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Kong X, Nguyen NV, Li Y, Sakr JS, Williams K, Sharifi S, Chau J, Bayrakci A, Mizuno S, Takahashi S, Kiyono T, Tawil R, Mortazavi A, Yokomori K. Engineered FSHD mutations results in D4Z4 heterochromatin disruption and feedforward DUX4 network activation. iScience 2024; 27:109357. [PMID: 38510139 PMCID: PMC10951985 DOI: 10.1016/j.isci.2024.109357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/20/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is linked to contraction of D4Z4 repeats on chromosome 4q with SMCHD1 mutations acting as a disease modifier. D4Z4 heterochromatin disruption and abnormal upregulation of the transcription factor DUX4, encoded in the D4Z4 repeat, are the hallmarks of FSHD. However, defining the precise effect of D4Z4 contraction has been difficult because D4Z4 repeats are primate-specific and DUX4 expression is very rare in highly heterogeneous patient myocytes. We generated isogenic mutant cell lines harboring D4Z4 and/or SMCHD1 mutations in a healthy human skeletal myoblast line. We found that the mutations affect D4Z4 heterochromatin differently, and that SMCHD1 mutation or disruption of DNA methylation stabilizes otherwise variegated DUX4 target activation in D4Z4 contraction mutant cells, demonstrating the critical role of modifiers. Our study revealed amplification of the DUX4 signal through downstream targets, H3.X/Y and LEUTX. Our results provide important insights into how rare DUX4 expression leads to FSHD pathogenesis.
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Affiliation(s)
- Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Nam Viet Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yumeng Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Jasmine Shaaban Sakr
- Department of Development and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Kate Williams
- Department of Development and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Sheila Sharifi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Jonathan Chau
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Altay Bayrakci
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center in Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Tohru Kiyono
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Ali Mortazavi
- Department of Development and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
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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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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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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: 0] [Impact Index Per Article: 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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Murphy K, Zhang A, Bittel AJ, Chen YW. Molecular and Phenotypic Changes in FLExDUX4 Mice. J Pers Med 2023; 13:1040. [PMID: 37511653 PMCID: PMC10381554 DOI: 10.3390/jpm13071040] [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: 03/17/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by the aberrant expression of the double homeobox 4 (DUX4) gene. The FLExDUX4 mouse model carries an inverted human DUX4 transgene which has leaky DUX4 transgene expression at a very low level. No overt muscle pathology was reported before 16 weeks. The purpose of this study is to track and characterize the FLExDUX4 phenotypes for a longer period, up to one year old. In addition, transcriptomic changes in the muscles of 2-month-old mice were investigated using RNA-seq. The results showed that male FLExDUX4 mice developed more severe phenotypes and at a younger age in comparison to the female mice. These include lower body and muscle weight, and muscle weakness measured by grip strength measurements. Muscle pathological changes were observed at older ages, including fibrosis, decreased size of type IIa and IIx myofibers, and the development of aggregates containing TDP-43 in type IIb myofibers. Muscle transcriptomic data identified early molecular changes in biological pathways regulating circadian rhythm and adipogenesis. The study suggests a slow progressive change in molecular and muscle phenotypes in response to the low level of DUX4 expression in the FLExDUX4 mice.
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Affiliation(s)
- Kelly Murphy
- Institute for Biomedical Sciences, The George Washington University, Washington, DC 20037, USA
| | - Aiping Zhang
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
| | - Adam J Bittel
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
| | - Yi-Wen Chen
- Institute for Biomedical Sciences, The George Washington University, Washington, DC 20037, USA
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Science, The George Washington University, Washington, DC 20037, USA
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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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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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8
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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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Pappalardo XG, Barra V. Losing DNA methylation at repetitive elements and breaking bad. Epigenetics Chromatin 2021; 14:25. [PMID: 34082816 PMCID: PMC8173753 DOI: 10.1186/s13072-021-00400-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/21/2021] [Indexed: 02/08/2023] Open
Abstract
Background DNA methylation is an epigenetic chromatin mark that allows heterochromatin formation and gene silencing. It has a fundamental role in preserving genome stability (including chromosome stability) by controlling both gene expression and chromatin structure. Therefore, the onset of an incorrect pattern of DNA methylation is potentially dangerous for the cells. This is particularly important with respect to repetitive elements, which constitute the third of the human genome. Main body Repetitive sequences are involved in several cell processes, however, due to their intrinsic nature, they can be a source of genome instability. Thus, most repetitive elements are usually methylated to maintain a heterochromatic, repressed state. Notably, there is increasing evidence showing that repetitive elements (satellites, long interspersed nuclear elements (LINEs), Alus) are frequently hypomethylated in various of human pathologies, from cancer to psychiatric disorders. Repetitive sequences’ hypomethylation correlates with chromatin relaxation and unscheduled transcription. If these alterations are directly involved in human diseases aetiology and how, is still under investigation. Conclusions Hypomethylation of different families of repetitive sequences is recurrent in many different human diseases, suggesting that the methylation status of these elements can be involved in preservation of human health. This provides a promising point of view towards the research of therapeutic strategies focused on specifically tuning DNA methylation of DNA repeats.
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Affiliation(s)
- Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95125, Catania, Italy.,National Council of Research, Institute for Biomedical Research and Innovation (IRIB), Unit of Catania, 95125, Catania, Italy
| | - Viviana Barra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy.
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10
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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: 16] [Impact Index Per Article: 5.3] [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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11
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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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12
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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: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [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 Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Experimental Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Remko Goossens
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Baziel van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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13
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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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14
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Ferguson MR, Poliachik SL, Budech CB, Gove NE, Carter GT, Wang LH, Miller DG, Shaw DW, Friedman SD. MRI change metrics of facioscapulohumeral muscular dystrophy: Stir and T1. Muscle Nerve 2018; 57:905-912. [DOI: 10.1002/mus.26038] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 12/04/2017] [Accepted: 12/09/2017] [Indexed: 01/07/2023]
Affiliation(s)
- Mark R. Ferguson
- Department of Radiology; Seattle Children's Hospital, 4800 Sandpoint Way, Room: L-MA.6.226; Seattle Washington 98105 USA
- Department of Radiology; University of Washington; Seattle Washington USA
| | - Sandra L. Poliachik
- Department of Radiology; Seattle Children's Hospital, 4800 Sandpoint Way, Room: L-MA.6.226; Seattle Washington 98105 USA
| | - Christopher B. Budech
- Department of Radiology; Seattle Children's Hospital, 4800 Sandpoint Way, Room: L-MA.6.226; Seattle Washington 98105 USA
| | - Nancy E. Gove
- Center for Clinical and Translational Research, Seattle Children's Research Institute; Seattle Washington USA
| | | | - Leo H. Wang
- Department of Neurology; University of Washington; Seattle Washington USA
| | - Daniel G. Miller
- Genome Sciences, University of Washington; Seattle Washington USA
| | - Dennis W.W. Shaw
- Department of Radiology; Seattle Children's Hospital, 4800 Sandpoint Way, Room: L-MA.6.226; Seattle Washington 98105 USA
- Department of Radiology; University of Washington; Seattle Washington USA
| | - Seth D. Friedman
- Department of Radiology; Seattle Children's Hospital, 4800 Sandpoint Way, Room: L-MA.6.226; Seattle Washington 98105 USA
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15
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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: 33] [Impact Index Per Article: 4.7] [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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Denny AP, Heather AK. Are Antioxidants a Potential Therapy for FSHD? A Review of the Literature. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:7020295. [PMID: 28690764 PMCID: PMC5485364 DOI: 10.1155/2017/7020295] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/27/2017] [Accepted: 05/03/2017] [Indexed: 11/21/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an inherited myopathy affecting approximately 1 in 7500 individuals worldwide. It is a progressive disease characterised by skeletal muscle weakness and wasting. A genetic mutation on the 4q35 chromosome results in the expression of the double homeobox 4 gene (DUX4) which drives oxidative stress, inflammation, toxicity, and atrophy within the skeletal muscle. FSHD is characterised by oxidative stress, and there is currently no cure and a lack of therapies for the disease. Antioxidants have been researched for many years, with investigators aiming to use antioxidants therapeutically for oxidative stress-associated diseases. This has included both natural and synthetic antioxidants. The use of antioxidants in preclinical or clinical models has been largely successful with a plethora of research reporting positive results. However, when translated to clinical trials, the use of antioxidants as a therapeutic intervention for a variety of disease has been largely unsuccessful. Moreover, specifically focusing on FSHD, limited research has been conducted on the use of antioxidants as a therapy in either preclinical or clinical models. This review summarises the current state of antioxidant use in the treatment of FSHD and discusses their potential avenue for therapeutic use for FSHD patients.
