101
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Ikeda M, Taniguchi-Ikeda M, Kato T, Shinkai Y, Tanaka S, Hagiwara H, Sasaki N, Masaki T, Matsumura K, Sonoo M, Kurahashi H, Saito F. Unexpected Mutations by CRISPR-Cas9 CTG Repeat Excision in Myotonic Dystrophy and Use of CRISPR Interference as an Alternative Approach. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:131-144. [PMID: 32637445 PMCID: PMC7321784 DOI: 10.1016/j.omtm.2020.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022]
Abstract
Myotonic dystrophy type 1 is the most common type of adult-onset muscular dystrophy. This is an autosomal dominant disorder and caused by the expansion of the CTG repeat in the 3′ untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. Messenger RNAs containing these expanded repeats form aggregates as nuclear RNA foci. Then, RNA binding proteins, including muscleblind-like 1, are sequestered to the RNA foci, leading to systemic abnormal RNA splicing. In this study, we used CRISPR-Cas9 genome editing to excise this CTG repeat. Dual cleavage at the 5′ and 3′ regions of the repeat using a conventional Cas9 nuclease and a double nicking with Cas9 nickase successfully excised the CTG repeat. Subsequently, the formation of the RNA foci was markedly reduced in patient-derived fibroblasts. However, contrary to expectations, a considerable amount of off-target digestions and on-target genomic rearrangements were observed using high-throughput genome-wide translocation sequencing. Finally, the suppression of DMPK transcripts using CRISPR interference significantly decreased the intensity of RNA foci. Our results indicate that close attention should be paid to the unintended mutations when double-strand breaks are generated by CRISPR-Cas9 for therapeutic purposes. Alternative approaches independent of double-strand breaks, including CRISPR interference, may be considered.
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Affiliation(s)
- Miki Ikeda
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
| | - Mariko Taniguchi-Ikeda
- Department of Clinical Genetics, Fujita Health University Hospital, Aichi 4701192, Japan.,Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 4701192, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 4701192, Japan
| | - Yasuko Shinkai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 4701192, Japan
| | - Sonoko Tanaka
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
| | - Hiroki Hagiwara
- Department of Medical Science, Teikyo University of Science, Uenohara Campus, Yamanashi 4090193, Japan
| | - Naomichi Sasaki
- Department of Medical Science, Teikyo University of Science, Senju Campus, Tokyo 1200045, Japan
| | - Toshihiro Masaki
- Department of Medical Science, Teikyo University of Science, Senju Campus, Tokyo 1200045, Japan
| | - Kiichiro Matsumura
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
| | - Masahiro Sonoo
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 4701192, Japan
| | - Fumiaki Saito
- Department of Neurology, School of Medicine, Teikyo University, Tokyo 1738606, Japan
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102
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Differences in splicing defects between the grey and white matter in myotonic dystrophy type 1 patients. PLoS One 2020; 15:e0224912. [PMID: 32407311 PMCID: PMC7224547 DOI: 10.1371/journal.pone.0224912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/24/2020] [Indexed: 12/11/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multi-system disorder caused by CTG repeats in the myotonic dystrophy protein kinase (DMPK) gene. This leads to the sequestration of splicing factors such as muscleblind-like 1/2 (MBNL1/2) and aberrant splicing in the central nervous system. We investigated the splicing patterns of MBNL1/2 and genes controlled by MBNL2 in several regions of the brain and between the grey matter (GM) and white matter (WM) in DM1 patients using RT-PCR. Compared with amyotrophic lateral sclerosis (ALS, as disease controls), the percentage of spliced-in parameter (PSI) for most of the examined exons were significantly altered in most of the brain regions of DM1 patients, except for the cerebellum. The splicing of many genes was differently regulated between the GM and WM in both DM1 and ALS. In 7 out of the 15 examined splicing events, the level of PSI change between DM1 and ALS was significantly higher in the GM than in the WM. The differences in alternative splicing between the GM and WM may be related to the effect of DM1 on the WM of the brain.
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103
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Itskovich SS, Gurunathan A, Clark J, Burwinkel M, Wunderlich M, Berger MR, Kulkarni A, Chetal K, Venkatasubramanian M, Salomonis N, Kumar AR, Lee LH. MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia. Nat Commun 2020; 11:2369. [PMID: 32398749 PMCID: PMC7217953 DOI: 10.1038/s41467-020-15733-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/25/2020] [Indexed: 02/06/2023] Open
Abstract
Despite growing awareness of the biologic features underlying MLL-rearranged leukemia, targeted therapies for this leukemia have remained elusive and clinical outcomes remain dismal. MBNL1, a protein involved in alternative splicing, is consistently overexpressed in MLL-rearranged leukemias. We found that MBNL1 loss significantly impairs propagation of murine and human MLL-rearranged leukemia in vitro and in vivo. Through transcriptomic profiling of our experimental systems, we show that in leukemic cells, MBNL1 regulates alternative splicing (predominantly intron exclusion) of several genes including those essential for MLL-rearranged leukemogenesis, such as DOT1L and SETD1A. We finally show that selective leukemic cell death is achievable with a small molecule inhibitor of MBNL1. These findings provide the basis for a new therapeutic target in MLL-rearranged leukemia and act as further validation of a burgeoning paradigm in targeted therapy, namely the disruption of cancer-specific splicing programs through the targeting of selectively essential RNA binding proteins.
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Affiliation(s)
- Svetlana S Itskovich
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Arun Gurunathan
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jason Clark
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Matthew Burwinkel
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mikaela R Berger
- College of Medicine, University of Cincinnati School of Medicine, Cincinnati, OH, 45267, USA
| | - Aishwarya Kulkarni
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Meenakshi Venkatasubramanian
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, 45229, USA
| | - Ashish R Kumar
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, 45229, USA
| | - Lynn H Lee
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, 45229, USA.
