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Huang M, Zhang Q, Jiao J, Shi J, Xu Y, Zhang C, Zhou R, Liu W, Liang Y, Chen H, Wang Y, Xu Z, Hu P. Comprehensive genetic analysis of facioscapulohumeral muscular dystrophy by Nanopore long-read whole-genome sequencing. J Transl Med 2024; 22:451. [PMID: 38741136 DOI: 10.1186/s12967-024-05259-8] [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: 12/10/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is a high-prevalence autosomal dominant neuromuscular disease characterized by significant clinical and genetic heterogeneity. Genetic diagnosis of FSHD remains a challenge because it cannot be detected by standard sequencing methods and requires a complex diagnosis workflow. METHODS We developed a comprehensive genetic FSHD detection method based on Oxford Nanopore Technologies (ONT) whole-genome sequencing. Using a case-control design, we applied this procedure to 29 samples and compared the results with those from optical genome mapping (OGM), bisulfite sequencing (BSS), and whole-exome sequencing (WES). RESULTS Using our ONT-based method, we identified 59 haplotypes (35 4qA and 24 4qB) among the 29 samples (including a mosaic sample), as well as the number of D4Z4 repeat units (RUs). The pathogenetic D4Z4 RU contraction identified by our ONT-based method showed 100% concordance with OGM results. The methylation levels of the most distal D4Z4 RU and the double homeobox 4 gene (DUX4) detected by ONT sequencing are highly consistent with the BSS results and showed excellent diagnostic efficiency. Additionally, our ONT-based method provided an independent methylation profile analysis of two permissive 4qA alleles, reflecting a more accurate scenario than traditional BSS. The ONT-based method detected 17 variations in three FSHD2-related genes from nine samples, showing 100% concordance with WES. CONCLUSIONS Our ONT-based FSHD detection method is a comprehensive method for identifying pathogenetic D4Z4 RU contractions, methylation level alterations, allele-specific methylation of two 4qA haplotypes, and variations in FSHD2-related genes, which will all greatly improve genetic testing for FSHD.
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Affiliation(s)
- Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Qinxin Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Jiao Jiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Jianquan Shi
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210006, People's Republic of China
| | - Yiyun Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Cuiping Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Wenwen Liu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Yixuan Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Hao Chen
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China.
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China.
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Salsi V, Vattemi GNA, Tupler RG. The FSHD jigsaw: are we placing the tiles in the right position? Curr Opin Neurol 2023; 36:455-463. [PMID: 37338810 PMCID: PMC10487374 DOI: 10.1097/wco.0000000000001176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
PURPOSE OF REVIEW Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common myopathies, involving over 870,000 people worldwide and over 20 FSHD national registries. Our purpose was to summarize the main objectives of the scientific community on this topic and the moving trajectories of research from the past to the present. RECENT FINDINGS To date, research is mainly oriented toward deciphering the molecular and pathogenetic basis of the disease by investigating DUX4-mediated muscle alterations. Accordingly, FSHD drug development has been escalating in the last years in an attempt to silence DUX4 or to block its downstream effectors. Breakthroughs in the field include the awareness that new biomarkers and outcome measures are required for tracking disease progression and patient stratification. The need to develop personalized therapeutic strategies is also crucial according to the phenotypic variability observed in FSHD subjects. SUMMARY We analysed 121 literature reports published between 2021 and 2023 to assess the most recent advances in FSHD clinical and molecular research.
