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Wilson VD, Bommart S, Passerieux E, Thomas C, Pincemail J, Picot MC, Mercier J, Portet F, Arbogast S, Laoudj-Chenivesse D. Muscle strength, quantity and quality and muscle fat quantity and their association with oxidative stress in patients with facioscapulohumeral muscular dystrophy: Effect of antioxidant supplementation. Free Radic Biol Med 2024; 219:112-126. [PMID: 38574978 DOI: 10.1016/j.freeradbiomed.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
The purpose of this study was to identify causes of quadriceps muscle weakness in facioscapulohumeral muscular dystrophy (FSHD). To this aim, we evaluated quadriceps muscle and fat volumes by magnetic resonance imaging and their relationships with muscle strength and oxidative stress markers in adult patients with FSHD (n = 32) and healthy controls (n = 7), and the effect of antioxidant supplementation in 20 of the 32 patients with FSHD (n = 10 supplementation and n = 10 placebo) (NCT01596803). Compared with healthy controls, the dominant quadriceps strength and quality (muscle strength per unit of muscle volume) were decreased in patients with FSHD. In addition, fat volume was increased, without changes in total muscle volume. Moreover, in patients with FSHD, the lower strength of the non-dominant quadriceps was associated with lower muscle quality compared with the dominant muscle. Antioxidant supplementation significantly changed muscle and fat volumes in the non-dominant quadriceps, and muscle quality in the dominant quadriceps. This was associated with improved muscle strength (both quadriceps) and antioxidant response. These findings suggest that quadriceps muscle strength decline may not be simply explained by atrophy and may be influenced also by the muscle intrinsic characteristics. As FSHD is associated with increased oxidative stress, supplementation might reduce oxidative stress and increase antioxidant defenses, promoting changes in muscle function.
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Affiliation(s)
- Vinicius Dias Wilson
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France; Centro Universitário Estácio de Belo Horizonte, Minas Gerais, Brazil.
| | - Sébastien Bommart
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France; Department of Radiology, CHU of Montpellier, Arnaud de Villeneuve Hospital, 34090, Montpellier, France.
| | - Emilie Passerieux
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France.
| | - Claire Thomas
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France; LBEPS, Univ Evry, IRBA, University Paris Saclay, 91025, Evry, France.
| | - Joël Pincemail
- Department of CREDEC, Department of Medical Chemistry, University Hospital of Liege, Sart Tilman, Liege, Belgium.
| | - Marie Christine Picot
- Department of Biostatistics and Epidemiology, University Hospital, Montpellier, France; CIC 1001-INSERM, Montpellier, France.
| | - Jacques Mercier
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France; Department of Clinical Physiology, CHU of Montpellier, Montpellier, France.
| | - Florence Portet
- Department of Clinical Physiology, CHU of Montpellier, Montpellier, France; U1061 INSERM, CHU de Montpellier, Montpellier University, France.
| | - Sandrine Arbogast
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France.
| | - Dalila Laoudj-Chenivesse
- PhyMedExp, Université de Montpellier, INSERM, CNRS, Montpellier, France; Department of Clinical Physiology, CHU of Montpellier, Montpellier, France.
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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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3
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Jiang J, Cai X, Qu H, Yao Q, He T, Yang M, Zhou H, Zhang X. Case report: Identification of facioscapulohumeral muscular dystrophy 1 in two siblings with normal phenotypic parents using optical genome mapping. Front Neurol 2024; 15:1258831. [PMID: 38361638 PMCID: PMC10867183 DOI: 10.3389/fneur.2024.1258831] [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: 07/14/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
Objective Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is one of the most common forms of autosomal-dominant muscular dystrophies characterized by variable disease penetrance due to shortened D4Z4 repeat units on 4q35. The molecular diagnosis of FSHD1 is usually made by Southern blotting, which is complex, time-consuming, and lacks clinical practicality. Therefore, in this study, optical genome mapping (OGM) is employed for the genetic diagnosis of FSHD1. Furthermore, epigenetic heterogeneity is determined from methylation analysis. Methods Genomic DNA samples from four members of the same family were subjected to whole-exome sequencing. OGM was used to identify structural variations in D4Z4, while sodium bisulfite sequencing helped identify the methylation levels of CpG sites in a region located distally to the D4Z4 array. A multidisciplinary team collected the clinical data, and comprehensive family analyses aided in the assessment of phenotypes and genotypes. Results Whole-exome sequencing did not reveal variants related to clinical phenotypes in the patients. OGM showed that the proband was a compound heterozygote for the 4qA allele with four and eight D4Z4 repeat units, whereas the affected younger brother had only one 4qA allele with four D4Z4 repeat units. Both the proband and her younger brother were found to display asymmetric weakness predominantly involving the facial, shoulder girdle, and upper arm muscles, whereas the younger brother had more severe clinical symptoms. The proband's father, who was found to be normal after a neurological examination, also carried the 4qA allele with eight D4Z4 repeat units. The unaffected mother exhibited 49 D4Z4 repeat units of the 4qA allele and a minor mosaic pattern with four D4Z4 repeat units of the 4qA allele. Consequently, the presence of the 4qA allele in the four D4Z4 repeat units strongly pointed to the occurrence of maternal germline mosaicism. The CpG6 methylation levels were lower in symptomatic patients compared to those in the asymptomatic parents. The older sister had lower clinical scores and ACSS and higher CpG6 methylation levels than that of her younger brother. Conclusions In this study, two siblings with FSHD1 with phenotypically normal parents were identified by OGM. Our findings suggest that the 4qA allele of four D4Z4 repeats was inherited through maternal germline mosaicism. The clinical phenotype heterogeneity is influenced by the CpG6 methylation levels. The results of this study greatly aid in the molecular diagnosis of FSHD1 and in also understanding the clinical phenotypic variability underlying the disease.
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Affiliation(s)
- Jieni Jiang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaotang Cai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Rehabilitation, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Haibo Qu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Radiology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qiang Yao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Tiantian He
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Mei Yang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Hui Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Rehabilitation, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xuemei Zhang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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4
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Lemmers RJLF, Butterfield R, van der Vliet PJ, de Bleecker JL, van der Pol L, Dunn DM, Erasmus CE, D'Hooghe M, Verhoeven K, Balog J, Bigot A, van Engelen B, Statland J, Bugiardini E, van der Stoep N, Evangelista T, Marini-Bettolo C, van den Bergh P, Tawil R, Voermans NC, Vissing J, Weiss RB, van der Maarel SM. Autosomal dominant in cis D4Z4 repeat array duplication alleles in facioscapulohumeral dystrophy. Brain 2024; 147:414-426. [PMID: 37703328 PMCID: PMC10834250 DOI: 10.1093/brain/awad312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/26/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) has a unique genetic aetiology resulting in partial chromatin relaxation of the D4Z4 macrosatellite repeat array on 4qter. This D4Z4 chromatin relaxation facilitates inappropriate expression of the transcription factor DUX4 in skeletal muscle. DUX4 is encoded by a retrogene that is embedded within the distal region of the D4Z4 repeat array. In the European population, the D4Z4 repeat array is usually organized in a single array that ranges between 8 and 100 units. D4Z4 chromatin relaxation and DUX4 derepression in FSHD is most often caused by repeat array contraction to 1-10 units (FSHD1) or by a digenic mechanism requiring pathogenic variants in a D4Z4 chromatin repressor like SMCHD1, combined with a repeat array between 8 and 20 units (FSHD2). With a prevalence of 1.5% in the European population, in cis duplications of the D4Z4 repeat array, where two adjacent D4Z4 arrays are interrupted by a spacer sequence, are relatively common but their relationship to FSHD is not well understood. In cis duplication alleles were shown to be pathogenic in FSHD2 patients; however, there is inconsistent evidence for the necessity of an SMCHD1 mutation for disease development. To explore the pathogenic nature of these alleles we compared in cis duplication alleles in FSHD patients with or without pathogenic SMCHD1 variant. For both groups we showed duplication-allele-specific DUX4 expression. We studied these alleles in detail using pulsed-field gel electrophoresis-based Southern blotting and molecular combing, emphasizing the challenges in the characterization of these rearrangements. Nanopore sequencing was instrumental to study the composition and methylation of the duplicated D4Z4 repeat arrays and to identify the breakpoints and the spacer sequence between the arrays. By comparing the composition of the D4Z4 repeat array of in cis duplication alleles in both groups, we found that specific combinations of proximal and distal repeat array sizes determine their pathogenicity. Supported by our algorithm to predict pathogenicity, diagnostic laboratories should now be furnished to accurately interpret these in cis D4Z4 repeat array duplications, alleles that can easily be missed in routine settings.
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Affiliation(s)
- Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | | | - Patrick J van der Vliet
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | | | - Ludo van der Pol
- University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Corrie E Erasmus
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Marc D'Hooghe
- Department of Neurology, Algemeen Ziekenhuis Sint-Jan, 8000, Brugge, Belgium
| | - Kristof Verhoeven
- Department of Neurology, Algemeen Ziekenhuis Sint-Jan, 8000, Brugge, Belgium
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Anne Bigot
- Sorbonne Université, Inserm UMRS974, Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France
| | - Baziel van Engelen
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | | | - Enrico Bugiardini
- National Hospital For Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Teresinha Evangelista
- Unité de Morphologie Neuromusculaire, Institut de Myologie, AP-HP, F-75013, Paris, France
| | - Chiara Marini-Bettolo
- The John Walton Muscular Dystrophy Research Centre, Faculty of Medical Sciences, Newcastle upon Tyne, NE1 3BZ, UK
| | | | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, NY 14642, Rochester, USA
| | - Nicol C Voermans
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - John Vissing
- Department of Neurology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
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5
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Zheng F, Qiu L, Chen L, Zheng Y, He Q, Lin X, Lin M, Lin Y, Fu Y, Wang N, Wang Z. An epigenetic basis for genetic anticipation in facioscapulohumeral muscular dystrophy type 1. Brain 2023; 146:e107-e110. [PMID: 37352893 DOI: 10.1093/brain/awad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/10/2023] [Indexed: 06/25/2023] Open
Affiliation(s)
- Fuze Zheng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Liangliang Qiu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Long Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Ying Zheng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Qifang He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xiaodan Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Minting Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Yi Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Ying Fu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Zhiqiang Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
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6
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Megalizzi D, Trastulli G, Caputo V, Colantoni L, Caltagirone C, Strafella C, Cascella R, Giardina E. Epigenetic profiling of the D4Z4 locus: Optimization of the protocol for studying DNA methylation at single CpG site level. Electrophoresis 2023; 44:1588-1594. [PMID: 37565369 DOI: 10.1002/elps.202300058] [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: 03/21/2023] [Revised: 06/27/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023]
Abstract
The alteration of epigenetic modifications, including DNA methylation, can contribute to the etiopathogenesis and progression of many diseases. Among them, facioscapulohumeral dystrophy (FSHD) is a muscular disorder characterized by the loss of repressive epigenetic features affecting the D4Z4 locus (4q35). As a consequence, these alterations are responsible for DNA hypomethylation and a transcriptional-active chromatin conformation change that, in turn, lead to the aberrant expression of DUX4 in muscle cells. In the present study, methylation levels of 29 CpG sites of the DR1 region (within each repeat unit of the D4Z4 macrosatellite) were assessed on 335 subjects by employing primers designed for enhancing the performance of the assay. First, the DR1 original primers were optimized by adding M13 oligonucleotide tails. Moreover, the DR1 reverse primer was replaced with a degenerate one. As a result, the protocol optimization allowed a better sequencing resolution and a more accurate evaluation of DR1 methylation levels. Moreover, the assessment of the repeatability of measurements proved the reliability and robustness of the assay. The optimized protocol emerges as an excellent method to detect methylation levels compatible with FSHD.
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Affiliation(s)
- Domenica Megalizzi
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Giulia Trastulli
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Claudia Strafella
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Emiliano Giardina
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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7
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Tapia Del Fierro A, den Hamer B, Benetti N, Jansz N, Chen K, Beck T, Vanyai H, Gurzau AD, Daxinger L, Xue S, Ly TTN, Wanigasuriya I, Iminitoff M, Breslin K, Oey H, Krom YD, van der Hoorn D, Bouwman LF, Johanson TM, Ritchie ME, Gouil QA, Reversade B, Prin F, Mohun T, van der Maarel SM, McGlinn E, Murphy JM, Keniry A, de Greef JC, Blewitt ME. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nat Commun 2023; 14:5466. [PMID: 37749075 PMCID: PMC10519958 DOI: 10.1038/s41467-023-40992-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets. Moreover, it also results in enhanced silencing at the facioscapulohumeral muscular dystrophy associated macrosatellite-array, D4Z4, resulting in enhanced repression of DUX4 encoded by this repeat. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against other epigenetic regulators, including PRC2 and CTCF, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1's role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.