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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104
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Bourefis AR, Campanari ML, Buee-Scherrer V, Kabashi E. Functional characterization of a FUS mutant zebrafish line as a novel genetic model for ALS. Neurobiol Dis 2020; 142:104935. [PMID: 32380281 DOI: 10.1016/j.nbd.2020.104935] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/22/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in Fused in sarcoma (FUS), an RNA-binding protein, are known to cause Amyotrophic Lateral Sclerosis (ALS). However, molecular mechanisms due to loss of FUS function remain unclear and controversial. Here, we report the characterization and phenotypic analysis of a deletion mutant of the unique FUS orthologue in zebrafish where Fus protein levels are depleted. The homozygous mutants displayed a reduced lifespan as well as impaired motor abilities associated with specific cellular deficits, including decreased motor neurons length and neuromuscular junctions (NMJ) fragmentation. Furthermore, we demonstrate that these cellular impairments are linked to the misregulation of mRNA expression of acetylcholine receptor (AChR) subunits and histone deacetylase 4, markers of denervation and reinnervation processes observed in ALS patients. In addition, fus loss of function alters tau transcripts favoring the expression of small tau isoforms. Overall, this new animal model extends our knowledge on FUS and supports the relevance of FUS loss of function in ALS physiopathology.
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Affiliation(s)
- Annis-Rayan Bourefis
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
| | - Maria-Letizia Campanari
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
| | | | - Edor Kabashi
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France.
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105
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Sznajder ŁJ, Scotti MM, Shin J, Taylor K, Ivankovic F, Nutter CA, Aslam FN, Subramony SH, Ranum LPW, Swanson MS. Loss of MBNL1 induces RNA misprocessing in the thymus and peripheral blood. Nat Commun 2020; 11:2022. [PMID: 32332745 PMCID: PMC7181699 DOI: 10.1038/s41467-020-15962-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/03/2020] [Indexed: 12/25/2022] Open
Abstract
The thymus is a primary lymphoid organ that plays an essential role in T lymphocyte maturation and selection during development of one arm of the mammalian adaptive immune response. Although transcriptional mechanisms have been well documented in thymocyte development, co-/post-transcriptional modifications are also important but have received less attention. Here we demonstrate that the RNA alternative splicing factor MBNL1, which is sequestered in nuclear RNA foci by C(C)UG microsatellite expansions in myotonic dystrophy (DM), is essential for normal thymus development and function. Mbnl1 129S1 knockout mice develop postnatal thymic hyperplasia with thymocyte accumulation. Transcriptome analysis indicates numerous gene expression and RNA mis-splicing events, including transcription factors from the TCF/LEF family. CNBP, the gene containing an intronic CCTG microsatellite expansion in DM type 2 (DM2), is coordinately expressed with MBNL1 in the developing thymus and DM2 CCTG expansions induce similar transcriptome alterations in DM2 blood, which thus serve as disease-specific biomarkers.
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Affiliation(s)
- Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA.
| | - Marina M Scotti
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Jihae Shin
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Katarzyna Taylor
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA.,Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Franjo Ivankovic
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Curtis A Nutter
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Faaiq N Aslam
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - S H Subramony
- Department of Neurology, Center for NeuroGenetics, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Laura P W Ranum
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - 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.
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106
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Shimoyama T, Hayashi H, Suzuki F, Nishiyama Y, Miyamoto Y, Aiba T, Shimizu W, Kimura K. Idiopathic ventricular fibrillation and the V1764fsX1786 frameshift mutation of the SCN5A gene in a myotonic dystrophy type 1 patient. J Clin Neurosci 2020; 74:242-244. [DOI: 10.1016/j.jocn.2020.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/08/2020] [Indexed: 10/25/2022]
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107
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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108
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Misra C, Bangru S, Lin F, Lam K, Koenig SN, Lubbers ER, Hedhli J, Murphy NP, Parker DJ, Dobrucki LW, Cooper TA, Tajkhorshid E, Mohler PJ, Kalsotra A. Aberrant Expression of a Non-muscle RBFOX2 Isoform Triggers Cardiac Conduction Defects in Myotonic Dystrophy. Dev Cell 2020; 52:748-763.e6. [PMID: 32109384 PMCID: PMC7098852 DOI: 10.1016/j.devcel.2020.01.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/25/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic genetic disorder caused by the CTG repeat expansion in the 3'-untranslated region of DMPK gene. Heart dysfunctions occur in ∼80% of DM1 patients and are the second leading cause of DM1-related deaths. Herein, we report that upregulation of a non-muscle splice isoform of RNA-binding protein RBFOX2 in DM1 heart tissue-due to altered splicing factor and microRNA activities-induces cardiac conduction defects in DM1 individuals. Mice engineered to express the non-muscle RBFOX240 isoform in heart via tetracycline-inducible transgenesis, or CRISPR/Cas9-mediated genome editing, reproduced DM1-related cardiac conduction delay and spontaneous episodes of arrhythmia. Further, by integrating RNA binding with cardiac transcriptome datasets from DM1 patients and mice expressing the non-muscle RBFOX2 isoform, we identified RBFOX240-driven splicing defects in voltage-gated sodium and potassium channels, which alter their electrophysiological properties. Thus, our results uncover a trans-dominant role for an aberrantly expressed RBFOX240 isoform in DM1 cardiac pathogenesis.
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Affiliation(s)
- Chaitali Misra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Feikai Lin
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Kin Lam
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Centers for Macromolecular Modeling, Bioinformatics and Experimental Molecular Imaging at Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Sara N Koenig
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, College of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Ellen R Lubbers
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, College of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Jamila Hedhli
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Centers for Macromolecular Modeling, Bioinformatics and Experimental Molecular Imaging at Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Nathaniel P Murphy
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, College of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Darren J Parker
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Lawrence W Dobrucki
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Centers for Macromolecular Modeling, Bioinformatics and Experimental Molecular Imaging at Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Centers for Macromolecular Modeling, Bioinformatics and Experimental Molecular Imaging at Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Peter J Mohler
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, College of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, USA.