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Affiliation(s)
- Valentina Salsi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena
| | - Gaetano Nicola Alfio Vattemi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Clinical Neurology, University of Verona, Verona, Italy
| | - Rossella Ginevra Tupler
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena
- Department of Molecular Cell and Cancer Biology
- Li Weibo Institute for Rare Diseases Research at the University of Massachusetts Medical School, Worcester, USA
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3
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Runfola V, Giambruno R, Caronni C, Pannese M, Andolfo A, Gabellini D. MATR3 is an endogenous inhibitor of DUX4 in FSHD muscular dystrophy. Cell Rep 2023; 42:113120. [PMID: 37703175 PMCID: PMC10591880 DOI: 10.1016/j.celrep.2023.113120] [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: 03/28/2023] [Revised: 07/07/2023] [Accepted: 08/25/2023] [Indexed: 09/15/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common neuromuscular disorders and has no cure. Due to an unknown molecular mechanism, FSHD displays overlapping manifestations with the neurodegenerative disease amyotrophic lateral sclerosis (ALS). FSHD is caused by aberrant gain of expression of the transcription factor double homeobox 4 (DUX4), which triggers a pro-apoptotic transcriptional program resulting in inhibition of myogenic differentiation and muscle wasting. Regulation of DUX4 activity is poorly known. We identify Matrin 3 (MATR3), whose mutation causes ALS and dominant distal myopathy, as a cellular factor controlling DUX4 expression and activity. MATR3 binds to the DUX4 DNA-binding domain and blocks DUX4-mediated gene expression, rescuing cell viability and myogenic differentiation of FSHD muscle cells, without affecting healthy muscle cells. Finally, we characterize a shorter MATR3 fragment that is necessary and sufficient to directly block DUX4-induced toxicity to the same extent as the full-length protein. Collectively, our data suggest MATR3 as a candidate for developing a treatment for FSHD.
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Affiliation(s)
- Valeria Runfola
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Roberto Giambruno
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
| | - Claudia Caronni
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Maria Pannese
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Annapaola Andolfo
- ProMeFa, Proteomics and Metabolomics Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
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Kakimoto T, Ogasawara A, Ishikawa K, Kurita T, Yoshida K, Harada S, Nonaka T, Inoue Y, Uchida K, Tateoka T, Ohta T, Kumagai S, Sasaki T, Aihara H. A Systemically Administered Unconjugated Antisense Oligonucleotide Targeting DUX4 Improves Muscular Injury and Motor Function in FSHD Model Mice. Biomedicines 2023; 11:2339. [PMID: 37760780 PMCID: PMC10525656 DOI: 10.3390/biomedicines11092339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/02/2023] [Accepted: 08/13/2023] [Indexed: 09/29/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), one of the most common muscular dystrophies, is caused by an abnormal expression of the DUX4 gene in skeletal muscles, resulting in muscle weakness. In this study, we investigated MT-DUX4-ASO, a novel gapmer antisense oligonucleotide (ASO). MT-DUX4-ASO decreased the expression of DUX4 and its target genes in FSHD patient-derived myoblasts. For the first time, we demonstrated that a systemically administered ASO, even without a ligand for drug delivery, could significantly improve muscle injury and motor function in the ACTA1-MCM/FLExDUX4 (DUX4-TG) mouse model of FSHD. Tamoxifen (TMX) injection transiently induces skeletal-muscle-specific DUX4 expression in DUX4-TG mice, while the skeletal muscles of TMX-untreated DUX4-TG mice have leaky DUX4 expression in a small subset of myofibers similar to those of FSHD patients. Subcutaneous 10 mg/kg of MT-DUX4-ASO at two-week intervals significantly suppressed muscular DUX4 target gene expression, histological muscle injury, and blood muscle injury marker elevation in TMX-untreated DUX4-TG mice. Notably, MT-DUX4-ASO at 10 mg/kg every other week significantly prevented the TMX-induced declines in treadmill test running speed and muscle force in DUX4-TG mice. Thus, the systemically administered unconjugated MT-DUX4-ASO suppressed disease progression in DUX4-TG mice, extending the potential of unconjugated ASOs as a promising FSHD treatment strategy.
