1
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Handal T, Juster S, Abu Diab M, Yanovsky-Dagan S, Zahdeh F, Aviel U, Sarel-Gallily R, Michael S, Bnaya E, Sebban S, Buganim Y, Drier Y, Mouly V, Kubicek S, van den Broek WJAA, Wansink DG, Epsztejn-Litman S, Eiges R. Differentiation shifts from a reversible to an irreversible heterochromatin state at the DM1 locus. Nat Commun 2024; 15:3270. [PMID: 38627364 PMCID: PMC11021500 DOI: 10.1038/s41467-024-47217-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Epigenetic defects caused by hereditary or de novo mutations are implicated in various human diseases. It remains uncertain whether correcting the underlying mutation can reverse these defects in patient cells. Here we show by the analysis of myotonic dystrophy type 1 (DM1)-related locus that in mutant human embryonic stem cells (hESCs), DNA methylation and H3K9me3 enrichments are completely abolished by repeat excision (CTG2000 expansion), whereas in patient myoblasts (CTG2600 expansion), repeat deletion fails to do so. This distinction between undifferentiated and differentiated cells arises during cell differentiation, and can be reversed by reprogramming of gene-edited myoblasts. We demonstrate that abnormal methylation in DM1 is distinctively maintained in the undifferentiated state by the activity of the de novo DNMTs (DNMT3b in tandem with DNMT3a). Overall, the findings highlight a crucial difference in heterochromatin maintenance between undifferentiated (sequence-dependent) and differentiated (sequence-independent) cells, thus underscoring the role of differentiation as a locking mechanism for repressive epigenetic modifications at the DM1 locus.
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Affiliation(s)
- Tayma Handal
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Sarah Juster
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Manar Abu Diab
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Shira Yanovsky-Dagan
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Fouad Zahdeh
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
| | - Uria Aviel
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Roni Sarel-Gallily
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, 91904, Israel
| | - Shir Michael
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Ester Bnaya
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel
| | - Shulamit Sebban
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Yotam Drier
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Vincent Mouly
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013, Paris, France
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Walther J A A van den Broek
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Derick G Wansink
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Silvina Epsztejn-Litman
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, The Eisenberg R&D Authority, Shaare Zedek Medical Center, Jerusalem, 91031, Israel.
- The Hebrew University School of Medicine, Jerusalem, 91120, Israel.
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2
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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3
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Pluripotent Stem Cells in Disease Modeling and Drug Discovery for Myotonic Dystrophy Type 1. Cells 2023; 12:cells12040571. [PMID: 36831237 PMCID: PMC9954118 DOI: 10.3390/cells12040571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a progressive multisystemic disease caused by the expansion of a CTG repeat tract within the 3' untranslated region (3' UTR) of the dystrophia myotonica protein kinase gene (DMPK). Although DM1 is considered to be the most frequent myopathy of genetic origin in adults, DM1 patients exhibit a vast diversity of symptoms, affecting many different organs. Up until now, different in vitro models from patients' derived cells have largely contributed to the current understanding of DM1. Most of those studies have focused on muscle physiopathology. However, regarding the multisystemic aspect of DM1, there is still a crucial need for relevant cellular models to cover the whole complexity of the disease and open up options for new therapeutic approaches. This review discusses how human pluripotent stem cell-based models significantly contributed to DM1 mechanism decoding, and how they provided new therapeutic strategies that led to actual phase III clinical trials.
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4
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Identification of Candidate mRNA Isoforms for Prostate Cancer-Risk SNPs Utilizing Iso-eQTL and sQTL Methods. Int J Mol Sci 2022; 23:ijms232012406. [PMID: 36293264 PMCID: PMC9604153 DOI: 10.3390/ijms232012406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) impacting the alternative splicing (AS) process (sQTLs) or isoform expression (iso-eQTL) are implicated as important cancer regulatory elements. To find the sQTL and iso-eQTL, we retrieved prostate cancer (PrCa) tissue RNA-seq and genotype data originating from 385 PrCa European patients from The Cancer Genome Atlas. We conducted RNA-seq analysis with isoform-based and splice event-based approaches. The MatrixEQTL was used to identify PrCa-associated sQTLs and iso-eQTLs. The overlap between sQTL and iso-eQTL with GWAS loci and those that are differentially expressed between cancer and normal tissue were identified. The cis-acting associations (FDR < 0.05) for PrCa-risk SNPs identified 42, 123, and 90 PrCa-associated cassette exons, intron retention, and mRNA isoforms belonging to 25, 95, and 83 genes, respectively; while assessment of trans-acting association (FDR < 0.05) yielded 59, 65, and 196 PrCa-associated cassette exons, intron retention and mRNA isoforms belonging to 35, 55, and 181 genes, respectively. The results suggest that functional PrCa-associated SNPs can play a role in PrCa genesis by making an important contribution to the dysregulation of AS and, consequently, impacting the expression of the mRNA isoforms.
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5
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Baud A, Derbis M, Tutak K, Sobczak K. Partners in crime: Proteins implicated in
RNA
repeat expansion diseases. WIRES RNA 2022; 13:e1709. [PMID: 35229468 PMCID: PMC9539487 DOI: 10.1002/wrna.1709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Baud
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Magdalena Derbis
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Katarzyna Tutak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
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Koehorst E, Odria R, Capó J, Núñez-Manchón J, Arbex A, Almendrote M, Linares-Pardo I, Natera-de Benito D, Saez V, Nascimento A, Ortez C, Rubio MÁ, Díaz-Manera J, Alonso-Pérez J, Lucente G, Rodriguez-Palmero A, Ramos-Fransi A, Martínez-Piñeiro A, Nogales-Gadea G, Suelves M. An Integrative Analysis of DNA Methylation Pattern in Myotonic Dystrophy Type 1 Samples Reveals a Distinct DNA Methylation Profile between Tissues and a Novel Muscle-Associated Epigenetic Dysregulation. Biomedicines 2022; 10:biomedicines10061372. [PMID: 35740394 PMCID: PMC9220235 DOI: 10.3390/biomedicines10061372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a progressive, non-treatable, multi-systemic disorder. To investigate the contribution of epigenetics to the complexity of DM1, we compared DNA methylation profiles of four annotated CpG islands (CpGis) in the DMPK locus and neighbouring genes, in distinct DM1 tissues and derived cells, representing six DM1 subtypes, by bisulphite sequencing. In blood, we found no differences in CpGi 74, 43 and 36 in DNA methylation profile. In contrast, a CTCF1 DNA methylation gradient was found with 100% methylation in congenital cases, 50% in childhood cases and 13% in juvenile cases. CTCF1 methylation correlated to disease severity and CTG expansion size. Notably, 50% of CTCF1 methylated cases showed methylation in the CTCF2 regions. Additionally, methylation was associated with maternal transmission. Interestingly, the evaluation of seven families showed that unmethylated mothers passed on an expansion of the CTG repeat, whereas the methylated mothers transmitted a contraction. The analysis of patient-derived cells showed that DNA methylation profiles were highly preserved, validating their use as faithful DM1 cellular models. Importantly, the comparison of DNA methylation levels of distinct DM1 tissues revealed a novel muscle-specific epigenetic signature with methylation of the CTCF1 region accompanied by demethylation of CpGi 43, a region containing an alternative DMPK promoter, which may decrease the canonical promoter activity. Altogether, our results showed a distinct DNA methylation profile across DM1 tissues and uncovered a novel and dual epigenetic signature in DM1 muscle samples, providing novel insights into the epigenetic changes associated with DM1.
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Affiliation(s)
- Emma Koehorst
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Renato Odria
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Júlia Capó
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Judit Núñez-Manchón
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Andrea Arbex
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Miriam Almendrote
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Ian Linares-Pardo
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Neuropediatric Department, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, L'Hospitalet de Llobregat, 08950 Barcelona, Spain
| | - Verónica Saez
- Neuromuscular Unit, Neuropediatric Department, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, L'Hospitalet de Llobregat, 08950 Barcelona, Spain
| | - Andrés Nascimento
- Neuromuscular Unit, Neuropediatric Department, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, L'Hospitalet de Llobregat, 08950 Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Neuropediatric Department, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, L'Hospitalet de Llobregat, 08950 Barcelona, Spain
| | - Miguel Ángel Rubio
- Neuromuscular Unit, Department of Neurology, Hospital del Mar, 08003 Barcelona, Spain
| | - Jordi Díaz-Manera
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Jorge Alonso-Pérez
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
| | - Giuseppe Lucente
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Agustín Rodriguez-Palmero
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Pediatric Neurology Unit, Department of Pediatrics, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Alba Ramos-Fransi
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Alicia Martínez-Piñeiro
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Gisela Nogales-Gadea
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Mònica Suelves
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
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7
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Barbé L, Finkbeiner S. Genetic and Epigenetic Interplay Define Disease Onset and Severity in Repeat Diseases. Front Aging Neurosci 2022; 14:750629. [PMID: 35592702 PMCID: PMC9110800 DOI: 10.3389/fnagi.2022.750629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Repeat diseases, such as fragile X syndrome, myotonic dystrophy, Friedreich ataxia, Huntington disease, spinocerebellar ataxias, and some forms of amyotrophic lateral sclerosis, are caused by repetitive DNA sequences that are expanded in affected individuals. The age at which an individual begins to experience symptoms, and the severity of disease, are partially determined by the size of the repeat. However, the epigenetic state of the area in and around the repeat also plays an important role in determining the age of disease onset and the rate of disease progression. Many repeat diseases share a common epigenetic pattern of increased methylation at CpG islands near the repeat region. CpG islands are CG-rich sequences that are tightly regulated by methylation and are often found at gene enhancer or insulator elements in the genome. Methylation of CpG islands can inhibit binding of the transcriptional regulator CTCF, resulting in a closed chromatin state and gene down regulation. The downregulation of these genes leads to some disease-specific symptoms. Additionally, a genetic and epigenetic interplay is suggested by an effect of methylation on repeat instability, a hallmark of large repeat expansions that leads to increasing disease severity in successive generations. In this review, we will discuss the common epigenetic patterns shared across repeat diseases, how the genetics and epigenetics interact, and how this could be involved in disease manifestation. We also discuss the currently available stem cell and mouse models, which frequently do not recapitulate epigenetic patterns observed in human disease, and propose alternative strategies to study the role of epigenetics in repeat diseases.