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Affiliation(s)
- Adam Philip Denny
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Alison Kay Heather
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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Casa V, Runfola V, Micheloni S, Aziz A, Dilworth FJ, Gabellini D. Polycomb repressive complex 1 provides a molecular explanation for repeat copy number dependency in FSHD muscular dystrophy. Hum Mol Genet 2017; 26:753-767. [PMID: 28040729 PMCID: PMC5409123 DOI: 10.1093/hmg/ddw426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/15/2016] [Indexed: 11/13/2022] Open
Abstract
Repression of repetitive elements is crucial to preserve genome integrity and has been traditionally ascribed to constitutive heterochromatin pathways. FacioScapuloHumeral Muscular Dystrophy (FSHD), one of the most common myopathies, is characterized by a complex interplay of genetic and epigenetic events. The main FSHD form is linked to a reduced copy number of the D4Z4 macrosatellite repeat on 4q35, causing loss of silencing and aberrant expression of the D4Z4-embedded DUX4 gene leading to disease. By an unknown mechanism, D4Z4 copy-number correlates with FSHD phenotype. Here we show that the DUX4 proximal promoter (DUX4p) is sufficient to nucleate the enrichment of both constitutive and facultative heterochromatin components and to mediate a copy-number dependent gene silencing. We found that both the CpG/GC dense DNA content and the repetitive nature of DUX4p arrays are important for their repressive ability. We showed that DUX4p mediates a copy number-dependent Polycomb Repressive Complex 1 (PRC1) recruitment, which is responsible for the copy-number dependent gene repression. Overall, we directly link genetic and epigenetic defects in FSHD by proposing a novel molecular explanation for the copy number-dependency in FSHD pathogenesis, and offer insight into the molecular functions of repeats in chromatin regulation.
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Affiliation(s)
- Valentina Casa
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Università Vita-Salute San Raffaele, Milan 20132, Italy
| | - Valeria Runfola
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Stefano Micheloni
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Arif Aziz
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - F Jeffrey Dilworth
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Dulbecco Telethon Institute, Milan 20132, Italy
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Sharma V, Pandey SN, Khawaja H, Brown KJ, Hathout Y, Chen YW. PARP1 Differentially Interacts with Promoter region of DUX4 Gene in FSHD Myoblasts. JOURNAL OF GENETIC SYNDROMES & GENE THERAPY 2016; 7:303. [PMID: 27722032 PMCID: PMC5051271 DOI: 10.4172/2157-7412.1000303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE The goal of the study is to identity proteins, which interact with the promoter region of double homeobox protein 4 (DUX4) gene known to be causative for the autosomal dominant disorder Facioscapulohumeral Muscular Dystrophy (FSHD). METHODS We performed a DNA pull down assay coupled with mass spectrometry analysis to identify proteins that interact with a DUX4 promoter probe in Rhabdomyosarcomca (RD) cells. We selected the top ranked protein poly (ADP-ribose) polymerase 1 (PARP1) from our mass spectrometry data for further ChIP-qPCR validation using patients' myoblasts. We then treated FSHD myoblasts with PARP1 inhibitors to investigate the role of PARP1 in the FSHD myoblasts. RESULTS In our mass spectrometry analysis, PARP1 was found to be the top ranked protein interacting preferentially with the DUX4 promoter probe in RD cells. We further validated this interaction by immunoblotting in RD cells (2-fold enrichment compared to proteins pulled down by a control probe, p<0.05) and ChIP-qPCR in patients' myoblasts (65-fold enrichment, p<0.01). Interestingly, the interaction was only observed in FSHD myoblasts but not in the control myoblasts. Upon further treatment of FSHD myoblasts with PARP1 inhibitors, we showed that treatment with a PARP1 inhibitor, 3-aminobenzamide (0.5 mM), for 24 h had a suppression of DUX4 (2.6 fold, p<0.05) and ZSCAN4, a gene previously shown to be upregulated by DUX4, (1.6 fold, p<0.01) in FSHD myoblasts. Treatment with fisetin (0.5 mM), a polyphenol compound with PARP1 inhibitory property, for 24 h also suppressed the expression of DUX4 (44.8 fold, p<0.01) and ZSCAN4 (2.2 fold, p<0.05) in the FSHD myoblasts. We further showed that DNA methyltransferase 1 (DNMT1), a gene regulated by PARP1 was also enriched at the DUX4 promoter in RD cells through immunoblotting (2-fold, p<0.01) and immortalized FSHD myoblasts (42-fold, p<0.01) but not control myoblasts through ChIP qPCR. CONCLUSION Our results showed that PARP1 and DNMT1 interacted with DUX4 promoter and may be involved in modulating DUX4 expression in FSHD.
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Affiliation(s)
- Vishakha Sharma
- Department of Molecular Medicine, George Washington University, Washington DC, USA
| | - Sachchida Nand Pandey
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Hunain Khawaja
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Kristy J Brown
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
| | - Yetrib Hathout
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
- Department of Integrative Systems Biology, George Washington University, Washington DC, USA
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Health System, Washington DC, USA
- Department of Integrative Systems Biology, George Washington University, Washington DC, USA
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Influence of Repressive Histone and DNA Methylation upon D4Z4 Transcription in Non-Myogenic Cells. PLoS One 2016; 11:e0160022. [PMID: 27467759 PMCID: PMC4965136 DOI: 10.1371/journal.pone.0160022] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 07/12/2016] [Indexed: 01/11/2023] Open
Abstract
We looked at a disease-associated macrosatellite array D4Z4 and focused on epigenetic factors influencing its chromatin state outside of the disease-context. We used the HCT116 cell line that contains the non-canonical polyadenylation (poly-A) signal required to stabilize somatic transcripts of the human double homeobox gene DUX4, encoded from D4Z4. In HCT116, D4Z4 is packaged into constitutive heterochromatin, characterized by DNA methylation and histone H3 tri-methylation at lysine 9 (H3K9me3), resulting in low basal levels of D4Z4-derived transcripts. However, a double knockout (DKO) of DNA methyltransferase genes, DNMT1 and DNMT3B, but not either alone, results in significant loss of DNA and H3K9 methylation. This is coupled with upregulation of transcript levels from the array, including DUX4 isoforms (DUX4-fl) that are abnormally expressed in somatic muscle in the disease Facioscapulohumeral muscular dystrophy (FSHD) along with DUX4 protein, as indicated indirectly by upregulation of bondafide targets of DUX4 in DKO but not HCT116 cells. Results from treatment with a chemical inhibitor of histone methylation in HCT116 suggest that in the absence of DNA hypomethylation, H3K9me3 loss alone is sufficient to facilitate DUX4-fl transcription. Additionally, characterization of a cell line from a patient with Immunodeficiency, Centromeric instability and Facial anomalies syndrome 1 (ICF1) possessing a non-canonical poly-A signal and DNA hypomethylation at D4Z4 showed DUX4 target gene upregulation in the patient when compared to controls in spite of retention of H3K9me3. Taken together, these data suggest that both DNA methylation and H3K9me3 are determinants of D4Z4 silencing. Moreover, we show that in addition to testis, there is appreciable expression of spliced and polyadenylated D4Z4 derived transcripts that contain the complete DUX4 open reading frame (ORF) along with DUX4 target gene expression in the thymus, suggesting that DUX4 may provide normal function in this somatic tissue.
