1
|
Chen L, Kong X, Johnston KG, Mortazavi A, Holmes TC, Tan Z, Yokomori K, Xu X. Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome Res 2024; 34:665-679. [PMID: 38777608 DOI: 10.1101/gr.278717.123] [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: 11/09/2023] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is linked to abnormal derepression of the transcription activator DUX4. This effect is localized to a low percentage of cells, requiring single-cell analysis. However, single-cell/nucleus RNA-seq cannot fully capture the transcriptome of multinucleated large myotubes. To circumvent these issues, we use multiplexed error-robust fluorescent in situ hybridization (MERFISH) spatial transcriptomics that allows profiling of RNA transcripts at a subcellular resolution. We simultaneously examined spatial distributions of 140 genes, including 24 direct DUX4 targets, in in vitro differentiated myotubes and unfused mononuclear cells (MNCs) of control, isogenic D4Z4 contraction mutant and FSHD patient samples, as well as the individual nuclei within them. We find myocyte nuclei segregate into two clusters defined by the expression of DUX4 target genes, which is exclusively found in patient/mutant nuclei, whereas MNCs cluster based on developmental states. Patient/mutant myotubes are found in "FSHD-hi" and "FSHD-lo" states with the former signified by high DUX4 target expression and decreased muscle gene expression. Pseudotime analyses reveal a clear bifurcation of myoblast differentiation into control and FSHD-hi myotube branches, with variable numbers of DUX4 target-expressing nuclei found in multinucleated FSHD-hi myotubes. Gene coexpression modules related to extracellular matrix and stress gene ontologies are significantly altered in patient/mutant myotubes compared with the control. We also identify distinct subpathways within the DUX4 gene network that may differentially contribute to the disease transcriptomic phenotype. Taken together, our MERFISH-based study provides effective gene network profiling of multinucleated cells and identifies FSHD-induced transcriptomic alterations during myoblast differentiation.
Collapse
Affiliation(s)
- Lujia Chen
- Department of Biomedical Engineering, University of California, Irvine, California 92697, USA
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Kevin G Johnston
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Ali Mortazavi
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Todd C Holmes
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Zhiqun Tan
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA;
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, California 92697, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA;
| | - Xiangmin Xu
- Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, California 92697, USA
- Department of Computer Science, University of California, Irvine, California 92697, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Greco A, Mul K, Jaeger MH, Dos Santos JC, Koenen H, de Jong L, Mann R, Fütterer J, Netea MG, Pruijn GJM, van Engelen BGM, Joosten LAB. IL-6 and TNF are Potential Inflammatory Biomarkers in Facioscapulohumeral Muscular Dystrophy. J Neuromuscul Dis 2024; 11:327-347. [PMID: 38250782 DOI: 10.3233/jnd-230063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Background FSHD is a highly prevalent inherited myopathy with a still poorly understood pathology. Objective To investigate whether proinflammatory cytokines are associated with FSHD and which specific innate immune cells are involved in its pathology. Methods First, we measured circulating cytokines in serum samples: IL-6 (FSHD, n = 150; HC, n = 98); TNF (FSHD, n = 150; HC, n = 59); IL-1α (FSHD, n = 150; HC, n = 66); IL-1β (FSHD, n = 150; HC, n = 98); MCP-1 (FSHD, n = 14; HC, n = 14); VEGF-A (FSHD, n = 14; HC, n = 14). Second, we tested trained immunity in monocytes (FSHD, n = 15; HC, n = 15) and NK cells (FSHD, n = 11; HC, n = 11). Next, we explored the cytokine production capacity of NK cells in response to different stimuli (FSHD, n = 39; HC, n = 22). Lastly, we evaluated the cytokine production of ex vivo stimulated MRI guided inflamed (TIRM+) and paired MRI guided non inflamed (TIRM-) muscle biopsies of 21 patients and of 8 HC muscle biopsies. Results We included a total of 190 FSHD patients (N = 190, 48±14 years, 49% men) and of 135 HC (N = 135, 44±15 years, 47% men). We found that FSHD patients had higher concentrations of IL-6 and TNF measured (a) in the circulation, (b) after ex-vivo stimulation of NK cells, and (c) in muscle specimens. Besides, IL-6 circulating concentrations, as well as its production by NK cells and IL-6 content of FSHD muscle specimens, showed a mild correlation with disease duration, disease severity, and muscle weakness. Conclusion These results show that IL-6 and TNF may contribute to FSHD pathology and suggest novel therapeutic targets. Additionally, the activation of NK cells in FSHD may be a novel pathway contributing to FSHD pathology.
