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Jia FF, Drew AP, Nicholson GA, Corbett A, Kumar KR. Facioscapulohumeral muscular dystrophy type 2: an update on the clinical, genetic, and molecular findings. Neuromuscul Disord 2021; 31:1101-1112. [PMID: 34711481 DOI: 10.1016/j.nmd.2021.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 11/25/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a common genetic disease of the skeletal muscle with a characteristic pattern of weakness. Facioscapulohumeral muscular dystrophy type 2 (FSHD2) accounts for approximately 5% of all cases of FSHD and describes patients without a D4Z4 repeat contraction on chromosome 4. Phenotypically FSHD2 shows virtually no difference from FSHD1 and both forms of FSHD arise via a common downstream mechanism of epigenetic derepression of the transcription factor DUX4 in skeletal muscle cells. This results in expression of DUX4 and target genes leading to skeletal muscle toxicity. Over the past decade, major progress has been made in our understanding of the genetic and epigenetic architecture that underlies FSHD2 pathogenesis, as well as the clinical manifestations and disease progression. These include the finding that FSHD2 is a digenic disease and that mutations in the genes SMCHD1, DNMT3B, and more recently LRIF1, can cause FSHD2. FSHD2 is complex and it is important that clinicians keep abreast of recent developments; this review aims to serve as an update of the clinical, genetic, and molecular research into this condition.
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Affiliation(s)
- Fangzhi Frank Jia
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia.
| | - Alexander P Drew
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.
| | - Garth Alexander Nicholson
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Alastair Corbett
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Kishore Raj Kumar
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
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2
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Goossens R, van den Boogaard ML, Lemmers RJLF, Balog J, van der Vliet PJ, Willemsen IM, Schouten J, Maggio I, van der Stoep N, Hoeben RC, Tapscott SJ, Geijsen N, Gonçalves MAFV, Sacconi S, Tawil R, van der Maarel SM. Intronic SMCHD1 variants in FSHD: testing the potential for CRISPR-Cas9 genome editing. J Med Genet 2019; 56:828-837. [PMID: 31676591 DOI: 10.1136/jmedgenet-2019-106402] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/04/2019] [Accepted: 09/21/2019] [Indexed: 01/14/2023]
Abstract
BACKGROUND Facioscapulohumeral dystrophy (FSHD) is associated with partial chromatin relaxation of the DUX4 retrogene containing D4Z4 macrosatellite repeats on chromosome 4, and transcriptional de-repression of DUX4 in skeletal muscle. The common form of FSHD, FSHD1, is caused by a D4Z4 repeat array contraction. The less common form, FSHD2, is generally caused by heterozygous variants in SMCHD1. METHODS We employed whole exome sequencing combined with Sanger sequencing to screen uncharacterised FSHD2 patients for extra-exonic SMCHD1 mutations. We also used CRISPR-Cas9 genome editing to repair a pathogenic intronic SMCHD1 variant from patient myoblasts. RESULTS We identified intronic SMCHD1 variants in two FSHD families. In the first family, an intronic variant resulted in partial intron retention and inclusion of the distal 14 nucleotides of intron 13 into the transcript. In the second family, a deep intronic variant in intron 34 resulted in exonisation of 53 nucleotides of intron 34. In both families, the aberrant transcripts are predicted to be non-functional. Deleting the pseudo-exon by CRISPR-Cas9 mediated genome editing in primary and immortalised myoblasts from the index case of the second family restored wild-type SMCHD1 expression to a level that resulted in efficient suppression of DUX4. CONCLUSIONS The estimated intronic mutation frequency of almost 2% in FSHD2, as exemplified by the two novel intronic SMCHD1 variants identified here, emphasises the importance of screening for intronic variants in SMCHD1. Furthermore, the efficient suppression of DUX4 after restoring SMCHD1 levels by genome editing of the mutant allele provides further guidance for therapeutic strategies.
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Affiliation(s)
- Remko Goossens
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Judit Balog
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Iris M Willemsen
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Julie Schouten
- Hubrecht Institute-KNAW and University Medical Center, Utrecht, The Netherlands.,Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht, The Netherlands
| | - Ignazio Maggio
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nienke van der Stoep
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob C Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephen J Tapscott
- Division of Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Niels Geijsen
- Hubrecht Institute-KNAW and University Medical Center, Utrecht, The Netherlands.,Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht, The Netherlands
| | - Manuel A F V Gonçalves
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sabrina Sacconi
- Peripheral Nervous System, Muscle and ALS Department, Université Côte d'Azur, Nice, France.,Institute for Research on Cancer and Aging of Nice, Faculty of Medicine, Université Côte d'Azur, Nice, France
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA
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Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, provides a powerful model of the complex interplay between genetic and epigenetic mechanisms of chromatin regulation. FSHD is caused by dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, aberrant expression of the DUX4 gene in skeletal muscle. DUX4 is a pioneer transcription factor that activates a program of gene expression during early human development, after which its expression is silenced in most somatic cells. When misexpressed in FSHD skeletal muscle, the DUX4 program leads to accumulated muscle pathology. Epigenetic regulators of the disease locus represent particularly attractive therapeutic targets for FSHD, as many are not global modifiers of the genome, and altering their expression or activity should allow correction of the underlying defect.