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Affiliation(s)
- Andres Tapia Del Fierro
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Natalia Benetti
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Hannah Vanyai
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lucia Daxinger
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Iromi Wanigasuriya
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Harald Oey
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dinja van der Hoorn
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Linde F Bouwman
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Quentin A Gouil
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Timothy Mohun
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | | | - Edwina McGlinn
- EMBL Australia, Monash University, Clayton, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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8
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Butterfield RJ, Dunn DM, Duval B, Moldt S, Weiss RB. Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing. Genome Res 2023; 33:1439-1454. [PMID: 37798116 PMCID: PMC10620044 DOI: 10.1101/gr.277871.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/02/2023] [Indexed: 10/07/2023]
Abstract
Fascioscapulohumeral muscular dystrophy (FSHD) is caused by a unique genetic mechanism that relies on contraction and hypomethylation of the D4Z4 macrosatellite array on the Chromosome 4q telomere allowing ectopic expression of the DUX4 gene in skeletal muscle. Genetic analysis is difficult because of the large size and repetitive nature of the array, a nearly identical array on the 10q telomere, and the presence of divergent D4Z4 arrays scattered throughout the genome. Here, we combine nanopore long-read sequencing with Cas9-targeted enrichment of 4q and 10q D4Z4 arrays for comprehensive genetic analysis including determination of the length of the 4q and 10q D4Z4 arrays with base-pair resolution. In the same assay, we differentiate 4q from 10q telomeric sequences, determine A/B haplotype, identify paralogous D4Z4 sequences elsewhere in the genome, and estimate methylation for all CpGs in the array. Asymmetric, length-dependent methylation gradients were observed in the 4q and 10q D4Z4 arrays that reach a hypermethylation point at approximately 10 D4Z4 repeat units, consistent with the known threshold of pathogenic D4Z4 contractions. High resolution analysis of individual D4Z4 repeat methylation revealed areas of low methylation near the CTCF/insulator region and areas of high methylation immediately preceding the DUX4 transcriptional start site. Within the DUX4 exons, we observed a waxing/waning methylation pattern with a 180-nucleotide periodicity, consistent with phased nucleosomes. Targeted nanopore sequencing complements recently developed molecular combing and optical mapping approaches to genetic analysis for FSHD by adding precision of the length measurement, base-pair resolution sequencing, and quantitative methylation analysis.
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Affiliation(s)
- Russell J Butterfield
- Department of Pediatrics, University of Utah, Salt Lake City, Utah 84108, USA;
- Department of Neurology, University of Utah, Salt Lake City, Utah 84132, USA
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Brett Duval
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Sarah Moldt
- Department of Pediatrics, University of Utah, Salt Lake City, Utah 84108, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
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9
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Strafella C, Caputo V, Bortolani S, Torchia E, Megalizzi D, Trastulli G, Monforte M, Colantoni L, Caltagirone C, Ricci E, Tasca G, Cascella R, Giardina E. Whole exome sequencing highlights rare variants in CTCF, DNMT1, DNMT3A, EZH2 and SUV39H1 as associated with FSHD. Front Genet 2023; 14:1235589. [PMID: 37674478 PMCID: PMC10477786 DOI: 10.3389/fgene.2023.1235589] [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: 06/06/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023] Open
Abstract
Introduction: Despite the progress made in the study of Facioscapulohumeral Dystrophy (FSHD), the wide heterogeneity of disease complicates its diagnosis and the genotype-phenotype correlation among patients and within families. In this context, the present work employed Whole Exome Sequencing (WES) to investigate known and unknown genetic contributors that may be involved in FSHD and may represent potential disease modifiers, even in presence of a D4Z4 Reduced Allele (DRA). Methods: A cohort of 126 patients with clinical signs of FSHD were included in the study, which were characterized by D4Z4 sizing, methylation analysis and WES. Specific protocols were employed for D4Z4 sizing and methylation analysis, whereas the Illumina® Next-Seq 550 system was utilized for WES. The study included both patients with a DRA compatible with FSHD diagnosis and patients with longer D4Z4 alleles. In case of patients harboring relevant variants from WES, the molecular analysis was extended to the family members. Results: The WES data analysis highlighted 20 relevant variants, among which 14 were located in known genetic modifiers (SMCHD1, DNMT3B and LRIF1) and 6 in candidate genes (CTCF, DNMT1, DNMT3A, EZH2 and SUV39H1). Most of them were found together with a permissive short (4-7 RU) or borderline/long DRA (8-20 RU), supporting the possibility that different genes can contribute to disease heterogeneity in presence of a FSHD permissive background. The segregation and methylation analysis among family members, together with clinical findings, provided a more comprehensive picture of patients. Discussion: Our results support FSHD pathomechanism being complex with a multigenic contribution by several known (SMCHD1, DNMT3B, LRIF1) and possibly other candidate genes (CTCF, DNMT1, DNMT3A, EZH2, SUV39H1) to disease penetrance and expressivity. Our results further emphasize the importance of extending the analysis of molecular findings within the proband's family, with the purpose of providing a broader framework for understanding single cases and allowing finer genotype-phenotype correlations in FSHD-affected families.
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Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Sara Bortolani
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Eleonora Torchia
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Domenica Megalizzi
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Giulia Trastulli
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Mauro Monforte
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Enzo Ricci
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Istituto di Neurologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giorgio Tasca
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trusts, Newcastle UponTyne, United Kingdom
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
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10
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Zheng F, Qiu L, Chen L, Zheng Y, Lin X, He J, Lin X, He Q, Lin Y, Lin L, Wang L, Lin F, Yang K, Lin M, Lin Y, Fu Y, Wang N, Wang Z. Association of 4qA-Specific Distal D4Z4 Hypomethylation With Disease Severity and Progression in Facioscapulohumeral Muscular Dystrophy. Neurology 2023; 101:e225-e237. [PMID: 37225433 PMCID: PMC10382269 DOI: 10.1212/wnl.0000000000207418] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/31/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND AND OBJECTIVES The objective of this study was to examine whether the regional methylation levels at the most distal D4Z4 repeat units (RU) in the 4qA-permissive haplotype were associated with disease severity and progression in facioscapulohumeral muscular dystrophy type 1 (FSHD1). METHODS This 21-year, retrospective, observational cohort study was conducted at the Fujian Neuromedical Center (FNMC) in China. Methylation levels of the most distal D4Z4 RU, including 10 CpGs, were assessed in all participants by bisulfite sequencing. Patients with FSHD1 were stratified into 4 groups based on methylation percentage quartiles, including LM1 (low methylation), LM2 (low to intermediate methylation), LM3 (intermediate to high methylation), and highest methylation (HM) levels. Patients received evaluations of motor function focusing on lower extremity (LE) progression at baseline and in follow-ups. FSHD clinical score (CS), age-corrected clinical severity scale (ACSS), and modified Rankin scale were used to assess motor function. RESULTS The methylation levels of the 10 CpGs were significantly lower in all 823 patients with genetically confirmed FSHD1 than in 341 healthy controls (HCs). CpG6 methylation levels could distinguish the following: (1) patients with FSHD1 from HCs; (2) symptomatic from asymptomatic/unaffected patients; (3) patients with LE involvement from those without LE involvement, with AUCs (95% CI) of 0.9684 (0.9584-0.9785), 0.7417 (0.6903-0.7931), and 0.6386 (0.5816-0.6956), respectively. Lower CpG6 methylation levels were correlated with higher CS (r = -0.392), higher ACSS (r = -0.432), and earlier onset age of first-ever muscle weakness (r = 0.297). For the LM1, LM2, LM3, and HM groups, the respective proportions of LE involvement were 52.9%, 44.2%, 36.9%, and 23.4%; and onset ages of LE involvement were 20, 26.5, 25, and 26.5 years. Cox regression analysis-adjusted for sex, age at examination, D4Z4 RU, and 4qA/B haplotype-showed that the LM1, LM2, and LM3 groups (i.e., groups with lower methylation levels) had a higher risk of independent ambulation loss, with HRs (95% CI) of 3.523 (1.565-7.930), 3.356 (1.458-7.727), and 2.956 (1.245-7.020), respectively. DISCUSSION 4q35 distal D4Z4 hypomethylation is correlated with disease severity and progression to lower extremity involvement.
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Affiliation(s)
- Fuze Zheng
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Liangliang Qiu
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Long Chen
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ying Zheng
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiaodan Lin
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Junjie He
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xin Lin
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qifang He
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yuhua Lin
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Lin Lin
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Lili Wang
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
| | - Feng Lin
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Kang Yang
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Minting Lin
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yi Lin
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ying Fu
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ning Wang
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
| | - Zhiqiang Wang
- From the Department of Neurology and Institute of Neurology of First Affiliated Hospital (F.Z., L.Q., L.C., Y.Z., Xiaodan Lin, J.H., Xin Lin, Q.H., Yuhua Lin, L.L., L.W., F.L., K.Y., M.L., Yi Lin, Y.F., N.W., Z.W.), Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou; and Department of Neurology (L.Q., Xin Lin, F.L., M.L., Yi Lin, Y.F., N.W., Z.W.), National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
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11
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Šikrová D, Testa AM, Willemsen I, van den Heuvel A, Tapscott SJ, Daxinger L, Balog J, van der Maarel SM. SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action. Commun Biol 2023; 6:677. [PMID: 37380887 DOI: 10.1038/s42003-023-05053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/17/2023] [Indexed: 06/30/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by the epigenetic derepression of the 4q-linked D4Z4 macrosatellite repeat resulting in inappropriate expression of the D4Z4 repeat-encoded DUX4 gene in skeletal muscle. In 5% of FSHD cases, D4Z4 chromatin relaxation is due to germline mutations in one of the chromatin modifiers SMCHD1, DNMT3B or LRIF1. The mechanism of SMCHD1- and LRIF1-mediated D4Z4 repression is not clear. We show that somatic loss-of-function of either SMCHD1 or LRIF1 does not result in D4Z4 chromatin changes and that SMCHD1 and LRIF1 form an auxiliary layer of D4Z4 repressive mechanisms. We uncover that SMCHD1, together with the long isoform of LRIF1, binds to the LRIF1 promoter and silences LRIF1 expression. The interdependency of SMCHD1 and LRIF1 binding differs between D4Z4 and the LRIF1 promoter, and both loci show different transcriptional responses to either early developmentally or somatically perturbed chromatin function of SMCHD1 and LRIF1.
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Affiliation(s)
- Darina Šikrová
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Alessandra M Testa
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
- Department of Biomedical Sciences, University of Padua, 35100, Padua, Italy
| | - Iris Willemsen
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Anita van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands.
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12
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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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13
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Amzali S, Wilson VD, Bommart S, Picot MC, Galas S, Mercier J, Poucheret P, Cristol JP, Arbogast S, Laoudj-Chenivesse D. Nutritional Status of Patients with Facioscapulohumeral Muscular Dystrophy. Nutrients 2023; 15:nu15071673. [PMID: 37049513 PMCID: PMC10096775 DOI: 10.3390/nu15071673] [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: 02/17/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
In patients with facioscapulohumeral muscular dystrophy (FSHD), a rare genetic neuromuscular disease, reduced physical performance is associated with lower blood levels of vitamin C, zinc, selenium, and increased oxidative stress markers. Supplementation of vitamin C, vitamin E, zinc, and selenium improves the quadriceps' physical performance. Here, we compared the nutritional status of 74 women and 85 men with FSHD. Calorie intake was lower in women with FSHD than in men. Moreover, we assessed vitamin C, vitamin E, zinc, copper, and selenium intakes in diet and their concentrations in the plasma. Vitamin E, copper, and zinc intake were lower in women with FSHD than in men, whereas plasma vitamin C, copper levels, and copper/zinc ratio were higher in women with FSHD than in men. The dietary intake and plasma concentrations of the studied vitamins and minerals were not correlated in both sexes. A well-balanced and varied diet might not be enough in patients with FSHD to correct the observed vitamin/mineral deficiencies. A low energy intake is a risk factor for suboptimal intake of proteins, vitamins, and minerals that are important for protein synthesis and other metabolic pathways and that might contribute to progressive muscle mass loss. Antioxidant supplementation and higher protein intake seem necessary to confer protection against oxidative stress and skeletal muscle mass loss.
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Affiliation(s)
- Sedda Amzali
- PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, 34295 Montpellier, France
| | - Vinicius Dias Wilson
- Departamento de Educação Física, Centro Universitário Estácio de Belo Horizonte, Belo Horizonte 30411-052, Minas Gerais, Brazil
- Pró-Reitoria de Assuntos Comunitários e Estudantis, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina 39100-000, Minas Gerais, Brazil
| | - Sébastien Bommart
- PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, 34295 Montpellier, France
- Service de Radiologie, Hôpital Arnaud-de-Villeneuve, CHU de Montpellier, 34295 Montpellier, France
| | - Marie-Christine Picot
- Clinical Research and Epidemiology Unit (Department of Medicale Information), Centre d'Investigation Clinique 1411 INSERM, CHU Montpellier, Univ Montpellier, CEDEX 5, 34295 Montpellier, France
| | - Simon Galas
- Institut des Biomolecules Max Mousseron (IBMM), Centre National de Recherche Scientifique (CNRS), University of Montpellier, ENSCM, 34000 Montpellier, France
| | - Jacques Mercier
- PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, 34295 Montpellier, France
- Department of Clinical Physiology, CHU of Montpellier, 34295 Montpellier, France
| | - Patrick Poucheret
- Qualisud, Université de Montpellier, CIRAD, Institut Agro, IRD, Avignon Université, Université de La Réunion, 34000 Montpellier, France
| | - Jean-Paul Cristol
- PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, 34295 Montpellier, France
- Department of Biochemistry, University Hospital of Montpellier, 34295 Montpellier, France
| | - Sandrine Arbogast
- PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, 34295 Montpellier, France
| | - Dalila Laoudj-Chenivesse
- PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, 34295 Montpellier, France
- Department of Clinical Physiology, CHU of Montpellier, 34295 Montpellier, France
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14
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Tihaya MS, Mul K, Balog J, de Greef JC, Tapscott SJ, Tawil R, Statland JM, van der Maarel SM. Facioscapulohumeral muscular dystrophy: the road to targeted therapies. Nat Rev Neurol 2023; 19:91-108. [PMID: 36627512 DOI: 10.1038/s41582-022-00762-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Advances in the molecular understanding of facioscapulohumeral muscular dystrophy (FSHD) have revealed that FSHD results from epigenetic de-repression of the DUX4 gene in skeletal muscle, which encodes a transcription factor that is active in early embryonic development but is normally silenced in almost all somatic tissues. These advances also led to the identification of targets for disease-altering therapies for FSHD, as well as an improved understanding of the molecular mechanism of the disease and factors that influence its progression. Together, these developments led the FSHD research community to shift its focus towards the development of disease-modifying treatments for FSHD. This Review presents advances in the molecular and clinical understanding of FSHD, discusses the potential targeted therapies that are currently being explored, some of which are already in clinical trials, and describes progress in the development of FSHD-specific outcome measures and assessment tools for use in future clinical trials.