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Affiliation(s)
- Tetsuhiro Kakimoto
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1 Muraoka-Higashi, Fujisawa-shi, Kanagawa 251-8555, Japan
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Knox RN, Eidahl JO, Wallace L, Choudury S, Rashnonejad A, Daman K, Guggenbiller M, Saad N, Hoover ME, Zhang L, Branson OE, Emerson CP, Freitas MA, Harper SQ. Post-Translational Modifications of the DUX4 Protein Impact Toxic Function in FSHD Cell Models. Ann Neurol 2023; 94:398-413. [PMID: 37186119 PMCID: PMC10777487 DOI: 10.1002/ana.26668] [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: 07/22/2022] [Revised: 04/12/2023] [Accepted: 04/22/2023] [Indexed: 05/17/2023]
Abstract
OBJECTIVE Facioscapulohumeral muscular dystrophy (FSHD) is caused by abnormal de-repression of the myotoxic transcription factor DUX4. Although the transcriptional targets of DUX4 are known, the regulation of DUX4 protein and the molecular consequences of this regulation are unclear. Here, we used in vitro models of FSHD to identify and characterize DUX4 post-translational modifications (PTMs) and their impact on the toxic function of DUX4. METHODS We immunoprecipitated DUX4 protein and performed mass spectrometry to identify PTMs. We then characterized DUX4 PTMs and potential enzyme modifiers using mutagenesis, proteomics, and biochemical assays in HEK293 and human myoblast cell lines. RESULTS We identified 17 DUX4 amino acids with PTMs, and generated 55 DUX4 mutants designed to prevent or mimic PTMs. Five mutants protected cells against DUX4-mediated toxicity and reduced the ability of DUX4 to transactivate FSHD biomarkers. These mutagenesis results suggested that DUX4 toxicity could be counteracted by serine/threonine phosphorylation and/or inhibition of arginine methylation. We therefore sought to identify modifying enzymes that could play a role in regulating DUX4 PTMs. We found several enzymes capable of modifying DUX4 protein in vitro, and confirmed that protein kinase A (PKA) and protein arginine methyltransferase (PRMT1) interact with DUX4. INTERPRETATION These results support that DUX4 is regulated by PTMs and set a foundation for developing FSHD drug screens based mechanistically on DUX4 PTMs and modifying enzymes. ANN NEUROL 2023;94:398-413.
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Affiliation(s)
- Renatta N. Knox
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63108
| | - Jocelyn O. Eidahl
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Lindsay Wallace
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Sarah Choudury
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Afrooz Rashnonejad
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Katelyn Daman
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical School, Worcester, MA 01655
| | - Matthew Guggenbiller
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Nizar Saad
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Michael E. Hoover
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Liwen Zhang
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Owen E. Branson
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Charles P. Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical School, Worcester, MA 01655
| | - Michael A. Freitas
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Scott Q. Harper
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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6
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Duranti E, Villa C. Influence of DUX4 Expression in Facioscapulohumeral Muscular Dystrophy and Possible Treatments. Int J Mol Sci 2023; 24:ijms24119503. [PMID: 37298453 DOI: 10.3390/ijms24119503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) represents the third most common form of muscular dystrophy and is characterized by muscle weakness and atrophy. FSHD is caused by the altered expression of the transcription factor double homeobox 4 (DUX4), which is involved in several significantly altered pathways required for myogenesis and muscle regeneration. While DUX4 is normally silenced in the majority of somatic tissues in healthy individuals, its epigenetic de-repression has been linked to FSHD, resulting in DUX4 aberrant expression and cytotoxicity in skeletal muscle cells. Understanding how DUX4 is regulated and functions could provide useful information not only to further understand FSHD pathogenesis, but also to develop therapeutic approaches for this disorder. Therefore, this review discusses the role of DUX4 in FSHD by examining the possible molecular mechanisms underlying the disease as well as novel pharmacological strategies targeting DUX4 aberrant expression.