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MESH Headings
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 4
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing
- Genetic Loci
- Genome, Human
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/classification
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Mutation
- Severity of Illness Index
- DNA Methyltransferase 3B
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Affiliation(s)
- Charis L Himeda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| | - Peter L Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
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Lemmers RJLF, van der Stoep N, Vliet PJVD, Moore SA, San Leon Granado D, Johnson K, Topf A, Straub V, Evangelista T, Mozaffar T, Kimonis V, Shaw ND, Selvatici R, Ferlini A, Voermans N, van Engelen B, Sacconi S, Tawil R, Lamers M, van der Maarel SM. SMCHD1 mutation spectrum for facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS) reveals disease-specific localisation of variants in the ATPase domain. J Med Genet 2019; 56:693-700. [PMID: 31243061 DOI: 10.1136/jmedgenet-2019-106168] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/11/2019] [Accepted: 05/15/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Variants in the Structural Maintenance of Chromosomes flexible Hinge Domain-containing protein 1 (SMCHD1) can cause facioscapulohumeral muscular dystrophy type 2 (FSHD2) and the unrelated Bosma arhinia microphthalmia syndrome (BAMS). In FSHD2, pathogenic variants are found anywhere in SMCHD1 while in BAMS, pathogenic variants are restricted to the extended ATPase domain. Irrespective of the phenotypic outcome, both FSHD2-associated and BAMS-associated SMCHD1 variants result in quantifiable local DNA hypomethylation. We compared FSHD2, BAMS and non-pathogenic SMCHD1 variants to derive genotype-phenotype relationships. METHODS Examination of SMCHD1 variants and methylation of the SMCHD1-sensitive FSHD locus DUX4 in 187 FSHD2 families, 41 patients with BAMS and in control individuals. Analysis of variants in a three-dimensional model of the ATPase domain of SMCHD1. RESULTS DUX4 methylation analysis is essential to establish pathogenicity of SMCHD1 variants. Although the FSHD2 mutation spectrum includes all types of variants covering the entire SMCHD1 locus, missense variants are significantly enriched in the extended ATPase domain. Identification of recurrent variants suggests disease-specific residues for FSHD2 and in BAMS, consistent with a largely disease-specific localisation of variants in SMCHD1. CONCLUSIONS The localisation of missense variants within the ATPase domain of SMCHD1 may contribute to the differences in phenotypic outcome.
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Affiliation(s)
| | - Nienke van der Stoep
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis, Leids Universitair Medisch Centrum, Leiden, The Netherlands
| | | | - Steven A Moore
- Department of Pathology, University of Iowa, Iowa City, Iowa, USA
| | | | - Katherine Johnson
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Ana Topf
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | | | - Tahseen Mozaffar
- Department of Neurology, University of California Irvine, Irvine, California, USA
| | - Virginia Kimonis
- Department of Pediatrics, University of California, Irvine, Irvine, California, USA
| | | | - Rita Selvatici
- Department of Medical Sciences; Medical Genetics Unit, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Dipartimento di Medicina Sperimentale e Diagnostica, Università di Ferrara, Ferrara, Italy
| | - Nicol Voermans
- Department of Neurology, Radboudumc, Nijmegen, Gelderland, The Netherlands
| | - Baziel van Engelen
- Department of Neurology, Radboudumc, Nijmegen, Gelderland, The Netherlands
| | - Sabrina Sacconi
- Centre de Référence Maladies Neuromusculaires, Hôpital Archet, Nice, France
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA
| | - Meindert Lamers
- Department of Cell and Chemical Biology, Leiden Universitair Medisch Centrum, Leiden, The Netherlands
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Cascella R, Strafella C, Caputo V, Galota RM, Errichiello V, Scutifero M, Petillo R, Marella GL, Arcangeli M, Colantoni L, Zampatti S, Ricci E, Deidda G, Politano L, Giardina E. Digenic Inheritance of Shortened Repeat Units of the D4Z4 Region and a Loss-of-Function Variant in SMCHD1 in a Family With FSHD. Front Neurol 2018; 9:1027. [PMID: 30546343 PMCID: PMC6279899 DOI: 10.3389/fneur.2018.01027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a neuromuscular disorder which is typically transmitted by an autosomal dominant pattern, although reduced penetrance and sporadic cases caused by de novo mutations, are often observed. FSHD may be caused by a contraction of a repetitive element, located on chromosome 4 (4q35). This locus is named D4Z4 and consists of 