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109
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Yadava RS, Kim YK, Mandal M, Mahadevan K, Gladman JT, Yu Q, Mahadevan MS. MBNL1 overexpression is not sufficient to rescue the phenotypes in a mouse model of RNA toxicity. Hum Mol Genet 2020; 28:2330-2338. [PMID: 30997488 DOI: 10.1093/hmg/ddz065] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 12/21/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is caused by an expanded (CTG)n tract in the 3'UTR of the DM protein kinase (DMPK) gene. The RNA transcripts produced from the expanded allele sequester or alter the function of RNA-binding proteins (MBNL1, CUGBP1, etc.). The sequestration of MBNL1 results in RNA-splicing defects that contribute to disease. Overexpression of MBNL1 in skeletal muscle has been shown to rescue some of the DM1 features in a mouse model and has been proposed as a therapeutic strategy for DM1. Here, we sought to confirm if overexpression of MBNL1 rescues the phenotypes in a different mouse model of RNA toxicity. Using an inducible mouse model of RNA toxicity in which expression of the mutant DMPK 3'UTR results in RNA foci formation, MBNL1 sequestration, splicing defects, myotonia and cardiac conduction defects, we find that MBNL1 overexpression did not rescue skeletal muscle function nor beneficially affect cardiac conduction. Surprisingly, MBNL1 overexpression also did not rescue myotonia, though variable rescue of Clcn1 splicing and other splicing defects was seen. Additionally, contrary to the previous study, we found evidence for increased muscle histopathology with MBNL1 overexpression. Overall, we did not find evidence for beneficial effects from overexpression of MBNL1 as a means to correct RNA toxicity mediated by mRNAs containing an expanded DMPK 3'UTR.
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Affiliation(s)
- Ramesh S Yadava
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Yun K Kim
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Mahua Mandal
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | | | - Jordan T Gladman
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Qing Yu
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Mani S Mahadevan
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
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110
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Abstract
Studies on myotonic dystrophy type 1 (DM1) have led to the RNA-mediated disease model for hereditary disorders caused by noncoding microsatellite expansions. This model proposes that DM1 disease manifestations are caused by a reversion to fetal RNA processing patterns in adult tissues due to the expression of toxic CUG RNA expansions (CUGexp) leading to decreased muscleblind-like, but increased CUGBP1/ETR3-like factor 1 (CELF1), alternative splicing activities. Here, we test this model in vivo, using the mouse HSA LR poly(CUG) model for DM1 and recombinant adeno-associated virus (rAAV)-mediated transduction of specific splicing factors. Surprisingly, systemic overexpression of HNRNPA1, not previously linked to DM1, also shifted DM1-relevant splicing targets to fetal isoforms, resulting in more severe muscle weakness/myopathy as early as 4 to 6 wk posttransduction, whereas rAAV controls were unaffected. Overexpression of HNRNPA1 promotes fetal exon inclusion of representative DM1-relevant splicing targets in differentiated myoblasts, and HITS-CLIP of rAAV-mycHnrnpa1-injected muscle revealed direct interactions of HNRNPA1 with these targets in vivo. Similar to CELF1, HNRNPA1 protein levels decrease during postnatal development, but are elevated in both regenerating mouse muscle and DM1 skeletal muscle. Our studies suggest that CUGexp RNA triggers abnormal expression of multiple nuclear RNA binding proteins, including CELF1 and HNRNPA1, that antagonize MBNL activity to promote fetal splicing patterns.
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111
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Huang K, Masuda A, Chen G, Bushra S, Kamon M, Araki T, Kinoshita M, Ohkawara B, Ito M, Ohno K. Inhibition of cyclooxygenase-1 by nonsteroidal anti-inflammatory drugs demethylates MeR2 enhancer and promotes Mbnl1 transcription in myogenic cells. Sci Rep 2020; 10:2558. [PMID: 32054946 PMCID: PMC7018979 DOI: 10.1038/s41598-020-59517-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Muscleblind-like 1 (MBNL1) is a ubiquitously expressed RNA-binding protein, which is highly expressed in skeletal muscle. Abnormally expanded CUG-repeats in the DMPK gene cause myotonic dystrophy type 1 (DM1) by sequestration of MBNL1 to nuclear RNA foci and by upregulation of another RNA-binding protein, CUG-binding protein 1 (CUGBP1). We previously reported that a nonsteroidal anti-inflammatory drug (NSAID), phenylbutazone, upregulates MBNL1 expression in DM1 mouse model by demethylation of MeR2, an enhancer element in Mbnl1 intron 1. NSAIDs inhibit cyclooxygenase (COX), which is comprised of COX-1 and COX-2 isoforms. In this study, we screened 29 NSAIDs in C2C12 myoblasts, and found that 13 NSAIDs enhanced Mbnl1 expression, where COX-1-selective NSAIDs upregulated Mbnl1 more than COX-2-selective NSAIDs. Consistently, knockdown of COX-1, but not of COX-2, upregulated MBNL1 expression in C2C12 myoblasts and myotubes, as well as in myotubes differentiated from DM1 patient-derived induced pluripotent stem cells (iPSCs). Luciferase assay showed that COX-1-knockdown augmented the MeR2 enhancer activity. Furthermore, bisulfite sequencing analysis demonstrated that COX-1-knockdown suppressed methylation of MeR2. These results suggest that COX-1 inhibition upregulates Mbnl1 transcription through demethylation of the MeR2 enhancer. Taken together, our study provides new insights into the transcriptional regulation of Mbnl1 by the COX-1-mediated pathway.
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Affiliation(s)
- Kun Huang
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Guiying Chen
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Samira Bushra
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masayoshi Kamon
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | | | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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112
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Swinnen B, Robberecht W, Van Den Bosch L. RNA toxicity in non-coding repeat expansion disorders. EMBO J 2020; 39:e101112. [PMID: 31721251 PMCID: PMC6939197 DOI: 10.15252/embj.2018101112] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 09/30/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022] Open
Abstract
Several neurodegenerative disorders like amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia (SCA) are caused by non-coding nucleotide repeat expansions. Different pathogenic mechanisms may underlie these non-coding repeat expansion disorders. While gain-of-function mechanisms, such as toxicity associated with expression of repeat RNA or toxicity associated with repeat-associated non-ATG (RAN) products, are most frequently connected with these disorders, loss-of-function mechanisms have also been implicated. We review the different pathways that have been linked to non-coding repeat expansion disorders such as C9ORF72-linked ALS/frontotemporal dementia (FTD), myotonic dystrophy, fragile X tremor/ataxia syndrome (FXTAS), SCA, and Huntington's disease-like 2. We discuss modes of RNA toxicity focusing on the identity and the interacting partners of the toxic RNA species. Using the C9ORF72 ALS/FTD paradigm, we further explore the efforts and different methods used to disentangle RNA vs. RAN toxicity. Overall, we conclude that there is ample evidence for a role of RNA toxicity in non-coding repeat expansion diseases.