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van den Boogaard ML, Lemmers RJLF, Balog J, Wohlgemuth M, Auranen M, Mitsuhashi S, van der Vliet PJ, Straasheijm KR, van den Akker RFP, Kriek M, Laurense-Bik MEY, Raz V, van Ostaijen-Ten Dam MM, Hansson KBM, van der Kooi EL, Kiuru-Enari S, Udd B, van Tol MJD, Nishino I, Tawil R, Tapscott SJ, van Engelen BGM, van der Maarel SM. Mutations in DNMT3B Modify Epigenetic Repression of the D4Z4 Repeat and the Penetrance of Facioscapulohumeral Dystrophy. Am J Hum Genet 2016; 98:1020-1029. [PMID: 27153398 PMCID: PMC4863565 DOI: 10.1016/j.ajhg.2016.03.013] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/15/2016] [Indexed: 01/08/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is associated with somatic chromatin relaxation of the D4Z4 repeat array and derepression of the D4Z4-encoded DUX4 retrogene coding for a germline transcription factor. Somatic DUX4 derepression is caused either by a 1-10 unit repeat-array contraction (FSHD1) or by mutations in SMCHD1, which encodes a chromatin repressor that binds to D4Z4 (FSHD2). Here, we show that heterozygous mutations in DNA methyltransferase 3B (DNMT3B) are a likely cause of D4Z4 derepression associated with low levels of DUX4 expression from the D4Z4 repeat and increased penetrance of FSHD. Recessive mutations in DNMT3B were previously shown to cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome. This study suggests that transcription of DUX4 in somatic cells is modified by variations in its epigenetic state and provides a basis for understanding the reduced penetrance of FSHD within families.
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Affiliation(s)
| | - Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Mariëlle Wohlgemuth
- Department of Neurology, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Mari Auranen
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Satomi Mitsuhashi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Patrick J van der Vliet
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Kirsten R Straasheijm
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Rob F P van den Akker
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Marjolein Kriek
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Marlies E Y Laurense-Bik
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | | | - Kerstin B M Hansson
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | | | - Sari Kiuru-Enari
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Bjarne Udd
- Neuromuscular Research Center, Department of Neurology, Tampere University Hospital and University of Tampere, 33520 Tampere, Finland
| | - Maarten J D van Tol
- Department of Pediatrics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Baziel G M van Engelen
- Department of Neurology, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.
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21
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Calandra P, Cascino I, Lemmers RJLF, Galluzzi G, Teveroni E, Monforte M, Tasca G, Ricci E, Moretti F, van der Maarel SM, Deidda G. Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2. J Med Genet 2016; 53:348-55. [PMID: 26831754 DOI: 10.1136/jmedgenet-2015-103436] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 12/28/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is associated with an epigenetic defect on 4qter. Two clinically indistinguishable forms of FSHD are known, FSHD1 and FSHD2. FSHD1 is caused by contraction of the highly polymorphic D4Z4 macrosatellite repeat array on chromosome 4q35. FSHD2 is caused by pathogenic mutations of the SMCHD1 gene.Both genetic defects lead to D4Z4 DNA hypomethylation. In the presence of a polymorphic polyadenylation signal (PAS), DNA hypomethylation leads to inappropriate expression of the D4Z4-encoded DUX4 transcription factor in skeletal muscle. Currently, hypomethylation is not diagnostic per se because of the interference of non-pathogenic arrays and the lack of information about the presence of DUX4-PAS. METHODS We investigated, by bisulfite sequencing, the DNA methylation levels of the region distal to the D4Z4 array selectively in PAS-positive alleles. RESULTS Comparison of FSHD1, FSHD2 and Control subjects showed a highly significant difference of methylation levels in all CpGs tested. Importantly, using a cohort of 112 samples, one of these CpGs (CpG6) is able to discriminate the affected individuals with a sensitivity of 0.95 supporting this assay potential for FSHD diagnosis. Moreover, our study showed a relationship between PAS-specific methylation and severity of the disease. CONCLUSIONS These data point to the CpGs distal to the D4Z4 array as a critical region reflecting multiple factors affecting the epigenetics of FSHD. Additionally, methylation analysis of this region allows the establishment of a rapid and sensitive tool for FSHD diagnosis.
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Affiliation(s)
- Patrizia Calandra
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo (Rome), Italy
| | - Isabella Cascino
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo (Rome), Italy
| | - Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Giuliana Galluzzi
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo (Rome), Italy
| | - Emanuela Teveroni
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo (Rome), Italy Institute of Pathology, Catholic University School of Medicine, Rome, Italy
| | - Mauro Monforte
- Institute of Neurology, Catholic University School of Medicine, Rome, Italy
| | | | - Enzo Ricci
- Institute of Neurology, Catholic University School of Medicine, Rome, Italy
| | - Fabiola Moretti
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo (Rome), Italy
| | | | - Giancarlo Deidda
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo (Rome), Italy
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22
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23
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Hewitt JE. Loss of epigenetic silencing of the DUX4 transcription factor gene in facioscapulohumeral muscular dystrophy. Hum Mol Genet 2015; 24:R17-23. [PMID: 26113644 DOI: 10.1093/hmg/ddv237] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/18/2015] [Indexed: 02/07/2023] Open
Abstract
Current genetic and molecular evidence best supports an epigenetic mechanism for facioscapulohumeral muscular dystrophy (FSHD), whereby de-repression of the D4Z4 macrosatellite array leads to aberrant expression of the DUX4 transcription factor in skeletal muscle. This de-repression is triggered by either array contraction or (more rarely) by mutation of the SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1) gene. Activation of DUX4 targets, including germline genes and several mammalian retrotransposons, then drives pathogenesis. A direct role for DUX4 mRNA in suppression of nonsense-mediated decay pathways has recently been demonstrated and may also contribute to muscle pathology. Loss of D4Z4 repression in FSHD is observed as hypomethylation of the array accompanied by loss of repressive chromatin marks. The molecular mechanisms of D4Z4 repression are poorly understood, but recent data have identified an Argonaute (AGO)-dependent siRNA pathway. Targeting this pathway by exogenous siRNAs could be a therapeutic strategy for FSHD.