11 to more than 100 repeated units (RU). The D4Z4 is normally hypermethylated and the genes located on this locus are silenced. In case of FSHD, the D4Z4 region is characterized by 1–10 repeats and results in the region being hypomethylated. However, 5% of FSHD cases do not carry the short allele of D4Z4 region. To date, two forms of FSHD (FSHD1 and FSHD2) are known. FSHD2 is usually observed in patients without the D4Z4 fragment contraction and carrying variants in SMCHD1 (18p11.32) gene. We report the case of a young adult patient who shows severe symptoms of FSHD. Preliminary genetic analysis did not clarify the phenotype, therefore we decided to study the family members by genetic and epigenetic approaches. The analysis of D4Z4 fragment resulted to be 8 RU in the affected proband and in his father; 26 RU in the mother and 25 RU in the maternal uncle. SMCHD1 analysis revealed a heterozygous variation within the exon 41. The variant was detected in the proband, her mother and the uncle. Furthermore, epigenetic analysis of CpG6 methylation regions showed significant hypomethylation in the affected patient (54%) and in the mother (56%), in contrast to the father (88%) and the uncle (81%) carrying higher methylation levels. The analysis of DR1 methylation levels reported hypomethylation for the proband (19%), the mother (11%), and the uncle (16%). The father showed normal DR1 methylation levels (>30%). Given these results, the combined inheritance of SMCHD1 variant and the short fragment might explain the severe FSHD phenotype displayed by the proband. On this subject, SMCHD1 analysis should be promoted in a larger number of patients, even in presence of D4Z4 contractions, to facilitate the genotype-phenotype correlation as well as, to enable a more precise diagnosis and prognosis of the disease.
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Affiliation(s)
- Raffaella Cascella
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy.,Department of Chemical-Toxicological and Pharmacological Evaluation of Drugs, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Claudia Strafella
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy.,Emotest Laboratory, Pozzuoli, Italy
| | - Valerio Caputo
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | | | - Valeria Errichiello
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | - Marianna Scutifero
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Roberta Petillo
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Gian Luca Marella
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Mauro Arcangeli
- Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
| | - Luca Colantoni
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | - Stefania Zampatti
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | - Enzo Ricci
- Institute of Neurology, Catholic University of the Sacred Heart, Rome, Italy
| | - Giancarlo Deidda
- Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo, Rome, Italy
| | - Luisa Politano
- Department of Experimental Medicine, Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Emiliano Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy.,Department of Biomedicine and Prevention Tor Vergata University, Rome, Italy
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6
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Integrating clinical and genetic observations in facioscapulohumeral muscular dystrophy. Curr Opin Neurol 2018; 29:606-13. [PMID: 27389814 DOI: 10.1097/wco.0000000000000360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
PURPOSE OF REVIEW This review gives an overview of the currently known key clinical and (epi)genetic aspects of facioscapulohumeral muscular dystrophy (FSHD) and provides perspectives to facilitate future research. RECENT FINDINGS Clinically, imaging studies have contributed to a detailed characterization of the FSHD phenotype, and a model is proposed with five stages of disease progression. A number of clinical trials have been conducted regarding exercise and diet aiming to reduce symptoms. Genetically, at least two different mechanisms (FSHD1 and FSHD2) lead to double homeobox 4 (DUX4) expression in skeletal myocytes, which is expected to be necessary for the disease. Disease severity is most likely determined by a combination of the D4Z4 repeat size and its epigenetic state. SUMMARY FSHD is one of the most common muscular dystrophies and is characterized by a typical distribution of muscle weakness. Progress has been made on clinical as well as on (epi)genetic aspects of the disease. Currently, there is no cure available for FSHD. For successful development of new treatments targeting the disease process, integration of clinical and pathogenetic knowledge is essential. A clinical trial toolbox that consists of patient registries, biomarkers and clinical outcome measures will be required to effectively conduct future clinical trials.
