front Genet 2024; 15:1360224. [PMID: 38596212 PMCID: PMC11002111 DOI: 10.3389/fgene.2024.1360224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/26/2024] [Indexed: 04/11/2024] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe genetic disorder characterized by progressive muscle degeneration, with respiratory and cardiac complications, caused by mutations in the DMD gene, encoding the protein dystrophin. Various DMD mutations result in different phenotypes and disease severity. Understanding genotype/phenotype correlations is essential to optimize clinical care, as mutation-specific therapies and innovative therapeutic approaches are becoming available. Disease modifier genes, trans-active variants influencing disease severity and phenotypic expressivity, may modulate the response to therapy, and become new therapeutic targets. Uncovering more disease modifier genes via extensive genomic mapping studies offers the potential to fine-tune prognostic assessments for individuals with DMD. This review provides insights into genotype/phenotype correlations and the influence of modifier genes in DMD.
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Affiliation(s)
| | | | - Giulio Piluso
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Luca Bello
- Department of Neurosciences DNS, University of Padova, Padova, Italy
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Chandrasekhar A, Mroczkowski HJ, Urraca N, Gross A, Bluske K, Thorpe E, Hagelstrom RT, Schonberg SA, Perry DL, Taft RJ, Kesari A. Genome sequencing detects a balanced pericentric inversion with breakpoints that impact the DMD and upstream region of POU3F4 genes. Am J Med Genet A 2024; 194:e63462. [PMID: 37929330 DOI: 10.1002/ajmg.a.63462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/11/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
We describe a family with two maternal half-brothers both of whom presented with muscular dystrophy, autism spectrum disorder, developmental delay, and sensorineural hearing loss. The elder brother had onset of features at ~3 months of age, followed by clinical confirmation of muscular dystrophy at 3 years. Skeletal biopsy staining at 4.7 years showed an absence of dystrophin protein which prompted extensive molecular testing over 4 years that included gene panels, targeted single-gene assays, arrays, and karyotyping, all of which failed to identify a clinically significant variant in the DMD gene. At 10 years of age, clinical whole-genome sequencing (cWGS) was performed, which revealed a novel hemizygous ~50.7 Mb balanced pericentric inversion on chromosome X that disrupts the DMD gene in both siblings, consistent with the muscular dystrophy phenotype. This inversion also impacts the upstream regulatory region of POU3F4, structural rearrangements which are known to cause hearing loss. The unaffected mother is a heterozygous carrier for the pericentric inversion. This finding illustrates the ability of cWGS to detect a wide breadth of disease-causing genomic variations including large genomic rearrangements.
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Affiliation(s)
| | - Henry J Mroczkowski
- Department of Pediatrics, University of Tennessee Health Science Center and Le Bonheur Children's Hospital, Memphis, Tennessee, USA
| | - Nora Urraca
- Department of Pediatrics, University of Tennessee Health Science Center and Le Bonheur Children's Hospital, Memphis, Tennessee, USA
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Xie Z, Sun C, Liu C, Lu Y, Chen B, Wu R, Liu Y, Liu R, Peng Q, Deng J, Meng L, Wang Z, Zhang W, Yuan Y. A new pseudoexon activation due to ultrarare branch point formation in Duchenne muscular dystrophy. Neuromuscul Disord 2024; 35:8-12. [PMID: 38194733 DOI: 10.1016/j.nmd.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/14/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024]
Abstract
Deep-intronic variants that create or enhance a splice site are increasingly reported as a significant cause of monogenic diseases. However, deep-intronic variants that activate pseudoexons by affecting a branch point are extremely rare in monogenic diseases. Here, we describe a novel deep-intronic DMD variant that created a branch point in a Duchenne muscular dystrophy (DMD) patient. A 7.0-year-old boy was enrolled because he was suspected of DMD based on his clinical, muscle imaging, and pathological features. Routine genetic testing did not discover a pathogenic DMD variant. We then performed muscle-derived dystrophin mRNA analysis and detected an aberrant pseudoexon-containing transcript. Further genomic Sanger sequencing and bioinformatic analyses revealed a novel deep-intronic splicing variant in DMD (NM_004006.2:c.5325+1759G>T), which created a new branch point sequence and thus activated a new dystrophin pseudoexon (NM_004006.2:r.5325_5326ins5325+1779_5325+1855). Our study highlights the significant role of branch point alterations in the pathogenesis of monogenic diseases.