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Affiliation(s)
- Jane E Hewitt
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
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24
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Jones TI, King OD, Himeda CL, Homma S, Chen JCJ, Beermann ML, Yan C, Emerson CP, Miller JB, Wagner KR, Jones PL. Individual epigenetic status of the pathogenic D4Z4 macrosatellite correlates with disease in facioscapulohumeral muscular dystrophy. Clin Epigenetics 2015; 7:37. [PMID: 25904990 PMCID: PMC4405830 DOI: 10.1186/s13148-015-0072-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/11/2015] [Indexed: 12/27/2022] Open
Abstract
Background Both forms of facioscapulohumeral muscular dystrophy (FSHD) are associated with aberrant epigenetic regulation of the chromosome 4q35 D4Z4 macrosatellite. Chromatin changes due to large deletions of heterochromatin (FSHD1) or mutations in chromatin regulatory proteins (FSHD2) lead to relaxation of epigenetic repression and increased expression of the deleterious double homeobox 4 (DUX4) gene encoded within the distal D4Z4 repeat. However, many individuals with the genetic requirements for FSHD remain asymptomatic throughout their lives. Here we investigated family cohorts of FSHD1 individuals who were either affected (manifesting) or without any discernible weakness (nonmanifesting/asymptomatic) and their unaffected family members to determine if individual epigenetic status and stability of repression at the contracted 4q35 D4Z4 array in myocytes correlates with FSHD disease. Results Family cohorts were analyzed for DNA methylation on the distal pathogenic 4q35 D4Z4 repeat on permissive A-type subtelomeres. We found DNA hypomethylation in FSHD1-affected subjects, hypermethylation in healthy controls, and distinctly intermediate levels of methylation in nonmanifesting subjects. We next tested if these differences in DNA methylation had functional relevance by assaying DUX4-fl expression and the stability of epigenetic repression of DUX4-fl in myogenic cells. Treatment with drugs that alter epigenetic status revealed that healthy cells were refractory to treatment, maintaining stable repression of DUX4, while FSHD1-affected cells were highly responsive to treatment and thus epigenetically poised to express DUX4. Myocytes from nonmanifesting subjects had significantly higher levels of DNA methylation and were more resistant to DUX4 activation in response to epigenetic drug treatment than cells from FSHD1-affected first-degree relatives containing the same contraction, indicating that the epigenetic status of the contracted D4Z4 array is reflective of disease. Conclusions The epigenetic status of the distal 4qA D4Z4 repeat correlates with FSHD disease; FSHD-affected subjects have hypomethylation, healthy unaffected subjects have hypermethylation, and nonmanifesting subjects have characteristically intermediate methylation. Thus, analysis of DNA methylation at the distal D4Z4 repeat could be used as a diagnostic indicator of developing clinical FSHD. In addition, the stability of epigenetic repression upstream of DUX4 expression is a key regulator of disease and a viable therapeutic target. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0072-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takako I Jones
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Oliver D King
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| | - Charis L Himeda
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| | - Sachiko Homma
- Neuromuscular Biology & Disease Group, Departments of Neurology and Physiology & Biophysics, Boston University School of Medicine, 72 E Concord St, Boston, MA 02118 USA
| | - Jennifer C J Chen
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| | - Mary Lou Beermann
- Neuromuscular Biology & Disease Group, Departments of Neurology and Physiology & Biophysics, Boston University School of Medicine, 72 E Concord St, Boston, MA 02118 USA
| | - Chi Yan
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; Key Lab of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan, 430070 People's Republic of China
| | - Charles P Emerson
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| | - Jeffrey B Miller
- Neuromuscular Biology & Disease Group, Departments of Neurology and Physiology & Biophysics, Boston University School of Medicine, 72 E Concord St, Boston, MA 02118 USA
| | - Kathryn R Wagner
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA ; The Hugo W. Moser Research Institute, Kennedy Krieger Institute, and the Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205 USA
| | - Peter L Jones
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
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DNA methylation analysis of the macrosatellite repeat associated with FSHD muscular dystrophy at single nucleotide level. PLoS One 2014; 9:e115278. [PMID: 25545674 PMCID: PMC4278900 DOI: 10.1371/journal.pone.0115278] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/23/2014] [Indexed: 11/26/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common inherited diseases of the skeletal muscle. It is characterized by asymmetric muscle weakness and variable penetrance. FSHD is linked to a reduction in copy number of the D4Z4 3.3 kb macrosatellite repeat, located in 4q35. This causes the epigenetic de-repression of FSHD candidate genes leading to disease. Nevertheless, the molecular mechanism responsible for silencing of FSHD candidate genes in healthy subjects is not fully understood. While a role for DNA methylation has been suggested, so far there is limited information regarding the methylation status of the 325 CpGs contained in each D4Z4 unit. Using a human/rodent monochromosomal hybrid cell line containing a single human chromosome 4, we performed an in depth analysis of DNA methylation for the majority of the CpGs inside D4Z4 at single nucleotide level. We found that D4Z4 is not uniformly methylated and that the level of DNA methylation does not correlate with the density of CpG dinucleotides. Moreover, in several D4Z4 regions characterized by near complete methylation, we found specific unmethylated CpGs. These elements are enriched in transcription factor binding sites that could be involved in muscle-specific D4Z4 activity. Our approach also detected differential methylation among different D4Z4 units, suggesting that the D4Z4 array is a mosaic of euchromatic and heterochromatic domains. Finally, we found that DNA methylation and histone de-acetylation are required to maintain FSHD candidate genes repressed. Taken together, our data underscore new players involved in the epigenetic regulation of the FSHD locus that could be targeted for therapeutic purposes.
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Friedman SD, Poliachik SL, Otto RK, Carter GT, Budech CB, Bird TD, Miller DG, Shaw DWW. Longitudinal features of STIR bright signal in FSHD. Muscle Nerve 2014; 49:257-60. [PMID: 23720194 DOI: 10.1002/mus.23911] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/26/2013] [Accepted: 05/13/2013] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Magnetic resonance imaging of muscle shows short tau-inversion recovery (STIR) brightness in autosomal dominant facioscapulohumeral muscular dystrophy (FSHD1) suggestive of active inflammation/injury. We measured the longitudinal stability/progression of this potential disease biomarker. METHODS Nine subjects underwent calf MRI imaging over 2 years. Two radiologists evaluated qualitative muscle changes. RESULTS In 3/9 subjects, calf muscles demonstrated moderate/severe STIR hyperintensity at Time 1 that had progressed to fatty replacement 2 years later (Time 2). In the remaining subjects, moderate/severe muscle STIR abnormalities, when present, were consistent between exams. Mild STIR+ elevations had roughly similar patterns between exams. CONCLUSIONS Moderate/severe STIR hyperintensities often foreshadow fatty replacement over a 2-year interval. Whether longer time courses are required to observe muscle degeneration and fatty replacement in some subjects remains to be explored.
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Zeng W, Chen YY, Newkirk DA, Wu B, Balog J, Kong X, Ball AR, Zanotti S, Tawil R, Hashimoto N, Mortazavi A, van der Maarel SM, Yokomori K. Genetic and epigenetic characteristics of FSHD-associated 4q and 10q D4Z4 that are distinct from non-4q/10q D4Z4 homologs. Hum Mutat 2014; 35:998-1010. [PMID: 24838473 DOI: 10.1002/humu.22593] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 05/06/2014] [Indexed: 12/15/2022]
Abstract
Facioscapulohumeral dystrophy (FSHD) is one of the most prevalent muscular dystrophies. The majority of FSHD cases are linked to a decreased copy number of D4Z4 macrosatellite repeats on chromosome 4q (FSHD1). Less than 5% of FSHD cases have no repeat contraction (FSHD2), most of which are associated with mutations of SMCHD1. FSHD is associated with the transcriptional derepression of DUX4 encoded within the D4Z4 repeat, and SMCHD1 contributes to its regulation. We previously found that the loss of heterochromatin mark (i.e., histone H3 lysine 9 tri-methylation (H3K9me3)) at D4Z4 is a hallmark of both FSHD1 and FSHD2. However, whether this loss contributes to DUX4 expression was unknown. Furthermore, additional D4Z4 homologs exist on multiple chromosomes, but they are largely uncharacterized and their relationship to 4q/10q D4Z4 was undetermined. We found that the suppression of H3K9me3 results in displacement of SMCHD1 at D4Z4 and increases DUX4 expression in myoblasts. The DUX4 open reading frame (ORF) is disrupted in D4Z4 homologs and their heterochromatin is unchanged in FSHD. The results indicate the significance of D4Z4 heterochromatin in DUX4 gene regulation and reveal the genetic and epigenetic distinction between 4q/10q D4Z4 and the non-4q/10q homologs, highlighting the special role of the 4q/10q D4Z4 chromatin and the DUX4 ORF in FSHD.
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Affiliation(s)
- Weihua Zeng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, California
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Tawil R, van der Maarel SM, Tapscott SJ. Facioscapulohumeral dystrophy: the path to consensus on pathophysiology. Skelet Muscle 2014; 4:12. [PMID: 24940479 PMCID: PMC4060068 DOI: 10.1186/2044-5040-4-12] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/13/2014] [Indexed: 01/07/2023] Open
Abstract
Although the pathophysiology of facioscapulohumeral dystrophy (FSHD) has been controversial over the last decades, progress in recent years has led to a model that incorporates these decades of findings and is gaining general acceptance in the FSHD research community. Here we review how the contributions from many labs over many years led to an understanding of a fundamentally new mechanism of human disease. FSHD is caused by inefficient repeat-mediated epigenetic repression of the D4Z4 macrosatellite repeat array on chromosome 4, resulting in the variegated expression of the DUX4 retrogene, encoding a double-homeobox transcription factor, in skeletal muscle. Normally expressed in the testis and epigenetically repressed in somatic tissues, DUX4 expression in skeletal muscle induces expression of many germline, stem cell, and other genes that might account for the pathophysiology of FSHD. Although some disagreements regarding the details of mechanisms remain in the field, the coalescing agreement on a central model of pathophysiology represents a pivot-point in FSHD research, transitioning the field from discovery-oriented studies to translational studies aimed at developing therapies based on a sound model of disease pathophysiology.