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7
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DeSimone AM, Pakula A, Lek A, Emerson CP. Facioscapulohumeral Muscular Dystrophy. Compr Physiol 2017; 7:1229-1279. [PMID: 28915324 DOI: 10.1002/cphy.c160039] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Facioscapulohumeral Muscular Dystrophy is a common form of muscular dystrophy that presents clinically with progressive weakness of the facial, scapular, and humeral muscles, with later involvement of the trunk and lower extremities. While typically inherited as autosomal dominant, facioscapulohumeral muscular dystrophy (FSHD) has a complex genetic and epigenetic etiology that has only recently been well described. The most prevalent form of the disease, FSHD1, is associated with the contraction of the D4Z4 microsatellite repeat array located on a permissive 4qA chromosome. D4Z4 contraction allows epigenetic derepression of the array, and possibly the surrounding 4q35 region, allowing misexpression of the toxic DUX4 transcription factor encoded within the terminal D4Z4 repeat in skeletal muscles. The less common form of the disease, FSHD2, results from haploinsufficiency of the SMCHD1 gene in individuals carrying a permissive 4qA allele, also leading to the derepression of DUX4, further supporting a central role for DUX4. How DUX4 misexpression contributes to FSHD muscle pathology is a major focus of current investigation. Misexpression of other genes at the 4q35 locus, including FRG1 and FAT1, and unlinked genes, such as SMCHD1, has also been implicated as disease modifiers, leading to several competing disease models. In this review, we describe recent advances in understanding the pathophysiology of FSHD, including the application of MRI as a research and diagnostic tool, the genetic and epigenetic disruptions associated with the disease, and the molecular basis of FSHD. We discuss how these advances are leading to the emergence of new approaches to enable development of FSHD therapeutics. © 2017 American Physiological Society. Compr Physiol 7:1229-1279, 2017.
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Affiliation(s)
- Alec M DeSimone
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Anna Pakula
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics and Genetics at Harvard Medical School, Boston, Massachusetts, USA
| | - Angela Lek
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics and Genetics at Harvard Medical School, Boston, Massachusetts, USA.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Gaillard MC, Puppo F, Roche S, Dion C, Campana ES, Mariot V, Chaix C, Vovan C, Mazaleyrat K, Tasmadjian A, Bernard R, Dumonceaux J, Attarian S, Lévy N, Nguyen K, Magdinier F, Bartoli M. Segregation between SMCHD1 mutation, D4Z4 hypomethylation and Facio-Scapulo-Humeral Dystrophy: a case report. BMC MEDICAL GENETICS 2016; 17:66. [PMID: 27634379 PMCID: PMC5025538 DOI: 10.1186/s12881-016-0328-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 09/09/2016] [Indexed: 12/22/2022]
Abstract
Background The main form of Facio-Scapulo-Humeral muscular Dystrophy is linked to copy number reduction of the 4q D4Z4 macrosatellite (FSHD1). In 5 % of cases, FSHD phenotype appears in the absence of D4Z4 reduction (FSHD2). In 70-80 % of these patients, variants of the SMCHD1 gene segregate with 4qA haplotypes and D4Z4 hypomethylation. Case presentation We report a family presenting with neuromuscular symptoms reminiscent of FSHD but without D4Z4 copy reduction. We characterized the 4q35 region using molecular combing, searched for mutation in the SMCHD1 gene and determined D4Z4 methylation level by sodium bisulfite sequencing. We further investigated the impact of the SMCHD1 mutation at the protein level and on the NMD-dependent degradation of transcript. In muscle, we observe moderate but significant reduction in D4Z4 methylation, not correlated with DUX4-fl expression. Exome sequencing revealed a heterozygous insertion of 7 bp in exon 37 of the SMCHD1 gene producing a loss of frame with premature stop codon 4 amino acids after the insertion (c.4614-4615insTATAATA). Both wild-type and mutated transcripts are detected. Conclusion The truncated protein is absent and the full-length protein level is similar in patients and controls indicating that in this family, FSHD is not associated with SMCHD1 haploinsufficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0328-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Camille Dion
- Aix Marseille Univ, INSERM, GMGF, Marseille, France
| | - Emmanuelle Salort Campana
- Aix Marseille Univ, INSERM, GMGF, Marseille, France.,APHM, Centre de Référence des Maladies Neuromusculaires et de la SLA, Hôpital de la Timone, Marseille, 13385, France
| | - Virginie Mariot
- Center of Research in Myology/ Institut de Myologie UMR974 - UPMC Université Paris 6/ Inserm /FRE3617- CNRS, Groupement Hospitalier de la Pitié Salpétrière, Paris, Cedex 13, France
| | - Charlene Chaix
- APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, 13385, France
| | - Catherine Vovan
- APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, 13385, France
| | | | | | - Rafaelle Bernard
- Aix Marseille Univ, INSERM, GMGF, Marseille, France.,APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, 13385, France
| | - Julie Dumonceaux