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Affiliation(s)
- Mara S Tihaya
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Karlien Mul
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jeffrey M Statland
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS, USA
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15
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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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16
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Caputo V, Megalizzi D, Fabrizio C, Termine A, Colantoni L, Caltagirone C, Giardina E, Cascella R, Strafella C. Update on the Molecular Aspects and Methods Underlying the Complex Architecture of FSHD. Cells 2022; 11:cells11172687. [PMID: 36078093 PMCID: PMC9454908 DOI: 10.3390/cells11172687] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the knowledge of the main mechanisms involved in facioscapulohumeral muscular dystrophy (FSHD), the high heterogeneity and variable penetrance of the disease complicate the diagnosis, characterization and genotype–phenotype correlation of patients and families, raising the need for further research and data. Thus, the present review provides an update of the main molecular aspects underlying the complex architecture of FSHD, including the genetic factors (related to D4Z4 repeated units and FSHD-associated genes), epigenetic elements (D4Z4 methylation status, non-coding RNAs and high-order chromatin interactions) and gene expression profiles (FSHD transcriptome signatures both at bulk tissue and single-cell level). In addition, the review will also describe the methods currently available for investigating the above-mentioned features and how the resulting data may be combined with artificial-intelligence-based pipelines, with the purpose of developing a multifunctional tool tailored to enhancing the knowledge of disease pathophysiology and progression and fostering the research for novel treatment strategies, as well as clinically useful biomarkers. In conclusion, the present review highlights how FSHD should be regarded as a disease characterized by a molecular spectrum of genetic and epigenetic factors, whose alteration plays a differential role in DUX4 repression and, subsequently, contributes to determining the FSHD phenotype.
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Affiliation(s)
- Valerio Caputo
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
| | - Domenica Megalizzi
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
| | - Carlo Fabrizio
- Data Science Unit, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
| | - Andrea Termine
- Data Science Unit, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavorial Neurology, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-0651501550
| | - Raffaella Cascella
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
| | - Claudia Strafella
- Genomic Medicine Laboratory-UILDM, Santa Lucia Foundation IRCCS, 00179 Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
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17
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Wang Z, Qiu L, Lin M, Chen L, Zheng F, Lin L, Lin F, Ye Z, Lin X, He J, Wang L, Lin X, He Q, Chen W, Lin Y, Fu Y, Wang N. Prevalence and disease progression of genetically-confirmed facioscapulohumeral muscular dystrophy type 1 (FSHD1) in China between 2001 and 2020: a nationwide population-based study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 18:100323. [PMID: 35024656 PMCID: PMC8671729 DOI: 10.1016/j.lanwpc.2021.100323] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is a rare disease, which is often underdiagnosed due to its heterogeneous presentations and complex molecular genetic basis, leading to a lack of population-based epidemiology data, especially of prevalence and disease progression. METHODS Fujian Neuromedical Centre (FNMC) is a diagnosis centre for clinical-genetic FSHD in China, and the only one employing pulsed-field gel electrophoresis (PFGE)-based Southern blotting for all FSHD1 genetic tests. Three sources distributed across all six spatial zones in China, were used to obtain information regarding FSHD1 events, namely, FNMC, Genetic and Myopathy Group (branches of the Neurology Society of the Chinese Medical Association), and "FSHD-China" (an organization supported by FSHD patients). During 2001-2020, all genetically-confirmed FSHD1 from China were registered in FNMC. Follow-up was conducted in the 20-year period to obtain data on disease progression, which was mainly described in terms of independent ambulation loss. FINDINGS Of the 1,744 FSHD1 genetic tests (total test number 1,802) included in the analysis, 997 (57.2%) patients from 620 families were diagnosed with FSHD1. The estimated prevalence of genetically-confirmed FSHD1 in China is 0.75 per million (95% confidence interval [CI], 0.70-0.79) during 2001-2020, with 0.78 (95% CI, 0.72-0.85) in males and 0.71 (95% CI, 0.65-0.78) in females. The estimated prevalence increased from 0.22 (95% CI, 0.19-0.26) per million in 2001-2015 to 0.53 (95% CI, 0.49-0.57) per million in 2016-2020 (p < 0.001). The prevalence in Fujian province was 7.10 per million, 4.66 per million, and 2.44 per million, during 2001-2020, 2001-2015, and 2016-2020, respectively. Among the 861 symptomatic plus asymptomatic patients of the total 997 patients, the median onset age at first-ever muscle weakness was 16 years of age (range 1-81); the median number of contracted D4Z4 repeats was 5 units (range 1-9); the median 4qA-allele-specific methylation level was 41% (range 14%-69%). Of the 977 symptomatic patients followed-up during 2001-2020, 117 patients (12.0%) lost independent ambulation. The expected duration from onset of first-ever muscle weakness to onset of independent ambulation loss was 40 years. The group with loss of independent ambulation had a smaller number of contracted D4Z4 repeats (p < 0.001) and had an earlier onset age of first-ever muscle weakness (p < 0.001) compared to the group without loss of independent ambulation. INTERPRETATION Our research captures the largest genetically-confirmed FSHD1 population worldwide, to calculate its prevalence of 0.75 per million in China from 2001 to 2020. Approximately 12.0% of symptomatic plus asymptomatic patients of FSHD1 will lose independent ambulation in 40 years from onset of first-ever muscle weakness. FUNDING This work has been supported by the grants (U2005201, 81870902, N.W.) and (81974193, 81671237, Z.Q.W.) from the National Natural Science Foundation of China; Joint Funds for the Innovation of Science and Technology of Fujian Province (2018Y9082) (N.W.), and the Key Clinical Specialty Discipline Construction Program of Fujian (N.W.).
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Affiliation(s)
- Zhiqiang Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Liangliang Qiu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Minting Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Long Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Fuze Zheng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Lin Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Feng Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Zhixian Ye
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xiaodan Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Junjie He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Lili Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xin Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Qifang He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Yi Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Ying Fu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
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18
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Heher P, Ganassi M, Weidinger A, Engquist EN, Pruller J, Nguyen TH, Tassin A, Declèves AE, Mamchaoui K, Grillari J, Kozlov AV, Zammit PS. Interplay between mitochondrial reactive oxygen species, oxidative stress and hypoxic adaptation in facioscapulohumeral muscular dystrophy: Metabolic stress as potential therapeutic target. Redox Biol 2022; 51:102251. [PMID: 35248827 PMCID: PMC8899416 DOI: 10.1016/j.redox.2022.102251] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is characterised by descending skeletal muscle weakness and wasting. FSHD is caused by mis-expression of the transcription factor DUX4, which is linked to oxidative stress, a condition especially detrimental to skeletal muscle with its high metabolic activity and energy demands. Oxidative damage characterises FSHD and recent work suggests metabolic dysfunction and perturbed hypoxia signalling as novel pathomechanisms. However, redox biology of FSHD remains poorly understood, and integrating the complex dynamics of DUX4-induced metabolic changes is lacking. Here we pinpoint the kinetic involvement of altered mitochondrial ROS metabolism and impaired mitochondrial function in aetiology of oxidative stress in FSHD. Transcriptomic analysis in FSHD muscle biopsies reveals strong enrichment for pathways involved in mitochondrial complex I assembly, nitrogen metabolism, oxidative stress response and hypoxia signalling. We found elevated mitochondrial ROS (mitoROS) levels correlate with increases in steady-state mitochondrial membrane potential in FSHD myogenic cells. DUX4 triggers mitochondrial membrane polarisation prior to oxidative stress generation and apoptosis through mitoROS, and affects mitochondrial health through lipid peroxidation. We identify complex I as the primary target for DUX4-induced mitochondrial dysfunction, with strong correlation between complex I-linked respiration and cellular oxygenation/hypoxia signalling activity in environmental hypoxia. Thus, FSHD myogenesis is uniquely susceptible to hypoxia-induced oxidative stress as a consequence of metabolic mis-adaptation. Importantly, mitochondria-targeted antioxidants rescue FSHD pathology more effectively than conventional antioxidants, highlighting the central involvement of disturbed mitochondrial ROS metabolism. This work provides a pathomechanistic model by which DUX4-induced changes in oxidative metabolism impair muscle function in FSHD, amplified when metabolic adaptation to varying O2 tension is required. Transcriptomics data from FSHD muscle indicates enrichment for disturbed mitochondrial pathways. Disturbed mitochondrial ROS metabolism correlates with mitochondrial membrane polarisation and myotube hypotrophy. DUX4-induced changes in mitochondrial function precede mitoROS generation and affect hypoxia signalling via complex I. FSHD is sensitive to environmental hypoxia, which increases ROS levels in FSHD myotubes. Hypotrophy in hypoxic FSHD myotubes is efficiently rescued with mitochondria-targeted antioxidants.
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19
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Jia FF, Drew AP, Nicholson GA, Corbett A, Kumar KR. Facioscapulohumeral muscular dystrophy type 2: an update on the clinical, genetic, and molecular findings. Neuromuscul Disord 2021; 31:1101-1112. [PMID: 34711481 DOI: 10.1016/j.nmd.2021.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 11/25/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a common genetic disease of the skeletal muscle with a characteristic pattern of weakness. Facioscapulohumeral muscular dystrophy type 2 (FSHD2) accounts for approximately 5% of all cases of FSHD and describes patients without a D4Z4 repeat contraction on chromosome 4. Phenotypically FSHD2 shows virtually no difference from FSHD1 and both forms of FSHD arise via a common downstream mechanism of epigenetic derepression of the transcription factor DUX4 in skeletal muscle cells. This results in expression of DUX4 and target genes leading to skeletal muscle toxicity. Over the past decade, major progress has been made in our understanding of the genetic and epigenetic architecture that underlies FSHD2 pathogenesis, as well as the clinical manifestations and disease progression. These include the finding that FSHD2 is a digenic disease and that mutations in the genes SMCHD1, DNMT3B, and more recently LRIF1, can cause FSHD2. FSHD2 is complex and it is important that clinicians keep abreast of recent developments; this review aims to serve as an update of the clinical, genetic, and molecular research into this condition.
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Affiliation(s)
- Fangzhi Frank Jia
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia.
| | - Alexander P Drew
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.
| | - Garth Alexander Nicholson
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Alastair Corbett
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Kishore Raj Kumar
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
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20
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Precise Epigenetic Analysis Using Targeted Bisulfite Genomic Sequencing Distinguishes FSHD1, FSHD2, and Healthy Subjects. Diagnostics (Basel) 2021; 11:diagnostics11081469. [PMID: 34441403 PMCID: PMC8393475 DOI: 10.3390/diagnostics11081469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/01/2021] [Accepted: 08/11/2021] [Indexed: 12/16/2022] Open
Abstract
The true prevalence of facioscapulohumeral muscular dystrophy (FSHD) is unknown due to difficulties with accurate clinical evaluation and the complexities of current genetic diagnostics. Interestingly, all forms of FSHD are linked to epigenetic changes in the chromosome 4q35 D4Z4 macrosatellite, suggesting that epigenetic analysis could provide an avenue for sequence-based FSHD diagnostics. However, studies assessing DNA methylation at the FSHD locus have produced conflicting results; thus, the utility of this technique as an FSHD diagnostic remains controversial. Here, we critically compared two protocols for epigenetic analysis of the FSHD region using bisulfite genomic sequencing: Jones et al., that contends to be individually diagnostic for FSHD1 and FSHD2, and Gaillard et al., that can identify some changes in DNA methylation levels between groups of clinically affected FSHD and healthy subjects, but is not individually diagnostic for any form of FSHD. We performed both sets of assays on the same genetically confirmed samples and showed that this discrepancy was due strictly to differences in amplicon specificity. We propose that the epigenetic status of the FSHD-associated D4Z4 arrays, when accurately assessed, is a diagnostic for genetic FSHD and can readily distinguish between healthy, FSHD1 and FSHD2. Thus, epigenetic diagnosis of FSHD, which can be performed on saliva DNA, will greatly increase accessibility to FSHD diagnostics for populations around the world.