Collapse
Affiliation(s)
- Anna Greco
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Karlien Mul
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martin H Jaeger
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jéssica C Dos Santos
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hans Koenen
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leon de Jong
- Department of Radiology, Nuclear Medicine and Anatomy, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ritse Mann
- Department of Radiology, Nuclear Medicine and Anatomy, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jurgen Fütterer
- Department of Radiology, Nuclear Medicine and Anatomy, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ger J M Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Baziel G M van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| |
Collapse
|
4
|
Butterfield RJ, Dunn DM, Duval B, Moldt S, Weiss RB. Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing. Genome Res 2023; 33:1439-1454. [PMID: 37798116 PMCID: PMC10620044 DOI: 10.1101/gr.277871.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/02/2023] [Indexed: 10/07/2023]
Abstract
Fascioscapulohumeral muscular dystrophy (FSHD) is caused by a unique genetic mechanism that relies on contraction and hypomethylation of the D4Z4 macrosatellite array on the Chromosome 4q telomere allowing ectopic expression of the DUX4 gene in skeletal muscle. Genetic analysis is difficult because of the large size and repetitive nature of the array, a nearly identical array on the 10q telomere, and the presence of divergent D4Z4 arrays scattered throughout the genome. Here, we combine nanopore long-read sequencing with Cas9-targeted enrichment of 4q and 10q D4Z4 arrays for comprehensive genetic analysis including determination of the length of the 4q and 10q D4Z4 arrays with base-pair resolution. In the same assay, we differentiate 4q from 10q telomeric sequences, determine A/B haplotype, identify paralogous D4Z4 sequences elsewhere in the genome, and estimate methylation for all CpGs in the array. Asymmetric, length-dependent methylation gradients were observed in the 4q and 10q D4Z4 arrays that reach a hypermethylation point at approximately 10 D4Z4 repeat units, consistent with the known threshold of pathogenic D4Z4 contractions. High resolution analysis of individual D4Z4 repeat methylation revealed areas of low methylation near the CTCF/insulator region and areas of high methylation immediately preceding the DUX4 transcriptional start site. Within the DUX4 exons, we observed a waxing/waning methylation pattern with a 180-nucleotide periodicity, consistent with phased nucleosomes. Targeted nanopore sequencing complements recently developed molecular combing and optical mapping approaches to genetic analysis for FSHD by adding precision of the length measurement, base-pair resolution sequencing, and quantitative methylation analysis.
Collapse
Affiliation(s)
- Russell J Butterfield
- Department of Pediatrics, University of Utah, Salt Lake City, Utah 84108, USA;
- Department of Neurology, University of Utah, Salt Lake City, Utah 84132, USA
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Brett Duval
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Sarah Moldt
- Department of Pediatrics, University of Utah, Salt Lake City, Utah 84108, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| |
Collapse
|
5
|
Strafella C, Caputo V, Bortolani S, Torchia E, Megalizzi D, Trastulli G, Monforte M, Colantoni L, Caltagirone C, Ricci E, Tasca G, Cascella R, Giardina E. Whole exome sequencing highlights rare variants in CTCF, DNMT1, DNMT3A, EZH2 and SUV39H1 as associated with FSHD. Front Genet 2023; 14:1235589. [PMID: 37674478 PMCID: PMC10477786 DOI: 10.3389/fgene.2023.1235589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023] Open
Abstract
Introduction: Despite the progress made in the study of Facioscapulohumeral Dystrophy (FSHD), the wide heterogeneity of disease complicates its diagnosis and the genotype-phenotype correlation among patients and within families. In this context, the present work employed Whole Exome Sequencing (WES) to investigate known and unknown genetic contributors that may be involved in FSHD and may represent potential disease modifiers, even in presence of a D4Z4 Reduced Allele (DRA). Methods: A cohort of 126 patients with clinical signs of FSHD were included in the study, which were characterized by D4Z4 sizing, methylation analysis and WES. Specific protocols were employed for D4Z4 sizing and methylation analysis, whereas the Illumina® Next-Seq 550 system was utilized for WES. The study included both patients with a DRA compatible with FSHD diagnosis and patients with longer D4Z4 alleles. In case of patients harboring relevant variants from WES, the molecular analysis was extended to the family members. Results: The WES data analysis highlighted 20 relevant variants, among which 14 were located in known genetic modifiers (SMCHD1, DNMT3B and LRIF1) and 6 in candidate genes (CTCF, DNMT1, DNMT3A, EZH2 and SUV39H1). Most of them were found together with a permissive short (4-7 RU) or borderline/long DRA (8-20 RU), supporting the possibility that different genes can contribute to disease heterogeneity in presence of a FSHD permissive background. The segregation and methylation analysis among family members, together with clinical findings, provided a more comprehensive picture of patients. Discussion: Our results support FSHD pathomechanism being complex with a multigenic contribution by several known (SMCHD1, DNMT3B, LRIF1) and possibly other candidate genes (CTCF, DNMT1, DNMT3A, EZH2, SUV39H1) to disease penetrance and expressivity. Our results further emphasize the importance of extending the analysis of molecular findings within the proband's family, with the purpose of providing a broader framework for understanding single cases and allowing finer genotype-phenotype correlations in FSHD-affected families.