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Affiliation(s)
- Elisa Duranti
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
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7
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Erdmann H, Scharf F, Gehling S, Benet-Pagès A, Jakubiczka S, Becker K, Seipelt M, Kleefeld F, Knop KC, Prott EC, Hiebeler M, Montagnese F, Gläser D, Vorgerd M, Hagenacker T, Walter MC, Reilich P, Neuhann T, Zenker M, Holinski-Feder E, Schoser B, Abicht A. Methylation of the 4q35 D4Z4 repeat defines disease status in facioscapulohumeral muscular dystrophy. Brain 2023; 146:1388-1402. [PMID: 36100962 DOI: 10.1093/brain/awac336] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/06/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic diagnosis of facioscapulohumeral muscular dystrophy (FSHD) remains a challenge in clinical practice as it cannot be detected by standard sequencing methods despite being the third most common muscular dystrophy. The conventional diagnostic strategy addresses the known genetic parameters of FSHD: the required presence of a permissive haplotype, a size reduction of the D4Z4 repeat of chromosome 4q35 (defining FSHD1) or a pathogenic variant in an epigenetic suppressor gene (consistent with FSHD2). Incomplete penetrance and epistatic effects of the underlying genetic parameters as well as epigenetic parameters (D4Z4 methylation) pose challenges to diagnostic accuracy and hinder prediction of clinical severity. In order to circumvent the known limitations of conventional diagnostics and to complement genetic parameters with epigenetic ones, we developed and validated a multistage diagnostic workflow that consists of a haplotype analysis and a high-throughput methylation profile analysis (FSHD-MPA). FSHD-MPA determines the average global methylation level of the D4Z4 repeat array as well as the regional methylation of the most distal repeat unit by combining bisulphite conversion with next-generation sequencing and a bioinformatics pipeline and uses these as diagnostic parameters. We applied the diagnostic workflow to a cohort of 148 patients and compared the epigenetic parameters based on FSHD-MPA to genetic parameters of conventional genetic testing. In addition, we studied the correlation of repeat length and methylation level within the most distal repeat unit with age-corrected clinical severity and age at disease onset in FSHD patients. The results of our study show that FSHD-MPA is a powerful tool to accurately determine the epigenetic parameters of FSHD, allowing discrimination between FSHD patients and healthy individuals, while simultaneously distinguishing FSHD1 and FSHD2. The strong correlation between methylation level and clinical severity indicates that the methylation level determined by FSHD-MPA accounts for differences in disease severity among individuals with similar genetic parameters. Thus, our findings further confirm that epigenetic parameters rather than genetic parameters represent FSHD disease status and may serve as a valuable biomarker for disease status.
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Affiliation(s)
- Hannes Erdmann
- Medical Genetics Center (MGZ), 80335 Munich, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | | | | | - Anna Benet-Pagès
- Medical Genetics Center (MGZ), 80335 Munich, Germany
- Institute of Neurogenomics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Sibylle Jakubiczka
- Institute of Human Genetics, Universitätsklinikum Magdeburg, Otto-von-Guericke Universität, 39120 Magdeburg, Germany
| | | | - Maria Seipelt
- Department of Neurology, Universitätsklinikum Marburg, Philipps-University Marburg, 35043 Marburg, Germany
| | - Felix Kleefeld
- Department of Neurology and Experimental Neurology, Charité Berlin, 10117 Berlin, Germany
| | | | | | - Miriam Hiebeler
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | - Federica Montagnese
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | | | - Matthias Vorgerd
- Department of Neurology, Berufgenossenschaftliches Universitätsklinikum Bergmannsheil, Ruhr-Universität Bochum, 44789 Bochum, Germany
| | - Tim Hagenacker
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, 45147 Essen, Germany
| | - Maggie C Walter
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | - Peter Reilich
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | | | - Martin Zenker
- Institute of Human Genetics, Universitätsklinikum Magdeburg, Otto-von-Guericke Universität, 39120 Magdeburg, Germany
| | - Elke Holinski-Feder
- Medical Genetics Center (MGZ), 80335 Munich, Germany
- Department of Medicine IV, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | - Angela Abicht