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21
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Schätzl T, Kaiser L, Deigner HP. Facioscapulohumeral muscular dystrophy: genetics, gene activation and downstream signalling with regard to recent therapeutic approaches: an update. Orphanet J Rare Dis 2021; 16:129. [PMID: 33712050 PMCID: PMC7953708 DOI: 10.1186/s13023-021-01760-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Whilst a disease-modifying treatment for Facioscapulohumeral muscular dystrophy (FSHD) does not exist currently, recent advances in complex molecular pathophysiology studies of FSHD have led to possible therapeutic approaches for its targeted treatment. Although the underlying genetics of FSHD have been researched extensively, there remains an incomplete understanding of the pathophysiology of FSHD in relation to the molecules leading to DUX4 gene activation and the downstream gene targets of DUX4 that cause its toxic effects. In the context of the local proximity of chromosome 4q to the nuclear envelope, a contraction of the D4Z4 macrosatellite induces lower methylation levels, enabling the ectopic expression of DUX4. This disrupts numerous signalling pathways that mostly result in cell death, detrimentally affecting skeletal muscle in affected individuals. In this regard different options are currently explored either to suppress the transcription of DUX4 gene, inhibiting DUX4 protein from its toxic effects, or to alleviate the symptoms triggered by its numerous targets.
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Affiliation(s)
- Teresa Schätzl
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054, Villingen-Schwenningen, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054, Villingen-Schwenningen, Germany
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104, Freiburg i. Br., Germany
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054, Villingen-Schwenningen, Germany.
- EXIM Department, Fraunhofer Institute IZI, Leipzig, Schillingallee 68, 18057, Rostock, Germany.
- Faculty of Science, Tuebingen University, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
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22
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Lemmers RJLF, van der Vliet PJ, Blatnik A, Balog J, Zidar J, Henderson D, Goselink R, Tapscott SJ, Voermans NC, Tawil R, Padberg GWAM, van Engelen BG, van der Maarel SM. Chromosome 10q-linked FSHD identifies DUX4 as principal disease gene. J Med Genet 2021; 59:180-188. [PMID: 33436523 DOI: 10.1136/jmedgenet-2020-107041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/05/2020] [Accepted: 11/14/2020] [Indexed: 01/24/2023]
Abstract
BACKGROUND Facioscapulohumeral dystrophy (FSHD) is an inherited muscular dystrophy clinically characterised by muscle weakness starting with the facial and upper extremity muscles. A disease model has been developed that postulates that failure in somatic repression of the transcription factor DUX4 embedded in the D4Z4 repeat on chromosome 4q causes FSHD. However, due to the position of the D4Z4 repeat close to the telomere and the complex genetic and epigenetic aetiology of FSHD, there is ongoing debate about the transcriptional deregulation of closely linked genes and their involvement in FSHD. METHOD Detailed genetic characterisation and gene expression analysis of patients with clinically confirmed FSHD and control individuals. RESULTS Identification of two FSHD families in which the disease is caused by repeat contraction and DUX4 expression from chromosome 10 due to a de novo D4Z4 repeat exchange between chromosomes 4 and 10. We show that the genetic lesion causal to FSHD in these families is physically separated from other candidate genes on chromosome 4. We demonstrate that muscle cell cultures from affected family members exhibit the characteristic molecular features of FSHD, including DUX4 and DUX4 target gene expression, without showing evidence for transcriptional deregulation of other chromosome 4-specific candidate genes. CONCLUSION This study shows that in rare situations, FSHD can occur on chromosome 10 due to an interchromosomal rearrangement with the FSHD locus on chromosome 4q. These findings provide further evidence that DUX4 derepression is the dominant disease pathway for FSHD. Hence, therapeutic strategies should focus on DUX4 as the primary target.
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Affiliation(s)
- Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Ana Blatnik
- Cancer Genetics Clinic, Institute of Oncology, Ljubljana, Slovenia
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Janez Zidar
- Division of Neurology, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Don Henderson
- Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA
| | - Rianne Goselink
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA
| | - George W A M Padberg
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Baziel Gm van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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23
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Bouwman LF, den Hamer B, Verveer EP, Lerink LJS, Krom YD, van der Maarel SM, de Greef JC. Dnmt3b regulates DUX4 expression in a tissue-dependent manner in transgenic D4Z4 mice. Skelet Muscle 2020; 10:27. [PMID: 33004076 PMCID: PMC7528343 DOI: 10.1186/s13395-020-00247-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/10/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is a skeletal muscle disorder that is caused by derepression of the transcription factor DUX4 in skeletal muscle cells. Apart from SMCHD1, DNMT3B was recently identified as a disease gene and disease modifier in FSHD. However, the exact role of DNMT3B at the D4Z4 repeat array remains unknown. METHODS To determine the role of Dnmt3b on DUX4 repression, hemizygous mice with a FSHD-sized D4Z4 repeat array (D4Z4-2.5 mice) were cross-bred with mice carrying an in-frame exon skipping mutation in Dnmt3b (Dnmt3bMommeD14 mice). Additionally, siRNA knockdowns of Dnmt3b were performed in mouse embryonic stem cells (mESCs) derived from the D4Z4-2.5 mouse model. RESULTS In mESCs derived from D4Z4-2.5 mice, Dnmt3b was enriched at the D4Z4 repeat array and DUX4 transcript levels were upregulated after a knockdown of Dnmt3b. In D4Z4-2.5/Dnmt3bMommeD14 mice, Dnmt3b protein levels were reduced; however, DUX4 RNA levels in skeletal muscles were not enhanced and no pathology was observed. Interestingly, D4Z4-2.5/Dnmt3bMommeD14 mice showed a loss of DNA methylation at the D4Z4 repeat array and significantly higher DUX4 transcript levels in secondary lymphoid organs. As these lymphoid organs seem to be more sensitive to epigenetic modifiers of the D4Z4 repeat array, different immune cell populations were quantified in the spleen and inguinal lymph nodes of D4Z4-2.5 mice crossed with Dnmt3bMommeD14 mice or Smchd1MommeD1 mice. Only in D4Z4-2.5/Smchd1MommeD1 mice the immune cell populations were disturbed. CONCLUSIONS Our data demonstrates that loss of Dnmt3b results in derepression of DUX4 in lymphoid tissues and mESCs but not in myogenic cells of D4Z4-2.5/Dnmt3bMommeD14 mice. In addition, the Smchd1MommeD1 variant seems to have a more potent role in DUX4 derepression. Our studies suggest that the immune system is particularly but differentially sensitive to D4Z4 chromatin modifiers which may provide a molecular basis for the yet underexplored immune involvement in FSHD.
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Affiliation(s)
- Linde F Bouwman
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Elwin P Verveer
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Lente J S Lerink
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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24
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Giacomucci G, Monforte M, Diaz-Manera J, Mul K, Fernandez Torrón R, Maggi L, Marini Bettolo C, Dahlqvist JR, Haberlova J, Camaño P, Gros M, Tartaglione T, Cristiano L, Gerevini S, Calandra P, Deidda G, Giardina E, Sacconi S, Straub V, Vissing J, Van Engelen B, Ricci E, Tasca G. Deep phenotyping of facioscapulohumeral muscular dystrophy type 2 by magnetic resonance imaging. Eur J Neurol 2020; 27:2604-2615. [PMID: 32697863 DOI: 10.1111/ene.14446] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND PURPOSE The aim was to define the radiological picture of facioscapulohumeral muscular dystrophy 2 (FSHD2) in comparison with FSHD1 and to explore correlations between imaging and clinical/molecular data. METHODS Upper girdle and/or lower limb muscle magnetic resonance imaging scans of 34 molecularly confirmed FSHD2 patients from nine European neuromuscular centres were analysed. T1-weighted and short-tau inversion recovery (STIR) sequences were used to evaluate the global pattern and to assess the extent of fatty replacement and muscle oedema. RESULTS The most frequently affected muscles were obliquus and transversus abdominis, semimembranosus, soleus and gluteus minimus in the lower limbs; trapezius, serratus anterior, latissimus dorsi and pectoralis major in the upper girdle. Iliopsoas, popliteus, obturator internus and tibialis posterior in the lower limbs and subscapularis, spinati, sternocleidomastoid and levator scapulae in the upper girdle were the most spared. Asymmetry and STIR hyperintensities were consistent features. The pattern of muscle involvement was similar to that of FSHD1, and the combined involvement of trapezius, abdominal and hamstring muscles, together with complete sparing of iliopsoas and subscapularis, was detected in 91% of patients. Peculiar differences were identified in a rostro-caudal gradient, a predominant involvement of lower limb muscles compared to the upper girdle, and in the higher percentage of STIR hyperintensities in FSHD2. CONCLUSION This multicentre study defines the pattern of muscle involvement in FSHD2, providing useful information for diagnostics and clinical trial design. Both similarities and differences between FSHD1 and FSHD2 were detected, which is also relevant to better understand the pathogenic mechanisms underlying the FSHD-related disease spectrum.
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Affiliation(s)
- G Giacomucci
- Istituto di Neurologia, Università Cattolica del Sacro Cuore, Roma, Italy
| | - M Monforte
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - J Diaz-Manera
- Neuromuscular Disorders Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - K Mul
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R Fernandez Torrón
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Neurology Department, Biodonostia Health Research Institute, Neuromuscular Area, Hospital Donostia, Basque Health Service, Doctor Begiristain, Donostia-San Sebastian, Spain
| | - L Maggi
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - C Marini Bettolo
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - J R Dahlqvist
- Copenhagen Neuromuscular Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - J Haberlova
- Department of Pediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - P Camaño
- Biodonostia, Neurosciences Area, Group of Neuromuscular Diseases; Biodonostia-Osakidetza Basque Health Service, Molecular Diagnostics Platform, San Sebastian, Spain
| | - M Gros
- Université Côte d'Azur (UCA), Peripheral Nervous System, Muscle and ALS Department, Pasteur 2 Hospital, Nice, France.,Université Côte d'Azur, Inserm, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - T Tartaglione
- Radiology Unit, Istituto Dermopatico dell'Immacolata-IRCCS-FLMM, Rome, Italy
| | - L Cristiano
- Radiology Unit, Istituto Dermopatico dell'Immacolata-IRCCS-FLMM, Rome, Italy
| | - S Gerevini
- Neuroradiology Department, IRCCS San Raffaele Hospital, Milan, Italy
| | - P Calandra
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo, Rome, Italy
| | - G Deidda
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo, Rome, Italy
| | - E Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation IRCSS-University of Rome 'Tor Vergata', Rome, Italy
| | - S Sacconi
- Université Côte d'Azur (UCA), Peripheral Nervous System, Muscle and ALS Department, Pasteur 2 Hospital, Nice, France.,Université Côte d'Azur, Inserm, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - V Straub
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - J Vissing
- Copenhagen Neuromuscular Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - B Van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E Ricci
- Istituto di Neurologia, Università Cattolica del Sacro Cuore, Roma, Italy.,Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - G Tasca
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
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25
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Rojas LA, Valentine E, Accorsi A, Maglio J, Shen N, Robertson A, Kazmirski S, Rahl P, Tawil R, Cadavid D, Thompson LA, Ronco L, Chang AN, Cacace AM, Wallace O. p38α Regulates Expression of DUX4 in a Model of Facioscapulohumeral Muscular Dystrophy. J Pharmacol Exp Ther 2020; 374:489-498. [DOI: 10.1124/jpet.119.264689] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
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Greco A, Goossens R, van Engelen B, van der Maarel SM. Consequences of epigenetic derepression in facioscapulohumeral muscular dystrophy. Clin Genet 2020; 97:799-814. [PMID: 32086799 PMCID: PMC7318180 DOI: 10.1111/cge.13726] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/08/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a common hereditary myopathy, is caused either by the contraction of the D4Z4 macrosatellite repeat at the distal end of chromosome 4q to a size of 1 to 10 repeat units (FSHD1) or by mutations in D4Z4 chromatin modifiers such as Structural Maintenance of Chromosomes Hinge Domain Containing 1 (FSHD2). These two genotypes share a phenotype characterized by progressive and often asymmetric muscle weakening and atrophy, and common epigenetic alterations of the D4Z4 repeat. All together, these epigenetic changes converge the two genetic forms into one disease and explain the derepression of the DUX4 gene, which is otherwise kept epigenetically silent in skeletal muscle. DUX4 is consistently transcriptionally upregulated in FSHD1 and FSHD2 skeletal muscle cells where it is believed to exercise a toxic effect. Here we provide a review of the recent literature describing the progress in understanding the complex genetic and epigenetic architecture of FSHD, with a focus on one of the consequences that these epigenetic changes inflict, the DUX4-induced immune deregulation cascade. Moreover, we review the latest therapeutic strategies, with particular attention to the potential of epigenetic correction of the FSHD locus.
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Affiliation(s)
- Anna Greco
- Department of Neurology, Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
- Department of Experimental Internal MedicineRadboud University Medical CenterNijmegenThe Netherlands
| | - Remko Goossens
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Baziel van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
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27
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Nikolic A, Jones TI, Govi M, Mele F, Maranda L, Sera F, Ricci G, Ruggiero L, Vercelli L, Portaro S, Villa L, Fiorillo C, Maggi L, Santoro L, Antonini G, Filosto M, Moggio M, Angelini C, Pegoraro E, Berardinelli A, Maioli MA, D’Angelo G, Di Muzio A, Siciliano G, Tomelleri G, D’Esposito M, Della Ragione F, Brancaccio A, Piras R, Rodolico C, Mongini T, Magdinier F, Salsi V, Jones PL, Tupler R. Interpretation of the Epigenetic Signature of Facioscapulohumeral Muscular Dystrophy in Light of Genotype-Phenotype Studies. Int J Mol Sci 2020; 21:ijms21072635. [PMID: 32290091 PMCID: PMC7178248 DOI: 10.3390/ijms21072635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 01/03/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is characterized by incomplete penetrance and intra-familial clinical variability. The disease has been associated with the genetic and epigenetic features of the D4Z4 repetitive elements at 4q35. Recently, D4Z4 hypomethylation has been proposed as a reliable marker in the FSHD diagnosis. We exploited the Italian Registry for FSHD, in which FSHD families are classified using the Clinical Comprehensive Evaluation Form (CCEF). A total of 122 index cases showing a classical FSHD phenotype (CCEF, category A) and 110 relatives were selected to test with the receiver operating characteristic (ROC) curve, the diagnostic and predictive value of D4Z4 methylation. Moreover, we performed DNA methylation analysis in selected large families with reduced penetrance characterized by the co-presence of subjects carriers of one D4Z4 reduced allele with no signs of disease or presenting the classic FSHD clinical phenotype. We observed a wide variability in the D4Z4 methylation levels among index cases revealing no association with clinical manifestation or disease severity. By extending the analysis to family members, we revealed the low predictive value of D4Z4 methylation in detecting the affected condition. In view of the variability in D4Z4 methylation profiles observed in our large cohort, we conclude that D4Z4 methylation does not mirror the clinical expression of FSHD. We recommend that measurement of this epigenetic mark must be interpreted with caution in clinical practice.