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Affiliation(s)
- Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Chengyue Sun
- Department of Neurology, Peking University People's Hospital, Beijing 100044, China
| | - Chang Liu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Yanyu Lu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Bin Chen
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Rui Wu
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong
| | - Yanru Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ran Liu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Qing Peng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China.
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing 100034, China.
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Berntsson SG, Matsson H, Kristoffersson A, Niemelä V, van Duyvenvoorde HA, Richel-van Assenbergh C, van der Klift HM, Casar-Borota O, Frykholm C, Landtblom AM. Case report: a novel deep intronic splice-altering variant in DMD as a cause of Becker muscular dystrophy. Front Genet 2023; 14:1226766. [PMID: 37795243 PMCID: PMC10546389 DOI: 10.3389/fgene.2023.1226766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
We present the case of a male patient who was ultimately diagnosed with Becker muscular dystrophy (BMD; MIM# 300376) after the onset of muscle weakness in his teens progressively led to significant walking difficulties in his twenties. A genetic diagnosis was pursued but initial investigation revealed no aberrations in the dystrophin gene (DMD), although immunohistochemistry and Western blot analysis suggested the diagnosis of dystrophinopathy. Eventually, after more than 10 years, an RNA analysis captured abnormal splicing where 154 nucleotides from intron 43 were inserted between exon 43 and 44 resulting in a frameshift and a premature stop codon. Normal splicing of the DMD gene was also observed. Additionally, a novel variant c.6291-13537A>G in DMD was confirmed in the genomic DNA of the patient. The predicted function of the variant aligns with the mRNA results. To conclude, we here demonstrate that mRNA analysis can guide the diagnosis of non-coding genetic variants in DMD.
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Affiliation(s)
| | - Hans Matsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Clinical Genetics, Rudbeck Laboratory, Uppsala University Hospital, Uppsala, Sweden
| | - Anna Kristoffersson
- Department of Medical Sciences, Neurology, Uppsala University, Uppsala, Sweden
| | - Valter Niemelä
- Department of Medical Sciences, Neurology, Uppsala University, Uppsala, Sweden
| | | | | | | | - Olivera Casar-Borota
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Clinical Pathology, Uppsala University Hospital, Uppsala, Sweden
| | - Carina Frykholm
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Clinical Genetics, Rudbeck Laboratory, Uppsala University Hospital, Uppsala, Sweden
| | - Anne-Marie Landtblom
- Department of Medical Sciences, Neurology, Uppsala University, Uppsala, Sweden
- Department of Clinical Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health, Linköping University, Linköping, Sweden
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Hildyard JCW, Piercy RJ. When Size Really Matters: The Eccentricities of Dystrophin Transcription and the Hazards of Quantifying mRNA from Very Long Genes. Biomedicines 2023; 11:2082. [PMID: 37509720 PMCID: PMC10377302 DOI: 10.3390/biomedicines11072082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
At 2.3 megabases in length, the dystrophin gene is enormous: transcription of a single mRNA requires approximately 16 h. Principally expressed in skeletal muscle, the dystrophin protein product protects the muscle sarcolemma against contraction-induced injury, and dystrophin deficiency results in the fatal muscle-wasting disease, Duchenne muscular dystrophy. This gene is thus of key clinical interest, and therapeutic strategies aimed at eliciting dystrophin restoration require quantitative analysis of its expression. Approaches for quantifying dystrophin at the protein level are well-established, however study at the mRNA level warrants closer scrutiny: measured expression values differ in a sequence-dependent fashion, with significant consequences for data interpretation. In this manuscript, we discuss these nuances of expression and present evidence to support a transcriptional model whereby the long transcription time is coupled to a short mature mRNA half-life, with dystrophin transcripts being predominantly nascent as a consequence. We explore the effects of such a model on cellular transcriptional dynamics and then discuss key implications for the study of dystrophin gene expression, focusing on both conventional (qPCR) and next-gen (RNAseq) approaches.