- Medical Genetics Center (MGZ), 80335 Munich, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
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D4Z4 Methylation Levels Combined with a Machine Learning Pipeline Highlight Single CpG Sites as Discriminating Biomarkers for FSHD Patients. Cells 2022; 11:cells11244114. [PMID: 36552879 PMCID: PMC9777431 DOI: 10.3390/cells11244114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/18/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
The study describes a protocol for methylation analysis integrated with Machine Learning (ML) algorithms developed to classify Facio-Scapulo-Humeral Dystrophy (FSHD) subjects. The DNA methylation levels of two D4Z4 regions (DR1 and DUX4-PAS) were assessed by an in-house protocol based on bisulfite sequencing and capillary electrophoresis, followed by statistical and ML analyses. The study involved two independent cohorts, namely a training group of 133 patients with clinical signs of FSHD and 150 healthy controls (CTRL) and a testing set of 27 FSHD patients and 25 CTRL. As expected, FSHD patients showed significantly reduced methylation levels compared to CTRL. We utilized single CpG sites to develop a ML pipeline able to discriminate FSHD subjects. The model identified four CpGs sites as the most relevant for the discrimination of FSHD subjects and showed high metrics values (accuracy: 0.94, sensitivity: 0.93, specificity: 0.96). Two additional models were developed to differentiate patients with lower D4Z4 size and patients who might carry pathogenic variants in FSHD genes, respectively. Overall, the present model enables an accurate classification of FSHD patients, providing additional evidence for DNA methylation as a powerful disease biomarker that could be employed for prioritizing subjects to be tested for FSHD.
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9
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Findlay AR, Weihl CC. Genetic-Based Treatment Strategies for Muscular Dystrophy and Congenital Myopathies. Continuum (Minneap Minn) 2022; 28:1800-1816. [PMID: 36537981 PMCID: PMC10496150 DOI: 10.1212/con.0000000000001203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW This article discusses the foundational concepts of genetic treatment strategies employed in neuromuscular medicine, as well as the importance of genetic testing as a requirement for applying gene-based therapy. RECENT FINDINGS Gene therapies have become a reality for several neuromuscular disorders. Exon-skipping and (in Europe) ribosomal read-through approaches are currently available to a subset of patients with Duchenne muscular dystrophy. Microdystrophin gene replacement has shown promise and is nearing the final stages of clinical trials. Numerous gene-based therapies for other muscular dystrophies and congenital myopathies are progressing toward approval as well. SUMMARY Muscular dystrophies and congenital myopathies are a heterogenous group of hereditary muscle disorders. Confirming a diagnosis with genetic testing is not only critical for guiding management, but also an actual prerequisite for current and future gene therapies. Recessive loss-of-function or dominant haploinsufficiency disorders may be treated with gene replacement strategies, whereas dominant negative and toxic gain-of-function disorders are best addressed with a variety of knockdown approaches. It is important to recognize that many therapeutics are mutation specific and will only benefit a subset of individuals with a specific disease.
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10
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Mariot V, Dumonceaux J. Gene Editing to Tackle Facioscapulohumeral Muscular Dystrophy. Front Genome Ed 2022; 4:937879. [PMID: 35910413 PMCID: PMC9334676 DOI: 10.3389/fgeed.2022.937879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is a skeletal muscle disease caused by the aberrant expression of the DUX4 gene in the muscle tissue. To date, different therapeutic approaches have been proposed, targeting DUX4 at the DNA, RNA or protein levels. The recent development of the clustered regularly interspaced short-palindromic repeat (CRISPR) based technology opened new avenues of research, and FSHD is no exception. For the first time, a cure for genetic muscular diseases can be considered. Here, we describe CRISPR-based strategies that are currently being investigated for FSHD. The different approaches include the epigenome editing targeting the DUX4 gene and its promoter, gene editing targeting the polyadenylation of DUX4 using TALEN, CRISPR/cas9 or adenine base editing and the CRISPR-Cas9 genome editing for SMCHD1. We also discuss challenges facing the development of these gene editing based therapeutics.