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Affiliation(s)
- Ana Nikolic
- Department of Science of Life, Institute of Biology, University of Modena and Reggio Emilia, 41125 Modena, Italy; (A.N.); (M.G.); (V.S.)
| | - Takako I Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (T.I.J.); (P.L.J.)
| | - Monica Govi
- Department of Science of Life, Institute of Biology, University of Modena and Reggio Emilia, 41125 Modena, Italy; (A.N.); (M.G.); (V.S.)
| | - Fabiano Mele
- Center for Genome Research, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Louise Maranda
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA 01605, USA;
| | - Francesco Sera
- Department of Public Health, Environments and Society, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - Giulia Ricci
- Department of Clinical and Experimental Medicine, Neurological Clinic, 56126 Pisa, Italy; (G.R.); (G.S.)
| | - Lucia Ruggiero
- Department of Neurosciences and Reproductive and Odontostomatologic Sciences, University Federico II, 80137 Naples, Italy; (L.R.); (L.S.)
| | - Liliana Vercelli
- Department of Neurosciences “Rita Levi Montalcini”, University of Turin, 10124 Turin, Italy; (L.V.); (T.M.)
| | - Simona Portaro
- Department of Neuroscience, Mental Health and Sensory Organs, S. Andrea Hospital, University of Rome “Sapienza”, 00185 Rome, Italy; (S.P.); (G.A.)
| | - Luisa Villa
- Department of Neuroscience, Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (L.V.); (M.M.)
| | - Chiara Fiorillo
- Pediatric Neurology and Neuromuscular Disorders Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16126 Genoa, Italy;
| | - Lorenzo Maggi
- IRCCS Foundation, C. Besta Neurological Institute, 20133 Milan, Italy;
| | - Lucio Santoro
- Department of Neurosciences and Reproductive and Odontostomatologic Sciences, University Federico II, 80137 Naples, Italy; (L.R.); (L.S.)
| | - Giovanni Antonini
- Department of Neuroscience, Mental Health and Sensory Organs, S. Andrea Hospital, University of Rome “Sapienza”, 00185 Rome, Italy; (S.P.); (G.A.)
| | | | - Maurizio Moggio
- Department of Neuroscience, Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (L.V.); (M.M.)
| | - Corrado Angelini
- Ospedale S.Camillo IRCCS, Lido di Venezia, 20126 Venezia, Italy;
| | - Elena Pegoraro
- Department of Neurosciences, University of Padua, 35128 Padua, Italy;
| | - Angela Berardinelli
- Neurology and Psychiatry, IRCCS Institute ‘C.Mondino’ Foundation, 27100 Pavia, Italy;
| | | | - Grazia D’Angelo
- Department of Neurorehabilitation, IRCCS Institute Eugenio Medea, 23842 Bosisio Parini, Italy;
| | - Antonino Di Muzio
- Center for Neuromuscular Disease, CeSI, University ‘‘G. D’Annunzio’’, 66100 Chieti, Italy;
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Neurological Clinic, 56126 Pisa, Italy; (G.R.); (G.S.)
| | - Giuliano Tomelleri
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Maurizio D’Esposito
- Institute of Genetics and Biophysics, A. Buzzati Traverso, IGB, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (M.D.); (F.D.R.); (A.B.)
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics, A. Buzzati Traverso, IGB, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (M.D.); (F.D.R.); (A.B.)
| | - Arianna Brancaccio
- Institute of Genetics and Biophysics, A. Buzzati Traverso, IGB, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy; (M.D.); (F.D.R.); (A.B.)
| | - Rachele Piras
- ASL8, Centro Sclerosi Multipla, 09126 Cagliari, Italy; (M.A.M.); (R.P.)
| | - Carmelo Rodolico
- Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy;
| | - Tiziana Mongini
- Department of Neurosciences “Rita Levi Montalcini”, University of Turin, 10124 Turin, Italy; (L.V.); (T.M.)
| | | | - Valentina Salsi
- Department of Science of Life, Institute of Biology, University of Modena and Reggio Emilia, 41125 Modena, Italy; (A.N.); (M.G.); (V.S.)
| | - Peter L. Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (T.I.J.); (P.L.J.)
| | - Rossella Tupler
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research at the University of Massachusetts Medical School, Worcester, MA 01605, USA
- Correspondence: ; Tel.: +39-059-2055414
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Qiu L, Ye Z, Lin L, Wang L, Lin X, He J, Lin F, Xu G, Cai N, Jin M, Chen H, Lin M, Wang N, Wang Z. Clinical and genetic features of somatic mosaicism in facioscapulohumeral dystrophy. J Med Genet 2020; 57:777-785. [PMID: 32170003 DOI: 10.1136/jmedgenet-2019-106638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/02/2020] [Accepted: 02/05/2020] [Indexed: 11/03/2022]
Abstract
PURPOSE To analyse the clinical spectrum, genetic features, specific D4Z4 hypomethylation status and genotype-phenotype correlations for somatic mosaicism in facioscapulohumeral dystrophy (FSHD). METHODS This was a prospective, hospital-based, case-control, observational study of 35 participants with FSHD with somatic mosaicism recruited over 10 years, with 17 penetrant patients and 18 non-penetrant mutation carriers. This study also included a univariate comparison of 17 paired mosaic and non-mosaic patients with FSHD. RESULTS Mosaic participants with FSHD varied in age of diagnosis (median 45; range 15-65 years), muscle strength (FSHD clinical score median 0; range 0-10 points), clinical severity (age-corrected clinical severity score (ACSS) median 0; range 0-467 points), D4Z4 repeats (median 3; range 2-5 units), mosaic proportion (median 55%; range 27%-72%) and D4Z4 methylation extent (median 49.82%; range 27.17%-64.51%). The genotypic severity scale and D4Z4 methylation extent were significantly associated with ACSS (p1=0.003; p2=0.002). Among the matched pairs, the 17 mosaic patients had shorter D4Z4 repeats, lower FSHD clinical scores and lower ACSS than non-mosaic patients. Additionally, 34 of 35 (97%) participants carried two mosaic arrays, while a single patient had three mosaic arrays (3%). Two cases also carried four-type non-mosaic arrays on chromosome 10 (translocation configuration). CONCLUSIONS Broadly, this large mosaic FSHD cohort exhibited significant clinical heterogeneity and relatively slight disease severity. Both genotypic severity scale and D4Z4 hypomethylation status served as modifiers of clinical phenotypes. Consistent with previous reports, mitotic interchromosomal/intrachromosomal gene conversion without crossover was here identified as a major genetic mechanism underlying mosaic FSHD.
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Affiliation(s)
- Liangliang Qiu
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhixian Ye
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Lin Lin
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Lili Wang
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiaodan Lin
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Junjie He
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Feng Lin
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Guorong Xu
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Naiqing Cai
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ming Jin
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Haizhu Chen
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Minting Lin
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Molecular Neurology, Fuzhou, China
| | - Ning Wang
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China .,Fujian Key Laboratory of Molecular Neurology, Fuzhou, China
| | - Zhiqiang Wang
- Department of Neurology, Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China .,Fujian Key Laboratory of Molecular Neurology, Fuzhou, China
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29
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Salsi V, Magdinier F, Tupler R. Does DNA Methylation Matter in FSHD? Genes (Basel) 2020; 11:E258. [PMID: 32121044 PMCID: PMC7140823 DOI: 10.3390/genes11030258] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) has been associated with the genetic and epigenetic molecular features of the CpG-rich D4Z4 repeat tandem array at 4q35. Reduced DNA methylation of D4Z4 repeats is considered part of the FSHD mechanism and has been proposed as a reliable marker in the FSHD diagnostic procedure. We considered the assessment of D4Z4 DNA methylation status conducted on distinct cohorts using different methodologies. On the basis of the reported results we conclude that the percentage of DNA methylation detected at D4Z4 does not correlate with the disease status. Overall, data suggest that in the case of FSHD1, D4Z4 hypomethylation is a consequence of the chromatin structure present in the contracted allele, rather than a proxy of its function. Besides, CpG methylation at D4Z4 DNA is reduced in patients presenting diseases unrelated to muscle progressive wasting, like Bosma Arhinia and Microphthalmia syndrome, a developmental disorder, as well as ICF syndrome. Consistent with these observations, the analysis of epigenetic reprogramming at the D4Z4 locus in human embryonic and induced pluripotent stem cells indicate that other mechanisms, independent from the repeat number, are involved in the control of the epigenetic structure at D4Z4.
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Affiliation(s)
- Valentina Salsi
- Department of Life Sciences, University of Modena and Reggio Emilia, 4, 41121 Modena, Italy;
| | | | - Rossella Tupler
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 4, 41121 Modena, Italy
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, 4, 41121 Modena, Italy
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01003, USA
- Li Weibo Institute for Rare Diseases Research at the University of Massachusetts Medical School, Worcester, MA 01003, USA
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30
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Roche S, Dion C, Broucqsault N, Laberthonnière C, Gaillard MC, Robin JD, Lagarde A, Puppo F, Vovan C, Chaix C, Campana ES, Attarian S, Bartoli M, Bernard R, Nguyen K, Magdinier F. Methylation hotspots evidenced by deep sequencing in patients with facioscapulohumeral dystrophy and mosaicism. NEUROLOGY-GENETICS 2019; 5:e372. [PMID: 31872053 PMCID: PMC6878839 DOI: 10.1212/nxg.0000000000000372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 10/04/2019] [Indexed: 11/15/2022]
Abstract
Objective To investigate the distribution of cytosine-guanine dinucleotide (CpG) sites with a variable level of DNA methylation of the D4Z4 macrosatellite element in patients with facioscapulohumeral dystrophy (FSHD). Methods By adapting bisulfite modification to deep sequencing, we performed a comprehensive analysis of D4Z4 methylation across D4Z4 repeats and adjacent 4qA sequence in DNA from patients with FSHD1, FSHD2, or mosaicism and controls. Results Using hierarchical clustering, we identified clusters with different levels of methylation and separated, thereby the different groups of samples (controls, FSHD1, and FSHD2) based on their respective level of methylation. We further show that deep sequencing-based methylation analysis discriminates mosaic cases for which methylation changes have never been evaluated previously. Conclusions Altogether, our approach offers a new high throughput tool for estimation of the D4Z4 methylation level in the different subcategories of patients having FSHD. This methodology allows for a comprehensive and discriminative analysis of different regions along the macrosatellite repeat and identification of focal regions or CpG sites differentially methylated in patients with FSHD1 and FSHD2 but also complex cases such as those presenting mosaicism.
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Affiliation(s)
- Stéphane Roche
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Camille Dion
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Natacha Broucqsault
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Camille Laberthonnière
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Marie-Cécile Gaillard
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Jérôme D Robin
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Arnaud Lagarde
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Francesca Puppo
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Catherine Vovan
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Charlene Chaix
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Emmanuelle Salort Campana
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Shahram Attarian
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Marc Bartoli
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Rafaelle Bernard
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Karine Nguyen
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
| | - Frédérique Magdinier
- Aix Marseille University, INSERM, MMG (S.R., C.D., N.B., C.L., M.-C.G., J.D.R., A.L., F.P., E.S.C., S.A., M.B., R.B., K.N., F.M.); Département de Génétique Médicale (A.L., C.V., C.C., R.B., K.N.), AP-HM, Hôpital de la Timone enfants, Marseille; and Centre de référence pour les maladies neuromusculaires et la SLA (E.S.C., S.A.), AP-HM, Hôpital de la Timone, Marseille, France
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31
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Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, provides a powerful model of the complex interplay between genetic and epigenetic mechanisms of chromatin regulation. FSHD is caused by dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, aberrant expression of the DUX4 gene in skeletal muscle. DUX4 is a pioneer transcription factor that activates a program of gene expression during early human development, after which its expression is silenced in most somatic cells. When misexpressed in FSHD skeletal muscle, the DUX4 program leads to accumulated muscle pathology. Epigenetic regulators of the disease locus represent particularly attractive therapeutic targets for FSHD, as many are not global modifiers of the genome, and altering their expression or activity should allow correction of the underlying defect.