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Affiliation(s)
- John C W Hildyard
- Comparative Neuromuscular Disease Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London NW1 0TU, UK
| | - Richard J Piercy
- Comparative Neuromuscular Disease Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London NW1 0TU, UK
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Folland C, Ganesh V, Weisburd B, McLean C, Kornberg AJ, O'Donnell-Luria A, Rehm HL, Stevanovski I, Chintalaphani SR, Kennedy P, Deveson IW, Ravenscroft G. Transcriptome and Genome Analysis Uncovers a DMD Structural Variant: A Case Report. Neurol Genet 2023; 9:e200064. [PMID: 37090938 PMCID: PMC10117699 DOI: 10.1212/nxg.0000000000200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/27/2023] [Indexed: 03/16/2023]
Abstract
Objective Duchenne muscular dystrophy (DMD) is caused by pathogenic variants in the dystrophin gene (DMD). Hypermethylated CGG expansions within DIP2B 5' UTR are associated with an intellectual development disorder. Here, we demonstrate the diagnostic utility of genomic short-read sequencing (SRS) and transcriptome sequencing to identify a novel DMD structural variant (SV) and a DIP2B CGG expansion in a patient with DMD for whom conventional diagnostic testing failed to yield a genetic diagnosis. Methods We performed genomic SRS, skeletal muscle transcriptome sequencing, and targeted programmable long-read sequencing (LRS). Results The proband had a typical DMD clinical presentation, autism spectrum disorder (ASD), and dystrophinopathy on muscle biopsy. Transcriptome analysis identified 6 aberrantly expressed genes; DMD and DIP2B were the strongest underexpression and overexpression outliers, respectively. Genomic SRS identified a 216 kb paracentric inversion (NC_000023.11: g.33162217-33378800) overlapping 2 DMD promoters. ExpansionHunter indicated an expansion of 109 CGG repeats within the 5' UTR of DIP2B. Targeted genomic LRS confirmed the SV and genotyped the DIP2B repeat expansion as 270 CGG repeats. Discussion Here, transcriptome data heavily guided genomic analysis to resolve a complex DMD inversion and a DIP2B repeat expansion. Longitudinal follow-up will be important for clarifying the clinical significance of the DIP2B genotype.
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Affiliation(s)
- Chiara Folland
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Vijay Ganesh
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Ben Weisburd
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Catriona McLean
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Andrew J Kornberg
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Anne O'Donnell-Luria
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Heidi L Rehm
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Igor Stevanovski
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Sanjog R Chintalaphani
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Paul Kennedy
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Ira W Deveson
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
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10
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Xie Z, Sun C, Liu C, Xie Z, Wei L, Yu J, Ling C, Guo X, Liu Y, Yu M, Leng Y, Meng L, Sun Y, Deng J, Leal SM, Schrauwen I, Wang Z, Yuan Y. Clinical, muscle imaging, and genetic characteristics of dystrophinopathies with deep-intronic DMD variants. J Neurol 2023; 270:925-37. [PMID: 36319768 DOI: 10.1007/s00415-022-11432-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Phenotypic heterogeneity within or between families with a same deep-intronic splice-altering variant in the DMD gene has never been systematically analyzed. This study aimed to determine the phenotypic and genetic characteristics of patients with deep-intronic DMD variants. METHODS Of 1338 male patients with a suspected dystrophinopathy, 38 were confirmed to have atypical pathogenic DMD variants via our comprehensive genetic testing approach. Of the 38 patients, 30 patients from 22 unrelated families with deep-intronic DMD variants underwent a detailed clinical and imaging assessment. RESULTS Nineteen different deep-intronic DMD variants were identified in the 30 patients, including 15 with Duchenne muscular dystrophy (DMD), 14 with Becker muscular dystrophy (BMD), and one with X-linked dilated cardiomyopathy. Of the 19 variants, 15 were single-nucleotide variants, 2 were structural variants (SVs), and 2 were pure-intronic large-scale SVs causing aberrant inclusion of other protein-coding genes sequences into the mature DMD transcripts. The trefoil with single fruit sign was observed in 18 patients and the concentric fatty infiltration pattern was observed in 2 patients. Remarkable phenotypic heterogeneity was observed not only in skeletal but also cardiac muscle involvement in 2 families harboring a same deep-intronic variant. Different skeletal muscle involvement between families with a same variant was observed in 4 families. High inter-individual phenotypic heterogeneity was observed within two BMD families and one DMD family. CONCLUSIONS Our study first highlights the variable phenotypic expressivity of deep-intronic DMD variants and demonstrates a new class of deep-intronic DMD variants, i.e., pure-intronic SVs involving other protein-coding genes.