- Center of Research in Myology/ Institut de Myologie UMR974 - UPMC Université Paris 6/ Inserm /FRE3617- CNRS, Groupement Hospitalier de la Pitié Salpétrière, Paris, Cedex 13, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM, GMGF, Marseille, France.,APHM, Centre de Référence des Maladies Neuromusculaires et de la SLA, Hôpital de la Timone, Marseille, 13385, France
| | - Nicolas Lévy
- Aix Marseille Univ, INSERM, GMGF, Marseille, France.,APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, 13385, France
| | - Karine Nguyen
- Aix Marseille Univ, INSERM, GMGF, Marseille, France.,APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, 13385, France
| | | | - Marc Bartoli
- Aix Marseille Univ, INSERM, GMGF, Marseille, France.,APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, 13385, France
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Mathias SR, Knowles EEM, Kent JW, McKay DR, Curran JE, de Almeida MAA, Dyer TD, Göring HHH, Olvera RL, Duggirala R, Fox PT, Almasy L, Blangero J, Glahn DC. Recurrent major depression and right hippocampal volume: A bivariate linkage and association study. Hum Brain Mapp 2015; 37:191-202. [PMID: 26485182 DOI: 10.1002/hbm.23025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/02/2015] [Indexed: 01/04/2023] Open
Abstract
Previous work has shown that the hippocampus is smaller in the brains of individuals suffering from major depressive disorder (MDD) than those of healthy controls. Moreover, right hippocampal volume specifically has been found to predict the probability of subsequent depressive episodes. This study explored the utility of right hippocampal volume as an endophenotype of recurrent MDD (rMDD). We observed a significant genetic correlation between the two traits in a large sample of Mexican American individuals from extended pedigrees (ρg = -0.34, p = 0.013). A bivariate linkage scan revealed a significant pleiotropic quantitative trait locus on chromosome 18p11.31-32 (LOD = 3.61). Bivariate association analysis conducted under the linkage peak revealed a variant (rs574972) within an intron of the gene SMCHD1 meeting the corrected significance level (χ(2) = 19.0, p = 7.4 × 10(-5)). Univariate association analyses of each phenotype separately revealed that the same variant was significant for right hippocampal volume alone, and also revealed a suggestively significant variant (rs12455524) within the gene DLGAP1 for rMDD alone. The results implicate right-hemisphere hippocampal volume as a possible endophenotype of rMDD, and in so doing highlight a potential gene of interest for rMDD risk.
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Affiliation(s)
- Samuel R Mathias
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.,Olin Neuropsychiatry Research Center, Institute of Living, Hartford, Connecticut
| | - Emma E M Knowles
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.,Olin Neuropsychiatry Research Center, Institute of Living, Hartford, Connecticut
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - D Reese McKay
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute, University of Texas Health Science Center at San Antonio, Texas.,University of Texas of the Rio Grande Valley, Brownsville, Texas
| | - Marcio A A de Almeida
- South Texas Diabetes and Obesity Institute, University of Texas Health Science Center at San Antonio, Texas.,University of Texas of the Rio Grande Valley, Brownsville, Texas
| | - Thomas D Dyer
- South Texas Diabetes and Obesity Institute, University of Texas Health Science Center at San Antonio, Texas.,University of Texas of the Rio Grande Valley, Brownsville, Texas
| | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,South Texas Diabetes and Obesity Institute, University of Texas Health Science Center at San Antonio, Texas.,University of Texas of the Rio Grande Valley, Brownsville, Texas
| | - Rene L Olvera
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Ravi Duggirala
- South Texas Diabetes and Obesity Institute, University of Texas Health Science Center at San Antonio, Texas.,University of Texas of the Rio Grande Valley, Brownsville, Texas
| | - Peter T Fox
- Research Imaging Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas.,South Texas Veterans Health System, San Antonio, Texas
| | - Laura Almasy
- South Texas Diabetes and Obesity Institute, University of Texas Health Science Center at San Antonio, Texas.,University of Texas of the Rio Grande Valley, Brownsville, Texas
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Health Science Center at San Antonio, Texas.,University of Texas of the Rio Grande Valley, Brownsville, Texas
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.,Olin Neuropsychiatry Research Center, Institute of Living, Hartford, Connecticut
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10
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Mayes MB, Morgan T, Winston J, Buxton DS, Kamat MA, Smith D, Williams M, Martin RL, Kleinjan DA, Cooper DN, Upadhyaya M, Chuzhanova N. Remotely acting SMCHD1 gene regulatory elements: in silico prediction and identification of potential regulatory variants in patients with FSHD. Hum Genomics 2015; 9:25. [PMID: 26446085 PMCID: PMC4597391 DOI: 10.1186/s40246-015-0047-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/01/2015] [Indexed: 12/03/2022] Open
Abstract