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Affiliation(s)
- Lise Barbé
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
| | - Steve Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Steve Finkbeiner,
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8
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Molecular Therapies for Myotonic Dystrophy Type 1: From Small Drugs to Gene Editing. Int J Mol Sci 2022; 23:ijms23094622. [PMID: 35563013 PMCID: PMC9101876 DOI: 10.3390/ijms23094622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy affecting many different body tissues, predominantly skeletal and cardiac muscles and the central nervous system. The expansion of CTG repeats in the DM1 protein-kinase (DMPK) gene is the genetic cause of the disease. The pathogenetic mechanisms are mainly mediated by the production of a toxic expanded CUG transcript from the DMPK gene. With the availability of new knowledge, disease models, and technical tools, much progress has been made in the discovery of altered pathways and in the potential of therapeutic intervention, making the path to the clinic a closer reality. In this review, we describe and discuss the molecular therapeutic strategies for DM1, which are designed to directly target the CTG genomic tract, the expanded CUG transcript or downstream signaling molecules.
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9
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de Pontual L, Tomé S. Overview of the Complex Relationship between Epigenetics Markers, CTG Repeat Instability and Symptoms in Myotonic Dystrophy Type 1. Int J Mol Sci 2022; 23:ijms23073477. [PMID: 35408837 PMCID: PMC8998570 DOI: 10.3390/ijms23073477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/05/2023] Open
Abstract
Among the trinucleotide repeat disorders, myotonic dystrophy type 1 (DM1) is one of the most complex neuromuscular diseases caused by an unstable CTG repeat expansion in the DMPK gene. DM1 patients exhibit high variability in the dynamics of CTG repeat instability and in the manifestations and progression of the disease. The largest expanded alleles are generally associated with the earliest and most severe clinical form. However, CTG repeat length alone is not sufficient to predict disease severity and progression, suggesting the involvement of other factors. Several data support the role of epigenetic alterations in clinical and genetic variability. By highlighting epigenetic alterations in DM1, this review provides a new avenue on how these changes can serve as biomarkers to predict clinical features and the mutation behavior.
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Affiliation(s)
| | - Stéphanie Tomé
- Correspondence: ; Tel.: +33-1-42-16-57-16; Fax: +33-1-42-16-57-00
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10
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Cardinali B, Provenzano C, Izzo M, Voellenkle C, Battistini J, Strimpakos G, Golini E, Mandillo S, Scavizzi F, Raspa M, Perfetti A, Baci D, Lazarevic D, Garcia-Manteiga JM, Gourdon G, Martelli F, Falcone G. Time-controlled and muscle-specific CRISPR/Cas9-mediated deletion of CTG-repeat expansion in the DMPK gene. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:184-199. [PMID: 34976437 PMCID: PMC8693309 DOI: 10.1016/j.omtn.2021.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9-mediated therapeutic gene editing is a promising technology for durable treatment of incurable monogenic diseases such as myotonic dystrophies. Gene-editing approaches have been recently applied to in vitro and in vivo models of myotonic dystrophy type 1 (DM1) to delete the pathogenic CTG-repeat expansion located in the 3′ untranslated region of the DMPK gene. In DM1-patient-derived cells removal of the expanded repeats induced beneficial effects on major hallmarks of the disease with reduction in DMPK transcript-containing ribonuclear foci and reversal of aberrant splicing patterns. Here, we set out to excise the triplet expansion in a time-restricted and cell-specific fashion to minimize the potential occurrence of unintended events in off-target genomic loci and select for the target cell type. To this aim, we employed either a ubiquitous promoter-driven or a muscle-specific promoter-driven Cas9 nuclease and tetracycline repressor-based guide RNAs. A dual-vector approach was used to deliver the CRISPR/Cas9 components into DM1 patient-derived cells and in skeletal muscle of a DM1 mouse model. In this way, we obtained efficient and inducible gene editing both in proliferating cells and differentiated post-mitotic myocytes in vitro as well as in skeletal muscle tissue in vivo.
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Affiliation(s)
- Beatrice Cardinali
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Claudia Provenzano
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Mariapaola Izzo
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Jonathan Battistini
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Georgios Strimpakos
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Elisabetta Golini
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Silvia Mandillo
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Ferdinando Scavizzi
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Marcello Raspa
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
| | - Alessandra Perfetti
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Denisa Baci
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | | | - Geneviève Gourdon
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Germana Falcone
- Institute of Biochemistry and Cell Biology, National Research Council, Monterotondo, 00015 Rome, Italy
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11
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Franck S, Couvreu De Deckersberg E, Bubenik JL, Markouli C, Barbé L, Allemeersch J, Hilven P, Duqué G, Swanson MS, Gheldof A, Spits C, Sermon KD. Myotonic dystrophy type 1 embryonic stem cells show decreased myogenic potential, increased CpG methylation at the DMPK locus and RNA mis-splicing. Biol Open 2022; 11:273965. [PMID: 35019138 PMCID: PMC8764412 DOI: 10.1242/bio.058978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Skeletal muscle tissue is severely affected in myotonic dystrophy type 1 (DM1) patients, characterised by muscle weakness, myotonia and muscle immaturity in the most severe congenital form of the disease. Previously, it was not known at what stage during myogenesis the DM1 phenotype appears. In this study we differentiated healthy and DM1 human embryonic stem cells to myoblasts and myotubes and compared their differentiation potential using a comprehensive multi-omics approach. We found myogenesis in DM1 cells to be abnormal with altered myotube generation compared to healthy cells. We did not find differentially expressed genes between DM1 and non-DM1 cell lines within the same developmental stage. However, during differentiation we observed an aberrant inflammatory response and increased CpG methylation upstream of the CTG repeat at the myoblast level and RNA mis-splicing at the myotube stage. We show that early myogenesis modelled in hESC reiterates the early developmental manifestation of DM1. Summary: Early developmental abnormalities in myotonic dystrophy type 1 are reiterated in vitro in myotubes differentiated from human embryonic stem cells that carry the mutation.
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Affiliation(s)
- Silvie Franck
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | | | - Jodi L Bubenik
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Christina Markouli
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Lise Barbé
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, 94107 CA, United States
| | | | - Pierre Hilven
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Geoffrey Duqué
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Alexander Gheldof
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium.,Center for Medical Genetics, UZ Brussel, Brussels 1090, Belgium
| | - Claudia Spits
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Karen D Sermon
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
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12
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Nuclear Envelope Alterations in Myotonic Dystrophy Type 1 Patient-Derived Fibroblasts. Int J Mol Sci 2022; 23:ijms23010522. [PMID: 35008948 PMCID: PMC8745202 DOI: 10.3390/ijms23010522] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/01/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a hereditary and multisystemic disease characterized by myotonia, progressive distal muscle weakness and atrophy. The molecular mechanisms underlying this disease are still poorly characterized, although there are some hypotheses that envisage to explain the multisystemic features observed in DM1. An emergent hypothesis is that nuclear envelope (NE) dysfunction may contribute to muscular dystrophies, particularly to DM1. Therefore, the main objective of the present study was to evaluate the nuclear profile of DM1 patient-derived and control fibroblasts and to determine the protein levels and subcellular distribution of relevant NE proteins in these cell lines. Our results demonstrated that DM1 patient-derived fibroblasts exhibited altered intracellular protein levels of lamin A/C, LAP1, SUN1, nesprin-1 and nesprin-2 when compared with the control fibroblasts. In addition, the results showed an altered location of these NE proteins accompanied by the presence of nuclear deformations (blebs, lobes and/or invaginations) and an increased number of nuclear inclusions. Regarding the nuclear profile, DM1 patient-derived fibroblasts had a larger nuclear area and a higher number of deformed nuclei and micronuclei than control-derived fibroblasts. These results reinforce the evidence that NE dysfunction is a highly relevant pathological characteristic observed in DM1.
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13
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Koehorst E, Núñez-Manchón J, Ballester-López A, Almendrote M, Lucente G, Arbex A, Chojnacki J, Vázquez-Manrique RP, Gómez-Escribano AP, Pintos-Morell G, Coll-Cantí J, Ramos-Fransi A, Martínez-Piñeiro A, Suelves M, Nogales-Gadea G. Characterization of RAN Translation and Antisense Transcription in Primary Cell Cultures of Patients with Myotonic Dystrophy Type 1. J Clin Med 2021; 10:jcm10235520. [PMID: 34884222 PMCID: PMC8658563 DOI: 10.3390/jcm10235520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Myotonic Dystrophy type 1 (DM1) is a muscular dystrophy with a multi-systemic nature. It was one of the first diseases in which repeat associated non-ATG (RAN) translation was described in 2011, but has not been further explored since. In order to enhance our knowledge of RAN translation in DM1, we decided to study the presence of DM1 antisense (DM1-AS) transcripts (the origin of the polyglutamine (polyGln) RAN protein) using RT-PCR and FISH, and that of RAN translation via immunoblotting and immunofluorescence in distinct DM1 primary cell cultures, e.g., myoblasts, skin fibroblasts and lymphoblastoids, from ten patients. DM1-AS transcripts were found in all DM1 cells, with a lower expression in patients compared to controls. Antisense RNA foci were found in the nuclei and cytoplasm of a subset of DM1 cells. The polyGln RAN protein was undetectable in all three cell types with both approaches. Immunoblots revealed a 42 kD polyGln containing protein, which was most likely the TATA-box-binding protein. Immunofluorescence revealed a cytoplasmic aggregate, which co-localized with the Golgi apparatus. Taken together, DM1-AS transcript levels were lower in patients compared to controls and a small portion of the transcripts included the expanded repeat. However, RAN translation was not present in patient-derived DM1 cells, or was in undetectable quantities for the available methods.