Collapse
Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Sara Bortolani
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Eleonora Torchia
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Domenica Megalizzi
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Giulia Trastulli
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Mauro Monforte
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Enzo Ricci
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Istituto di Neurologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giorgio Tasca
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trusts, Newcastle UponTyne, United Kingdom
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Medical Genetics Laboratory, Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| |
Collapse
|
6
|
Šikrová D, Testa AM, Willemsen I, van den Heuvel A, Tapscott SJ, Daxinger L, Balog J, van der Maarel SM. SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action. Commun Biol 2023; 6:677. [PMID: 37380887 DOI: 10.1038/s42003-023-05053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/17/2023] [Indexed: 06/30/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by the epigenetic derepression of the 4q-linked D4Z4 macrosatellite repeat resulting in inappropriate expression of the D4Z4 repeat-encoded DUX4 gene in skeletal muscle. In 5% of FSHD cases, D4Z4 chromatin relaxation is due to germline mutations in one of the chromatin modifiers SMCHD1, DNMT3B or LRIF1. The mechanism of SMCHD1- and LRIF1-mediated D4Z4 repression is not clear. We show that somatic loss-of-function of either SMCHD1 or LRIF1 does not result in D4Z4 chromatin changes and that SMCHD1 and LRIF1 form an auxiliary layer of D4Z4 repressive mechanisms. We uncover that SMCHD1, together with the long isoform of LRIF1, binds to the LRIF1 promoter and silences LRIF1 expression. The interdependency of SMCHD1 and LRIF1 binding differs between D4Z4 and the LRIF1 promoter, and both loci show different transcriptional responses to either early developmentally or somatically perturbed chromatin function of SMCHD1 and LRIF1.
Collapse
Affiliation(s)
- Darina Šikrová
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Alessandra M Testa
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
- Department of Biomedical Sciences, University of Padua, 35100, Padua, Italy
| | - Iris Willemsen
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Anita van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
|
10
|
CRISPR mediated targeting of DUX4 distal regulatory element represses DUX4 target genes dysregulated in Facioscapulohumeral muscular dystrophy. Sci Rep 2021; 11:12598. [PMID: 34131248 PMCID: PMC8206090 DOI: 10.1038/s41598-021-92096-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/04/2021] [Indexed: 11/08/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a debilitating muscle disease that currently does not have an effective cure or therapy. The abnormal reactivation of DUX4, an embryonic gene that is epigenetically silenced in somatic tissues, is causal to FSHD. Disease-specific reactivation of DUX4 has two common characteristics, the presence of a non-canonical polyadenylation sequence within exon 3 of DUX4 that stabilizes pathogenic transcripts, and the loss of repressive chromatin modifications at D4Z4, the macrosatellite repeat which encodes DUX4. We used CRISPR/Cas9 to silence DUX4 using two independent approaches. We deleted the DUX4 pathogenic polyadenylation signal, which resulted in downregulation of pathogenic DUX4-fl transcripts. In another approach, we transcriptionally repressed DUX4 by seeding heterochromatin using the dCas9-KRAB platform within exon 3. These feasibility of targeting DUX4 experiments were initially tested in a non-myogenic carcinoma cell line that we have previously characterized. Subsequently, in an immortalized patient myoblast cell line, we demonstrated that targeting DUX4 by either approach led to substantial downregulation of not only pathogenic DUX4 transcripts, but also a subset of its target genes that are known biomarkers of FSHD. These findings offer proof-of-concept of the effect of silencing the polyadenylation sequence on pathogenic DUX4 expression.
Collapse
|
11
|
Gene Editing Targeting the DUX4 Polyadenylation Signal: A Therapy for FSHD? J Pers Med 2020; 11:jpm11010007. [PMID: 33374516 PMCID: PMC7822190 DOI: 10.3390/jpm11010007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 01/26/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD, OMIM: 158900, 158901) is the most common dystrophy in adults and so far, there is no treatment. Different loci of the disease have been characterized and they all lead to the aberrant expression of the DUX4 protein, which impairs the function of the muscle, ultimately leading to cell death. Here, we used gene editing to try to permanently shut down DUX4 expression by targeting its poly(A) sequence. We used transcription activator-like effector nucleases (TALEN) and CRISPR-Cas9 nucleases in vitro on FSHD myoblasts. More than 150 TOPO clones were sequenced and only indels were observed in 4%. Importantly, in 2 of them, the DUX4 poly(A) signal was eliminated at the genomic level but DUX4 mRNA was still produced thanks to the use of a non-canonical upstream poly(A) signal sequence. These experiments show that targeting DUX4 PAS at the genomic level might not be an appropriate gene editing strategy for FSHD therapy.
Collapse
|
12
|
DUX4 Expression in FSHD Muscles: Focus on Its mRNA Regulation. J Pers Med 2020; 10:jpm10030073. [PMID: 32731450 PMCID: PMC7564753 DOI: 10.3390/jpm10030073] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is the most frequent muscular disease in adults. FSHD is characterized by a weakness and atrophy of a specific set of muscles located in the face, the shoulder, and the upper arms. FSHD patients may present different genetic defects, but they all present epigenetic alterations of the D4Z4 array located on the subtelomeric part of chromosome 4, leading to chromatin relaxation and, ultimately, to the aberrant expression of one gene called DUX4. Once expressed, DUX4 triggers a cascade of deleterious events, eventually leading to muscle dysfunction and cell death. Here, we review studies on DUX4 expression in skeletal muscle to determine the genetic/epigenetic factors and regulatory proteins governing DUX4 expression, with particular attention to the different transcripts and their very low expression in muscle.