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Affiliation(s)
- Rabi Tawil
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Stephen J Tapscott
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Neurology, University of Washington, Seattle, WA 98105, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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Facioscapulohumeral muscular dystrophy. Biochim Biophys Acta Mol Basis Dis 2014; 1852:607-14. [PMID: 24882751 DOI: 10.1016/j.bbadis.2014.05.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 12/18/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is characterized by a typical and asymmetric pattern of muscle involvement and disease progression. Two forms of FSHD, FSHD1 and FSHD2, have been identified displaying identical clinical phenotype but different genetic and epigenetic basis. Autosomal dominant FSHD1 (95% of patients) is characterized by chromatin relaxation induced by pathogenic contraction of a macrosatellite repeat called D4Z4 located on the 4q subtelomere (FSHD1 patients harbor 1 to 10 D4Z4 repeated units). Chromatin relaxation is associated with inappropriate expression of DUX4, a retrogene, which in muscles induces apoptosis and inflammation. Consistent with this hypothesis, individuals carrying zero repeat on chromosome 4 do not develop FSHD1. Not all D4Z4 contracted alleles cause FSHD. Distal to the last D4Z4 unit, a polymorphic site with two allelic variants has been identified: 4qA and 4qB. 4qA is in cis with a functional polyadenylation consensus site. Only contractions on 4qA alleles are pathogenic because the DUX4 transcript is polyadenylated and translated into stable protein. FSHD2 is instead a digenic disease. Chromatin relaxation of the D4Z4 locus is caused by heterozygous mutations in the SMCHD1 gene encoding a protein essential for chromatin condensation. These patients also harbor at least one 4qA allele in order to express stable DUX4 transcripts. FSHD1 and FSHD2 may have an additive effect: patients harboring D4Z4 contraction and SMCHD1 mutations display a more severe clinical phenotype than with either defect alone. Knowledge of the complex genetic and epigenetic defects causing these diseases is essential in view of designing novel therapeutic strategies. This article is part of a Special Issue entitled: Neuromuscular Diseases: Pathology and Molecular Pathogenesis.
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Sacconi S, Desnuelle C. Dystrophie musculaire facio-scapulo-humérale de type 2. Rev Neurol (Paris) 2013; 169:564-72. [DOI: 10.1016/j.neurol.2013.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 02/28/2013] [Indexed: 12/01/2022]
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Block GJ, Narayanan D, Amell AM, Petek LM, Davidson KC, Bird TD, Tawil R, Moon RT, Miller DG. Wnt/β-catenin signaling suppresses DUX4 expression and prevents apoptosis of FSHD muscle cells. Hum Mol Genet 2013; 22:4661-72. [PMID: 23821646 DOI: 10.1093/hmg/ddt314] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy is a dominantly inherited myopathy associated with chromatin relaxation of the D4Z4 macrosatellite array on chromosome 4. DUX4 is encoded within each unit of the D4Z4 array where it is normally transcriptionally silenced and packaged as constitutive heterochromatin. Truncation of the array to less than 11 D4Z4 units (FSHD1) or mutations in SMCHD1 (FSHD2) results in chromatin relaxation and a small percentage of cultured myoblasts from these individuals exhibit infrequent bursts of DUX4 expression. There are no cellular or animal models to determine the trigger of the DUX4 producing transcriptional bursts and there has been a failure to date to detect the protein in significant numbers of cells from FSHD-affected individuals. Here, we demonstrate for the first time that myotubes generated from FSHD patients express sufficient amounts of DUX4 to undergo DUX4-dependent apoptosis. We show that activation of the Wnt/β-catenin signaling pathway suppresses DUX4 transcription in FSHD1 and FSHD2 myotubes and can rescue DUX4-mediated myotube apoptosis. In addition, reduction of mRNA transcripts from Wnt pathway genes β-catenin, Wnt3A and Wnt9B results in DUX4 activation. We propose that Wnt/β-catenin signaling is important for transcriptional repression of DUX4 and identify a novel group of therapeutic targets for the treatment of FSHD.
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Intrinsic epigenetic regulation of the D4Z4 macrosatellite repeat in a transgenic mouse model for FSHD. PLoS Genet 2013; 9:e1003415. [PMID: 23593020 PMCID: PMC3616921 DOI: 10.1371/journal.pgen.1003415] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 02/11/2013] [Indexed: 11/19/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is a progressive muscular dystrophy caused by decreased epigenetic repression of the D4Z4 macrosatellite repeats and ectopic expression of DUX4, a retrogene encoding a germline transcription factor encoded in each repeat. Unaffected individuals generally have more than 10 repeats arrayed in the subtelomeric region of chromosome 4, whereas the most common form of FSHD (FSHD1) is caused by a contraction of the array to fewer than 10 repeats, associated with decreased epigenetic repression and variegated expression of DUX4 in skeletal muscle. We have generated transgenic mice carrying D4Z4 arrays from an FSHD1 allele and from a control allele. These mice recapitulate important epigenetic and DUX4 expression attributes seen in patients and controls, respectively, including high DUX4 expression levels in the germline, (incomplete) epigenetic repression in somatic tissue, and FSHD–specific variegated DUX4 expression in sporadic muscle nuclei associated with D4Z4 chromatin relaxation. In addition we show that DUX4 is able to activate similar functional gene groups in mouse muscle cells as it does in human muscle cells. These transgenic mice therefore represent a valuable animal model for FSHD and will be a useful resource to study the molecular mechanisms underlying FSHD and to test new therapeutic intervention strategies. Facioscapulohumeral dystrophy (FSHD) is a progressive muscle disorder that is associated with contraction and chromatin relaxation of the D4Z4 macrosatellite repeat on chromosome 4q. Each unit of the repeat contains a copy of the primate-specific DUX4 retrogene, encoding a germline transcription factor that is repressed in somatic tissue. In FSHD, somatic repression of the DUX4 gene is compromised, leading to a variegated expression pattern of DUX4 in muscle cells. The complex (epi)genetic etiology of FSHD has long hampered the generation of a faithful animal model, and thus far the role of FSHD candidate genes has only been studied in model organisms by overexpression approaches. Here we present two transgenic mouse models containing either patient- or control-sized D4Z4 repeats. In our mice, the regulation of the FSHD locus is preserved in both lines, and only in the disease model somatic derepression and variegated expression of DUX4 is observed. These mice thus reflect many aspects of the complex regulation of DUX4 expression in humans. These models may therefore become valuable tools in understanding the in vivo regulation and function of DUX4, its role in FSHD, and the evaluation of therapeutic strategies.
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Hartweck LM, Anderson LJ, Lemmers RJ, Dandapat A, Toso EA, Dalton JC, Tawil R, Day JW, van der Maarel SM, Kyba M. A focal domain of extreme demethylation within D4Z4 in FSHD2. Neurology 2013; 80:392-9. [PMID: 23284062 DOI: 10.1212/wnl.0b013e31827f075c] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Facioscapulohumeral muscular dystrophy (FSHD) is a neuromuscular disease with an unclear genetic mechanism. Most patients have a contraction of the D4Z4 macrosatellite repeat array at 4qter, which is thought to cause partial demethylation (FSHD1) of the contracted allele. Demethylation has been surveyed at 3 restriction enzyme sites in the first repeat and only a single site across the entire array, and current models postulate that a generalized D4Z4 chromatin alteration causes FSHD. The background of normal alleles has confounded the study of epigenetic alterations; however, rare patients (FSHD2) have a form of the disease in which demethylation is global, i.e., on all D4Z4 elements throughout the genome. Our objective was to take advantage of the global nature of FSHD2 to identify where disease-relevant methylation changes occur within D4Z4. METHODS Using bisulfite sequencing of DNA from blood and myoblast cells, methylation levels at 74 CpG sites across 3 disparate regions within D4Z4 were measured in FSHD2 patients and controls. RESULTS We found that rates of demethylation caused by FSHD2 are not consistent across D4Z4. We identified a focal region of extreme demethylation within a 5' domain, which we named DR1. Other D4Z4 regions, including the DUX4 ORF, were hypomethylated but to a much lesser extent. CONCLUSIONS These data challenge the simple view that FSHD is caused by a broad "opening" of D4Z4 and lead us to postulate that the region of focal demethylation is the site of action of the key D4Z4 chromatin regulatory factors that go awry in FSHD.