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Affiliation(s)
- Emma Koehorst
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
| | - Judit Núñez-Manchón
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
| | - Alfonsina Ballester-López
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (R.P.V.-M.); (A.P.G.-E.)
| | - Miriam Almendrote
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Giuseppe Lucente
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Andrea Arbex
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | | | - Rafael P. Vázquez-Manrique
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (R.P.V.-M.); (A.P.G.-E.)
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Ana Pilar Gómez-Escribano
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (R.P.V.-M.); (A.P.G.-E.)
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Guillem Pintos-Morell
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Reference Unit for Hereditary Metabolic Disorders (MetabERN), Vall d’Hebron University Hospital, 08035 Barcelona, Spain
| | - Jaume Coll-Cantí
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Alba Ramos-Fransi
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Alicia Martínez-Piñeiro
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Mònica Suelves
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
| | - Gisela Nogales-Gadea
- Neuromuscular and Neuropediatric Research Group, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (E.K.); (J.N.-M.); (A.B.-L.); (M.A.); (G.L.); (A.A.); (G.P.-M.); (J.C.-C.); (A.R.-F.); (A.M.-P.); (M.S.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (R.P.V.-M.); (A.P.G.-E.)
- Correspondence: ; Tel.: +34-930330530
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14
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Visconti VV, Centofanti F, Fittipaldi S, Macrì E, Novelli G, Botta A. Epigenetics of Myotonic Dystrophies: A Minireview. Int J Mol Sci 2021; 22:ijms222212594. [PMID: 34830473 PMCID: PMC8623789 DOI: 10.3390/ijms222212594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/19/2021] [Accepted: 11/20/2021] [Indexed: 12/14/2022] Open
Abstract
Myotonic dystrophy type 1 and 2 (DM1 and DM2) are two multisystemic autosomal dominant disorders with clinical and genetic similarities. The prevailing paradigm for DMs is that they are mediated by an in trans toxic RNA mechanism, triggered by untranslated CTG and CCTG repeat expansions in the DMPK and CNBP genes for DM1 and DM2, respectively. Nevertheless, increasing evidences suggest that epigenetics can also play a role in the pathogenesis of both diseases. In this review, we discuss the available information on epigenetic mechanisms that could contribute to the DMs outcome and progression. Changes in DNA cytosine methylation, chromatin remodeling and expression of regulatory noncoding RNAs are described, with the intent of depicting an epigenetic signature of DMs. Epigenetic biomarkers have a strong potential for clinical application since they could be used as targets for therapeutic interventions avoiding changes in DNA sequences. Moreover, understanding their clinical significance may serve as a diagnostic indicator in genetic counselling in order to improve genotype–phenotype correlations in DM patients.
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Affiliation(s)
- Virginia Veronica Visconti
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Federica Centofanti
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Simona Fittipaldi
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Elisa Macrì
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
- IRCCS (Institute for Treatment and Research) Neuromed, 86077 Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Annalisa Botta
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (F.C.); (S.F.); (E.M.); (G.N.)
- Correspondence: ; Tel.: +39-6-7259-6078
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15
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De Serres-Bérard T, Pierre M, Chahine M, Puymirat J. Deciphering the mechanisms underlying brain alterations and cognitive impairment in congenital myotonic dystrophy. Neurobiol Dis 2021; 160:105532. [PMID: 34655747 DOI: 10.1016/j.nbd.2021.105532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/24/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic and heterogeneous disorder caused by the expansion of CTG repeats in the 3' UTR of the myotonic dystrophy protein kinase (DMPK) gene. There is a congenital form (CDM1) of the disease characterized by severe hypotonia, respiratory insufficiency as well as developmental delays and intellectual disabilities. CDM1 infants manifest important brain structure abnormalities present from birth while, in contrast, older patients with adult-onset DM1 often present neurodegenerative features and milder progressive cognitive deficits. Promising therapies targeting central molecular mechanisms contributing to the symptoms of adult-onset DM1 are currently in development, but their relevance for treating cognitive impairment in CDM1, which seems to be a partially distinct neurodevelopmental disorder, remain to be elucidated. Here, we provide an update on the clinical presentation of CDM1 and review recent in vitro and in vivo models that have provided meaningful insights on its consequences in development, with a particular focus on the brain. We discuss how enhanced toxic gain-of-function of the mutated DMPK transcripts with larger CUG repeats and the resulting dysregulation of RNA-binding proteins may affect the developing cortex in utero. Because the methylation of CpG islets flanking the trinucleotide repeats has emerged as a strong biomarker of CDM1, we highlight the need to investigate the tissue-specific impacts of these chromatin modifications in the brain. Finally, we outline promising potential therapeutic treatments for CDM1 and propose future in vitro and in vivo models with great potential to shed light on this disease.
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Affiliation(s)
- Thiéry De Serres-Bérard
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, Canada; CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada
| | - Marion Pierre
- CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada
| | - Mohamed Chahine
- CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada.
| | - Jack Puymirat
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
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16
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Yang B, Borgeaud AC, Buřičová M, Aeschbach L, Rodríguez-Lima O, Ruiz Buendía GA, Cinesi C, Taylor AS, Baubec T, Dion V. Expanded CAG/CTG repeats resist gene silencing mediated by targeted Epigenome editing. Hum Mol Genet 2021; 31:386-398. [PMID: 34494094 PMCID: PMC8825355 DOI: 10.1093/hmg/ddab255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 05/08/2021] [Accepted: 08/25/2021] [Indexed: 11/14/2022] Open
Abstract
Expanded CAG/CTG repeat disorders affect over 1 in 2500 individuals worldwide. Potential therapeutic avenues include gene silencing and modulation of repeat instability. However, there are major mechanistic gaps in our understanding of these processes, which prevent the rational design of an efficient treatment. To address this, we developed a novel system, ParB/ANCHOR-mediated Inducible Targeting (PInT), in which any protein can be recruited at will to a GFP reporter containing an expanded CAG/CTG repeat. Previous studies have implicated the histone deacetylase HDAC5 and the DNA methyltransferase DNMT1 as modulators of repeat instability via mechanisms that are not fully understood. Using PInT, we found no evidence that HDAC5 or DNMT1 modulate repeat instability upon targeting to the expanded repeat, suggesting that their effect is independent of local chromatin structure. Unexpectedly, we found that expanded CAG/CTG repeats reduce the effectiveness of gene silencing mediated by targeting HDAC5 and DNMT1. The repeat-length effect in gene silencing by HDAC5 was abolished by a small molecule inhibitor of HDAC3. Our results have important implications on the design of epigenome editing approaches for expanded CAG/CTG repeat disorders. PInT is a versatile synthetic system to study the effect of any sequence of interest on epigenome editing.
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Affiliation(s)
- Bin Yang
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Alicia C Borgeaud
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland.,UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ, Cardiff, United Kingdom
| | - Marcela Buřičová
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ, Cardiff, United Kingdom
| | - Lorène Aeschbach
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Oscar Rodríguez-Lima
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Gustavo A Ruiz Buendía
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Cinzia Cinesi
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Alysha S Taylor
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ, Cardiff, United Kingdom
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ, Cardiff, United Kingdom
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17
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Morales F, Corrales E, Zhang B, Vásquez M, Santamaría-Ulloa C, Quesada H, Sirito M, Estecio MR, Monckton DG, Krahe R. Myotonic dystrophy type 1 (DM1) clinical sub-types and CTCF site methylation status flanking the CTG expansion are mutant allele length-dependent. Hum Mol Genet 2021; 31:262-274. [PMID: 34432028 DOI: 10.1093/hmg/ddab243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a complex disease with a wide spectrum of symptoms. The exact relationship between mutant CTG repeat expansion size and clinical outcome remains unclear. DM1 congenital patients (CDM) inherit the largest expanded alleles, which are associated with abnormal and increased DNA methylation flanking the CTG repeat. However, DNA methylation at the DMPK locus remains understudied. Its relationship to DM1 clinical subtypes, expansion size and age-at-onset is not yet completely understood. Using pyrosequencing-based methylation analysis on 225 blood DNA samples from Costa Rican DM1 patients, we determined that the size of the estimated progenitor allele length (ePAL) is not only a good discriminator between CDM and non-CDM cases (with an estimated threshold at 653 CTG repeats), but also for all DM1 clinical subtypes. Secondly, increased methylation at both CTCF sites upstream and downstream of the expansion was almost exclusively present in CDM cases. Thirdly, levels of abnormal methylation were associated with clinical subtype, age and ePAL, with strong correlations between these variables. Fourthly, both ePAL and the intergenerational expansion size were significantly associated with methylation status. Finally, methylation status was associated with ePAL and maternal inheritance, with almost exclusively maternal transmission of CDM. In conclusion, increased DNA methylation at the CTCF sites flanking the DM1 expansion could be linked to ePAL, and both increased methylation and the ePAL could be considered biomarkers for the CDM phenotype.
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Affiliation(s)
- Fernando Morales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Eyleen Corrales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Baili Zhang
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Melissa Vásquez
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Carolina Santamaría-Ulloa
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Hazel Quesada
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Mario Sirito
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Marcos R Estecio
- Department of Epigenetics & Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Ralf Krahe
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
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18
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Breton É, Légaré C, Overend G, Guay SP, Monckton D, Mathieu J, Gagnon C, Richer L, Gallais B, Bouchard L. DNA methylation at the DMPK gene locus is associated with cognitive functions in myotonic dystrophy type 1. Epigenomics 2020; 12:2051-2064. [PMID: 33301350 DOI: 10.2217/epi-2020-0328] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: Myotonic dystrophy type 1 (DM1) is caused by an unstable trinucleotide (CTG) expansion at the DMPK gene locus. Cognitive dysfunctions are often observed in the condition. We investigated the association between DMPK blood DNA methylation (DNAm) and cognitive functions in DM1, considering expansion length and variant repeats (VRs). Method: Data were obtained from 115 adult-onset DM1 patients. Molecular analyses consisted of pyrosequencing, small pool PCR and Southern blot hybridization. Cognitive functions were assessed by validated neuropsychological tests. Results: For patients without VRs (n = 103), blood DNAm at baseline independently contributed to predict cognitive functions 9 years later. Patients with VRs (n = 12) had different DNAm and cognitive profiles. Conclusion: DNAm allows to better understand DM1-related cognitive dysfunction etiology.