Collapse
|
13
|
Jiang S, Williams K, Kong X, Zeng W, Nguyen NV, Ma X, Tawil R, Yokomori K, Mortazavi A. Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei. PLoS Genet 2020; 16:e1008754. [PMID: 32365093 PMCID: PMC7224571 DOI: 10.1371/journal.pgen.1008754] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/14/2020] [Accepted: 04/03/2020] [Indexed: 12/22/2022] Open
Abstract
FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is thought to be the pathogenic cause of FSHD, DUX4 is lowly expressed in patient samples, and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we performed bulk RNA-seq on a 6-day differentiation time-course in primary FSHD2 patient myoblasts. We identify a set of 54 genes upregulated in FSHD2 cells, termed FSHD-induced genes. Using single-cell and single-nucleus RNA-seq on myoblasts and differentiated myotubes, respectively, we captured, for the first time, DUX4 expressed at the single-nucleus level in a native state. We identified two populations of FSHD myotube nuclei based on low or high enrichment of DUX4 and FSHD-induced genes ("FSHD-Lo" and "FSHD Hi", respectively). FSHD-Hi myotube nuclei coexpress multiple DUX4 target genes including DUXA, LEUTX and ZSCAN4, and also upregulate cell cycle-related genes with significant enrichment of E2F target genes and p53 signaling activation. We found more FSHD-Hi nuclei than DUX4-positive nuclei, and confirmed with in situ RNA/protein detection that DUX4 transcribed in only one or two nuclei is sufficient for DUX4 protein to activate target genes across multiple nuclei within the same myotube. DUXA (the DUX4 paralog) is more widely expressed than DUX4, and depletion of DUXA suppressed the expression of LEUTX and ZSCAN4 in late, but not early, differentiation. The results suggest that the DUXA can take over the role of DUX4 to maintain target gene expression. These results provide a possible explanation as to why it is easier to detect DUX4 target genes than DUX4 itself in patient cells and raise the possibility of a self-sustaining network of gene dysregulation triggered by the limited DUX4 expression.
Collapse
Affiliation(s)
- Shan Jiang
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Katherine Williams
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Weihua Zeng
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Nam Viet Nguyen
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Xinyi Ma
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KY); (AM)
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KY); (AM)
| |
Collapse
|
14
|
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.
Collapse
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
| | | |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Young E, Abid HZ, Kwok PY, Riethman H, Xiao M. Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping. PLoS Genet 2020; 16:e1008347. [PMID: 31986135 PMCID: PMC7004388 DOI: 10.1371/journal.pgen.1008347] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/06/2020] [Accepted: 10/15/2019] [Indexed: 12/03/2022] Open
Abstract
Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.
Collapse
Affiliation(s)
- Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Heba Z. Abid
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA, United States of America
- Department of Dermatology, University of California–San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California–San Francisco, San Francisco, CA, United States of America
| | - Harold Riethman
- Medical Diagnostic & Translational Sciences, Old Dominium University, Norfolk, VA, United States of America
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
- Institute of Molecular Medicine and Infectious Disease in the School of Medicine, Drexel University, Philadelphia, PA, United States of America
| |
Collapse
|
17
|
Zheng Y, Kong L, Xu H, Lu Y, Zhao X, Yang Y, Yu G, Li P, Liang F, Jin H, Kong X. Rapid prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy 1 by combined Bionano optical mapping and karyomapping. Prenat Diagn 2019; 40:317-323. [PMID: 31711258 PMCID: PMC7065173 DOI: 10.1002/pd.5607] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022]
Abstract
Purpose To explore the feasibility of performing rapid prenatal diagnoses of FSHD1 using a combination of Bianano optical mapping and linkage‐based karyomapping. Methods DNA specimens from a family that had been previously diagnosed with FSHD1 using Southern Blot analysis were used for this study. Genetic diagnosis of the proband, fetus chorionic amniotic fluid, and aborted fetal tissue was performed using Bianano optical mapping (BOM) together with linkage‐based karyomapping. Results BOM analysis showed that the proband's 4q35.2 region contained four D4Z4 repeats and the 4qA permissible allele, consistent with the previous FSHD1 diagnosis obtained by Southern Blotting. BOM analysis of the fetus' 4q35.2 region was consistent with that of the proband. Karyomap analysis revealed that the fetus inherited the affected chromosome segment from the proband. After genetic counseling, the couple choose termination of pregnancy, and we performed gene diagnosis of the abortus tissue by BOM. Conclusions Bianano optical mapping can determine the number of D4Z4 repeats and exclude interference of the 10q26.3 homologous region, and in combination with karyomapping, can be used for rapid and accurate prenatal diagnosis of FSHD1.
Collapse
Affiliation(s)
- Yuting Zheng
- Genetics and Prenatal Diagnostic Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Hui Xu
- Genetics and Prenatal Diagnostic Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongjie Lu
- Genetics and Prenatal Diagnostic Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuechao Zhao
- Genetics and Prenatal Diagnostic Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuxia Yang
- Genetics and Prenatal Diagnostic Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Pidong Li
- Grandomics Biosciences, Beijing, China
| | - Fan Liang
- Grandomics Biosciences, Beijing, China
| | | | - Xiangdong Kong
- Genetics and Prenatal Diagnostic Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
18
|
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.