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Affiliation(s)
- Lynn M Hartweck
- Department of Pediatrics and Lillehei Heart Institute, Minneapolis, MN, USA
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van der Maarel SM, Miller DG, Tawil R, Filippova GN, Tapscott SJ. Facioscapulohumeral muscular dystrophy: consequences of chromatin relaxation. Curr Opin Neurol 2012; 25:614-20. [PMID: 22892954 PMCID: PMC3653067 DOI: 10.1097/wco.0b013e328357f22d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
PURPOSE OF REVIEW In recent years, we have seen remarkable progress in our understanding of the disease mechanism underlying facioscapulohumeral muscular dystrophy (FSHD). The purpose of this review is to provide a comprehensive overview of our current understanding of the disease mechanism and to discuss the observations supporting the possibility of a developmental defect in this disorder. RECENT FINDINGS In the majority of cases, FSHD is caused by contraction of the D4Z4 repeat array (FSHD1). This results in local chromatin relaxation and stable expression of the DUX4 retrogene in skeletal muscle, but only when a polymorphic DUX4 polyadenylation signal is present. In some cases (FSHD2), D4Z4 chromatin relaxation and stable DUX4 expression occur in the absence of D4Z4 array contraction. DUX4 is a germline transcription factor and its expression in skeletal muscle leads to activation of early stem cell and germline programs and transcriptional activation of retroelements. SUMMARY Recent studies have provided a plausible disease mechanism for FSHD in which FSHD results from inappropriate expression of the germline transcription factor DUX4. The genes regulated by DUX4 suggest several mechanisms of muscle damage, and provide potential biomarkers and therapeutic targets that should be investigated in future studies.
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35
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The epigenetics of facioscapulohumeral muscular dystrophy. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Giussani M, Cardone MF, Bodega B, Ginelli E, Meneveri R. Evolutionary history of linked D4Z4 and Beta satellite clusters at the FSHD locus (4q35). Genomics 2012; 100:289-96. [PMID: 22824653 PMCID: PMC3488192 DOI: 10.1016/j.ygeno.2012.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/21/2012] [Accepted: 07/12/2012] [Indexed: 01/10/2023]
Abstract
We performed a detailed genomic investigation of the chimpanzee locus syntenic to human chromosome 4q35.2, associated to the facioscapulohumeral dystrophy. Two contigs of approximately 150 kb and 200 kb were derived from PTR chromosomes 4q35 and 3p12, respectively: both regions showed a very similar sequence organization, including D4Z4 and Beta satellite linked clusters. Starting from these findings, we derived a hypothetical evolutionary history of human 4q35, 10q26 and 3p12 chromosome regions focusing on the D4Z4–Beta satellite linked organization. The D4Z4 unit showed an open reading frame (DUX4) at both PTR 4q35 and 3p12 regions; furthermore some subregions of the Beta satellite unit showed a high degree of conservation between chimpanzee and humans. In conclusion, this paper provides evidence that at the 4q subtelomere the linkage between D4Z4 and Beta satellite arrays is a feature that appeared late during evolution and is conserved between chimpanzee and humans.
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Affiliation(s)
- Marta Giussani
- Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy.
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Jones TI, Chen JCJ, Rahimov F, Homma S, Arashiro P, Beermann ML, King OD, Miller JB, Kunkel LM, Emerson CP, Wagner KR, Jones PL. Facioscapulohumeral muscular dystrophy family studies of DUX4 expression: evidence for disease modifiers and a quantitative model of pathogenesis. Hum Mol Genet 2012; 21:4419-30. [PMID: 22798623 DOI: 10.1093/hmg/dds284] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), the most prevalent myopathy afflicting both children and adults, is predominantly associated with contractions in the 4q35-localized macrosatellite D4Z4 repeat array. Recent studies have proposed that FSHD pathology is caused by the misexpression of the DUX4 (double homeobox 4) gene resulting in production of a pathogenic protein, DUX4-FL, which has been detected in FSHD, but not in unaffected control myogenic cells and muscle tissue. Here, we report the analysis of DUX4 mRNA and protein expression in a much larger collection of myogenic cells and muscle biopsies derived from biceps and deltoid muscles of FSHD affected subjects and their unaffected first-degree relatives. We confirmed that stable DUX4-fl mRNA and protein were expressed in myogenic cells and muscle tissues derived from FSHD affected subjects, including several genetically diagnosed adult FSHD subjects yet to show clinical manifestations of the disease in the assayed muscles. In addition, we report DUX4-fl mRNA and protein expression in muscle biopsies and myogenic cells from genetically unaffected relatives of the FSHD subjects, although at a significantly lower frequency. These results establish that DUX4-fl expression per se is not sufficient for FSHD muscle pathology and indicate that quantitative modifiers of DUX4-fl expression and/or function and family genetic background are determinants of FSHD muscle disease progression.
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Abstract
DUX4, a homeobox-containing gene present in a tandem array, is implicated in facioscapulohumeral muscular dystrophy (FSHD), a dominant autosomal disease. New findings about DUX4 have raised as many fundamental questions about the molecular pathology of this unique disease as they have answered. This review discusses recent studies addressing the question of whether there is extensive FSHD-related transcription dysregulation in adult-derived myoblasts and myotubes, the precursors for muscle repair. Two models for the role of DUX4 in FSHD are presented. One involves transient pathogenic expression of DUX4 in many cells in the muscle lineage before the myoblast stage resulting in a persistent, disease-related transcription profile ('Majority Rules'), which might be enhanced by subsequent oscillatory expression of DUX4. The other model emphasizes the toxic effects of inappropriate expression of DUX4 in only an extremely small percentage of FSHD myoblasts or myotube nuclei ('Minority Rules'). The currently favored Minority Rules model is not supported by recent studies of transcription dysregulation in FSHD myoblasts and myotubes. It also presents other difficulties, for example, explaining the expression of full-length DUX4 transcripts in FSHD fibroblasts. The Majority Rules model is the simpler explanation of findings about FSHD-associated gene expression and the DUX4-encoded homeodomain-type protein.
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Friedman SD, Poliachik SL, Carter GT, Budech CB, Bird TD, Shaw DWW. The magnetic resonance imaging spectrum of facioscapulohumeral muscular dystrophy. Muscle Nerve 2012; 45:500-6. [PMID: 22431082 DOI: 10.1002/mus.22342] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Facioscapulohumeral muscular dystrophy (FSHD) is associated with a repeat contraction in the D4Z4 gene locus on chromosome 4q35. We used a one-step quantitative magnetic resonance imaging (MRI) method to evaluate muscle, edema, and fat in patients spanning the range of severity. METHODS Fifteen patients with FSHD were compared with 10 healthy subjects using non-negative linear least-squares fitting of 32-echo relaxation data (T2). The results were compared with a biexponential approach for characterizing muscle/fat ratio and T2 relaxation measurements from fat-suppressed inversion recovery. RESULTS Increased T2 signal consistent with edema was common in FSHD subjects, a pattern not present in healthy controls. A varied pattern of edema and fatty replacement in muscles was shown. CONCLUSIONS As a discrete biomarker, edema may be useful for following the clinical course of FSHD. Future work toward optimizing measurement is discussed.
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Affiliation(s)
- Seth D Friedman
- Department of Radiology, Seattle Children's Hospital, 4800 Sandpoint Way, Room R4488, Seattle, Washington 98105, USA.