Background Facioscapulohumeral dystrophy (FSHD) is commonly associated with contraction of the D4Z4 macro-satellite repeat on chromosome 4q35 (FSHD1) or mutations in the SMCHD1 gene (FSHD2). Recent studies have shown that the clinical manifestation of FSHD1 can be modified by mutations in the SMCHD1 gene within a given family. The absence of either D4Z4 contraction or SMCHD1 mutations in a small cohort of patients suggests that the disease could also be due to disruption of gene regulation. In this study, we postulated that mutations responsible for exerting a modifier effect on FSHD might reside within remotely acting regulatory elements that have the potential to interact at a distance with their cognate gene promoter via chromatin looping. To explore this postulate, genome-wide Hi-C data were used to identify genomic fragments displaying the strongest interaction with the SMCHD1 gene. These fragments were then narrowed down to shorter regions using ENCODE and FANTOM data on transcription factor binding sites and epigenetic marks characteristic of promoters, enhancers and silencers. Results We identified two regions, located respectively ~14 and ~85 kb upstream of the SMCHD1 gene, which were then sequenced in 229 FSHD/FSHD-like patients (200 with D4Z4 repeat units <11). Three heterozygous sequence variants were found ~14 kb upstream of the SMCHD1 gene. One of these variants was found to be of potential functional significance based on DNA methylation analysis. Further functional ascertainment will be required in order to establish the clinical/functional significance of the variants found. Conclusions In this study, we propose an improved approach to predict the possible locations of remotely acting regulatory elements that might influence the transcriptional regulation of their associated gene(s). It represents a new way to screen for disease-relevant mutations beyond the immediate vicinity of the specific disease gene. It promises to be useful for investigating disorders in which mutations could occur in remotely acting regulatory elements. Electronic supplementary material The online version of this article (doi:10.1186/s40246-015-0047-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mary B Mayes
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Taniesha Morgan
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Jincy Winston
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Daniel S Buxton
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Mihir Anant Kamat
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.,Present address: Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Debbie Smith
- Blood Sciences Department and Bristol Genetics Laboratory, Southmead Hospital, Westbury-on-Trym, Bristol, BS10 5NB, UK
| | - Maggie Williams
- Blood Sciences Department and Bristol Genetics Laboratory, Southmead Hospital, Westbury-on-Trym, Bristol, BS10 5NB, UK
| | - Rebecca L Martin
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Dirk A Kleinjan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Meena Upadhyaya
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Nadia Chuzhanova
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
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11
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de la Kethulle de Ryhove L, Ansseau E, Nachtegael C, Pieters K, Vanderplanck C, Geens M, Sermon K, Wilton SD, Coppée F, Lagneaux L, Belayew A. The Role of D4Z4-Encoded Proteins in the Osteogenic Differentiation of Mesenchymal Stromal Cells Isolated from Bone Marrow. Stem Cells Dev 2015; 24:2674-86. [PMID: 26192274 DOI: 10.1089/scd.2014.0575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is associated with an activation of the double homeobox 4 (DUX4) gene, which we previously identified within the D4Z4 repeated elements in the 4q35 subtelomeric region. The pathological DUX4 mRNA is derived from the most distal D4Z4 unit and extends unexpectedly within the flanking pLAM region, which provides an intron and polyadenylation signal. The conditions that are required to develop FSHD are a permissive allele providing the polyadenylation signal and hypomethylation of the D4Z4 repeat array compared with the healthy muscle. The DUX4 protein is a 52-kDa transcription factor that initiates a large gene deregulation cascade leading to muscle atrophy, inflammation, differentiation defects, and oxidative stress, which are the key features of FSHD. DUX4 is a retrogene that is normally expressed in germline cells and is submitted to repeat-induced silencing in adult tissues. Since DUX4 mRNAs have been detected in human embryonic and induced pluripotent stem cells, we investigated whether they could also be expressed in human mesenchymal stromal cells (hMSCs). We found that DUX4 mRNAs were induced during the differentiation of hMSCs into osteoblasts and that this process involved DUX4 and new longer protein forms (58 and 70 kDa). A DUX4 mRNA with a more distant 5' start site was characterized that presented a 60-codon reading frame extension and encoded the 58-kDa protein. Transfections of hMSCs with an antisense oligonucleotide targeting DUX4 mRNAs decreased both the 52- and 58-kDa protein levels and confirmed their identity. Gain- and loss-of-function experiments in hMSCs suggested these DUX4 proteins had opposite roles in osteogenic differentiation as evidenced by the alkaline phosphatase activity and calcium deposition. Differentiation was delayed by the 58-kDa DUX4 expression and it was increased by 52-kDa DUX4. These data indicate a role for DUX4 protein forms in the osteogenic differentiation of hMSCs.