Collapse
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
Collapse
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;
| |
Collapse
|
19
|
Zhang Q, Xu X, Ding L, Li H, Xu C, Gong Y, Liu Y, Mu T, Leigh D, Cram DS, Tang S. Clinical application of single-molecule optical mapping to a multigeneration FSHD1 pedigree. Mol Genet Genomic Med 2019; 7:e565. [PMID: 30666819 PMCID: PMC6418370 DOI: 10.1002/mgg3.565] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 01/06/2023] Open
Abstract
Introduction Facioscapulohumeral muscular dystrophy 1 (FSHD1) is a relatively common autosomal dominant adult muscular dystrophy with variable disease penetrance. The disease is caused by shortening of a D4Z4 repeat array located near the telomere of chromosome 4 at 4q35. This causes activation of a dormant gene DUX4, permitting aberrant DUX4 expression which is toxic to muscles. Molecular diagnosis of FSHD1 by Southern blot hybridization or FISH combing is difficult and time consuming, requiring specialist laboratories. As an alternative, we apply a novel approach for the diagnosis of FSHD1 utilizing single‐molecule optical mapping (SMOM). Methods Long DNA molecules with BssS1 enzyme marking were subjected to SMOM on the Bionano Genomics platform to determine the number of D4Z4 repeats. Southern blot and molecular combing were used to confirm the FSHD1 haplotypes. Results In a study of a five‐generation FSHD1 pedigree, SMOM correctly diagnosed the disease and normal haplotypes, identifying the founder 4qA disease allele as having 4 D4Z4 repeat units. Southern blot and molecular combing analysis confirmed the SMOM results for the 4qA disease and 4qB nondisease alleles. Conclusion Based on our findings, we propose that SMOM is a reliable and accurate technique suitable for the molecular diagnosis of FSHD1.
Collapse
Affiliation(s)
- Qian Zhang
- Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueqin Xu
- Wenzhou Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, China
| | - Lirong Ding
- Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huanzheng Li
- Wenzhou Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, China
| | - Chengyang Xu
- Wenzhou Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, China
| | - Yuyan Gong
- Berry Genomics Corporation, Beijing, China
| | - Ying Liu
- Berry Genomics Corporation, Beijing, China
| | - Ting Mu
- Berry Genomics Corporation, Beijing, China
| | - Don Leigh
- The First Hospital of Kunming, Kunming, China
| | | | - Shaohua Tang
- Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Wenzhou Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, China
| |
Collapse
|
20
|
Haynes P, Bomsztyk K, Miller DG. Sporadic DUX4 expression in FSHD myocytes is associated with incomplete repression by the PRC2 complex and gain of H3K9 acetylation on the contracted D4Z4 allele. Epigenetics Chromatin 2018; 11:47. [PMID: 30122154 PMCID: PMC6100714 DOI: 10.1186/s13072-018-0215-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 08/10/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy 1 (FSHD1) has an autosomal dominant pattern of inheritance and primarily affects skeletal muscle. The genetic cause of FSHD1 is contraction of the D4Z4 macrosatellite array on chromosome 4 alleles associated with a permissive haplotype causing infrequent sporadic expression of the DUX4 gene. Epigenetically, the contracted D4Z4 array has decreased cytosine methylation and an open chromatin structure. Despite these genetic and epigenetic changes, the majority of FSHD myoblasts are able to repress DUX4 transcription. In this study we hypothesized that histone modifications distinguish DUX4 expressing and non-expressing cells from the same individuals. RESULTS FSHD myocytes containing the permissive 4qA haplotype with a long terminal D4Z4 unit were sorted into DUX4 expressing and non-expressing groups. We found similar CpG hypomethylation between the groups of FSHD-affected cells suggesting that CpG hypomethylation is not sufficient to trigger DUX4 expression. A survey of histone modifications present at the D4Z4 region during cell lineage commitment revealed that this region is bivalent in FSHD iPS cells with both H3K4me3 activating and H3K27me3 repressive marks present, making D4Z4 poised for DUX4 activation in pluripotent cells. After lineage commitment, the D4Z4 region becomes univalent with H3K27me3 in FSHD and non-FSHD control myoblasts and a concomitant increase in H3K4me3 in a small fraction of cells. Chromatin immunoprecipitation (ChIP) for histone modifications, chromatin modifier proteins and chromatin structural proteins on sorted FSHD myocytes revealed that activating H3K9Ac modifications were ~ fourfold higher in DUX4 expressing FSHD myocytes, while the repressive H3K27me3 modification was ~ fourfold higher at the permissive allele in DUX4 non-expressing FSHD myocytes from the same cultures. Similarly, we identified EZH2, a member of the polycomb repressive complex involved in H3K27 methylation, to be present more frequently on the permissive allele in DUX4 non-expressing FSHD myocytes. CONCLUSIONS These results implicate PRC2 as the complex primarily responsible for DUX4 repression in the setting of FSHD and H3K9 acetylation along with reciprocal loss of H3K27me3 as key epigenetic events that result in DUX4 expression. Future studies focused on events that trigger H3K9Ac or augment PRC2 complex activity in a small fraction of nuclei may expose additional drug targets worthy of study.
Collapse
Affiliation(s)
- Premi Haynes
- Departments of Pediatrics and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Karol Bomsztyk
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Daniel G Miller
- Departments of Pediatrics and Genome Sciences, University of Washington, Seattle, WA, USA. .,University of Washington, Campus Box 358056, 850 Republican Street, Room N416, Seattle, WA, 98109, USA.