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Asymmetric bidirectional transcription from the FSHD-causing D4Z4 array modulates DUX4 production. PLoS One 2012; 7:e35532. [PMID: 22536400 PMCID: PMC3334996 DOI: 10.1371/journal.pone.0035532] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 03/17/2012] [Indexed: 01/08/2023] Open
Abstract
Facioscapulohumeral Disease (FSHD) is a dominantly inherited progressive myopathy associated with aberrant production of the transcription factor, Double Homeobox Protein 4 (DUX4). The expression of DUX4 depends on an open chromatin conformation of the D4Z4 macrosatellite array and a specific haplotype on chromosome 4. Even when these requirements are met, DUX4 transcripts and protein are only detectable in a subset of cells indicating that additional constraints govern DUX4 production. Since the direction of transcription, along with the production of non-coding antisense transcripts is an important regulatory feature of other macrosatellite repeats, we developed constructs that contain the non-coding region of a single D4Z4 unit flanked by genes that report transcriptional activity in the sense and antisense directions. We found that D4Z4 contains two promoters that initiate sense and antisense transcription within the array, and that antisense transcription predominates. Transcriptional start sites for the antisense transcripts, as well as D4Z4 regions that regulate the balance of sense and antisense transcripts were identified. We show that the choice of transcriptional direction is reversible but not mutually exclusive, since sense and antisense reporter activity was often present in the same cell and simultaneously upregulated during myotube formation. Similarly, levels of endogenous sense and antisense D4Z4 transcripts were upregulated in FSHD myotubes. These studies offer insight into the autonomous distribution of muscle weakness that is characteristic of FSHD.
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41
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Neguembor MV, Gabellini D. In junk we trust: repetitive DNA, epigenetics and facioscapulohumeral muscular dystrophy. Epigenomics 2012; 2:271-87. [PMID: 22121874 DOI: 10.2217/epi.10.8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant myopathy with a peculiar etiology. Unlike most genetic disorders, FSHD is not caused by mutations in a protein-coding gene. Instead, it is associated with contraction of the D4Z4 macrosatellite repeat array located at 4q35. Interestingly, D4Z4 deletion is not sufficient per se to cause FSHD. Moreover, the disease severity, its rate of progression and the distribution of muscle weakness display great variability even among close family relatives. Hence, additional genetic and epigenetic events appear to be required for FSHD pathogenesis. Indeed, recent findings suggest that virtually all levels of epigenetic regulation, from DNA methylation to higher order chromosomal architecture, exhibit alterations in the disease locus causing deregulation of 4q35 gene expression, ultimately leading to FSHD.
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Affiliation(s)
- Maria V Neguembor
- International PhD Program in Cellular & Molecular Biology, Vita-Salute San Raffaele University, Milan, Italy
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Leidenroth A, Sorte HS, Gilfillan G, Ehrlich M, Lyle R, Hewitt JE. Diagnosis by sequencing: correction of misdiagnosis from FSHD2 to LGMD2A by whole-exome analysis. Eur J Hum Genet 2012; 20:999-1003. [PMID: 22378277 DOI: 10.1038/ejhg.2012.42] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We studied and validated facioscapulohumeral muscular dystrophy (FSHD) samples from patients without a D4Z4 contraction (FSHD2 or 'phenotypic FSHD'). For this, we developed non-radioactive protocols to test D4Z4 allele constitution and DNA methylation, and applied these to samples from the Coriell Institute Cell Repository. The D4Z4 sizing showed two related subjects to have classic chromosome 4 contraction-dependent FSHD1. A third sample (GM17726) did not have a short chromosome 4 fragment, and had been assigned as non-4q FSHD (FSHD2). We tested D4Z4 haplotype and methylation for this individual but found both to be inconsistent with this diagnosis. Using exome sequencing, we identified two known pathogenic mutations in CAPN3 (Arg490Gln and Thr184Argfs(*)36), indicating a case of LGMD2A rather than FSHD. Our study shows how a wrong diagnosis can easily be corrected by whole-exome sequencing by constraining the variant analysis to candidate genes after the data have been generated. This new way of 'diagnosis by sequencing' is likely to become common place in genetic diagnostic laboratories. We also publish a digoxigenin-labeled Southern protocol to test D4Z4 methylation. Our data supports hypomethylation as a good epigenetic predictor for FSHD2. The non-radioactive protocol will help to make this assay more accessible to clinical diagnostic laboratories and the wider FSHD research community.
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Affiliation(s)
- Andreas Leidenroth
- Centre for Genetics and Genomics, School of Biology, Queen's Medical Centre, The University of Nottingham, Nottingham, UK
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Richards M, Coppée F, Thomas N, Belayew A, Upadhyaya M. Facioscapulohumeral muscular dystrophy (FSHD): an enigma unravelled? Hum Genet 2011; 131:325-40. [PMID: 21984394 DOI: 10.1007/s00439-011-1100-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 09/26/2011] [Indexed: 01/02/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the third most common muscular dystrophy after the dystrophinopathies and myotonic dystrophy and is associated with a typical pattern of muscle weakness. Most patients with FSHD carry a large deletion in the polymorphic D4Z4 macrosatellite repeat array at 4q35 and present with 1-10 repeats whereas non-affected individuals possess 11-150 repeats. An almost identical repeat array is present at 10q26 and the high sequence identity between these two arrays can cause difficulties in molecular diagnosis. Each 3.3-kb D4Z4 unit contains a DUX4 (double homeobox 4) gene that, among others, is activated upon contraction of the 4q35 repeat array due to the induction of chromatin remodelling of the 4qter region. A number of 4q subtelomeric sequence variants are now recognised, although FSHD only occurs in association with three 'permissive' haplotypes, each of which is associated with a polyadenylation signal located immediately distal of the last D4Z4 unit. The resulting poly-A tail appears to stabilise DUX4 mRNAs transcribed from this most distal D4Z4 unit in FSHD muscle cells. Synthesis of both the DUX4 transcripts and protein in FSHD muscle cells induces significant cell toxicity. DUX4 is a transcription factor that may target several genes which results in a deregulation cascade which inhibits myogenesis, sensitises cells to oxidative stress and induces muscle atrophy, thus recapitulating many of the key molecular features of FSHD.
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Affiliation(s)
- Mark Richards
- School of Medicine, Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
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Sacconi S, Camaño P, de Greef JC, Lemmers RJLF, Salviati L, Boileau P, Lopez de Munain Arregui A, van der Maarel SM, Desnuelle C. Patients with a phenotype consistent with facioscapulohumeral muscular dystrophy display genetic and epigenetic heterogeneity. J Med Genet 2011; 49:41-6. [PMID: 21984748 DOI: 10.1136/jmedgenet-2011-100101] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To identify the genetic and epigenetic defects in patients presenting with a facioscapulohumeral (FSHD) clinical phenotype without D4Z4 contractions on chromosome 4q35 tested by linear gel electrophoresis and Southern blot analysis. DESIGN AND PATIENTS The authors studied 16 patients displaying an FSHD-like phenotype, with normal cardiovascular and respiratory function, a myopathic pattern on electromyography, and a muscle biopsy being normal or displaying only mild and aspecific dystrophic changes. They sequenced the genes calpain 3 (CAPN3), valosin containing protein (VCP) and four-and-a-half LIM domains protein 1 (FHL1), and they analysed the D4Z4 repeat arrays by extensive genotyping and DNA methylation analysis. RESULTS The authors identified one patient carrying a complex rearrangement in the FSHD locus that masked the D4Z4 contraction associated with FSHD1 in standard genetic testing, one patient with somatic mosaicism for the D4Z4 4q35 contraction, six patients that were diagnosed as having FSHD2, four patients with CAPN3 mutations and two patients with a VCP mutation, No mutations were detected in FHL1, and in two patients, the authors could not identify the genetic defect. CONCLUSIONS In patients presenting with an FSHD-like clinical phenotype with a negative molecular testing for FSHD, consider (1) detailed genetic testing including D4Z4 contraction of permissive hybrid D4Z4 repeat arrays, p13E-11 probe deletions, and D4Z4 hypomethylation in the absence of repeat contraction as observed in FSHD2; (2) mutations in CAPN3 even in the absence of protein deficiency on western blot analysis; and (3) VCP mutations even in the absence of cognitive impairment, Paget disease and typical inclusion in muscle biopsy.
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Affiliation(s)
- Sabrina Sacconi
- Centre de référence des Maladies neuromusculaires and CNRS UMR6543, Nice University Hospital, Nice, France.