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Affiliation(s)
- Bart Swinnen
- Department of NeurosciencesExperimental NeurologyLeuven Brain Institute (LBI)KU Leuven – University of LeuvenLeuvenBelgium
- Laboratory of NeurobiologyVIB, Center for Brain & Disease ResearchLeuvenBelgium
- Department of NeurologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Wim Robberecht
- Department of NeurosciencesExperimental NeurologyLeuven Brain Institute (LBI)KU Leuven – University of LeuvenLeuvenBelgium
- Laboratory of NeurobiologyVIB, Center for Brain & Disease ResearchLeuvenBelgium
- Department of NeurologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Ludo Van Den Bosch
- Department of NeurosciencesExperimental NeurologyLeuven Brain Institute (LBI)KU Leuven – University of LeuvenLeuvenBelgium
- Laboratory of NeurobiologyVIB, Center for Brain & Disease ResearchLeuvenBelgium
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113
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Dosage effect of multiple genes accounts for multisystem disorder of myotonic dystrophy type 1. Cell Res 2019; 30:133-145. [PMID: 31853004 PMCID: PMC7015062 DOI: 10.1038/s41422-019-0264-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/09/2019] [Indexed: 12/19/2022] Open
Abstract
Multisystem manifestations in myotonic dystrophy type 1 (DM1) may be due to dosage reduction in multiple genes induced by aberrant expansion of CTG repeats in DMPK, including DMPK, its neighboring genes (SIX5 or DMWD) and downstream MBNL1. However, direct evidence is lacking. Here, we develop a new strategy to generate mice carrying multigene heterozygous mutations to mimic dosage reduction in one step by injection of haploid embryonic stem cells with mutant Dmpk, Six5 and Mbnl1 into oocytes. The triple heterozygous mutant mice exhibit adult-onset DM1 phenotypes. With the additional mutation in Dmwd, the quadruple heterozygous mutant mice recapitulate many major manifestations in congenital DM1. Moreover, muscle stem cells in both models display reduced stemness, providing a unique model for screening small molecules for treatment of DM1. Our results suggest that the complex symptoms of DM1 result from the reduced dosage of multiple genes.
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114
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Casci I, Krishnamurthy K, Kour S, Tripathy V, Ramesh N, Anderson EN, Marrone L, Grant RA, Oliver S, Gochenaur L, Patel K, Sterneckert J, Gleixner AM, Donnelly CJ, Ruepp MD, Sini AM, Zuccaro E, Pennuto M, Pasinelli P, Pandey UB. Muscleblind acts as a modifier of FUS toxicity by modulating stress granule dynamics and SMN localization. Nat Commun 2019; 10:5583. [PMID: 31811140 PMCID: PMC6898697 DOI: 10.1038/s41467-019-13383-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
Mutations in fused in sarcoma (FUS) lead to amyotrophic lateral sclerosis (ALS) with varying ages of onset, progression and severity. This suggests that unknown genetic factors contribute to disease pathogenesis. Here we show the identification of muscleblind as a novel modifier of FUS-mediated neurodegeneration in vivo. Muscleblind regulates cytoplasmic mislocalization of mutant FUS and subsequent accumulation in stress granules, dendritic morphology and toxicity in mammalian neuronal and human iPSC-derived neurons. Interestingly, genetic modulation of endogenous muscleblind was sufficient to restore survival motor neuron (SMN) protein localization in neurons expressing pathogenic mutations in FUS, suggesting a potential mode of suppression of FUS toxicity. Upregulation of SMN suppressed FUS toxicity in Drosophila and primary cortical neurons, indicating a link between FUS and SMN. Our data provide in vivo evidence that muscleblind is a dominant modifier of FUS-mediated neurodegeneration by regulating FUS-mediated ALS pathogenesis.
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Affiliation(s)
- Ian Casci
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Karthik Krishnamurthy
- Department of Neuroscience, Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Jefferson University, Philadelphia, PA, USA
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Vadreenath Tripathy
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Nandini Ramesh
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lara Marrone
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Rogan A Grant
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Stacie Oliver
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lauren Gochenaur
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Krishani Patel
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Amanda M Gleixner
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Live Like Lou Center for ALS Research, Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christopher J Donnelly
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Live Like Lou Center for ALS Research, Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marc-David Ruepp
- UK Dementia Research Institute at King's College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9NU, UK
| | - Antonella M Sini
- Department of Biomedical Sciences (DBS), University of Padova, Padova, Italy
| | - Emanuela Zuccaro
- Department of Biomedical Sciences (DBS), University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Maria Pennuto
- Department of Biomedical Sciences (DBS), University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Piera Pasinelli
- Department of Neuroscience, Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Jefferson University, Philadelphia, PA, USA
| | - Udai Bhan Pandey
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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115
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López Castel A, Overby SJ, Artero R. MicroRNA-Based Therapeutic Perspectives in Myotonic Dystrophy. Int J Mol Sci 2019; 20:ijms20225600. [PMID: 31717488 PMCID: PMC6888406 DOI: 10.3390/ijms20225600] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 12/20/2022] Open
Abstract
Myotonic dystrophy involves two types of chronically debilitating rare neuromuscular diseases: type 1 (DM1) and type 2 (DM2). Both share similarities in molecular cause, clinical signs, and symptoms with DM2 patients usually displaying milder phenotypes. It is well documented that key clinical symptoms in DM are associated with a strong mis-regulation of RNA metabolism observed in patient’s cells. This mis-regulation is triggered by two leading DM-linked events: the sequestration of Muscleblind-like proteins (MBNL) and the mis-regulation of the CUGBP RNA-Binding Protein Elav-Like Family Member 1 (CELF1) that cause significant alterations to their important functions in RNA processing. It has been suggested that DM1 may be treatable through endogenous modulation of the expression of MBNL and CELF1 proteins. In this study, we analyzed the recent identification of the involvement of microRNA (miRNA) molecules in DM and focus on the modulation of these miRNAs to therapeutically restore normal MBNL or CELF1 function. We also discuss additional prospective miRNA targets, the use of miRNAs as disease biomarkers, and additional promising miRNA-based and miRNA-targeting drug development strategies. This review provides a unifying overview of the dispersed data on miRNA available in the context of DM.