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Konstantonis D, Kekou K, Papaefthymiou P, Vastardis H, Konstantoni N, Athanasiou M, Svingou M, Margariti A, Panousopoulou A. Orofacial Muscle Weakening in Facioscapulohumeral Muscular Dystrophy (FSHD) Patients. CHILDREN 2022; 9:children9010096. [PMID: 35053721 PMCID: PMC8774153 DOI: 10.3390/children9010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/02/2022]
Abstract
Background: Facioscapulohumeral muscular dystrophy is the third most commonly found type of muscular dystrophy. The aim of this study was to correlate the D4Z4 repeat array fragment size to the orofacial muscle weakening exhibited in a group of patients with a genetically supported diagnosis of FSHD. Methods: Molecular genetic analysis was performed for 52 patients (27 female and 25 male) from a group that consisted of 36 patients with autosomal dominant pedigrees and 16 patients with either sporadic or unknown family status. The patients were tested with the southern blotting technique, using EcoRI/Avrll double digestion, and fragments were detected by a p13E-11 telomeric probe. Spearman’s correlation was used to compare the fragment size with the degree of muscle weakening found in the forehead, periocular and perioral muscles. Results: A positive non-significant correlation between the DNA fragment size and severity of muscle weakness was found for the forehead (r = 0.27; p = 0187), the periocular (r = 0.24; p = 0.232) and the left and right perioral (r = 0.29; p = 0.122), (r = 0.32; p = 0.085) muscles. Conclusions: Although FSHD patients exhibited a decrease in muscular activity related to the forehead, perioral, and periocular muscles the genotype–phenotype associations confirmed a weak to moderate non-significant correlation between repeat size and the severity of muscle weakness. Orofacial muscle weakening and its association with a D4Z4 contraction alone may not have the significance to serve as a prognostic biomarker, due to the weak to moderate association. Further studies with larger sample sizes are needed to determine the degree of genetic involvement in the facial growth in FSHD patients.
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Affiliation(s)
- Dimitrios Konstantonis
- Department of Orthodontics, School of Dentistry, National and Kapodistrian University of Athens, GR-115 27 Athens, Greece;
- Clinic of Orthodontics and Pediatric Dentistry, Center of Dental Medicine, University of Zurich, CH-8032 Zurich, Switzerland
- Correspondence:
| | - Kyriaki Kekou
- Laboratory of Medical Genetics, Children’s Hospital Agia Sophia, National and Kapodistrian University of Athens, GR-115 27 Athens, Greece; (K.K.); (M.S.)
| | - Petros Papaefthymiou
- Department of Orthodontics, Faculty of Dentistry, Marmara University, Istanbul 34854, Turkey;
| | - Heleni Vastardis
- Department of Orthodontics, School of Dentistry, National and Kapodistrian University of Athens, GR-115 27 Athens, Greece;
| | - Nikoleta Konstantoni
- ATX Braces & Smile Aligners, In Private Practice of Orthodontics, 1601 E Pflugerville Pkwy Building 2, Pflugerville, TX 78660, USA;
| | - Maria Athanasiou
- Athensbestsmiles, In Private Practice of Orthodontics, 49 Alopekis, GR-106 76 Athens, Greece;
| | - Maria Svingou
- Laboratory of Medical Genetics, Children’s Hospital Agia Sophia, National and Kapodistrian University of Athens, GR-115 27 Athens, Greece; (K.K.); (M.S.)
| | - Anastasia Margariti
- Department of Elderly Medicine, University Hospital Sussex NHS Foundation Trust, St. Richard’s Hospital, Spitalfield Ln, Chichester PO19 6SE, UK;
| | - Angeliki Panousopoulou
- Department of Neurology, Korgialenio-Benakio Hellenic Red Cross Hospital, GR-115 26 Athens, Greece;
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