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Affiliation(s)
- Édith Breton
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.,Groupe de recherche interdisciplinaire sur les maladies neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital de Jonquière, Saguenay, Québec G7X 7X2, Canada
| | - Cécilia Légaré
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.,Groupe de recherche interdisciplinaire sur les maladies neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital de Jonquière, Saguenay, Québec G7X 7X2, Canada
| | - Gayle Overend
- Institute of Molecular, Cell & Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Simon-Pierre Guay
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.,Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Darren Monckton
- Institute of Molecular, Cell & Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Jean Mathieu
- Groupe de recherche interdisciplinaire sur les maladies neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital de Jonquière, Saguenay, Québec G7X 7X2, Canada.,Centre de recherche Charles-Le-Moyne-Saguenay-Lac-Saint-Jean sur les innovations en santé (CR-CSIS), Université de Sherbrooke, Saguenay, Québec G7H 5H6, Canada
| | - Cynthia Gagnon
- Groupe de recherche interdisciplinaire sur les maladies neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital de Jonquière, Saguenay, Québec G7X 7X2, Canada.,Centre de recherche Charles-Le-Moyne-Saguenay-Lac-Saint-Jean sur les innovations en santé (CR-CSIS), Université de Sherbrooke, Saguenay, Québec G7H 5H6, Canada
| | - Louis Richer
- Groupe de recherche interdisciplinaire sur les maladies neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital de Jonquière, Saguenay, Québec G7X 7X2, Canada.,Department of Health Sciences, Université du Québec à Chicoutimi (UQAC), Saguenay, Québec G7H 2B1, Canada
| | - Benjamin Gallais
- Groupe de recherche interdisciplinaire sur les maladies neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital de Jonquière, Saguenay, Québec G7X 7X2, Canada.,Centre de recherche Charles-Le-Moyne-Saguenay-Lac-Saint-Jean sur les innovations en santé (CR-CSIS), Université de Sherbrooke, Saguenay, Québec G7H 5H6, Canada.,ÉCOBES - Recherche et transfert, Cégep de Jonquière, Saguenay, Québec G7X 7W2, Canada
| | - Luigi Bouchard
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.,Groupe de recherche interdisciplinaire sur les maladies neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital de Jonquière, Saguenay, Québec G7X 7X2, Canada.,Department of Medical Biology, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital de Chicoutimi, Saguenay, Québec G7H 5H6, Canada
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19
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Franck S, Barbé L, Ardui S, De Vlaeminck Y, Allemeersch J, Dziedzicka D, Spits C, Vanroye F, Hilven P, Duqué G, Vermeesch JR, Gheldof A, Sermon K. MSH2 knock-down shows CTG repeat stability and concomitant upstream demethylation at the DMPK locus in myotonic dystrophy type 1 human embryonic stem cells. Hum Mol Genet 2020; 29:3566-3577. [PMID: 33242073 DOI: 10.1093/hmg/ddaa250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is caused by expansion of a CTG repeat in the DMPK gene, where expansion size and somatic mosaicism correlates with disease severity and age of onset. While it is known that the mismatch repair protein MSH2 contributes to the unstable nature of the repeat, its role on other disease-related features, such as CpG methylation upstream of the repeat, is unknown. In this study, we investigated the effect of an MSH2 knock-down (MSH2KD) on both CTG repeat dynamics and CpG methylation pattern in human embryonic stem cells (hESC) carrying the DM1 mutation. Repeat size in MSH2 wild-type (MSH2WT) and MSH2KD DM1 hESC was determined by PacBio sequencing and CpG methylation by bisulfite massive parallel sequencing. We found stabilization of the CTG repeat concurrent with a gradual loss of methylation upstream of the repeat in MSH2KD cells, while the repeat continued to expand and upstream methylation remained unchanged in MSH2WT control lines. Repeat instability was re-established and biased towards expansions upon MSH2 transgenic re-expression in MSH2KD lines while upstream methylation was not consistently re-established. We hypothesize that the hypermethylation at the mutant DM1 locus is promoted by the MMR machinery and sustained by a constant DNA repair response, establishing a potential mechanistic link between CTG repeat instability and upstream CpG methylation. Our work represents a first step towards understanding how epigenetic alterations and repair pathways connect and contribute to the DM1 pathology.
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Affiliation(s)
- Silvie Franck
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Lise Barbé
- Center for systems and Therapeutics, Gladstone Institutes, Finkbeiner lab, San Francisco, CA 94158, USA
| | - Simon Ardui
- Center of Human Genetics, University Hospital Leuven, KU Leuven, Laboratory for Cytogenetics and Genome Research, Leuven 3000, Belgium
| | - Yannick De Vlaeminck
- Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | | | - Dominika Dziedzicka
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Claudia Spits
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Fien Vanroye
- Laboratory HIV/STD, Institute of Tropical Medicine Antwerp, Antwerp 2000, Belgium
| | - Pierre Hilven
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Geoffrey Duqué
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Joris R Vermeesch
- Center of Human Genetics, University Hospital Leuven, KU Leuven, Laboratory for Cytogenetics and Genome Research, Leuven 3000, Belgium
| | - Alexander Gheldof
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium.,Center of Medical Genetics, UZ Brussel, Brussels 1090, Belgium
| | - Karen Sermon
- Department Reproduction and Genetics, Vrije Universiteit Brussel, Brussels 1090, Belgium
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20
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Abstract
Neuromuscular disorders are a heterogeneous group of conditions affecting the neuromuscular system. The aim of this article is to review the major epigenetic findings in motor neuron diseases and major hereditary muscular dystrophies. DNA methylation changes are observed in both hereditary and sporadic forms, and combining DNA methylation analysis with mutational screening holds the potential for better diagnostic and prognostic accuracy. Novel, less toxic and more selective epigenetic drugs are designed and tested in animal and cell culture models of neuromuscular disorders, and non-coding RNAs are being investigated as either disease biomarkers or targets of therapeutic approaches to restore gene expression levels. Overall, neuromuscular disorder epigenetic biomarkers have a strong potential for clinical applications in the near future.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy
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21
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Ruiz Buendía GA, Leleu M, Marzetta F, Vanzan L, Tan JY, Ythier V, Randall EL, Marques AC, Baubec T, Murr R, Xenarios I, Dion V. Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion. SCIENCE ADVANCES 2020; 6:eaaz4012. [PMID: 32656337 PMCID: PMC7334000 DOI: 10.1126/sciadv.aaz4012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation and thereby affect both gene expression and repeat instability. Here, we tested this hypothesis by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD-derived cells. We find that allele sizes ranging from 15 to 1700 repeats displayed similar chromatin interaction profiles. This was true for both loci and for alleles with different DNA methylation levels and CTCF binding. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the conformation of the surrounding chromatin. We conclude that CAG/CTG repeat expansions are not enough to alter chromatin conformation in cis. Therefore, it is unlikely that changes in chromatin interactions drive repeat instability or changes in gene expression in these disorders.
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Affiliation(s)
- Gustavo A. Ruiz Buendía
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Flavia Marzetta
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ludovica Vanzan
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Jennifer Y. Tan
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Victor Ythier
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Emma L. Randall
- UK Dementia Research Institute at Cardiff University at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK
| | - Ana C. Marques
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Rabih Murr
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK
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22
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Recovery in the Myogenic Program of Congenital Myotonic Dystrophy Myoblasts after Excision of the Expanded (CTG) n Repeat. Int J Mol Sci 2019; 20:ijms20225685. [PMID: 31766224 PMCID: PMC6888582 DOI: 10.3390/ijms20225685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022] Open
Abstract
The congenital form of myotonic dystrophy type 1 (cDM) is caused by the large-scale expansion of a (CTG•CAG)n repeat in DMPK and DM1-AS. The production of toxic transcripts with long trinucleotide tracts from these genes results in impairment of the myogenic differentiation capacity as cDM’s most prominent morpho-phenotypic hallmark. In the current in vitro study, we compared the early differentiation programs of isogenic cDM myoblasts with and without a (CTG)2600 repeat obtained by gene editing. We found that excision of the repeat restored the ability of cDM myoblasts to engage in myogenic fusion, preventing the ensuing myotubes from remaining immature. Although the cDM-typical epigenetic status of the DM1 locus and the expression of genes therein were not altered upon removal of the repeat, analyses at the transcriptome and proteome level revealed that early abnormalities in the temporal expression of differentiation regulators, myogenic progression markers, and alternative splicing patterns before and immediately after the onset of differentiation became normalized. Our observation that molecular and cellular features of cDM are reversible in vitro and can be corrected by repeat-directed genome editing in muscle progenitors, when already committed and poised for myogenic differentiation, is important information for the future development of gene therapy for different forms of myotonic dystrophy type 1 (DM1).
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23
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Lanni S, Pearson CE. Molecular genetics of congenital myotonic dystrophy. Neurobiol Dis 2019; 132:104533. [PMID: 31326502 DOI: 10.1016/j.nbd.2019.104533] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/29/2019] [Accepted: 07/11/2019] [Indexed: 12/26/2022] Open
Abstract
Myotonic Dystrophy type 1 (DM1) is a neuromuscular disease showing strong genetic anticipation, and is caused by the expansion of a CTG repeat tract in the 3'-UTR of the DMPK gene. Congenital Myotonic Dystrophy (CDM1) represents the most severe form of the disease, with prenatal onset, symptoms distinct from adult onset DM1, and a high rate of perinatal mortality. CDM1 is usually associated with very large CTG expansions, but this correlation is not absolute and cannot explain the distinct clinical features and the strong bias for maternal transmission. This review focuses upon the molecular and epigenetic factors that modulate disease severity and might be responsible for CDM1. Changes in the epigenetic status of the DM1 locus and in gene expression have recently been observed. Increasing evidence supports a role of a CTCF binding motif as a cis-element, upstream of the DMPK CTG tract, whereby CpG methylation of this site regulates the interaction of the insulator protein CTCF as a modulating trans-factor responsible for the inheritance and expression of CDM1.