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Affiliation(s)
- Arturo López Castel
- Translational Genomics Group, Incliva Health Research Institute, Burjassot, 46100 Valencia, Spain
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (Eri Biotecmed), University of Valencia, Burjassot, 46100 Valencia, Spain
- Correspondence: (A.L.C.); (R.A.)
| | - Sarah Joann Overby
- Translational Genomics Group, Incliva Health Research Institute, Burjassot, 46100 Valencia, Spain
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (Eri Biotecmed), University of Valencia, Burjassot, 46100 Valencia, Spain
| | - Rubén Artero
- Translational Genomics Group, Incliva Health Research Institute, Burjassot, 46100 Valencia, Spain
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (Eri Biotecmed), University of Valencia, Burjassot, 46100 Valencia, Spain
- Correspondence: (A.L.C.); (R.A.)
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116
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Correction of Glycogen Synthase Kinase 3β in Myotonic Dystrophy 1 Reduces the Mutant RNA and Improves Postnatal Survival of DMSXL Mice. Mol Cell Biol 2019; 39:MCB.00155-19. [PMID: 31383751 DOI: 10.1128/mcb.00155-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/01/2019] [Indexed: 11/20/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystem neuromuscular disease without cure. One of the possible therapeutic approaches for DM1 is correction of the RNA-binding proteins CUGBP1 and MBNL1, misregulated in DM1. CUGBP1 activity is controlled by glycogen synthase kinase 3β (GSK3β), which is elevated in skeletal muscle of patients with DM1, and inhibitors of GSK3 were suggested as therapeutic molecules to correct CUGBP1 activity in DM1. Here, we describe that correction of GSK3β with a small-molecule inhibitor of GSK3, tideglusib (TG), not only normalizes the GSK3β-CUGBP1 pathway but also reduces the mutant DMPK mRNA in myoblasts from patients with adult DM1 and congenital DM1 (CDM1). Correction of GSK3β in a mouse model of DM1 (HSALR mice) with TG also reduces the levels of CUG-containing RNA, normalizing a number of CUGBP1- and MBNL1-regulated mRNA targets. We also found that the GSK3β-CUGBP1 pathway is abnormal in skeletal muscle and brain of DMSXL mice, expressing more than 1,000 CUG repeats, and that the correction of this pathway with TG increases postnatal survival and improves growth and neuromotor activity of DMSXL mice. These findings show that the inhibitors of GSK3, such as TG, may correct pathology in DM1 and CDM1 via several pathways.
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117
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Mondragon-Gonzalez R, Azzag K, Selvaraj S, Yamamoto A, Perlingeiro RCR. Transplantation studies reveal internuclear transfer of toxic RNA in engrafted muscles of myotonic dystrophy 1 mice. EBioMedicine 2019; 47:553-562. [PMID: 31446083 PMCID: PMC6796515 DOI: 10.1016/j.ebiom.2019.08.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 08/05/2019] [Accepted: 08/14/2019] [Indexed: 12/11/2022] Open
Abstract
Background Stem cell transplantation represents a potential therapeutic option for muscular dystrophies (MD). However, to date, most reports have utilized mouse models for recessive types of MD. Here we performed studies to determine whether myotonic dystrophy 1 (DM1), an autosomal dominant type of MD, could benefit from cell transplantation. Methods We injected human pluripotent stem (PS) cell-derived myogenic progenitors into the muscles of a novel mouse model combining immunodeficiency and skeletal muscle pathology of DM1 and investigated transplanted mice for engraftment as well as for the presence of RNA foci and alternative splicing pattern. Findings Engraftment was clearly observed in recipient mice, but unexpectedly, we detected RNA foci in donor-derived engrafted myonuclei. These foci proved to be pathogenic as we observed MBNL1 sequestration and abnormal alternative splicing in donor-derived transcripts. Interpretation It has been assumed that toxic CUG repeat-containing RNA forms foci in situ in the nucleus in which it is expressed, but these data suggest that CUG repeat-containing RNA may also exit the nucleus and traffic to other nuclei in the syncytial myofiber, where it can exert pathological effects. Fund This project was supported by funds from the LaBonte/Shawn family and NIH grants R01 AR055299 and AR071439 (R.C.R.P.). R.M-G. was funded by CONACyT-Mexico (#394378).
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Affiliation(s)
- Ricardo Mondragon-Gonzalez
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Mexico City, Mexico
| | - Karim Azzag
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Sridhar Selvaraj
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Ami Yamamoto
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Rita C R Perlingeiro
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
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118
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Reddy K, Jenquin JR, Cleary JD, Berglund JA. Mitigating RNA Toxicity in Myotonic Dystrophy using Small Molecules. Int J Mol Sci 2019; 20:E4017. [PMID: 31426500 PMCID: PMC6720693 DOI: 10.3390/ijms20164017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 12/26/2022] Open
Abstract
This review, one in a series on myotonic dystrophy (DM), is focused on the development and potential use of small molecules as therapeutics for DM. The complex mechanisms and pathogenesis of DM are covered in the associated reviews. Here, we examine the various small molecule approaches taken to target the DNA, RNA, and proteins that contribute to disease onset and progression in myotonic dystrophy type 1 (DM1) and 2 (DM2).
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Affiliation(s)
- Kaalak Reddy
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA.
| | - Jana R Jenquin
- Center for NeuroGenetics and Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32608, USA
| | - John D Cleary
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - J Andrew Berglund
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA.
- Center for NeuroGenetics and Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32608, USA.