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MESH Headings
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 4
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing
- Genetic Loci
- Genome, Human
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/classification
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Mutation
- Severity of Illness Index
- DNA Methyltransferase 3B
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Affiliation(s)
- Charis L Himeda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| | - Peter L Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
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Mueller AL, O'Neill A, Jones TI, Llach A, Rojas LA, Sakellariou P, Stadler G, Wright WE, Eyerman D, Jones PL, Bloch RJ. Muscle xenografts reproduce key molecular features of facioscapulohumeral muscular dystrophy. Exp Neurol 2019; 320:113011. [PMID: 31306642 DOI: 10.1016/j.expneurol.2019.113011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/17/2019] [Accepted: 07/09/2019] [Indexed: 12/07/2022]
Abstract
Aberrant expression of DUX4, a gene unique to humans and primates, causes Facioscapulohumeral Muscular Dystrophy-1 (FSHD), yet the pathogenic mechanism is unknown. As transgenic overexpression models have largely failed to replicate the genetic changes seen in FSHD, many studies of endogenously expressed DUX4 have been limited to patient biopsies and myogenic cell cultures, which never fully differentiate into mature muscle fibers. We have developed a method to xenograft immortalized human muscle precursor cells from patients with FSHD and first-degree relative controls into the tibialis anterior muscle compartment of immunodeficient mice, generating human muscle xenografts. We report that FSHD cells mature into organized and innervated human muscle fibers with minimal contamination of murine myonuclei. They also reconstitute the satellite cell niche within the xenografts. FSHD xenografts express DUX4 and DUX4 downstream targets, retain the 4q35 epigenetic signature of their original donors, and express a novel protein biomarker of FSHD, SLC34A2. Ours is the first scalable, mature in vivo human model of FSHD. It should be useful for studies of the pathogenic mechanism of the disease as well as for testing therapeutic strategies targeting DUX4 expression.
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Affiliation(s)
- Amber L Mueller
- Department of Physiology, University of Maryland, Baltimore, 655 W, Baltimore St., Baltimore, MD 21201, United States of America
| | - Andrea O'Neill
- Department of Physiology, University of Maryland, Baltimore, 655 W, Baltimore St., Baltimore, MD 21201, United States of America
| | - Takako I Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, NV 89557, United States of America
| | - Anna Llach
- Department of Physiology, University of Maryland, Baltimore, 655 W, Baltimore St., Baltimore, MD 21201, United States of America
| | - Luis Alejandro Rojas
- Fulcrum Therapeutics, 26 Landsdowne St., Cambridge, MA 02139, United States of America
| | - Paraskevi Sakellariou
- Department of Physiology, University of Maryland, Baltimore, 655 W, Baltimore St., Baltimore, MD 21201, United States of America; FAME Laboratory Department of Exercise Science, University of Thessaly, Karies, Trikala 42100, Greece
| | - Guido Stadler
- Department of Cell Biology, UT Southwestern Medical Center Dallas, TX 75390, United States of America
| | - Woodring E Wright
- Department of Cell Biology, UT Southwestern Medical Center Dallas, TX 75390, United States of America
| | - David Eyerman
- Fulcrum Therapeutics, 26 Landsdowne St., Cambridge, MA 02139, United States of America
| | - Peter L Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, NV 89557, United States of America
| | - Robert J Bloch
- Department of Physiology, University of Maryland, Baltimore, 655 W, Baltimore St., Baltimore, MD 21201, United States of America.
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33
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Lemmers RJLF, van der Stoep N, Vliet PJVD, Moore SA, San Leon Granado D, Johnson K, Topf A, Straub V, Evangelista T, Mozaffar T, Kimonis V, Shaw ND, Selvatici R, Ferlini A, Voermans N, van Engelen B, Sacconi S, Tawil R, Lamers M, van der Maarel SM. SMCHD1 mutation spectrum for facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS) reveals disease-specific localisation of variants in the ATPase domain. J Med Genet 2019; 56:693-700. [PMID: 31243061 DOI: 10.1136/jmedgenet-2019-106168] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/11/2019] [Accepted: 05/15/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Variants in the Structural Maintenance of Chromosomes flexible Hinge Domain-containing protein 1 (SMCHD1) can cause facioscapulohumeral muscular dystrophy type 2 (FSHD2) and the unrelated Bosma arhinia microphthalmia syndrome (BAMS). In FSHD2, pathogenic variants are found anywhere in SMCHD1 while in BAMS, pathogenic variants are restricted to the extended ATPase domain. Irrespective of the phenotypic outcome, both FSHD2-associated and BAMS-associated SMCHD1 variants result in quantifiable local DNA hypomethylation. We compared FSHD2, BAMS and non-pathogenic SMCHD1 variants to derive genotype-phenotype relationships. METHODS Examination of SMCHD1 variants and methylation of the SMCHD1-sensitive FSHD locus DUX4 in 187 FSHD2 families, 41 patients with BAMS and in control individuals. Analysis of variants in a three-dimensional model of the ATPase domain of SMCHD1. RESULTS DUX4 methylation analysis is essential to establish pathogenicity of SMCHD1 variants. Although the FSHD2 mutation spectrum includes all types of variants covering the entire SMCHD1 locus, missense variants are significantly enriched in the extended ATPase domain. Identification of recurrent variants suggests disease-specific residues for FSHD2 and in BAMS, consistent with a largely disease-specific localisation of variants in SMCHD1. CONCLUSIONS The localisation of missense variants within the ATPase domain of SMCHD1 may contribute to the differences in phenotypic outcome.
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Affiliation(s)
| | - Nienke van der Stoep
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis, Leids Universitair Medisch Centrum, Leiden, The Netherlands
| | | | - Steven A Moore
- Department of Pathology, University of Iowa, Iowa City, Iowa, USA
| | | | - Katherine Johnson
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Ana Topf
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | | | - Tahseen Mozaffar
- Department of Neurology, University of California Irvine, Irvine, California, USA
| | - Virginia Kimonis
- Department of Pediatrics, University of California, Irvine, Irvine, California, USA
| | | | - Rita Selvatici
- Department of Medical Sciences; Medical Genetics Unit, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Dipartimento di Medicina Sperimentale e Diagnostica, Università di Ferrara, Ferrara, Italy
| | - Nicol Voermans
- Department of Neurology, Radboudumc, Nijmegen, Gelderland, The Netherlands
| | - Baziel van Engelen
- Department of Neurology, Radboudumc, Nijmegen, Gelderland, The Netherlands
| | - Sabrina Sacconi
- Centre de Référence Maladies Neuromusculaires, Hôpital Archet, Nice, France
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA
| | - Meindert Lamers
- Department of Cell and Chemical Biology, Leiden Universitair Medisch Centrum, Leiden, The Netherlands
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Banerji CRS, Panamarova M, Pruller J, Figeac N, Hebaishi H, Fidanis E, Saxena A, Contet J, Sacconi S, Severini S, Zammit PS. Dynamic transcriptomic analysis reveals suppression of PGC1α/ERRα drives perturbed myogenesis in facioscapulohumeral muscular dystrophy. Hum Mol Genet 2019; 28:1244-1259. [PMID: 30462217 PMCID: PMC6452176 DOI: 10.1093/hmg/ddy405] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 01/06/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy, linked to epigenetic derepression of D4Z4 repeats on chromosome 4q, leading to ectopic DUX4 expression. FSHD patient myoblasts have defective myogenic differentiation, forming smaller myotubes with reduced myosin content. However, molecular mechanisms driving such disrupted myogenesis in FSHD are poorly understood. We performed high-throughput morphological analysis describing FSHD and control myogenesis, revealing altered myogenic differentiation results in hypotrophic myotubes. Employing polynomial models and an empirical Bayes approach, we established eight critical time points during which human healthy and FSHD myogenesis differ. RNA-sequencing at these eight nodal time points in triplicate, provided temporal depth for a multivariate regression analysis, allowing assessment of interaction between progression of differentiation and FSHD disease status. Importantly, the unique size and structure of our data permitted identification of many novel FSHD pathomechanisms undetectable by previous approaches. For further analysis here, we selected pathways that control mitochondria: of interest considering known alterations in mitochondrial structure and function in FSHD muscle, and sensitivity of FSHD cells to oxidative stress. Notably, we identified suppression of mitochondrial biogenesis, in particular via peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC1α), the cofactor and activator of oestrogen-related receptor α (ERRα). PGC1α knock-down caused hypotrophic myotubes to form from control myoblasts. Known ERRα agonists and safe food supplements biochanin A, daidzein or genistein, each rescued the hypotrophic FSHD myotube phenotype. Together our work describes transcriptomic changes in high resolution that occur during myogenesis in FSHD ex vivo, identifying suppression of the PGC1α-ERRα axis leading to perturbed myogenic differentiation, which can effectively be rescued by readily available food supplements.
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Affiliation(s)
- Christopher R S Banerji
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
- Department of Computer Science, University College London, London, UK
- Centre of Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, UK
| | - Maryna Panamarova
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Johanna Pruller
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Nicolas Figeac
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Husam Hebaishi
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Efthymios Fidanis
- Genomics Research Platform, Biomedical Research Centre at Guy’s and St Thomas’ Trust and Kings College London, Guy’s Hospital, London, UK
| | - Alka Saxena
- Genomics Research Platform, Biomedical Research Centre at Guy’s and St Thomas’ Trust and Kings College London, Guy’s Hospital, London, UK
| | - Julian Contet
- Institute for Research on Cancer and Aging of Nice, Faculty of Medicine, Université Côte d'Azur, Nice, Cedex, France
| | - Sabrina Sacconi
- Institute for Research on Cancer and Aging of Nice, Faculty of Medicine, Université Côte d'Azur, Nice, Cedex, France
- Peripheral Nervous System, Muscle and ALS Department, Université Côte d'Azur, Nice, France
| | - Simone Severini
- Department of Computer Science, University College London, London, UK
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
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Facioscapulohumeral muscular dystrophy (FSHD) molecular diagnosis: from traditional technology to the NGS era. Neurogenetics 2019; 20:57-64. [PMID: 30911870 DOI: 10.1007/s10048-019-00575-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/17/2019] [Indexed: 02/08/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a genetic neuromuscular disorder which mainly affects the muscles of the face, shoulder, and upper arms. FSHD is generally associated with the contraction of D4Z4 macrosatellite repeats on 4q35 chromosome or mutations in SMCHD1, which are responsible of the toxic expression of DUX4 in muscle tissue. Despite the recent application of NGS techniques in the clinical practice, the molecular diagnosis of FSHD is still performed with dated techniques such as Southern blotting. The diagnosis of FSHD requires therefore specific skills on both modern and less modern analytical protocols. Considering that clinical and molecular diagnosis of FSHD is challenging, it is not surprising that only few laboratories offer a comprehensive characterization of FSHD, which requires the education of professionals on traditional techniques even in the era of NGS. In conclusion, the study of FSHD provides an excellent example of using classical and modern molecular technologies which are equally necessary for the analysis of DNA repetitive traits associated with specific disorders.
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de Greef JC, Krom YD, den Hamer B, Snider L, Hiramuki Y, van den Akker RFP, Breslin K, Pakusch M, Salvatori DCF, Slütter B, Tawil R, Blewitt ME, Tapscott SJ, van der Maarel SM. Smchd1 haploinsufficiency exacerbates the phenotype of a transgenic FSHD1 mouse model. Hum Mol Genet 2019; 27:716-731. [PMID: 29281018 DOI: 10.1093/hmg/ddx437] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 12/18/2017] [Indexed: 11/12/2022] Open
Abstract
In humans, a copy of the DUX4 retrogene is located in each unit of the D4Z4 macrosatellite repeat that normally comprises 8-100 units. The D4Z4 repeat has heterochromatic features and does not express DUX4 in somatic cells. Individuals with facioscapulohumeral muscular dystrophy (FSHD) have a partial failure of somatic DUX4 repression resulting in the presence of DUX4 protein in sporadic muscle nuclei. Somatic DUX4 derepression is caused by contraction of the D4Z4 repeat to 1-10 units (FSHD1) or by heterozygous mutations in genes responsible for maintaining the D4Z4 chromatin structure in a repressive state (FSHD2). One of the FSHD2 genes is the structural maintenance of chromosomes hinge domain 1 (SMCHD1) gene. SMCHD1 mutations have also been identified in FSHD1; patients carrying a contracted D4Z4 repeat and a SMCHD1 mutation are more severely affected than relatives with only a contracted repeat or a SMCHD1 mutation. To evaluate the modifier role of SMCHD1, we crossbred mice carrying a contracted D4Z4 repeat (D4Z4-2.5 mice) with mice that are haploinsufficient for Smchd1 (Smchd1MommeD1 mice). D4Z4-2.5/Smchd1MommeD1 mice presented with a significantly reduced body weight and developed skin lesions. The same skin lesions, albeit in a milder form, were also observed in D4Z4-2.5 mice, suggesting that reduced Smchd1 levels aggravate disease in the D4Z4-2.5 mouse model. Our study emphasizes the evolutionary conservation of the SMCHD1-dependent epigenetic regulation of the D4Z4 repeat array and further suggests that the D4Z4-2.5/Smchd1MommeD1 mouse model may be used to unravel the function of DUX4 in non-muscle tissues like the skin.