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Affiliation(s)
- Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto M5G 0A4, Ontario, Canada
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto M5G 0A4, Ontario, Canada; University of Toronto, Program of Molecular Genetics, Canada.
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24
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Légaré C, Overend G, Guay SP, Monckton DG, Mathieu J, Gagnon C, Bouchard L. DMPK gene DNA methylation levels are associated with muscular and respiratory profiles in DM1. NEUROLOGY-GENETICS 2019; 5:e338. [PMID: 31334355 PMCID: PMC6568328 DOI: 10.1212/nxg.0000000000000338] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/03/2022]
Abstract
Objective To assess the effects of dystrophia myotonica protein kinase (DMPK) DNA methylation (DNAme) epivariation on muscular and respiratory profiles in patients with myotonic dystrophy type 1 (DM1). Methods Phenotypes were assessed with standardized measures. Pyrosequencing of bisulfite-treated DNA was used to quantify DNAme levels in blood from 90 patients with DM1 (adult form). Modal CTG repeat length was assessed using small-pool PCR. The presence of Acil-sensitive variant repeats was also tested. Results DNAme levels upstream of the CTG expansion (exon and intron 11) were correlated with modal CTG repeat length (rs = −0.224, p = 0.040; rs = −0.317, p = 0.003; and rs = −0.241, p = 0.027), whereas correlations were observed with epivariations downstream of the CTG repeats (rs = 0.227; p = 0.037). The presence of a variant repeat was associated with higher DNAme levels at multiple CpG sites (up to 10% higher; p = 0.001). Stepwise multiple linear regression modeling showed that DNAme contributed significantly and independently to explain phenotypic variability in ankle dorsiflexor (3 CpGs: p = 0.001, 0.013, and 0.001), grip (p = 0.089), and pinch (p = 0.028) strengths and in forced vital capacity (2 CpGs: p = 0.002 and 0.021) and maximal inspiratory pressure (p = 0.012). Conclusions In addition to the CTG repeat length, DMPK epivariations independently explain phenotypic variability in DM1 and could thus improve prognostic accuracy for patients.
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Affiliation(s)
- Cécilia Légaré
- Department of Biochemistry (C.L., S.-P.G., L.B.), Université de Sherbrooke, Sherbrooke; ECOGENE-21 Biocluster (C.L., S.-P.G., L.B.), Chicoutimi, Québec, Canada; Groupe de Recherche interdisciplinaire sur les maladies neuromusculaires (C.L., J.M., C.G., L.B.), Saguenay, Canada; Institute of Molecular (G.O., D.G.M.), Cell and Systems Biology, University of Glasgow, United Kingdom; and Centre de Recherche Charles-Le-Moyne-Saguenay-Lac-StJean sur les innovations en santé (J.M., C.G.), Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
| | - Gayle Overend
- Department of Biochemistry (C.L., S.-P.G., L.B.), Université de Sherbrooke, Sherbrooke; ECOGENE-21 Biocluster (C.L., S.-P.G., L.B.), Chicoutimi, Québec, Canada; Groupe de Recherche interdisciplinaire sur les maladies neuromusculaires (C.L., J.M., C.G., L.B.), Saguenay, Canada; Institute of Molecular (G.O., D.G.M.), Cell and Systems Biology, University of Glasgow, United Kingdom; and Centre de Recherche Charles-Le-Moyne-Saguenay-Lac-StJean sur les innovations en santé (J.M., C.G.), Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
| | - Simon-Pierre Guay
- Department of Biochemistry (C.L., S.-P.G., L.B.), Université de Sherbrooke, Sherbrooke; ECOGENE-21 Biocluster (C.L., S.-P.G., L.B.), Chicoutimi, Québec, Canada; Groupe de Recherche interdisciplinaire sur les maladies neuromusculaires (C.L., J.M., C.G., L.B.), Saguenay, Canada; Institute of Molecular (G.O., D.G.M.), Cell and Systems Biology, University of Glasgow, United Kingdom; and Centre de Recherche Charles-Le-Moyne-Saguenay-Lac-StJean sur les innovations en santé (J.M., C.G.), Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
| | - Darren G Monckton
- Department of Biochemistry (C.L., S.-P.G., L.B.), Université de Sherbrooke, Sherbrooke; ECOGENE-21 Biocluster (C.L., S.-P.G., L.B.), Chicoutimi, Québec, Canada; Groupe de Recherche interdisciplinaire sur les maladies neuromusculaires (C.L., J.M., C.G., L.B.), Saguenay, Canada; Institute of Molecular (G.O., D.G.M.), Cell and Systems Biology, University of Glasgow, United Kingdom; and Centre de Recherche Charles-Le-Moyne-Saguenay-Lac-StJean sur les innovations en santé (J.M., C.G.), Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
| | - Jean Mathieu
- Department of Biochemistry (C.L., S.-P.G., L.B.), Université de Sherbrooke, Sherbrooke; ECOGENE-21 Biocluster (C.L., S.-P.G., L.B.), Chicoutimi, Québec, Canada; Groupe de Recherche interdisciplinaire sur les maladies neuromusculaires (C.L., J.M., C.G., L.B.), Saguenay, Canada; Institute of Molecular (G.O., D.G.M.), Cell and Systems Biology, University of Glasgow, United Kingdom; and Centre de Recherche Charles-Le-Moyne-Saguenay-Lac-StJean sur les innovations en santé (J.M., C.G.), Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
| | - Cynthia Gagnon
- Department of Biochemistry (C.L., S.-P.G., L.B.), Université de Sherbrooke, Sherbrooke; ECOGENE-21 Biocluster (C.L., S.-P.G., L.B.), Chicoutimi, Québec, Canada; Groupe de Recherche interdisciplinaire sur les maladies neuromusculaires (C.L., J.M., C.G., L.B.), Saguenay, Canada; Institute of Molecular (G.O., D.G.M.), Cell and Systems Biology, University of Glasgow, United Kingdom; and Centre de Recherche Charles-Le-Moyne-Saguenay-Lac-StJean sur les innovations en santé (J.M., C.G.), Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
| | - Luigi Bouchard
- Department of Biochemistry (C.L., S.-P.G., L.B.), Université de Sherbrooke, Sherbrooke; ECOGENE-21 Biocluster (C.L., S.-P.G., L.B.), Chicoutimi, Québec, Canada; Groupe de Recherche interdisciplinaire sur les maladies neuromusculaires (C.L., J.M., C.G., L.B.), Saguenay, Canada; Institute of Molecular (G.O., D.G.M.), Cell and Systems Biology, University of Glasgow, United Kingdom; and Centre de Recherche Charles-Le-Moyne-Saguenay-Lac-StJean sur les innovations en santé (J.M., C.G.), Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
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25
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Wang Y, Hao L, Wang H, Santostefano K, Thapa A, Cleary J, Li H, Guo X, Terada N, Ashizawa T, Xia G. Therapeutic Genome Editing for Myotonic Dystrophy Type 1 Using CRISPR/Cas9. Mol Ther 2018; 26:2617-2630. [PMID: 30274788 PMCID: PMC6225032 DOI: 10.1016/j.ymthe.2018.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/30/2018] [Accepted: 09/06/2018] [Indexed: 12/18/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is caused by a CTG nucleotide repeat expansion within the 3' UTR of the Dystrophia Myotonica protein kinase gene. In this study, we explored therapeutic genome editing using CRISPR/Cas9 via targeted deletion of expanded CTG repeats and targeted insertion of polyadenylation signals in the 3' UTR upstream of the CTG repeats to eliminate toxic RNA CUG repeats. We found paired SpCas9 or SaCas9 guide RNA induced deletion of expanded CTG repeats. However, this approach incurred frequent inversion in both the mutant and normal alleles. In contrast, the insertion of polyadenylation signals in the 3' UTR upstream of the CTG repeats eliminated toxic RNA CUG repeats, which led to phenotype reversal in differentiated neural stem cells, forebrain neurons, cardiomyocytes, and skeletal muscle myofibers. We concluded that targeted insertion of polyadenylation signals in the 3' UTR is a viable approach to develop therapeutic genome editing for DM1.
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Affiliation(s)
- Yanlin Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Henan 450000, China
| | - Lei Hao
- Department of Neurology, The Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Hongcai Wang
- Department of Neurology, Affiliated Hospital of Binzhou Medical University, Binzhou City, Shandong Province, China; Department of Neurology, University of New Mexico, Albuquerque, NM, USA
| | - Katherine Santostefano
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Arjun Thapa
- Department of Neurology, University of New Mexico, Albuquerque, NM, USA
| | - John Cleary
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Hui Li
- Department of Neurology, University of Wisconsin, Madison, WI, USA
| | - Xiuming Guo
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Naohiro Terada
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Tetsuo Ashizawa
- Houston Methodist Neurological Institute and Research Institute, 6670 Bertner Ave. R11-117, Houston, TX, USA
| | - Guangbin Xia
- Department of Neurology, University of New Mexico, Albuquerque, NM, USA; Department of Neuroscience, University of New Mexico, Albuquerque, NM, USA.
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26
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Nakamori M, Hamanaka K, Thomas JD, Wang ET, Hayashi YK, Takahashi MP, Swanson MS, Nishino I, Mochizuki H. Aberrant Myokine Signaling in Congenital Myotonic Dystrophy. Cell Rep 2017; 21:1240-1252. [PMID: 29091763 PMCID: PMC5689469 DOI: 10.1016/j.celrep.2017.10.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/02/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023] Open
Abstract
Myotonic dystrophy types 1 (DM1) and 2 (DM2) are dominantly inherited neuromuscular disorders caused by a toxic gain of function of expanded CUG and CCUG repeats, respectively. Although both disorders are clinically similar, congenital myotonic dystrophy (CDM), a severe DM form, is found only in DM1. CDM is also characterized by muscle fiber immaturity not observed in adult DM, suggesting specific pathological mechanisms. Here, we revealed upregulation of the interleukin-6 (IL-6) myokine signaling pathway in CDM muscles. We also found a correlation between muscle immaturity and not only IL-6 expression but also expanded CTG repeat length and CpG methylation status upstream of the repeats. Aberrant CpG methylation was associated with transcriptional dysregulation at the repeat locus, increasing the toxic RNA burden that upregulates IL-6. Because the IL-6 pathway is involved in myocyte maturation and muscle atrophy, our results indicate that enhanced RNA toxicity contributes to severe CDM phenotypes through aberrant IL-6 signaling.