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11
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Okubo M, Noguchi S, Awaya T, Hosokawa M, Tsukui N, Ogawa M, Hayashi S, Komaki H, Mori-Yoshimura M, Oya Y, Takahashi Y, Fukuyama T, Funato M, Hosokawa Y, Kinoshita S, Matsumura T, Nakamura S, Oshiro A, Terashima H, Nagasawa T, Sato T, Shimada Y, Tokita Y, Hagiwara M, Ogata K, Nishino I. RNA-seq analysis, targeted long-read sequencing and in silico prediction to unravel pathogenic intronic events and complicated splicing abnormalities in dystrophinopathy. Hum Genet 2023; 142:59-71. [PMID: 36048237 DOI: 10.1007/s00439-022-02485-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/24/2022] [Indexed: 01/18/2023]
Abstract
Dystrophinopathy is caused by alterations in DMD. Approximately 1% of patients remain genetically undiagnosed, because intronic variations are not detected by standard methods. Here, we combined laboratory and in silico analyses to identify disease-causing genomic variants in genetically undiagnosed patients and determine the regulatory mechanisms underlying abnormal DMD transcript generation. DMD transcripts from 20 genetically undiagnosed dystrophinopathy patients in whom no exon variants were identified, despite dystrophin deficiency on muscle biopsy, were analyzed by transcriptome sequencing. Genome sequencing captured intronic variants and their effects were interpreted using in silico tools. Targeted long-read sequencing was applied in cases with suspected structural genomic abnormalities. Abnormal DMD transcripts were detected in 19 of 20 cases; Exonization of intronic sequences in 15 cases, exon skipping in one case, aberrantly spliced and polyadenylated transcripts in two cases and transcription termination in one case. Intronic single nucleotide variants, chromosomal rearrangements and nucleotide repeat expansion were identified in DMD gene as pathogenic causes of transcript alteration. Our combined analysis approach successfully identified pathogenic events. Detection of diseasing-causing mechanisms in DMD transcripts could inform the therapeutic options for patients with dystrophinopathy.
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12
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Soderstrom CI, Larsen J, Owen C, Gifondorwa D, Beidler D, Yong FH, Conrad P, Neubert H, Moore SA, Hassanein M. Development and Validation of a Western Blot Method to Quantify Mini-Dystrophin in Human Skeletal Muscle Biopsies. AAPS J 2022; 25:12. [PMID: 36539515 PMCID: PMC10034579 DOI: 10.1208/s12248-022-00776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a degenerative muscular disease affecting roughly one in 5000 males at birth. The disease is often caused by inherited X-linked recessive pathogenic variants in the dystrophin gene, but may also arise from de novo mutations. Disease-causing variants include nonsense, out of frame deletions or duplications that result in loss of dystrophin protein expression. There is currently no cure for DMD and the few treatment options available aim at slowing muscle degradation. New advances in gene therapy and understanding of dystrophin (DYS) expression in other muscular dystrophies have opened new opportunities for treatment. Therefore, reliable methods are needed to monitor dystrophin expression and assess the efficacy of new therapies for muscular dystrophies such as DMD and Becker muscular dystrophy (BMD). Here, we describe the validation of a novel Western blot (WB) method for the quantitation of mini-dystrophin protein in human skeletal muscle tissues that is easy to adopt in most laboratory settings. This WB method was assessed through precision, accuracy, selectivity, dilution linearity, stability, and repeatability. Based on mini-DYS standard performance, the assay has a dynamic range of 0.5-15 ng protein (per 5 µg total protein per lane), precision of 3.3 to 25.5%, and accuracy of - 7.5 to 3.3%. Our stability assessment showed that the protein is stable after 4 F/T cycles, up to 2 h at RT and after 7 months at - 70°C. Furthermore, our WB method was compared to the results from our recently published LC-MS method. Workflow for our quantitative WB method to determine mini-dystrophin levels in muscle tissues (created in Biorender.com). Step 1 involves protein extraction from skeletal muscle tissue lysates from control, DMD, or BMD biospecimen. Step 2 measures total protein concentrations. Step 3 involves running gel electrophoresis with wild-type dystrophin (wt-DYS) from muscle tissue extracts alongside mini-dystrophin STD curve and mini-DYS and protein normalization with housekeeping GAPDH.