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Affiliation(s)
- Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lauren Snider
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yosuke Hiramuki
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rob F P van den Akker
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Miha Pakusch
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | - Bram Slütter
- Divisions of Biopharmaceutics & Drug Delivery Technology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,University of Melbourne, Melbourne, Australia
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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The Clinical Utility of Epigenetics: A Case Study. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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38
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Lin XD, He JJ, Lin F, Chen HZ, Xu LQ, Hu W, Cai NQ, Lin MT, Wang N, Wang ZQ, Xu GR. A "Triple Trouble" Case of Facioscapulohumeral Muscular Dystrophy Accompanied by Peripheral Neuropathy and Myoclonic Epilepsy. Chin Med J (Engl) 2018; 131:2164-2171. [PMID: 30203790 PMCID: PMC6144853 DOI: 10.4103/0366-6999.240797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Facioscapulohumeral muscular dystrophy (FSHD) is characterized by asymmetric muscular deficit of facial, shoulder-girdle muscles, and descending to lower limb muscles, but it exists in several extramuscular manifestations or overlapping syndromes. Herein, we report a "complex disease plus" patient with FSHD1, accompanied by peripheral neuropathy and myoclonic epilepsy. Methods Standard clinical assessments, particular auxiliary examination, histological analysis, and molecular analysis were performed through the new Comprehensive Clinical Evaluation Form, pulsed-field gel electrophoresis-based Southern blot, Multiplex Ligation-dependent Probe Amplification (MLPA), whole exome sequencing (WES), and targeted methylation sequencing. Results The patient presented with mild facial weakness, humeral poly-hill sign, scapular winging, peroneal weakness, drop foot, pes cavus, and myoclonic epilepsy. Furthermore, electrophysiology revealed severely demyelinated and axonal injury. The muscle and nerve biopsy revealed broadly fiber Type II grouping atrophy and myelinated nerve fibers that significantly decreased with thin myelinated fibers and onion bulbs changes. Generalized sharp and sharp-slow wave complexes on electroencephalography support the diagnosis toward myoclonic epilepsy. In addition, molecular testing demonstrated a co-segregated 20-kb 4q35-EcoRI fragment and permissive allele A, which corresponded with D4Z4 hypomethylation status in the family. Both the patient's mother and brother only presented the typical FSHD but lacked overlapping syndromes. However, no mutations for hereditary peripheral neuropathy and myoclonic epilepsy were discovered by MLPA and WES. Conclusions The present study described a "tripe trouble" with FSHD, peripheral neuropathy, and myoclonic epilepsy, adding the spectrum of overlapping syndromes and contributing to the credible diagnosis of atypical phenotype. It would provide a direct clue on medical care and genetic counseling.
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Affiliation(s)
- Xiao-Dan Lin
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Jun-Jie He
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Feng Lin
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Hai-Zhu Chen
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Liu-Qing Xu
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Wei Hu
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Nai-Qing Cai
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Min-Ting Lin
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University; Fujian Key Laboratory of Molecular Neurology, Fuzhou, Fujian 350005, China
| | - Zhi-Qiang Wang
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University; Fujian Key Laboratory of Molecular Neurology, Fuzhou, Fujian 350005, China
| | - Guo-Rong Xu
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
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Cascella R, Strafella C, Caputo V, Galota RM, Errichiello V, Scutifero M, Petillo R, Marella GL, Arcangeli M, Colantoni L, Zampatti S, Ricci E, Deidda G, Politano L, Giardina E. Digenic Inheritance of Shortened Repeat Units of the D4Z4 Region and a Loss-of-Function Variant in SMCHD1 in a Family With FSHD. Front Neurol 2018; 9:1027. [PMID: 30546343 PMCID: PMC6279899 DOI: 10.3389/fneur.2018.01027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a neuromuscular disorder which is typically transmitted by an autosomal dominant pattern, although reduced penetrance and sporadic cases caused by de novo mutations, are often observed. FSHD may be caused by a contraction of a repetitive element, located on chromosome 4 (4q35). This locus is named D4Z4 and consists of 11 to more than 100 repeated units (RU). The D4Z4 is normally hypermethylated and the genes located on this locus are silenced. In case of FSHD, the D4Z4 region is characterized by 1–10 repeats and results in the region being hypomethylated. However, 5% of FSHD cases do not carry the short allele of D4Z4 region. To date, two forms of FSHD (FSHD1 and FSHD2) are known. FSHD2 is usually observed in patients without the D4Z4 fragment contraction and carrying variants in SMCHD1 (18p11.32) gene. We report the case of a young adult patient who shows severe symptoms of FSHD. Preliminary genetic analysis did not clarify the phenotype, therefore we decided to study the family members by genetic and epigenetic approaches. The analysis of D4Z4 fragment resulted to be 8 RU in the affected proband and in his father; 26 RU in the mother and 25 RU in the maternal uncle. SMCHD1 analysis revealed a heterozygous variation within the exon 41. The variant was detected in the proband, her mother and the uncle. Furthermore, epigenetic analysis of CpG6 methylation regions showed significant hypomethylation in the affected patient (54%) and in the mother (56%), in contrast to the father (88%) and the uncle (81%) carrying higher methylation levels. The analysis of DR1 methylation levels reported hypomethylation for the proband (19%), the mother (11%), and the uncle (16%). The father showed normal DR1 methylation levels (>30%). Given these results, the combined inheritance of SMCHD1 variant and the short fragment might explain the severe FSHD phenotype displayed by the proband. On this subject, SMCHD1 analysis should be promoted in a larger number of patients, even in presence of D4Z4 contractions, to facilitate the genotype-phenotype correlation as well as, to enable a more precise diagnosis and prognosis of the disease.
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Affiliation(s)
- Raffaella Cascella
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy.,Department of Chemical-Toxicological and Pharmacological Evaluation of Drugs, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Claudia Strafella
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy.,Emotest Laboratory, Pozzuoli, Italy
| | - Valerio Caputo
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | | | - Valeria Errichiello
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | - Marianna Scutifero
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Roberta Petillo
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Gian Luca Marella
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Mauro Arcangeli
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | - Luca Colantoni
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | - Stefania Zampatti
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | - Enzo Ricci
- Institute of Neurology, Catholic University of the Sacred Heart, Rome, Italy
| | - Giancarlo Deidda
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo, Rome, Italy
| | - Luisa Politano
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Emiliano Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy.,Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
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Kashevarova AA, Nazarenko LP, Skryabin NA, Nikitina TV, Vasilyev SA, Tolmacheva EN, Lopatkina ME, Salyukova OA, Chechetkina NN, Vorotelyak EA, Kalabusheva EP, Fishman VS, Kzhyshkowska J, Graziano C, Magini P, Romeo G, Lebedev IN. A mosaic intragenic microduplication of LAMA1 and a constitutional 18p11.32 microduplication in a patient with keratosis pilaris and intellectual disability. Am J Med Genet A 2018; 176:2395-2403. [PMID: 30244536 DOI: 10.1002/ajmg.a.40478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/23/2017] [Accepted: 06/28/2018] [Indexed: 11/06/2022]
Abstract
The application of array-based comparative genomic hybridization and next-generation sequencing has identified many chromosomal microdeletions and microduplications in patients with different pathological phenotypes. Different copy number variations are described within the short arm of chromosome 18 in patients with skin diseases. In particular, full or partial monosomy 18p has also been associated with keratosis pilaris. Here, for the first time, we report a young male patient with intellectual disability, diabetes mellitus (type I), and keratosis pilaris, who exhibited a de novo 45-kb microduplication of exons 4-22 of LAMA1, located at 18p11.31, and a 432-kb 18p11.32 microduplication of paternal origin containing the genes METTL4, NDC80, and CBX3P2 and exons 1-15 of the SMCHD1 gene. The microduplication of LAMA1 was identified in skin fibroblasts but not in lymphocytes, whereas the larger microduplication was present in both tissues. We propose LAMA1 as a novel candidate gene for keratosis pilaris. Although inherited from a healthy father, the 18p11.32 microduplication, which included relevant genes, could also contribute to phenotype manifestation.
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Affiliation(s)
- Anna A Kashevarova
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,Laboratory of Human Ontogenetics, National Research Tomsk State University, Tomsk, Russia
| | - Lyudmila P Nazarenko
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,Chair of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - Nikolay A Skryabin
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,Laboratory of Human Ontogenetics, National Research Tomsk State University, Tomsk, Russia
| | - Tatiana V Nikitina
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Stanislav A Vasilyev
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,Laboratory of Human Ontogenetics, National Research Tomsk State University, Tomsk, Russia
| | - Ekaterina N Tolmacheva
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Mariya E Lopatkina
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Olga A Salyukova
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,Chair of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - Nataliya N Chechetkina
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Ekaterina A Vorotelyak
- Laboratory of Cell Biology, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina P Kalabusheva
- Laboratory of Cell Biology, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Veniamin S Fishman
- Institute of Cytology and Genetics, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Julia Kzhyshkowska
- Laboratory for Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russia.,Department of Innate Immunity and Tolerance, Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
| | - Claudio Graziano
- Medical Genetics Unit, Policlinico S. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, Policlinico S. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- Medical Genetics Unit, Policlinico S. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Igor N Lebedev
- Laboratory of Cytogenetics, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,Laboratory of Human Ontogenetics, National Research Tomsk State University, Tomsk, Russia.,Chair of Medical Genetics, Siberian State Medical University, Tomsk, Russia
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41
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Mah JK, Chen YW. A Pediatric Review of Facioscapulohumeral Muscular Dystrophy. JOURNAL OF PEDIATRIC NEUROLOGY 2018; 16:222-231. [PMID: 30923442 PMCID: PMC6435288 DOI: 10.1055/s-0037-1604197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Facioscapulohumeral dystrophy is one of the most common forms of muscular dystrophies worldwide. It is a complex and heterogeneous disease secondary to insufficient epigenetic repression of D4Z4 repeats and aberrant expression of DUX4 in skeletal muscles. Type 1 facioscapulohumeral muscular dystrophy (FSHD) is caused by contraction of D4Z4 repeats on 4q35, whereas type 2 FSHD is associated with mutations of the SMCHD1 or DNMT3B gene in the presence of a disease-permissive 4qA haplotype. Classical FSHD is a slowly progressive disorder with gradual-onset of muscle atrophy and a descending pattern of muscle weakness. In contrast, early-onset FSHD is associated with a large deletion of D4Z4 repeats and a more severe disease phenotype, including early loss of independent ambulation as well as extramuscular manifestations, such as retinal vasculopathy, hearing loss, and central nervous system (CNS) involvement. However, the correlation between D4Z4 repeats and disease severity remains imprecise. The current standard of care guidelines offers comprehensive assessment and symptomatic management of secondary complications. Several clinical trials are currently underway for FSHD. New and emerging treatments focus on correcting the transcriptional misregulation of D4Z4 and reversing the cytotoxic effects of DUX4. Other potential therapeutic targets include reduction of inflammation, improving muscle mass, and activating compensatory molecular pathways. The utility of disease-modifying treatments will depend on selection of sensitive clinical endpoints as well as validation of muscle magnetic resonance imaging (MRI) and other biomarkers to detect meaningful changes in disease progression. Correction of the epigenetic defects using new gene editing as well as other DUX4 silencing technologies offers potential treatment options for many individuals with FSHD.
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Affiliation(s)
- Jean K. Mah
- Department of Pediatrics and Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children’s National Health System, Washington, District of Columbia, United States
- Department of Integrative Systems Biology, George Washington University, Washington, District of Columbia, United States
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42
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Leung DG, Wang X, Barker PB, Carrino JA, Wagner KR. Multivoxel proton magnetic resonance spectroscopy in facioscapulohumeral muscular dystrophy. Muscle Nerve 2018; 57:958-963. [PMID: 29266323 DOI: 10.1002/mus.26048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 12/11/2017] [Accepted: 12/15/2017] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Facioscapulohumeral muscular dystrophy (FSHD) is a hereditary disorder that causes progressive muscle wasting. This study evaluates the use of proton magnetic resonance spectroscopy (1 H MRS) as a biomarker of muscle strength and function in FSHD. METHODS Thirty-six individuals with FSHD and 15 healthy controls underwent multivoxel 1 H MRS of a cross-section of the mid-thigh. Concentrations of creatine, intramyocellular and extramyocellular lipids, and trimethylamine (TMA)-containing compounds in skeletal muscle were calculated. Metabolite concentrations for individuals with FSHD were compared with those of controls. The relationship between metabolite concentrations and muscle strength was also examined. RESULTS The TMA/creatine (Cr) ratio in individuals with FSHD was reduced compared with controls. The TMA/Cr ratio in the hamstrings also showed a moderate linear correlation with muscle strength. DISCUSSION 1 H MRS offers a potential method of detecting early muscle pathology in FSHD prior to the development of fat infiltration. Muscle Nerve 57: 958-963, 2018.
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Affiliation(s)
- Doris G Leung
- Center for Genetic Muscle Disorders, Hugo W. Moser Research Institute at Kennedy Krieger Institute, 716 North Broadway, Room 411, Baltimore, Maryland, 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xin Wang
- Department of Radiation Oncology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Peter B Barker
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John A Carrino
- Department of Radiology and Imaging, Hospital for Special Surgery, New York, New York, USA
| | - Kathryn R Wagner
- Center for Genetic Muscle Disorders, Hugo W. Moser Research Institute at Kennedy Krieger Institute, 716 North Broadway, Room 411, Baltimore, Maryland, 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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43
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Lemmers RJ, van der Vliet PJ, Balog J, Goeman JJ, Arindrarto W, Krom YD, Straasheijm KR, Debipersad RD, Özel G, Sowden J, Snider L, Mul K, Sacconi S, van Engelen B, Tapscott SJ, Tawil R, van der Maarel SM. Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2. Eur J Hum Genet 2017; 26:94-106. [PMID: 29162933 DOI: 10.1038/s41431-017-0015-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 11/09/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy is caused by incomplete repression of the transcription factor DUX4 in skeletal muscle as a consequence of D4Z4 macrosatellite repeat contraction in chromosome 4q35 (FSHD1) or variants in genes encoding D4Z4 chromatin repressors (FSHD2). A clinical hallmark of FSHD is variability in onset and progression suggesting the presence of disease modifiers. A well-known cis modifier is the polymorphic DUX4 polyadenylation signal (PAS) that defines FSHD permissive alleles: D4Z4 chromatin relaxation on non-permissive alleles which lack the DUX4-PAS cannot cause disease in the absence of stable DUX4 mRNA. We have explored the nature and relevance of a common variant of the major FSHD haplotype 4A161, which is defined by 1.6 kb size difference of the most distal D4Z4 repeat unit. While the short variant (4A161S) has been extensively studied, we demonstrate that the long variant (4A161L) is relatively common in the European population, is capable of expressing DUX4, but that DUX4 mRNA processing differs from 4A161S. While we do not find evidence for a difference in disease severity between FSHD carriers of an 4A161S or 4A161L allele, our study does uncover biallelic DUX4 expression in FSHD2 patients. Compared to control individuals, we observed an increased frequency of FSHD2 patients homozygous for disease permissive alleles, and who are thus capable of biallelic DUX4 expression, while SMCHD1 variant carriers with only one permissive allele were significantly more often asymptomatic. This suggests that biallelic DUX4 expression lowers the threshold for disease presentation and is a modifier for disease severity in FSHD2.