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119
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Taylor K, Sznajder LJ, Cywoniuk P, Thomas JD, Swanson MS, Sobczak K. MBNL splicing activity depends on RNA binding site structural context. Nucleic Acids Res 2019; 46:9119-9133. [PMID: 29955876 PMCID: PMC6158504 DOI: 10.1093/nar/gky565] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/16/2018] [Indexed: 02/02/2023] Open
Abstract
Muscleblind-like (MBNL) proteins are conserved RNA-binding factors involved in alternative splicing (AS) regulation during development. While AS is controlled by distribution of MBNL paralogs and isoforms, the affinity of these proteins for specific RNA-binding regions and their location within transcripts, it is currently unclear how RNA structure impacts MBNL-mediated AS regulation. Here, we defined the RNA structural determinants affecting MBNL-dependent AS activity using both cellular and biochemical assays. While enhanced inclusion of MBNL-regulated alternative exons is controlled by the arrangement and number of MBNL binding sites within unstructured RNA, when these sites are embedded in a RNA hairpin MBNL binds preferentially to one side of stem region. Surprisingly, binding of MBNL proteins to RNA targets did not entirely correlate with AS efficiency. Moreover, comparison of MBNL proteins revealed structure-dependent competitive behavior between the paralogs. Our results showed that the structure of targeted RNAs is a prevalent component of the mechanism of alternative splicing regulation by MBNLs.
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Affiliation(s)
- Katarzyna Taylor
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA
| | - Piotr Cywoniuk
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - James D Thomas
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA.,Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Maurice S Swanson
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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120
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Lo Scrudato M, Poulard K, Sourd C, Tomé S, Klein AF, Corre G, Huguet A, Furling D, Gourdon G, Buj-Bello A. Genome Editing of Expanded CTG Repeats within the Human DMPK Gene Reduces Nuclear RNA Foci in the Muscle of DM1 Mice. Mol Ther 2019; 27:1372-1388. [PMID: 31253581 PMCID: PMC6697452 DOI: 10.1016/j.ymthe.2019.05.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is caused by a CTG repeat expansion located in the 3' UTR of the DMPK gene. Expanded DMPK transcripts aggregate into nuclear foci and alter the function of RNA-binding proteins, leading to defects in the alternative splicing of numerous pre-mRNAs. To date, there is no curative treatment for DM1. Here we investigated a gene-editing strategy using the CRISPR-Cas9 system from Staphylococcus aureus (Sa) to delete the CTG repeats in the human DMPK locus. Co-expression of SaCas9 and selected pairs of single-guide RNAs (sgRNAs) in cultured DM1 patient-derived muscle line cells carrying 2,600 CTG repeats resulted in targeted DNA deletion, ribonucleoprotein foci disappearance, and correction of splicing abnormalities in various transcripts. Furthermore, a single intramuscular injection of recombinant AAV vectors expressing CRISPR-SaCas9 components in the tibialis anterior muscle of DMSXL (myotonic dystrophy mouse line carrying the human DMPK gene with >1,000 CTG repeats) mice decreased the number of pathological RNA foci in myonuclei. These results establish the proof of concept that genome editing of a large trinucleotide expansion is feasible in muscle and may represent a useful strategy to be further developed for the treatment of myotonic dystrophy.
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Affiliation(s)
- Mirella Lo Scrudato
- Genethon, INSERM UMR_S951, Univ Evry, Université Paris Saclay, 91000 Evry, France
| | - Karine Poulard
- Genethon, INSERM UMR_S951, Univ Evry, Université Paris Saclay, 91000 Evry, France
| | - Célia Sourd
- Genethon, INSERM UMR_S951, Univ Evry, Université Paris Saclay, 91000 Evry, France
| | - Stéphanie Tomé
- INSERM UMR 1163, Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, 75015 Paris, France
| | - Arnaud F Klein
- INSERM, Association Institut de Myologie, Centre de Recherche en Myologie, Sorbonne Université, 75013 Paris, France
| | - Guillaume Corre
- Genethon, INSERM UMR_S951, Univ Evry, Université Paris Saclay, 91000 Evry, France
| | - Aline Huguet
- INSERM UMR 1163, Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, 75015 Paris, France
| | - Denis Furling
- INSERM, Association Institut de Myologie, Centre de Recherche en Myologie, Sorbonne Université, 75013 Paris, France
| | - Geneviève Gourdon
- INSERM UMR 1163, Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, 75015 Paris, France
| | - Ana Buj-Bello
- Genethon, INSERM UMR_S951, Univ Evry, Université Paris Saclay, 91000 Evry, France.
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121
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Lee KY, Chang HC, Seah C, Lee LJ. Deprivation of Muscleblind-Like Proteins Causes Deficits in Cortical Neuron Distribution and Morphological Changes in Dendritic Spines and Postsynaptic Densities. Front Neuroanat 2019; 13:75. [PMID: 31417371 PMCID: PMC6682673 DOI: 10.3389/fnana.2019.00075] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Myotonic dystrophy (Dystrophia Myotonica; DM) is the most common adult-onset muscular dystrophy and its brain symptoms seriously affect patients’ quality of life. It is caused by extended (CTG)n expansions at 3′-UTR of DMPK gene (DM type 1, DM1) or (CCTG)n repeats in the intron 1 of CNBP gene (DM type 2, DM2) and the sequestration of Muscleblind-like (MBNL) family proteins by transcribed (CUG)n RNA hairpin is the main pathogenic mechanism for DM. The MBNL proteins are splicing factors regulating posttranscriptional RNA during development. Previously, Mbnl knockout (KO) mouse lines showed molecular and phenotypic evidence that recapitulate DM brains, however, detailed morphological study has not yet been accomplished. In our studies, control (Mbnl1+/+; Mbnl2cond/cond; Nestin-Cre−/−), Mbnl2 conditional KO (2KO, Mbnl1+/+; Mbnl2cond/cond; Nestin-Cre+/−) and Mbnl1/2 double KO (DKO, Mbnl1ΔE3/ΔE3; Mbnl2cond/cond; Nestin-Cre+/−) mice were generated by crossing three individual lines. Immunohistochemistry for evaluating density and distribution of cortical neurons; Golgi staining for depicting the dendrites/dendritic spines; and electron microscopy for analyzing postsynaptic ultrastructure were performed. We found distributional defects in cortical neurons, reduction in dendritic complexity, immature dendritic spines and alterations of postsynaptic densities (PSDs) in the mutants. In conclusion, loss of function of Mbnl1/2 caused fundamental defects affecting neuronal distribution, dendritic morphology and postsynaptic architectures that are reminiscent of predominantly immature and fetal phenotypes in DM patients.