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Affiliation(s)
| | - Jennifer Larsen
- Early Clinical Development, Precision Medicine, Cambridge, MA, USA
| | - Carolina Owen
- Early Clinical Development, Precision Medicine, Cambridge, MA, USA
| | - David Gifondorwa
- Clinical Assay Group, Global Product Development (GPD), Pfizer Inc, Groton, Connecticut, USA
| | - David Beidler
- Early Clinical Development, Precision Medicine, Pfizer Inc., 1 Portland, Cambridge, Massachusetts, 02139, USA
| | - Florence H Yong
- Biostatistics, Early Clinical Development, Worldwide Research & Development, Pfizer Inc., Cambridge, MA, USA
| | - Patricia Conrad
- Early Clinical Development, Precision Medicine, Cambridge, MA, USA
| | - Hendrik Neubert
- Biomedicine Design, Worldwide Research & Development, Pfizer Inc., Andover, Massachusetts, USA
| | - Steven A Moore
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, 52242, USA
| | - Mohamed Hassanein
- Early Clinical Development, Precision Medicine, Pfizer Inc., 1 Portland, Cambridge, Massachusetts, 02139, USA.
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13
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Bruels CC, Littel HR, Daugherty AL, Stafki S, Estrella EA, McGaughy ES, Truong D, Badalamenti JP, Pais L, Ganesh VS, O'Donnell-Luria A, Stalker HJ, Wang Y, Collins C, Behlmann A, Lemmers RJLF, van der Maarel SM, Laine R, Ghosh PS, Darras BT, Zingariello CD, Pacak CA, Kunkel LM, Kang PB. Diagnostic capabilities of nanopore long-read sequencing in muscular dystrophy. Ann Clin Transl Neurol 2022; 9:1302-1309. [PMID: 35734998 PMCID: PMC9380148 DOI: 10.1002/acn3.51612] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/05/2022] Open
Abstract
Many individuals with muscular dystrophies remain genetically undiagnosed despite clinical diagnostic testing, including exome sequencing. Some may harbor previously undetected structural variants (SVs) or cryptic splice sites. We enrolled 10 unrelated families: nine had muscular dystrophy but lacked complete genetic diagnoses and one had an asymptomatic DMD duplication. Nanopore genomic long-read sequencing identified previously undetected pathogenic variants in four individuals: an SV in DMD, an SV in LAMA2, and two single nucleotide variants in DMD that alter splicing. The DMD duplication in the asymptomatic individual was in tandem. Nanopore sequencing may help streamline genetic diagnostic approaches for muscular dystrophy.
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Affiliation(s)
- Christine C Bruels
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, Minnesota, 55455
| | - Hannah R Littel
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, Minnesota, 55455
| | - Audrey L Daugherty
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, Minnesota, 55455
| | - Seth Stafki
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, Minnesota, 55455
| | - Elicia A Estrella
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Emily S McGaughy
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, 32610
| | - Don Truong
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, Minnesota, 55455
| | - Jonathan P Badalamenti
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Lynn Pais
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Vijay S Ganesh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Heather J Stalker
- Division of Genetics, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, 32610
| | - Yang Wang
- PerkinElmer Genomics, Pittsburgh, Pennsylvania
| | | | | | | | | | - Regina Laine
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Partha S Ghosh
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Basil T Darras
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Carla D Zingariello
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, 32610
| | - Christina A Pacak
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, Minnesota, 55455
| | - Louis M Kunkel
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Peter B Kang
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, Minnesota, 55455.,Institute for Translational Neuroscience, University of Minnesota Medical School, Minneapolis, Minnesota, 55455
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