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Affiliation(s)
- Richard Jlf Lemmers
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.
| | | | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Jelle J Goeman
- Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Netherlands
| | - Wibowo Arindrarto
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - Yvonne D Krom
- Department of Neurology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Rashmie D Debipersad
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Gizem Özel
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Janet Sowden
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Lauren Snider
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Karlien Mul
- Neuromuscular Centre Nijmegen, Department of Neurology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Sabrina Sacconi
- Centre de référence des Maladies neuromusculaires and CNRS UMR6543, Nice University Hospital, Nice, France
| | - Baziel van Engelen
- Neuromuscular Centre Nijmegen, Department of Neurology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
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DeSimone AM, Pakula A, Lek A, Emerson CP. Facioscapulohumeral Muscular Dystrophy. Compr Physiol 2017; 7:1229-1279. [PMID: 28915324 DOI: 10.1002/cphy.c160039] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Facioscapulohumeral Muscular Dystrophy is a common form of muscular dystrophy that presents clinically with progressive weakness of the facial, scapular, and humeral muscles, with later involvement of the trunk and lower extremities. While typically inherited as autosomal dominant, facioscapulohumeral muscular dystrophy (FSHD) has a complex genetic and epigenetic etiology that has only recently been well described. The most prevalent form of the disease, FSHD1, is associated with the contraction of the D4Z4 microsatellite repeat array located on a permissive 4qA chromosome. D4Z4 contraction allows epigenetic derepression of the array, and possibly the surrounding 4q35 region, allowing misexpression of the toxic DUX4 transcription factor encoded within the terminal D4Z4 repeat in skeletal muscles. The less common form of the disease, FSHD2, results from haploinsufficiency of the SMCHD1 gene in individuals carrying a permissive 4qA allele, also leading to the derepression of DUX4, further supporting a central role for DUX4. How DUX4 misexpression contributes to FSHD muscle pathology is a major focus of current investigation. Misexpression of other genes at the 4q35 locus, including FRG1 and FAT1, and unlinked genes, such as SMCHD1, has also been implicated as disease modifiers, leading to several competing disease models. In this review, we describe recent advances in understanding the pathophysiology of FSHD, including the application of MRI as a research and diagnostic tool, the genetic and epigenetic disruptions associated with the disease, and the molecular basis of FSHD. We discuss how these advances are leading to the emergence of new approaches to enable development of FSHD therapeutics. © 2017 American Physiological Society. Compr Physiol 7:1229-1279, 2017.
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Affiliation(s)
- Alec M DeSimone
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Anna Pakula
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics and Genetics at Harvard Medical School, Boston, Massachusetts, USA
| | - Angela Lek
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics and Genetics at Harvard Medical School, Boston, Massachusetts, USA.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Teveroni E, Pellegrino M, Sacconi S, Calandra P, Cascino I, Farioli-Vecchioli S, Puma A, Garibaldi M, Morosetti R, Tasca G, Ricci E, Trevisan CP, Galluzzi G, Pontecorvi A, Crescenzi M, Deidda G, Moretti F. Estrogens enhance myoblast differentiation in facioscapulohumeral muscular dystrophy by antagonizing DUX4 activity. J Clin Invest 2017; 127:1531-1545. [PMID: 28263188 DOI: 10.1172/jci89401] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 01/12/2017] [Indexed: 01/28/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder that is characterized by extreme variability in symptoms, with females being less severely affected than males and presenting a higher proportion of asymptomatic carriers. The sex-related factors involved in the disease are not known. Here, we have utilized myoblasts isolated from FSHD patients (FSHD myoblasts) to investigate the effect of estrogens on muscle properties. Our results demonstrated that estrogens counteract the differentiation impairment of FSHD myoblasts without affecting cell proliferation or survival. Estrogen effects are mediated by estrogen receptor β (ERβ), which reduces chromatin occupancy and transcriptional activity of double homeobox 4 (DUX4), a protein whose aberrant expression has been implicated in FSHD pathogenesis. During myoblast differentiation, we observed that the levels and activity of DUX4 increased progressively and were associated with its enhanced recruitment in the nucleus. ERβ interfered with this recruitment by relocalizing DUX4 in the cytoplasm. This work identifies estrogens as a potential disease modifier that underlie sex-related differences in FSHD by protecting against myoblast differentiation impairments in this disease.
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Jones TI, Himeda CL, Perez DP, Jones PL. Large family cohorts of lymphoblastoid cells provide a new cellular model for investigating facioscapulohumeral muscular dystrophy. Neuromuscul Disord 2017; 27:221-238. [PMID: 28161093 PMCID: PMC5815870 DOI: 10.1016/j.nmd.2016.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/11/2016] [Indexed: 01/26/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is associated with aberrant epigenetic regulation of the chromosome 4q35 D4Z4 macrosatellite repeat. The resulting DNA hypomethylation and relaxation of epigenetic repression leads to increased expression of the deleterious DUX4-fl mRNA encoded within the distal D4Z4 repeat. With the typical late onset of muscle weakness, prevalence of asymptomatic individuals, and an autosomal dominant mode of inheritance, FSHD is often passed on from one generation to the next and affects multiple individuals within a family. Here we have characterized unique collections of 114 lymphoblastoid cell lines (LCLs) generated from 12 multigenerational FSHD families, including 56 LCLs from large, genetically homogeneous families in Utah. We found robust expression of DUX4-fl in most FSHD LCLs and a good correlation between DNA hypomethylation and repeat length. In addition, DUX4-fl levels can be manipulated using epigenetic drugs as in myocytes, suggesting that some epigenetic pathways regulating DUX4-fl in myocytes are maintained in LCLs. Overall, these FSHD LCLs provide an alternative cellular model in which to study many aspects of D4Z4, DUX4, and FSHD gene regulation in a background of low genetic variation. Significantly, these non-adherent immortal LCLs are amenable for high-throughput screening of potential therapeutics targeting DUX4-fl mRNA or protein expression.
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Affiliation(s)
- Takako I Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Charis L Himeda
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Daniel P Perez
- FSH Society, 450 Bedford Street, Lexington, MA 02420, USA.
| | - Peter L Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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47
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Shaw ND, Brand H, Kupchinsky ZA, Bengani H, Plummer L, Jones TI, Erdin S, Williamson KA, Rainger J, Stortchevoi A, Samocha K, Currall BB, Dunican DS, Collins RL, Willer JR, Lek A, Lek M, Nassan M, Pereira S, Kammin T, Lucente D, Silva A, Seabra CM, Chiang C, An Y, Ansari M, Rainger JK, Joss S, Smith JC, Lippincott MF, Singh SS, Patel N, Jing JW, Law JR, Ferraro N, Verloes A, Rauch A, Steindl K, Zweier M, Scheer I, Sato D, Okamoto N, Jacobsen C, Tryggestad J, Chernausek S, Schimmenti LA, Brasseur B, Cesaretti C, García-Ortiz JE, Buitrago TP, Silva OP, Hoffman JD, Mühlbauer W, Ruprecht KW, Loeys BL, Shino M, Kaindl AM, Cho CH, Morton CC, Meehan RR, van Heyningen V, Liao EC, Balasubramanian R, Hall JE, Seminara SB, Macarthur D, Moore SA, Yoshiura KI, Gusella JF, Marsh JA, Graham JM, Lin AE, Katsanis N, Jones PL, Crowley WF, Davis EE, FitzPatrick DR, Talkowski ME. SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. Nat Genet 2017; 49:238-248. [PMID: 28067909 PMCID: PMC5473428 DOI: 10.1038/ng.3743] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
Arhinia, or absence of the nose, is a rare malformation of unknown etiology that is often accompanied by ocular and reproductive defects. Sequencing of 40 people with arhinia revealed that 84% of probands harbor a missense mutation localized to a constrained region of SMCHD1 encompassing the ATPase domain. SMCHD1 mutations cause facioscapulohumeral muscular dystrophy type 2 (FSHD2) via a trans-acting loss-of-function epigenetic mechanism. We discovered shared mutations and comparable DNA hypomethylation patterning between these distinct disorders. CRISPR/Cas9-mediated alteration of smchd1 in zebrafish yielded arhinia-relevant phenotypes. Transcriptome and protein analyses in arhinia probands and controls showed no differences in SMCHD1 mRNA or protein abundance but revealed regulatory changes in genes and pathways associated with craniofacial patterning. Mutations in SMCHD1 thus contribute to distinct phenotypic spectra, from craniofacial malformation and reproductive disorders to muscular dystrophy, which we speculate to be consistent with oligogenic mechanisms resulting in pleiotropic outcomes.
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Affiliation(s)
- Natalie D Shaw
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Harrison Brand
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Zachary A Kupchinsky
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Hemant Bengani
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Lacey Plummer
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Takako I Jones
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Serkan Erdin
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kathleen A Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Joe Rainger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kaitlin Samocha
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin B Currall
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Donncha S Dunican
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Ryan L Collins
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason R Willer
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Angela Lek
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Malik Nassan
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Shahrin Pereira
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tammy Kammin
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexandra Silva
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Catarina M Seabra
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- GABBA Program, University of Porto, Porto, Portugal
| | - Colby Chiang
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yu An
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Morad Ansari
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Jacqueline K Rainger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Shelagh Joss
- West of Scotland Genetics Service, South Glasgow University Hospitals, Glasgow, UK
| | - Jill Clayton Smith
- Faculty of Medical and Human Sciences, Institute of Human Development, Manchester Centre for Genomic Medicine, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Margaret F Lippincott
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sylvia S Singh
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Nirav Patel
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jenny W Jing
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jennifer R Law
- Division of Pediatric Endocrinology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nalton Ferraro
- Department of Oral and Maxillofacial Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alain Verloes
- Department of Genetics, Robert Debré Hospital, Paris, France
| | - Anita Rauch
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Ianina Scheer
- Department of Diagnostic Imaging, Children's Hospital, Zurich, Switzerland
| | - Daisuke Sato
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Christina Jacobsen
- Division of Endocrinology and Genetics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jeanie Tryggestad
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Steven Chernausek
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Lisa A Schimmenti
- Departments of Otorhinolaryngology and Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin Brasseur
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Claudia Cesaretti
- Medical Genetics Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Jose E García-Ortiz
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | | | | | - Jodi D Hoffman
- Divisions of Genetics and Maternal Fetal Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Wolfgang Mühlbauer
- Department of Plastic and Aesthetic Surgery, ATOS Klinik, Munich, Germany
| | - Klaus W Ruprecht
- Department of Ophthalmology, University Hospital of the Saarland, Homburg, Germany
| | - Bart L Loeys
- Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Masato Shino
- Department of Otolaryngology and Head and Neck Surgery, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Angela M Kaindl
- Biology and Neurobiology, Charité-University Medicine Berlin and Berlin Institute of Health, Berlin, Germany
| | - Chie-Hee Cho
- Department of Diagnostic, Interventional and Pediatric Radiology, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Cynthia C Morton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Eric C Liao
- Center for Regenerative Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Ravikumar Balasubramanian
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Janet E Hall
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Stephanie B Seminara
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel Macarthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - James F Gusella
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - John M Graham
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Angela E Lin
- Medical Genetics, MassGeneral Hospital for Children and Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Peter L Jones
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - William F Crowley
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Michael E Talkowski
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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48
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Lemmers RJLF. Analyzing Copy Number Variation Using Pulsed-Field Gel Electrophoresis: Providing a Genetic Diagnosis for FSHD1. Methods Mol Biol 2017; 1492:107-125. [PMID: 27822859 DOI: 10.1007/978-1-4939-6442-0_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The myopathy facioscapulohumeral muscular dystrophy type 1 (FSHD1) is caused by copy number variation of the D4Z4 macrosatellite repeat on chromosome 4. In unaffected individuals the number of 3.3 kb D4Z4 units varies between 8 and 100, whereas 1-10 units are seen in FSHD1 cases. A homologous and heterogenous D4Z4 array can be found on chromosome 10q, but contractions of this array are typically not associated with FSHD. Discriminating between the chromosome 4 and chromosome 10 D4Z4 arrays, as well as determining the array size, requires the use of pulsed-field gel electrophoresis, Southern blotting, and the isolation of high-quality DNA.
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Affiliation(s)
- Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, 2333, ZA, Leiden, The Netherlands.
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