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van der Maarel SM, Tawil R, Tapscott SJ. Facioscapulohumeral muscular dystrophy and DUX4: breaking the silence. Trends Mol Med 2011; 17:252-8. [PMID: 21288772 PMCID: PMC3092836 DOI: 10.1016/j.molmed.2011.01.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 12/14/2010] [Accepted: 01/03/2011] [Indexed: 01/10/2023]
Abstract
Autosomal dominant facioscapulohumeral muscular dystrophy (FSHD) has an unusual pathogenic mechanism. FSHD is caused by deletion of a subset of D4Z4 macrosatellite repeat units in the subtelomere of chromosome 4q. Recent studies provide compelling evidence that a retrotransposed gene in the D4Z4 repeat, DUX4, is expressed in the human germline and then epigenetically silenced in somatic tissues. In FSHD, the combination of inefficient chromatin silencing of the D4Z4 repeat and polymorphisms on the FSHD-permissive alleles that stabilize the DUX4 mRNAs emanating from the repeat result in inappropriate DUX4 protein expression in muscle cells. FSHD is thereby the first example of a human disease caused by the inefficient repression of a retrogene in a macrosatellite repeat array.
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Affiliation(s)
- Silvère M van der Maarel
- Leiden University Medical Center, Department of Human Genetics, Albinusdreef 2, 2333 ZA, Leiden, Netherlands. Phone: +31 71 526 9480, Fax: +31 71 526 8285
| | - Rabi Tawil
- University of Rochester Medical Center, Department of Neurology, POBox 673, 601 Elmwood Avenue, Rochester, NY 14642 USA. Phone: 1-585-275-6372, FAX: 1-585-273-1255
| | - Stephen J. Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 USA. Phone: 1-206-667-4499, FAX 1-206-667-6524
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Distrofia muscolare facio-scapolo-omerale. Neurologia 2011. [DOI: 10.1016/s1634-7072(11)70626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Wallace LM, Garwick SE, Mei W, Belayew A, Coppee F, Ladner KJ, Guttridge D, Yang J, Harper SQ. DUX4, a candidate gene for facioscapulohumeral muscular dystrophy, causes p53-dependent myopathy in vivo. Ann Neurol 2010; 69:540-52. [PMID: 21446026 DOI: 10.1002/ana.22275] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 08/31/2010] [Accepted: 09/17/2010] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Facioscapulohumeral muscular dystrophy (FSHD) is associated with D4Z4 repeat contraction on human chromosome 4q35. This genetic lesion does not result in complete loss or mutation of any gene. Consequently, the pathogenic mechanisms underlying FSHD have been difficult to discern. In leading FSHD pathogenesis models, D4Z4 contractions are proposed to cause epigenetic changes, which ultimately increase expression of genes with myopathic potential. Although no gene has been conclusively linked to FSHD development, recent evidence supports a role for the D4Z4-encoded DUX4 gene in FSHD. In this study, our objective was to test the in vivo myopathic potential of DUX4. METHODS We delivered DUX4 to zebrafish and mouse muscle by transposon-mediated transgenesis and adeno-associated viral vectors, respectively. RESULTS Overexpression of DUX4, which encodes a transcription factor, caused abnormalities associated with muscular dystrophy in zebrafish and mice. This toxicity required DNA binding, because a DUX4 DNA binding domain mutant produced no abnormalities. Importantly, we found the myopathic effects of DUX4 were p53 dependent, as p53 inhibition mitigated DUX4 toxicity in vitro, and muscles from p53 null mice were resistant to DUX4-induced damage. INTERPRETATION Our work demonstrates the myopathic potential of DUX4 in animal muscle. Considering previous studies showed DUX4 was elevated in FSHD patient muscles, our data support the hypothesis that DUX4 overexpression contributes to FSHD development. Moreover, we provide a p53-dependent mechanism for DUX4 toxicity that is consistent with previous studies showing p53 pathway activation in FSHD muscles. Our work justifies further investigation of DUX4 and the p53 pathway in FSHD pathogenesis.
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Affiliation(s)
- Lindsay M Wallace
- Molecular, Cellular, and Developmental Biology Graduate Program, Ohio State University, Columbus, USA
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48
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de Greef JC, Lemmers RJLF, Camaño P, Day JW, Sacconi S, Dunand M, van Engelen BGM, Kiuru-Enari S, Padberg GW, Rosa AL, Desnuelle C, Spuler S, Tarnopolsky M, Venance SL, Frants RR, van der Maarel SM, Tawil R. Clinical features of facioscapulohumeral muscular dystrophy 2. Neurology 2010; 75:1548-54. [PMID: 20975055 PMCID: PMC2974464 DOI: 10.1212/wnl.0b013e3181f96175] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE In some 5% of patients with facioscapulohumeral muscular dystrophy (FSHD), no D4Z4 repeat contraction on chromosome 4q35 is observed. Such patients, termed patients with FSHD2, show loss of DNA methylation and heterochromatin markers at the D4Z4 repeat that are similar to patients with D4Z4 contractions (FSHD1). This commonality suggests that a change in D4Z4 chromatin structure unifies FSHD1 and FSHD2. The aim of our study was to critically evaluate the clinical features in patients with FSHD2 in order to establish whether these patients are phenotypically identical to FSHD1 and to establish the effects of the (epi-) genotype on the phenotype. METHODS This cross-sectional study studied 33 patients with FSHD2 from 27 families, the largest cohort described to date. All patients were clinically assessed using a standardized clinical evaluation form. Genotype analysis was performed by pulsed field gel electrophoresis and PCR; D4Z4 methylation was studied by methylation-sensitive Southern blot analysis. RESULTS FSHD2 is identical to FSHD1 in its clinical presentation. Notable differences include a higher incidence (67%) of sporadic cases and the absence of gender differences in disease severity in FSHD2. Overall, average disease severity in FSHD2 was similar to that reported in FSHD1 and was not influenced by D4Z4 repeat size. In FSHD2, a small effect of the degree of hypomethylation on disease severity was observed. CONCLUSIONS Clinically, patients with FSHD2 are indistinguishable from patients with FSHD1. The present data suggest that FSHD1 and FSHD2 are the result of the same pathophysiologic process.
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Affiliation(s)
- J C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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de Greef JC, Lemmers RJLF, van Engelen BGM, Sacconi S, Venance SL, Frants RR, Tawil R, van der Maarel SM. Common epigenetic changes of D4Z4 in contraction-dependent and contraction-independent FSHD. Hum Mutat 2009; 30:1449-59. [PMID: 19728363 DOI: 10.1002/humu.21091] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), caused by partial deletion of the D4Z4 macrosatellite repeat on chromosome 4q, has a complex genetic and epigenetic etiology. To develop FSHD, D4Z4 contraction needs to occur on a specific genetic background. Only contractions associated with the 4qA161 haplotype cause FSHD. In addition, contraction of the D4Z4 repeat in FSHD patients is associated with significant D4Z4 hypomethylation. To date, however, the methylation status of contracted repeats on nonpathogenic haplotypes has not been studied. We have performed a detailed methylation study of the D4Z4 repeat on chromosome 4q and on a highly homologous repeat on chromosome 10q. We show that patients with a D4Z4 deletion (FSHD1) have D4Z4-restricted hypomethylation. Importantly, controls with a D4Z4 contraction on a nonpathogenic chromosome 4q haplotype or on chromosome 10q also demonstrate hypomethylation. In 15 FSHD families without D4Z4 contractions but with at least one 4qA161 haplotype (FSHD2), we observed D4Z4-restricted hypomethylation on chromosomes 4q and 10q. This finding implies that a genetic defect resulting in D4Z4 hypomethylation underlies FSHD2. In conclusion, we describe two ways to develop FSHD: (1) contraction-dependent or (2) contraction-independent D4Z4 hypomethylation on the 4qA161 subtelomere.
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Affiliation(s)
- Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Abstract
PURPOSE OF REVIEW The purpose of this review is to discuss the role of muscle biopsy in the current age of genetic testing. RECENT FINDINGS The diagnostic approach to patients with suspected genetically determined myopathies has been altered by recent advances in molecular diagnostic technologies and by the increased number of conditions for which the genetic alterations have been identified. Myopathological aspects can narrow down the differential diagnosis when the clinical phenotype is not informative enough and can help guide the molecular investigation. SUMMARY Here, we review genetic and myopathological aspects of selected genetically determined myopathies.
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