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Young E, Pastor S, Rajagopalan R, McCaffrey J, Sibert J, Mak ACY, Kwok PY, Riethman H, Xiao M. High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres. Nucleic Acids Res 2017; 45:e73. [PMID: 28180280 PMCID: PMC5605236 DOI: 10.1093/nar/gkx017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 02/07/2017] [Indexed: 01/22/2023] Open
Abstract
Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG)n repeat tracts. We establish detailed maps for subtelomere gap regions in the human reference sequence, detect many new large subtelomeric variants and demonstrate the feasibility of long-range haplotyping through segmentally duplicated subtelomere regions. These features make the method a uniquely valuable new tool for improving the quality of genome assemblies in complex DNA regions. Based on single molecule mapping of telomere-terminal DNA fragments, we provide proof of principle for a novel method to estimate telomere lengths linked to distinguishable telomeric haplotypes; this single-telomere genotyping method may ultimately enable delineation of human cis elements involved in telomere length regulation.
Collapse
Affiliation(s)
- Eleanor Young
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Steven Pastor
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | | | - Jennifer McCaffrey
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Justin Sibert
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Angel C Y Mak
- Cardiovascular Research Institute, University of California, San Francisco, CA, 94158 USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, CA, 94158 USA
| | - Harold Riethman
- Old Dominion University, Medical Diagnostic and Translational Sciences, Norfolk, VA, 23529 USA
| | - Ming Xiao
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA.,Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, 19102 USA
| |
Collapse
|
23
|
Newkirk DA, Chen YY, Chien R, Zeng W, Biesinger J, Flowers E, Kawauchi S, Santos R, Calof AL, Lander AD, Xie X, Yokomori K. The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome. Clin Epigenetics 2017; 9:89. [PMID: 28855971 PMCID: PMC5574093 DOI: 10.1186/s13148-017-0391-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cornelia de Lange syndrome (CdLS) is a multisystem developmental disorder frequently associated with heterozygous loss-of-function mutations of Nipped-B-like (NIPBL), the human homolog of Drosophila Nipped-B. NIPBL loads cohesin onto chromatin. Cohesin mediates sister chromatid cohesion important for mitosis but is also increasingly recognized as a regulator of gene expression. In CdLS patient cells and animal models, expression changes of multiple genes with little or no sister chromatid cohesion defect suggests that disruption of gene regulation underlies this disorder. However, the effect of NIPBL haploinsufficiency on cohesin binding, and how this relates to the clinical presentation of CdLS, has not been fully investigated. Nipbl haploinsufficiency causes CdLS-like phenotype in mice. We examined genome-wide cohesin binding and its relationship to gene expression using mouse embryonic fibroblasts (MEFs) from Nipbl+/- mice that recapitulate the CdLS phenotype. RESULTS We found a global decrease in cohesin binding, including at CCCTC-binding factor (CTCF) binding sites and repeat regions. Cohesin-bound genes were found to be enriched for histone H3 lysine 4 trimethylation (H3K4me3) at their promoters; were disproportionately downregulated in Nipbl mutant MEFs; and displayed evidence of reduced promoter-enhancer interaction. The results suggest that gene activation is the primary cohesin function sensitive to Nipbl reduction. Over 50% of significantly dysregulated transcripts in mutant MEFs come from cohesin target genes, including genes involved in adipogenesis that have been implicated in contributing to the CdLS phenotype. CONCLUSIONS Decreased cohesin binding at the gene regions is directly linked to disease-specific expression changes. Taken together, our Nipbl haploinsufficiency model allows us to analyze the dosage effect of cohesin loading on CdLS development.
Collapse
Affiliation(s)
- Daniel A. Newkirk
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- Department of Computer Sciences, University of California, Irvine, CA 92697 USA
| | - Yen-Yun Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- Current address: ResearchDx Inc., 5 Mason, Irvine, CA 92618 USA
| | - Richard Chien
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- Current address: Thermo Fisher Scientific, Inc., 180 Oyster Point Blvd South, San Francisco, CA 94080 USA
| | - Weihua Zeng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- Current address: Department of Developmental & Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92697 USA
| | - Jacob Biesinger
- Department of Computer Sciences, University of California, Irvine, CA 92697 USA
- Current address: Verily Life Scienceds, 1600 Amphitheatre Pkwy, Mountain View, CA 94043 USA
| | - Ebony Flowers
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
- California State University Long Beach, Long Beach, CA 90840 USA
- Current address: UT Southwestern Medical Center, 5323 Harry Hines Blvd, NA8.124, Dallas, TX 75390 USA
| | - Shimako Kawauchi
- Department of Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA 92697 USA
| | - Rosaysela Santos
- Department of Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA 92697 USA
| | - Anne L. Calof
- Department of Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA 92697 USA
| | - Arthur D. Lander
- Department of Developmental & Cell Biology, School of Biological Sciences, University of California, Irvine, CA 92697 USA
| | - Xiaohui Xie
- Department of Computer Sciences, University of California, Irvine, CA 92697 USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697 USA
| |
Collapse
|
24
|
Mason AG, Slieker RC, Balog J, Lemmers RJLF, Wong CJ, Yao Z, Lim JW, Filippova GN, Ne E, Tawil R, Heijmans BT, Tapscott SJ, van der Maarel SM. SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes. Skelet Muscle 2017; 7:12. [PMID: 28587678 PMCID: PMC5461771 DOI: 10.1186/s13395-017-0129-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/24/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance. METHODS To investigate the global effects of harboring heterozygous SMCHD1 mutations on DNA methylation in humans, we combined 450k methylation analysis on mononuclear monocytes from female heterozygous SMCHD1 mutation carriers and unaffected controls with reduced representation bisulfite sequencing (RRBS) on FSHD2 and control myoblast cell lines. Candidate loci were then evaluated for SMCHD1 binding using ChIP-qPCR and expression was evaluated using RT-qPCR. RESULTS We identified a limited number of clustered autosomal loci with CpG hypomethylation in SMCHD1 mutation carriers: the protocadherin (PCDH) cluster on chromosome 5, the transfer RNA (tRNA) and 5S rRNA clusters on chromosome 1, the HOXB and HOXD clusters on chromosomes 17 and 2, respectively, and the D4Z4 repeats on chromosomes 4 and 10. Furthermore, minor increases in RNA expression were seen in FSHD2 myoblasts for some of the PCDHβ cluster isoforms, tRNA isoforms, and a HOXB isoform in comparison to controls, in addition to the previously reported effects on DUX4 expression. SMCHD1 was bound at DNAseI hypersensitivity sites known to regulate the PCDHβ cluster and at the chromosome 1 tRNA cluster, with decreased binding in SMCHD1 mutation carriers at the PCDHβ cluster sites. CONCLUSIONS Our study is the first to investigate the global methylation effects in humans resulting from heterozygous mutations in SMCHD1. Our results suggest that SMCHD1 acts as a repressor on a limited set of autosomal gene clusters, as an observed reduction in methylation associates with a loss of SMCHD1 binding and increased expression for some of the loci.