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Affiliation(s)
- Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan.
| | - Kohei Hamanaka
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - James D Thomas
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Yukiko K Hayashi
- Department of Pathophysiology, Tokyo Medical University, Shinjuku, Tokyo 160-0022, Japan
| | - Masanori P Takahashi
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Department of Functional Diagnostic Science, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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27
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Provenzano C, Cappella M, Valaperta R, Cardani R, Meola G, Martelli F, Cardinali B, Falcone G. CRISPR/Cas9-Mediated Deletion of CTG Expansions Recovers Normal Phenotype in Myogenic Cells Derived from Myotonic Dystrophy 1 Patients. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 9:337-348. [PMID: 29246312 PMCID: PMC5684470 DOI: 10.1016/j.omtn.2017.10.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/11/2017] [Accepted: 10/11/2017] [Indexed: 02/05/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is the most common adult-onset muscular dystrophy, characterized by progressive myopathy, myotonia, and multi-organ involvement. This dystrophy is an inherited autosomal dominant disease caused by a (CTG)n expansion within the 3′ untranslated region of the DMPK gene. Expression of the mutated gene results in production of toxic transcripts that aggregate as nuclear foci and sequester RNA-binding proteins, resulting in mis-splicing of several transcripts, defective translation, and microRNA dysregulation. No effective therapy is yet available for treatment of the disease. In this study, myogenic cell models were generated from myotonic dystrophy patient-derived fibroblasts. These cells exhibit typical disease-associated ribonuclear aggregates, containing CUG repeats and muscleblind-like 1 protein, and alternative splicing alterations. We exploited these cell models to develop new gene therapy strategies aimed at eliminating the toxic mutant repeats. Using the CRISPR/Cas9 gene-editing system, the repeat expansions were removed, therefore preventing nuclear foci formation and splicing alterations. Compared with the previously reported strategies of inhibition/degradation of CUG expanded transcripts by various techniques, the advantage of this approach is that affected cells can be permanently reverted to a normal phenotype.
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Affiliation(s)
- Claudia Provenzano
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, Rome, Italy
| | - Marisa Cappella
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, Rome, Italy; DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Rea Valaperta
- Molecular Biology Laboratory, Policlinico San Donato-IRCCS, San Donato Milanese, Milan, Italy
| | - Rosanna Cardani
- Muscle Histopathology and Molecular Biology Laboratory, Policlinico San Donato-IRCCS, San Donato Milanese, Milan, Italy
| | - Giovanni Meola
- Department of Neurology, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy; Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Fabio Martelli
- Molecular Cardiology Laboratory, Policlinico San Donato-IRCCS, San Donato Milanese, Milan, Italy
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, Rome, Italy.
| | - Germana Falcone
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, Rome, Italy.
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28
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Gudde AEEG, van Heeringen SJ, de Oude AI, van Kessel IDG, Estabrook J, Wang ET, Wieringa B, Wansink DG. Antisense transcription of the myotonic dystrophy locus yields low-abundant RNAs with and without (CAG)n repeat. RNA Biol 2017; 14:1374-1388. [PMID: 28102759 PMCID: PMC5711456 DOI: 10.1080/15476286.2017.1279787] [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: 11/10/2016] [Revised: 12/21/2016] [Accepted: 12/30/2016] [Indexed: 12/20/2022] Open
Abstract
The unstable (CTG·CAG)n trinucleotide repeat in the myotonic dystrophy type 1 (DM1) locus is bidirectionally transcribed from genes with terminal overlap. By transcription in the sense direction, the DMPK gene produces various alternatively spliced mRNAs with a (CUG)n repeat in their 3' UTR. Expression in opposite orientation reportedly yields (CAG)n-repeat containing RNA, but both structure and biologic significance of this antisense gene (DM1-AS) are largely unknown. Via a combinatorial approach of computational and experimental analyses of RNA from unaffected individuals and DM1 patients we discovered that DM1-AS spans >6 kb, contains alternative transcription start sites and uses alternative polyadenylation sites up- and downstream of the (CAG)n repeat. Moreover, its primary transcripts undergo alternative splicing, whereby the (CAG)n segment is removed as part of an intron. Thus, in patients a mixture of DM1-AS RNAs with and without expanded (CAG)n repeat are produced. DM1-AS expression appears upregulated in patients, but transcript abundance remains very low in all tissues analyzed. Our data suggest that DM1-AS transcripts belong to the class of long non-coding RNAs. These and other biologically relevant implications for how (CAG)n-expanded transcripts may contribute to DM1 pathology can now be explored experimentally.
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Affiliation(s)
- Anke E. E. G. Gudde
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Simon J. van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Amanda I. de Oude
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | | | - Joseph Estabrook
- Department of Molecular Genetics and Microbiology, Center for Neurogenetics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for Neurogenetics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Bé Wieringa
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G. Wansink
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
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29
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Rohilla KJ, Gagnon KT. RNA biology of disease-associated microsatellite repeat expansions. Acta Neuropathol Commun 2017; 5:63. [PMID: 28851463 PMCID: PMC5574247 DOI: 10.1186/s40478-017-0468-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.
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30
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Barbé L, Lanni S, López-Castel A, Franck S, Spits C, Keymolen K, Seneca S, Tomé S, Miron I, Letourneau J, Liang M, Choufani S, Weksberg R, Wilson MD, Sedlacek Z, Gagnon C, Musova Z, Chitayat D, Shannon P, Mathieu J, Sermon K, Pearson CE. CpG Methylation, a Parent-of-Origin Effect for Maternal-Biased Transmission of Congenital Myotonic Dystrophy. Am J Hum Genet 2017; 100:488-505. [PMID: 28257691 PMCID: PMC5339342 DOI: 10.1016/j.ajhg.2017.01.033] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/26/2017] [Indexed: 12/13/2022] Open
Abstract
CTG repeat expansions in DMPK cause myotonic dystrophy (DM1) with a continuum of severity and ages of onset. Congenital DM1 (CDM1), the most severe form, presents distinct clinical features, large expansions, and almost exclusive maternal transmission. The correlation between CDM1 and expansion size is not absolute, suggesting contributions of other factors. We determined CpG methylation flanking the CTG repeat in 79 blood samples from 20 CDM1-affected individuals; 21, 27, and 11 individuals with DM1 but not CDM1 (henceforth non-CDM1) with maternal, paternal, and unknown inheritance; and collections of maternally and paternally derived chorionic villus samples (7 CVSs) and human embryonic stem cells (4 hESCs). All but two CDM1-affected individuals showed high levels of methylation upstream and downstream of the repeat, greater than non-CDM1 individuals (p = 7.04958 × 10−12). Most non-CDM1 individuals were devoid of methylation, where one in six showed downstream methylation. Only two non-CDM1 individuals showed upstream methylation, and these were maternally derived childhood onset, suggesting a continuum of methylation with age of onset. Only maternally derived hESCs and CVSs showed upstream methylation. In contrast, paternally derived samples (27 blood samples, 3 CVSs, and 2 hESCs) never showed upstream methylation. CTG tract length did not strictly correlate with CDM1 or methylation. Thus, methylation patterns flanking the CTG repeat are stronger indicators of CDM1 than repeat size. Spermatogonia with upstream methylation may not survive due to methylation-induced reduced expression of the adjacent SIX5, thereby protecting DM1-affected fathers from having CDM1-affected children. Thus, DMPK methylation may account for the maternal bias for CDM1 transmission, larger maternal CTG expansions, age of onset, and clinical continuum, and may serve as a diagnostic indicator.
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31
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Ueki J, Nakamori M, Nakamura M, Nishikawa M, Yoshida Y, Tanaka A, Morizane A, Kamon M, Araki T, Takahashi MP, Watanabe A, Inagaki N, Sakurai H. Myotonic dystrophy type 1 patient-derived iPSCs for the investigation of CTG repeat instability. Sci Rep 2017; 7:42522. [PMID: 28211918 PMCID: PMC5304155 DOI: 10.1038/srep42522] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/09/2017] [Indexed: 02/08/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is an autosomal-dominant multi-system disease caused by expanded CTG repeats in dystrophia myotonica protein kinase (DMPK). The expanded CTG repeats are unstable and can increase the length of the gene with age, which worsens the symptoms. In order to establish a human stem cell system suitable for the investigation of repeat instability, DM1 patient-derived iPSCs were generated and differentiated into three cell types commonly affected in DM1, namely cardiomyocytes, neurons and myocytes. Then we precisely analysed the CTG repeat lengths in these cells. Our DM1-iPSCs showed a gradual lengthening of CTG repeats with unchanged repeat distribution in all cell lines depending on the passage numbers of undifferentiated cells. However, the average CTG repeat length did not change significantly after differentiation into different somatic cell types. We also evaluated the chromatin accessibility in DM1-iPSCs using ATAC-seq. The chromatin status in DM1 cardiomyocytes was closed at the DMPK locus as well as at SIX5 and its promoter region, whereas it was open in control, suggesting that the epigenetic modifications may be related to the CTG repeat expansion in DM1. These findings may help clarify the role of repeat instability in the CTG repeat expansion in DM1.