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Affiliation(s)
| | - Eugénie Ansseau
- 1 Laboratory of Molecular Biology, University of Mons , Mons, Belgium
| | | | - Karlien Pieters
- 2 Laboratory of Clinical Cell Therapy, Institut Jules Bordet, Université Libre de Bruxelles , Brussels, Belgium
| | | | - Mieke Geens
- 3 Department of Embryology and Genetics, Vrije Universiteit Brussel , Jette, Belgium
| | - Karen Sermon
- 3 Department of Embryology and Genetics, Vrije Universiteit Brussel , Jette, Belgium
| | - Steve D Wilton
- 4 Centre for Comparative Genomics, Murdoch University , Murdoch, and The University of Western Australia, Crawley, and Western Australian Neuroscience Institute, Nedlands, Western Australia, Australia
| | - Frédérique Coppée
- 1 Laboratory of Molecular Biology, University of Mons , Mons, Belgium
| | - Laurence Lagneaux
- 2 Laboratory of Clinical Cell Therapy, Institut Jules Bordet, Université Libre de Bruxelles , Brussels, Belgium
| | - Alexandra Belayew
- 1 Laboratory of Molecular Biology, University of Mons , Mons, Belgium
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12
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Daxinger L, Tapscott SJ, van der Maarel SM. Genetic and epigenetic contributors to FSHD. Curr Opin Genet Dev 2015; 33:56-61. [PMID: 26356006 PMCID: PMC4674299 DOI: 10.1016/j.gde.2015.08.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/08/2015] [Accepted: 08/21/2015] [Indexed: 11/28/2022]
Abstract
Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant muscle disorder characterized by distinct chromatin changes including DNA hypomethylation of the D4Z4 macrosatellite repeat array on a disease-permissive 4qA allele and aberrant expression of the D4Z4-embedded DUX4 retrogene in skeletal muscle. Insufficient epigenetic repression of the D4Z4 repeat is the result of at least two different genetic mechanisms leading to two forms of disease, FSHD1 and FSHD2. In the case of FSHD1, a contraction of the D4Z4 repeat array is disease causing whereas FSHD2 is most often caused by mutations in the structural maintenance of chromosomes hinge domain 1 (SMCHD1) gene. Recent studies indicate that a combination of genetic and epigenetic factors that act on the D4Z4 repeat array determine the probability of DUX4 expression in skeletal muscle and disease penetrance and progression.
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Affiliation(s)
- Lucia Daxinger
- 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
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13
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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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14
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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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15
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van den Boogaard ML, Lemmers RJFL, Camaño P, van der Vliet PJ, Voermans N, van Engelen BGM, Lopez de Munain A, Tapscott SJ, van der Stoep N, Tawil R, van der Maarel SM. Double SMCHD1 variants in FSHD2: the synergistic effect of two SMCHD1 variants on D4Z4 hypomethylation and disease penetrance in FSHD2. Eur J Hum Genet 2015; 24:78-85. [PMID: 25782668 DOI: 10.1038/ejhg.2015.55] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/17/2015] [Accepted: 02/20/2015] [Indexed: 01/03/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) predominantly affects the muscles in the face, trunk and upper extremities and is marked by large clinical variability in disease onset and progression. FSHD is associated with partial chromatin relaxation of the D4Z4 repeat array on chromosome 4 and the somatic expression of the D4Z4 encoded DUX4 gene. The most common form, FSHD1, is caused by a contraction of the D4Z4 repeat array on chromosome 4 to a size of 1-10 units. FSHD2, the less common form of FSHD, is most often caused by heterozygous variants in the chromatin modifier SMCHD1, which is involved in the maintenance of D4Z4 methylation. We identified three families in which the proband carries two potentially damaging SMCHD1 variants. We investigated whether these variants were located in cis or in trans and determined their functional consequences by detailed clinical information and D4Z4 methylation studies. In the first family, both variants in trans were shown to act synergistically on D4Z4 hypomethylation and disease penetrance, in the second family both SMCHD1 function-affecting variants were located in cis while in the third family one of the two variants did not affect function. This study demonstrates that having two SMCHD1 missense variants that affect function is compatible with life in males and females, which is remarkable considering its role in X inactivation in mice. The study also highlights the variability in SMCHD1 variants underlying FSHD2 and the predictive value of D4Z4 methylation analysis in determining the functional consequences of SMCHD1 variants of unknown significance.