Collapse
Affiliation(s)
- Amanda G Mason
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Roderick C Slieker
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Judit Balog
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Chao-Jen Wong
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Zizhen Yao
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jong-Won Lim
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Galina N Filippova
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Enrico Ne
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Bas T Heijmans
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, Leiden, The Netherlands
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Balog J, Thijssen PE, Shadle S, Straasheijm KR, van der Vliet PJ, Krom YD, van den Boogaard ML, de Jong A, F Lemmers RJL, Tawil R, Tapscott SJ, van der Maarel SM. Increased DUX4 expression during muscle differentiation correlates with decreased SMCHD1 protein levels at D4Z4. Epigenetics 2016; 10:1133-42. [PMID: 26575099 PMCID: PMC4844215 DOI: 10.1080/15592294.2015.1113798] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy is caused by incomplete epigenetic repression of the transcription factor DUX4 in skeletal muscle. A copy of DUX4 is located within each unit of the D4Z4 macrosatellite repeat array and its derepression in somatic cells is caused by either repeat array contraction (FSHD1) or by mutations in the chromatin repressor SMCHD1 (FSHD2). While DUX4 expression has thus far only been detected in FSHD muscle and muscle cell cultures, and increases with in vitro myogenic differentiation, the D4Z4 chromatin structure has only been studied in proliferating myoblasts or non-myogenic cells. We here show that SMCHD1 protein levels at D4Z4 decline during muscle cell differentiation and correlate with DUX4 derepression. In FSHD2, but not FSHD1, the loss of SMCHD1 repressor activity is partially compensated by increased Polycomb Repressive Complex 2 (PRC2)–mediated H3K27 trimethylation at D4Z4, a situation that can be mimicked by SMCHD1 knockdown in control myotubes. In contrast, moderate overexpression of SMCHD1 results in DUX4 silencing in FSHD1 and FSHD2 myotubes demonstrating that DUX4 derepression in FSHD is reversible. Together, we show that in FSHD1 and FSHD2 the decline in SMCHD1 protein levels during muscle cell differentiation renders skeletal muscle sensitive to DUX4.
Collapse
Affiliation(s)
- Judit Balog
- a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands
| | - Peter E Thijssen
- a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands
| | - Sean Shadle
- b Division of Human Biology; Fred Hutchinson Cancer Research Center; Seattle 98109 , Washington , United States of America
| | - Kirsten R Straasheijm
- a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands
| | - Patrick J van der Vliet
- a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands
| | - Yvonne D Krom
- a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands
| | | | - Annika de Jong
- a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands
| | - Richard J L F Lemmers
- a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands
| | - Rabi Tawil
- c Neuromuscular Disease Unit; Department of Neurology; University of Rochester Medical Center; Rochester 14642 , New York , United States of America
| | - Stephen J Tapscott
- b Division of Human Biology; Fred Hutchinson Cancer Research Center; Seattle 98109 , Washington , United States of America
| | - Silvère M van der Maarel
- a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
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.