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Affiliation(s)
- Junko Ueki
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.,Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Nakamura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Misato Nishikawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Azusa Tanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Asuka Morizane
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masayoshi Kamon
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Masanori P Takahashi
- Department of Neurology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Functional Diagnostic Science, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akira Watanabe
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hidetoshi Sakurai
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
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32
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van Agtmaal EL, André LM, Willemse M, Cumming SA, van Kessel IDG, van den Broek WJAA, Gourdon G, Furling D, Mouly V, Monckton DG, Wansink DG, Wieringa B. CRISPR/Cas9-Induced (CTG⋅CAG) n Repeat Instability in the Myotonic Dystrophy Type 1 Locus: Implications for Therapeutic Genome Editing. Mol Ther 2017; 25:24-43. [PMID: 28129118 PMCID: PMC5363205 DOI: 10.1016/j.ymthe.2016.10.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 12/15/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is caused by (CTG⋅CAG)n-repeat expansion within the DMPK gene and thought to be mediated by a toxic RNA gain of function. Current attempts to develop therapy for this disease mainly aim at destroying or blocking abnormal properties of mutant DMPK (CUG)n RNA. Here, we explored a DNA-directed strategy and demonstrate that single clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-cleavage in either its 5' or 3' unique flank promotes uncontrollable deletion of large segments from the expanded trinucleotide repeat, rather than formation of short indels usually seen after double-strand break repair. Complete and precise excision of the repeat tract from normal and large expanded DMPK alleles in myoblasts from unaffected individuals, DM1 patients, and a DM1 mouse model could be achieved at high frequency by dual CRISPR/Cas9-cleavage at either side of the (CTG⋅CAG)n sequence. Importantly, removal of the repeat appeared to have no detrimental effects on the expression of genes in the DM1 locus. Moreover, myogenic capacity, nucleocytoplasmic distribution, and abnormal RNP-binding behavior of transcripts from the edited DMPK gene were normalized. Dual sgRNA-guided excision of the (CTG⋅CAG)n tract by CRISPR/Cas9 technology is applicable for developing isogenic cell lines for research and may provide new therapeutic opportunities for patients with DM1.
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Affiliation(s)
- Ellen L van Agtmaal
- Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Laurène M André
- Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Marieke Willemse
- Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Sarah A Cumming
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Ingeborg D G van Kessel
- Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Walther J A A van den Broek
- Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
| | - Geneviève Gourdon
- Inserm UMR 1163, 75015 Paris, France; Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, 75270 Paris, France
| | - Denis Furling
- UPMC Université Paris 06, Inserm UMRS974, CNRS FRE3617, Center for Research in Myology, Sorbonne Universités, 75252 Paris, France
| | - Vincent Mouly
- UPMC Université Paris 06, Inserm UMRS974, CNRS FRE3617, Center for Research in Myology, Sorbonne Universités, 75252 Paris, France
| | - Darren G Monckton
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Derick G Wansink
- Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands.
| | - Bé Wieringa
- Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands.
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33
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Gudde AEEG, González-Barriga A, van den Broek WJAA, Wieringa B, Wansink DG. A low absolute number of expanded transcripts is involved in myotonic dystrophy type 1 manifestation in muscle. Hum Mol Genet 2016; 25:1648-62. [PMID: 26908607 PMCID: PMC4805313 DOI: 10.1093/hmg/ddw042] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/09/2016] [Indexed: 12/15/2022] Open
Abstract
Muscular manifestation of myotonic dystrophy type 1 (DM1), a common inheritable degenerative multisystem disorder, is mainly caused by expression of RNA from a (CTG·CAG)n-expanded DM1 locus. Here, we report on comparative profiling of expression of normal and expanded endogenous or transgenic transcripts in skeletal muscle cells and biopsies from DM1 mouse models and patients in order to help us in understanding the role of this RNA-mediated toxicity. In tissue of HSALR mice, the most intensely used ‘muscle-only’ model in the DM1 field, RNA from the α-actin (CTG)250 transgene was at least 1000-fold more abundant than that from the Dmpk gene, or the DMPK gene in humans. Conversely, the DMPK transgene in another line, DM500/DMSXL mice, was expressed ∼10-fold lower than the endogenous gene. Temporal regulation of expanded RNA expression differed between models. Onset of expression occurred remarkably late in HSALR myoblasts during in vitro myogenesis whereas Dmpk or DMPK (trans)genes were expressed throughout proliferation and differentiation phases. Importantly, quantification of absolute transcript numbers revealed that normal and expanded Dmpk/DMPK transcripts in mouse models and DM1 patients are low-abundance RNA species. Northern blotting, reverse transcriptase–quantitative polymerase chain reaction, RNA-sequencing and fluorescent in situ hybridization analyses showed that they occur at an absolute number between one and a few dozen molecules per cell. Our findings refine the current RNA dominance theory for DM1 pathophysiology, as anomalous factor binding to expanded transcripts and formation of soluble or insoluble ribonucleoprotein aggregates must be nucleated by only few expanded DMPK transcripts and therefore be a small numbers game.
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Affiliation(s)
- Anke E E G Gudde
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Anchel González-Barriga
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Walther J A A van den Broek
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Bé Wieringa
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
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34
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Buckley L, Lacey M, Ehrlich M. Epigenetics of the myotonic dystrophy-associated DMPK gene neighborhood. Epigenomics 2016; 8:13-31. [PMID: 26756355 PMCID: PMC4863877 DOI: 10.2217/epi.15.104] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: Identify epigenetic marks in the vicinity of DMPK (linked to myotonic dystrophy, DM1) that help explain tissue-specific differences in its expression. Materials & methods: At DMPK and its flanking genes (DMWD, SIX5, BHMG1 and RSPH6A), we analyzed many epigenetic and transcription profiles from myoblasts, myotubes, skeletal muscle, heart and 30 nonmuscle samples. Results: In the DMPK gene neighborhood, muscle-associated DNA hypermethylation and hypomethylation, enhancer chromatin, and CTCF binding were seen. Myogenic DMPK hypermethylation correlated with high expression and decreased alternative promoter usage. Testis/sperm hypomethylation of BHMG1 and RSPH6A was associated with testis-specific expression. G-quadruplex (G4) motifs and sperm-specific hypomethylation were found near the DM1-linked CTG repeats within DMPK. Conclusion: Tissue-specific epigenetic features in DMPK and neighboring genes help regulate its expression. G4 motifs in DMPK DNA and RNA might contribute to DM1 pathology.
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Affiliation(s)
- Lauren Buckley
- Human Genetics Program, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lacey
- Tulane Cancer Center & Department of Mathematics, Tulane University, New Orleans, LA 70112, USA
| | - Melanie Ehrlich
- Human Genetics Program, Center for Bioinformatics & Genomics, Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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Santoro M, Fontana L, Masciullo M, Bianchi MLE, Rossi S, Leoncini E, Novelli G, Botta A, Silvestri G. Expansion size and presence of CCG/CTC/CGG sequence interruptions in the expanded CTG array are independently associated to hypermethylation at the DMPK locus in myotonic dystrophy type 1 (DM1). Biochim Biophys Acta Mol Basis Dis 2015; 1852:2645-52. [PMID: 26391753 DOI: 10.1016/j.bbadis.2015.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Massimo Santoro
- Fondazione Don Carlo Gnocchi, Via Capecelatro 66, 20148 Milan, Italy.
| | - Luana Fontana
- Department of Biomedicine and Prevention, University of Tor Vergata, Via Montpellier 1, 00133 Rome, Italy.
| | | | - Maria Laura Ester Bianchi
- Department of Geriatrics, Neuroscience and Orthopedics, Institute of Neurology, UCSC, Largo F. Vito 1, 00168 Rome Italy.
| | - Salvatore Rossi
- Department of Geriatrics, Neuroscience and Orthopedics, Institute of Neurology, UCSC, Largo F. Vito 1, 00168 Rome Italy.
| | - Emanuele Leoncini
- Institute of Public Health, Section of Hygiene, UCSC, Largo F. Vito 1, 00168 Rome, Italy.
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Tor Vergata, Via Montpellier 1, 00133 Rome, Italy.
| | - Annalisa Botta
- Department of Biomedicine and Prevention, University of Tor Vergata, Via Montpellier 1, 00133 Rome, Italy.
| | - Gabriella Silvestri
- Department of Geriatrics, Neuroscience and Orthopedics, Institute of Neurology, UCSC, Largo F. Vito 1, 00168 Rome Italy.
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36
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Michel L, Huguet-Lachon A, Gourdon G. Sense and Antisense DMPK RNA Foci Accumulate in DM1 Tissues during Development. PLoS One 2015; 10:e0137620. [PMID: 26339785 PMCID: PMC4560382 DOI: 10.1371/journal.pone.0137620] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 08/20/2015] [Indexed: 01/22/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is caused by an unstable expanded CTG repeat located within the DMPK gene 3’UTR. The nature, severity and age at onset of DM1 symptoms are very variable in patients. Different forms of the disease are described, among which the congenital form (CDM) is the most severe. Molecular mechanisms of DM1 are well characterized for the adult form and involve accumulation of mutant DMPK RNA forming foci in the nucleus. These RNA foci sequester proteins from the MBNL family and deregulate CELF proteins. These proteins are involved in many cellular mechanisms such as alternative splicing, transcriptional, translational and post-translational regulation miRNA regulation as well as mRNA polyadenylation and localization. All these mechanisms can be impaired in DM1 because of the deregulation of CELF and MBNL functions. The mechanisms involved in CDM are not clearly described. In order to get insight into the mechanisms underlying CDM, we investigated if expanded RNA nuclear foci, one of the molecular hallmarks of DM1, could be detected in human DM1 fetal tissues, as well as in embryonic and neonatal tissues from transgenic mice carrying the human DMPK gene with an expanded CTG repeat. We observed very abundant RNA foci formed by sense DMPK RNA and, to a lesser extent, antisense DMPK RNA foci. Sense DMPK RNA foci clearly co-localized with MBNL1 and MBNL2 proteins. In addition, we studied DMPK sense and antisense expression during development in the transgenic mice. We found that DMPK sense and antisense transcripts are expressed from embryonic and fetal stages in heart, muscle and brain and are regulated during development. These results suggest that mechanisms underlying DM1 and CDM involved common players including toxic expanded RNA forming numerous nuclear foci at early stages during development.