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Affiliation(s)
| | - Richard J F L Lemmers
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pilar Camaño
- Neurosciences, BioDonostia Health Research Institute, Hospital Donostia, San Sebastián, Spain
| | | | - Nicol Voermans
- Department of Neurology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - Adolfo Lopez de Munain
- Neurosciences, BioDonostia Health Research Institute, Hospital Donostia, San Sebastián, Spain
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, MN, USA
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16
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miRNA expression in control and FSHD fetal human muscle biopsies. PLoS One 2015; 10:e0116853. [PMID: 25692472 PMCID: PMC4333765 DOI: 10.1371/journal.pone.0116853] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022] Open
Abstract
Background Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal-dominant disorder and is one of the most common forms of muscular dystrophy. We have recently shown that some hallmarks of FSHD are already expressed in fetal FSHD biopsies, thus opening a new field of investigation for mechanisms leading to FSHD. As microRNAs (miRNAs) play an important role in myogenesis and muscle disorders, in this study we compared miRNAs expression levels during normal and FSHD muscle development. Methods Muscle biopsies were obtained from quadriceps of both healthy control and FSHD1 fetuses with ages ranging from 14 to 33 weeks of development. miRNA expression profiles were analyzed using TaqMan Human MicroRNA Arrays. Results During human skeletal muscle development, in control muscle biopsies we observed changes for 4 miRNAs potentially involved in secondary muscle fiber formation and 5 miRNAs potentially involved in fiber maturation. When we compared the miRNA profiles obtained from control and FSHD biopsies, we did not observe any differences in the muscle specific miRNAs. However, we identified 8 miRNAs exclusively expressed in FSHD1 samples (miR-330, miR-331-5p, miR-34a, miR-380-3p, miR-516b, miR-582-5p, miR-517* and miR-625) which could represent new biomarkers for this disease. Their putative targets are mainly involved in muscle development and morphogenesis. Interestingly, these FSHD1 specific miRNAs do not target the genes previously described to be involved in FSHD. Conclusions This work provides new candidate mechanisms potentially involved in the onset of FSHD pathology. Whether these FSHD specific miRNAs cause deregulations during fetal development, or protect against the appearance of the FSHD phenotype until the second decade of life still needs to be investigated.
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17
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Jones TI, Yan C, Sapp PC, McKenna-Yasek D, Kang PB, Quinn C, Salameh JS, King OD, Jones PL. Identifying diagnostic DNA methylation profiles for facioscapulohumeral muscular dystrophy in blood and saliva using bisulfite sequencing. Clin Epigenetics 2014; 6:23. [PMID: 25400706 PMCID: PMC4232706 DOI: 10.1186/1868-7083-6-23] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/17/2014] [Indexed: 12/20/2022] Open
Abstract
Background Facioscapulohumeral muscular dystrophy (FSHD) is linked to chromatin relaxation due to epigenetic changes at the 4q35 D4Z4 macrosatellite array. Molecular diagnostic criteria for FSHD are complex and involve analysis of high molecular weight (HMW) genomic DNA isolated from lymphocytes, followed by multiple restriction digestions, pulse-field gel electrophoresis (PFGE), and Southern blotting. A subject is genetically diagnosed as FSHD1 if one of the 4q alleles shows a contraction in the D4Z4 array to below 11 repeats, while maintaining at least 1 repeat, and the contraction is in cis with a disease-permissive A-type subtelomere. FSHD2 is contraction-independent and cannot be diagnosed or excluded by this common genetic diagnostic procedure. However, FSHD1 and FSHD2 are linked by epigenetic deregulation, assayed as DNA hypomethylation, of the D4Z4 array on FSHD-permissive alleles. We have developed a PCR-based assay that identifies the epigenetic signature for both types of FSHD, distinguishing FSHD1 from FSHD2, and can be performed on genomic DNA isolated from blood, saliva, or cultured cells. Results Samples were obtained from healthy controls or patients clinically diagnosed with FSHD, and include both FSHD1 and FSHD2. The genomic DNAs were subjected to bisulfite sequencing analysis for the distal 4q D4Z4 repeat with an A-type subtelomere and the DUX4 5’ promoter region. We compared genomic DNA isolated from saliva and blood from the same individuals and found similar epigenetic signatures. DNA hypomethylation was restricted to the contracted 4qA chromosome in FSHD1 patients while healthy control subjects were hypermethylated. Candidates for FSHD2 showed extreme DNA hypomethylation on the 4qA DUX4 gene body as well as all analyzed DUX4 5’ sequences. Importantly, our assay does not amplify the D4Z4 arrays with non-permissive B-type subtelomeres and accurately excludes the arrays with non-permissive A-type subtelomeres. Conclusions We have developed an assay to identify changes in DNA methylation on the pathogenic distal 4q D4Z4 repeat. We show that the DNA methylation profile of saliva reflects FSHD status. This assay can distinguish FSHD from healthy controls, differentiate FSHD1 from FSHD2, does not require HMW genomic DNA or PFGE, and can be performed on either cultured cells, tissue, blood, or saliva samples. Electronic supplementary material The online version of this article (doi:10.1186/1868-7083-6-23) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takako I Jones
- The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Chi Yan
- The Wellstone Program & The Department of Cell and Developmental Biology, 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, Wuhan, 430070 P.R. China
| | - Peter C Sapp
- The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Diane McKenna-Yasek
- The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Peter B Kang
- Department of Pediatrics, Division of Pediatric Neurology, University of Florida College of Medicine, 1600 SW Archer Road, Gainesville, FL 32607 USA
| | - Colin Quinn
- The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; Department of Neurology, Hospital of the University of Pennsylvania, 3400 Spruce St, 3 Gates, Philadelphia, PA 19104 USA
| | - Johnny S Salameh
- The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Oliver D King
- The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Department of Neurology, 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, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Peter L Jones
- The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Department of Neurology, 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, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
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