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Affiliation(s)
- Kuang-Yung Lee
- Department of Neurology, Chang Gung Memorial Hospital, Keelung, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ho-Ching Chang
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Carol Seah
- Department of Neurology, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Li-Jen Lee
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
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122
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Hale MA, Johnson NE, Berglund JA. Repeat-associated RNA structure and aberrant splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194405. [PMID: 31323433 DOI: 10.1016/j.bbagrm.2019.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Over 30 hereditary disorders attributed to the expansion of microsatellite repeats have been identified. Despite variant nucleotide content, number of consecutive repeats, and different locations in the genome, many of these diseases have pathogenic RNA gain-of-function mechanisms. The repeat-containing RNAs can form structures in vitro predicted to contribute to the disease through assembly of intracellular RNA aggregates termed foci. The expanded repeat RNAs within these foci sequester RNA binding proteins (RBPs) with important roles in the regulation of RNA metabolism, most notably alternative splicing (AS). These deleterious interactions lead to downstream alterations in transcriptome-wide AS directly linked with disease symptoms. This review summarizes existing knowledge about the association between the repeat RNA structures and RBPs as well as the resulting aberrant AS patterns, specifically in the context of myotonic dystrophy. The connection between toxic, structured RNAs and dysregulation of AS in other repeat expansion diseases is also discussed. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Melissa A Hale
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nicholas E Johnson
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J Andrew Berglund
- The RNA Institute, Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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Ubiquitination of MBNL1 Is Required for Its Cytoplasmic Localization and Function in Promoting Neurite Outgrowth. Cell Rep 2019; 22:2294-2306. [PMID: 29490267 DOI: 10.1016/j.celrep.2018.02.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/19/2017] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
The Muscleblind-like protein family (MBNL) plays an important role in regulating the transition between differentiation and pluripotency and in the pathogenesis of myotonic dystrophy type 1 (DM1), a CTG expansion disorder. How different MBNL isoforms contribute to the differentiation and are affected in DM1 has not been investigated. Here, we show that the MBNL1 cytoplasmic, but not nuclear, isoform promotes neurite morphogenesis and reverses the morphological defects caused by expanded CUG RNA. Cytoplasmic MBNL1 is polyubiquitinated by lysine 63 (K63). Reduced cytoplasmic MBNL1 in the DM1 mouse brain is consistent with the reduced extent of K63 ubiquitination. Expanded CUG RNA induced the deubiqutination of cytoplasmic MBNL1, which resulted in nuclear translocation and morphological impairment that could be ameliorated by inhibiting K63-linked polyubiquitin chain degradation. Our results suggest that K63-linked ubiquitination of MBNL1 is required for its cytoplasmic localization and that deubiquitination of cytoplasmic MBNL1 is pathogenic in the DM1 brain.
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124
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André LM, van Cruchten RTP, Willemse M, Wansink DG. (CTG)n repeat-mediated dysregulation of MBNL1 and MBNL2 expression during myogenesis in DM1 occurs already at the myoblast stage. PLoS One 2019; 14:e0217317. [PMID: 31116797 PMCID: PMC6530876 DOI: 10.1371/journal.pone.0217317] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a severe neuromuscular disorder caused by the expression of trinucleotide repeat-containing DMPK transcripts. Abnormally expanded (CUG)n repeats in these transcripts form hairpin-like structures that cause the RNA to accumulate in the cell nucleus by sequestering isoforms of the Muscleblind (MBNL) family, tissue-specific regulators of developmentally programmed, post-transcriptional processes in RNA metabolism. Through this mechanism, the function of MBNL in RNA processing becomes dominantly perturbed, which eventually leads to aberrant alternative splicing and the expression of foetal splice variants of a wide variety of proteins, including the MBNL isoforms themselves. Here, we employ a patient-derived muscle cell model for DM1 to examine in detail the expression of MBNL RNA and protein variants during myogenic differentiation. This DM1 model consists of a panel of isogenic myoblast cell lines that either contain a pathogenic DMPK allele with a congenital mutation of 2600 triplets, or lack this expanded repeat through CRISPR/Cas9-mediated gene editing. We found that the temporal expression levels of MBNL1, MBNL2 and MBNL3 RNAs are not influenced by presence of the (CTG)2600 repeat during myogenesis in vitro. However, throughout myoblast proliferation and differentiation to myotubes a disproportionate inclusion of MBNL1 exon 5 and MBNL2 exons 5 and 8 occurs in cells with the (CTG)2600 repeat. As a consequence, a reduced quantity and imbalanced collection of splice variants of MBNL1 and MBNL2 accumulates in both the cytoplasm and the nucleus of DM1 myoblasts and myotubes. We thus propose that both the quantitative and qualitative changes in the intracellular partitioning of MBNL proteins are a pivotal cause of skeletal muscle problems in DM1, starting already in muscle progenitor cells.
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Affiliation(s)
- Laurène M. André
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Remco T. P. van Cruchten
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Marieke Willemse
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G. Wansink
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
- * E-mail:
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125
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Voellenkle C, Perfetti A, Carrara M, Fuschi P, Renna LV, Longo M, Sain SB, Cardani R, Valaperta R, Silvestri G, Legnini I, Bozzoni I, Furling D, Gaetano C, Falcone G, Meola G, Martelli F. Dysregulation of Circular RNAs in Myotonic Dystrophy Type 1. Int J Mol Sci 2019; 20:ijms20081938. [PMID: 31010208 PMCID: PMC6515344 DOI: 10.3390/ijms20081938] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/10/2019] [Accepted: 04/17/2019] [Indexed: 01/03/2023] Open
Abstract
Circular RNAs (circRNAs) constitute a recently re-discovered class of non-coding RNAs functioning as sponges for miRNAs and proteins, affecting RNA splicing and regulating transcription. CircRNAs are generated by “back-splicing”, which is the linking covalently of 3′- and 5′-ends of exons. Thus, circRNA levels might be deregulated in conditions associated with altered RNA-splicing. Significantly, growing evidence indicates their role in human diseases. Specifically, myotonic dystrophy type 1 (DM1) is a multisystemic disorder caused by expanded CTG repeats in the DMPK gene which results in abnormal mRNA-splicing. In this investigation, circRNAs expressed in DM1 skeletal muscles were identified by analyzing RNA-sequencing data-sets followed by qPCR validation. In muscle biopsies, out of nine tested, four transcripts showed an increased circular fraction: CDYL, HIPK3, RTN4_03, and ZNF609. Their circular fraction values correlated with skeletal muscle strength and with splicing biomarkers of disease severity, and displayed higher values in more severely affected patients. Moreover, Receiver-Operating-Characteristics curves of these four circRNAs discriminated DM1 patients from controls. The identified circRNAs were also detectable in peripheral-blood-mononuclear-cells (PBMCs) and the plasma of DM1 patients, but they were not regulated significantly. Finally, increased circular fractions of RTN4_03 and ZNF609 were also observed in differentiated myogenic cell lines derived from DM1 patients. In conclusion, this pilot study identified circRNA dysregulation in DM1 patients.