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MESH Headings
- Alternative Splicing
- Animals
- Animals, Newborn
- Brain/metabolism
- Brain/pathology
- CCAAT-Enhancer-Binding Protein-delta/genetics
- CCAAT-Enhancer-Binding Protein-delta/metabolism
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Disease Models, Animal
- Embryo, Mammalian
- Gene Expression Regulation, Developmental
- Humans
- Mice
- Mice, Transgenic
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Myocardium/metabolism
- Myocardium/pathology
- Myotonic Dystrophy/genetics
- Myotonic Dystrophy/metabolism
- Myotonic Dystrophy/pathology
- Myotonin-Protein Kinase/genetics
- Myotonin-Protein Kinase/metabolism
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Signal Transduction
- Trinucleotide Repeat Expansion
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Affiliation(s)
- Lise Michel
- Inserm UMR 1163, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Aline Huguet-Lachon
- Inserm UMR 1163, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Geneviève Gourdon
- Inserm UMR 1163, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- * E-mail:
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37
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Yanovsky-Dagan S, Avitzour M, Altarescu G, Renbaum P, Eldar-Geva T, Schonberger O, Mitrani-Rosenbaum S, Levy-Lahad E, Birnbaum RY, Gepstein L, Epsztejn-Litman S, Eiges R. Uncovering the Role of Hypermethylation by CTG Expansion in Myotonic Dystrophy Type 1 Using Mutant Human Embryonic Stem Cells. Stem Cell Reports 2015; 5:221-31. [PMID: 26190529 PMCID: PMC4618658 DOI: 10.1016/j.stemcr.2015.06.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 12/28/2022] Open
Abstract
CTG repeat expansion in DMPK, the cause of myotonic dystrophy type 1 (DM1), frequently results in hypermethylation and reduced SIX5 expression. The contribution of hypermethylation to disease pathogenesis and the precise mechanism by which SIX5 expression is reduced are unknown. Using 14 different DM1-affected human embryonic stem cell (hESC) lines, we characterized a differentially methylated region (DMR) near the CTGs. This DMR undergoes hypermethylation as a function of expansion size in a way that is specific to undifferentiated cells and is associated with reduced SIX5 expression. Using functional assays, we provide evidence for regulatory activity of the DMR, which is lost by hypermethylation and may contribute to DM1 pathogenesis by causing SIX5 haplo-insufficiency. This study highlights the power of hESCs in disease modeling and describes a DMR that functions both as an exon coding sequence and as a regulatory element whose activity is epigenetically hampered by a heritable mutation. We identify a disease-associated, differentially methylated region in DM1 hESCs CTG expansion size correlates with the degree of methylation specifically in DM1 hESCs DMPK hypermethylation hampers the activity of a regulatory element for SIX5 DM1 hESCs provide an opportunity to study diseased cardiomyocytes in vitro
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Affiliation(s)
- Shira Yanovsky-Dagan
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel
| | - Michal Avitzour
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel
| | - Gheona Altarescu
- Zohar PGD Lab, Medical Genetics Institute, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel
| | - Paul Renbaum
- Zohar PGD Lab, Medical Genetics Institute, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel
| | - Talia Eldar-Geva
- IVF Unit, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel
| | - Oshrat Schonberger
- IVF Unit, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel
| | - Stella Mitrani-Rosenbaum
- Goldyne Savad Institute for Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem 91240, Israel
| | - Ephrat Levy-Lahad
- Zohar PGD Lab, Medical Genetics Institute, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel
| | - Ramon Y Birnbaum
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Lior Gepstein
- Sohnis Family Research Laboratory for Cardiac Electrophysiology and Regenerative Medicine, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Silvina Epsztejn-Litman
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel.
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38
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Mateos-Aierdi AJ, Goicoechea M, Aiastui A, Fernández-Torrón R, Garcia-Puga M, Matheu A, López de Munain A. Muscle wasting in myotonic dystrophies: a model of premature aging. Front Aging Neurosci 2015. [PMID: 26217220 PMCID: PMC4496580 DOI: 10.3389/fnagi.2015.00125] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1 or Steinert’s disease) and type 2 (DM2) are multisystem disorders of genetic origin. Progressive muscular weakness, atrophy and myotonia are the most prominent neuromuscular features of these diseases, while other clinical manifestations such as cardiomyopathy, insulin resistance and cataracts are also common. From a clinical perspective, most DM symptoms are interpreted as a result of an accelerated aging (cataracts, muscular weakness and atrophy, cognitive decline, metabolic dysfunction, etc.), including an increased risk of developing tumors. From this point of view, DM1 could be described as a progeroid syndrome since a notable age-dependent dysfunction of all systems occurs. The underlying molecular disorder in DM1 consists of the existence of a pathological (CTG) triplet expansion in the 3′ untranslated region (UTR) of the Dystrophia Myotonica Protein Kinase (DMPK) gene, whereas (CCTG)n repeats in the first intron of the Cellular Nucleic acid Binding Protein/Zinc Finger Protein 9(CNBP/ZNF9) gene cause DM2. The expansions are transcribed into (CUG)n and (CCUG)n-containing RNA, respectively, which form secondary structures and sequester RNA-binding proteins, such as the splicing factor muscleblind-like protein (MBNL), forming nuclear aggregates known as foci. Other splicing factors, such as CUGBP, are also disrupted, leading to a spliceopathy of a large number of downstream genes linked to the clinical features of these diseases. Skeletal muscle regeneration relies on muscle progenitor cells, known as satellite cells, which are activated after muscle damage, and which proliferate and differentiate to muscle cells, thus regenerating the damaged tissue. Satellite cell dysfunction seems to be a common feature of both age-dependent muscle degeneration (sarcopenia) and muscle wasting in DM and other muscle degenerative diseases. This review aims to describe the cellular, molecular and macrostructural processes involved in the muscular degeneration seen in DM patients, highlighting the similarities found with muscle aging.
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Affiliation(s)
- Alba Judith Mateos-Aierdi
- Neuroscience Area, Biodonostia Health Research Institute San Sebastián, Spain ; CIBERNED, Instituto Carlos III, Ministerio de Economía y Competitividad Madrid, Spain
| | - Maria Goicoechea
- Neuroscience Area, Biodonostia Health Research Institute San Sebastián, Spain ; CIBERNED, Instituto Carlos III, Ministerio de Economía y Competitividad Madrid, Spain
| | - Ana Aiastui
- CIBERNED, Instituto Carlos III, Ministerio de Economía y Competitividad Madrid, Spain ; Cell Culture Platform, Biodonostia Health Research Institute, San Sebastián Spain
| | - Roberto Fernández-Torrón
- Neuroscience Area, Biodonostia Health Research Institute San Sebastián, Spain ; CIBERNED, Instituto Carlos III, Ministerio de Economía y Competitividad Madrid, Spain ; Department of Neurology, Hospital Universitario Donostia, San Sebastián Spain
| | - Mikel Garcia-Puga
- Oncology Area, Biodonostia Health Research Institute San Sebastián, Spain
| | - Ander Matheu
- Oncology Area, Biodonostia Health Research Institute San Sebastián, Spain
| | - Adolfo López de Munain
- Neuroscience Area, Biodonostia Health Research Institute San Sebastián, Spain ; CIBERNED, Instituto Carlos III, Ministerio de Economía y Competitividad Madrid, Spain ; Department of Neurology, Hospital Universitario Donostia, San Sebastián Spain ; Department of Neuroscience, Universidad del País Vasco UPV-EHU San Sebastián, Spain
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39
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Abstract
Approximately 40 human diseases are associated with expansion of repeat sequences. These expansions can reside within coding or non-coding parts of the genes, affecting the host gene function. The presence of such expansions results in the production of toxic RNA and/or protein or causes transcriptional repression and silencing of the host gene. Although the molecular mechanisms of expansion diseases are not well understood, mounting evidence suggests that transcription through expanded repeats plays an essential role in disease pathology. The presence of an expansion can affect RNA polymerase transcription, leading to dysregulation of transcription-associated processes, such as RNA splicing, formation of RNA/DNA hybrids (R-loops), production of antisense, short non-coding and bidirectional RNA transcripts. In the present review, we summarize current advances in this field and discuss possible roles of transcriptional defects in disease pathology.
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40
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Rodríguez R, Hernández-Hernández O, Magaña JJ, González-Ramírez R, García-López ES, Cisneros B. Altered nuclear structure in myotonic dystrophy type 1-derived fibroblasts. Mol Biol Rep 2014; 42:479-88. [PMID: 25307018 DOI: 10.1007/s11033-014-3791-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 10/03/2014] [Indexed: 12/14/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystem genetic disorder caused by a triplet nucleotide repeat expansion in the 3' untranslated region of the Dystrophia Myotonica-Protein Kinase (DMPK) gene. DMPK gene transcripts containing CUG expanded repeats accumulate in nuclear foci and ultimately cause altered splicing/gene expression of numerous secondary genes. The study of primary cell cultures derived from patients with DM1 has allowed the identification and further characterization of molecular mechanisms underlying the pathology in the natural context of the disease. In this study we show for the first time impaired nuclear structure in fibroblasts of DM1 patients. DM1-derived fibroblasts exhibited altered localization of the nuclear envelope (NE) proteins emerin and lamins A/C and B1 with concomitant increased size and altered shape of nuclei. Abnormal NE organization is more common in DM1 fibroblasts containing abundant nuclear foci, implying expression of the expanded RNA as determinant of nuclear defects. That transient expression of the DMPK 3' UTR containing 960 CTG but not with the 3' UTR lacking CTG repeats is sufficient to generate NE disruption in normal fibroblasts confirms the direct impact of mutant RNA on NE architecture. We also evidence nucleoli distortion in DM1 fibroblasts by immunostaining of the nucleolar protein fibrillarin, implying a broader effect of the mutant RNA on nuclear structure. In summary, these findings reveal that NE disruption, a hallmark of laminopathy disorders, is a novel characteristic of DM1.
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Affiliation(s)
- R Rodríguez
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Av. IPN 2508 Col Zacatenco, 07360, Mexico, D.F, Mexico
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