Collapse
|
29
|
Clinical, muscle pathological, and genetic features of Japanese facioscapulohumeral muscular dystrophy 2 (FSHD2) patients with SMCHD1 mutations. Neuromuscul Disord 2016; 26:300-8. [DOI: 10.1016/j.nmd.2016.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 02/28/2016] [Accepted: 03/07/2016] [Indexed: 11/21/2022]
|
30
|
Himeda CL, Jones TI, Jones PL. CRISPR/dCas9-mediated Transcriptional Inhibition Ameliorates the Epigenetic Dysregulation at D4Z4 and Represses DUX4-fl in FSH Muscular Dystrophy. Mol Ther 2016; 24:527-35. [PMID: 26527377 PMCID: PMC4786914 DOI: 10.1038/mt.2015.200] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/21/2015] [Indexed: 12/16/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most prevalent myopathies, affecting males and females of all ages. Both forms of the disease are linked by epigenetic derepression of the D4Z4 macrosatellite repeat array at chromosome 4q35, leading to aberrant expression of D4Z4-encoded RNAs in skeletal muscle. Production of full-length DUX4 (DUX4-fl) mRNA from the derepressed D4Z4 array results in misexpression of DUX4-FL protein and its transcriptional targets, and apoptosis, ultimately leading to accumulated muscle pathology. Returning the chromatin at the FSHD locus to its nonpathogenic, epigenetically repressed state would simultaneously affect all D4Z4 RNAs, inhibiting downstream pathogenic pathways, and is thus an attractive therapeutic strategy. Advances in CRISPR/Cas9-based genome editing make it possible to target epigenetic modifiers to an endogenous disease locus, although reports to date have focused on more typical genomic regions. Here, we demonstrate that a CRISPR/dCas9 transcriptional inhibitor can be specifically targeted to the highly repetitive FSHD macrosatellite array and alter the chromatin to repress expression of DUX4-fl in primary FSHD myocytes. These results implicate the promoter and exon 1 of DUX4 as potential therapeutic targets and demonstrate the utility of CRISPR technology for correction of the epigenetic dysregulation in FSHD.
Collapse
Affiliation(s)
- Charis L Himeda
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Takako I Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Peter L Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- The Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| |
Collapse
|
31
|
Molecular combing compared to Southern blot for measuring D4Z4 contractions in FSHD. Neuromuscul Disord 2015; 25:945-51. [PMID: 26420234 DOI: 10.1016/j.nmd.2015.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 11/21/2022]
Abstract
We compare molecular combing to Southern blot in the analysis of the facioscapulohumeral muscular dystrophy type 1 locus (FSHD1) on chromosome 4q35-qter (chr 4q) in genomic DNA specimens sent to a clinical laboratory for FSHD testing. A de-identified set of 87 genomic DNA specimens determined by Southern blot as normal (n = 71), abnormal with D4Z4 macrosatellite repeat array contractions (n = 7), indeterminate (n = 6), borderline (n = 2), or mosaic (n = 1) was independently re-analyzed by molecular combing in a blinded fashion. The molecular combing results were identical to the Southern blot results in 75 (86%) of cases. All contractions (n = 7) and mosaics (n = 1) detected by Southern blot were confirmed by molecular combing. Of the 71 samples with normal Southern blot results, 67 (94%) had concordant molecular combing results. The four discrepancies were either mosaic (n = 2), rearranged (n = 1), or borderline by molecular combing (n = 1). All indeterminate Southern blot results (n = 6) were resolved by molecular combing as either normal (n = 4), borderline (n = 1), or rearranged (n = 1). The two borderline Southern blot results showed a D4Z4 contraction on the chr 4qA allele and a normal result by molecular combing. Molecular combing overcomes a number of technical limitations of Southern blot by providing direct visualization of D4Z4 macrosatellite repeat arrays on specific chr 4q and chr 10q alleles and more precise D4Z4 repeat sizing. This study suggests that molecular combing has superior analytical validity compared to Southern blot for determining D4Z4 contraction size, detecting mosaicism, and resolving borderline and indeterminate Southern blot results. Further studies are needed to establish the clinical validity and diagnostic accuracy of these findings in FSHD.
Collapse
|
32
|
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.
Collapse
Affiliation(s)
- Jane E Hewitt
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| |
Collapse
|
33
|
Himeda CL, Jones TI, Jones PL. Facioscapulohumeral muscular dystrophy as a model for epigenetic regulation and disease. Antioxid Redox Signal 2015; 22:1463-82. [PMID: 25336259 PMCID: PMC4432493 DOI: 10.1089/ars.2014.6090] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Aberrant epigenetic regulation is an integral aspect of many diseases and complex disorders. Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, is caused by disrupted genetic and epigenetic regulation of a macrosatellite repeat. FSHD provides a powerful model to investigate disease-relevant epigenetic modifiers and general mechanisms of epigenetic regulation that govern gene expression. RECENT ADVANCES In the context of a genetically permissive allele, the one aspect of FSHD that is consistent across all known cases is the aberrant epigenetic state of the disease locus. In addition, certain mutations in the chromatin regulator SMCHD1 (structural maintenance of chromosomes hinge-domain protein 1) are sufficient to cause FSHD2 and enhance disease severity in FSHD1. Thus, there are multiple pathways to generate the epigenetic dysregulation required for FSHD. CRITICAL ISSUES Why do some individuals with the genetic requirements for FSHD develop disease pathology, while others remain asymptomatic? Similarly, disease progression is highly variable among individuals. What are the relative contributions of genetic background and environmental factors in determining disease manifestation, progression, and severity in FSHD? What is the interplay between epigenetic factors regulating the disease locus and which, if any, are viable therapeutic targets? FUTURE DIRECTIONS Epigenetic regulation represents a potentially powerful therapeutic target for FSHD. Determining the epigenetic signatures that are predictive of disease severity and identifying the spectrum of disease modifiers in FSHD are vital to the development of effective therapies.
Collapse
Affiliation(s)
- Charis L Himeda
- The Wellstone Program and the Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School , Worcester, Massachusetts
| | | | | |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|