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Affiliation(s)
- Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Alessandra Perfetti
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Matteo Carrara
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Paola Fuschi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Laura Valentina Renna
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Marialucia Longo
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Simona Baghai Sain
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Rosanna Cardani
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Rea Valaperta
- Research Laboratories, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Gabriella Silvestri
- Department of Geriatrics, Orthopaedic and Neuroscience, Institute of Neurology, Catholic University of Sacred Heart, Fondazione Policlinico Gemelli, 00168 Rome, Italy.
| | - Ivano Legnini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Irene Bozzoni
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Denis Furling
- Sorbonne Université, INSERM, Association Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France.
| | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri, 27100 Pavia, Italy.
| | - Germana Falcone
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, 00015 Rome, Italy.
| | - Giovanni Meola
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
- Department of Neurology, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy.
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
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126
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Intrinsically cell-penetrating multivalent and multitargeting ligands for myotonic dystrophy type 1. Proc Natl Acad Sci U S A 2019; 116:8709-8714. [PMID: 30975744 DOI: 10.1073/pnas.1820827116] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Developing highly active, multivalent ligands as therapeutic agents is challenging because of delivery issues, limited cell permeability, and toxicity. Here, we report intrinsically cell-penetrating multivalent ligands that target the trinucleotide repeat DNA and RNA in myotonic dystrophy type 1 (DM1), interrupting the disease progression in two ways. The oligomeric ligands are designed based on the repetitive structure of the target with recognition moieties alternating with bisamidinium groove binders to provide an amphiphilic and polycationic structure, mimicking cell-penetrating peptides. Multiple biological studies suggested the success of our multivalency strategy. The designed oligomers maintained cell permeability and exhibited no apparent toxicity both in cells and in mice at working concentrations. Furthermore, the oligomers showed important activities in DM1 cells and in a DM1 liver mouse model, reducing or eliminating prominent DM1 features. Phenotypic recovery of the climbing defect in adult DM1 Drosophila was also observed. This design strategy should be applicable to other repeat expansion diseases and more generally to DNA/RNA-targeted therapeutics.
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127
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Ravel-Chapuis A, Al-Rewashdy A, Bélanger G, Jasmin BJ. Pharmacological and physiological activation of AMPK improves the spliceopathy in DM1 mouse muscles. Hum Mol Genet 2019; 27:3361-3376. [PMID: 29982462 DOI: 10.1093/hmg/ddy245] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/28/2018] [Indexed: 12/26/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a debilitating multisystemic disorder caused by a triplet repeat expansion in the 3' untranslated region of dystrophia myotonica protein kinase mRNAs. Mutant mRNAs accumulate in the nucleus of affected cells and misregulate RNA-binding proteins, thereby promoting characteristic missplicing events. However, little is known about the signaling pathways that may be affected in DM1. Here, we investigated the status of activated protein kinase (AMPK) signaling in DM1 skeletal muscle and found that the AMPK pathway is markedly repressed in a DM1 mouse model (human skeletal actin-long repeat, HSALR) and patient-derived DM1 myoblasts. Chronic pharmacological activation of AMPK signaling in DM1 mice with 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) has multiple beneficial effects on the DM1 phenotype. Indeed, a 6-week AICAR treatment of DM1 mice promoted expression of a slower, more oxidative phenotype, improved muscle histology and corrected several events associated with RNA toxicity. Importantly, AICAR also had a dose-dependent positive effect on the spliceopathy in patient-derived DM1 myoblasts. In separate experiments, we also show that chronic treatment of DM1 mice with resveratrol as well as voluntary wheel running also rescued missplicing events in muscle. Collectively, our findings demonstrate the therapeutic potential of chronic AMPK stimulation both physiologically and pharmacologically for DM1 patients.
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Affiliation(s)
- Aymeric Ravel-Chapuis
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ali Al-Rewashdy
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Guy Bélanger
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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128
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Kim EY, Barefield DY, Vo AH, Gacita AM, Schuster EJ, Wyatt EJ, Davis JL, Dong B, Sun C, Page P, Dellefave-Castillo L, Demonbreun A, Zhang HF, McNally EM. Distinct pathological signatures in human cellular models of myotonic dystrophy subtypes. JCI Insight 2019; 4:122686. [PMID: 30730308 DOI: 10.1172/jci.insight.122686] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/31/2019] [Indexed: 01/06/2023] Open
Abstract
Myotonic dystrophy (DM) is the most common autosomal dominant muscular dystrophy and encompasses both skeletal muscle and cardiac complications. DM is nucleotide repeat expansion disorder in which type 1 (DM1) is due to a trinucleotide repeat expansion on chromosome 19 and type 2 (DM2) arises from a tetranucleotide repeat expansion on chromosome 3. Developing representative models of DM in animals has been challenging due to instability of nucleotide repeat expansions, especially for DM2, which is characterized by nucleotide repeat expansions often greater than 5,000 copies. To investigate mechanisms of human DM, we generated cellular models of DM1 and DM2. We used regulated MyoD expression to reprogram urine-derived cells into myotubes. In this myogenic cell model, we found impaired dystrophin expression, in the presence of muscleblind-like 1 (MBNL1) foci, and aberrant splicing in DM1 but not in DM2 cells. We generated induced pluripotent stem cells (iPSC) from healthy controls and DM1 and DM2 subjects, and we differentiated these into cardiomyocytes. DM1 and DM2 cells displayed an increase in RNA foci concomitant with cellular differentiation. iPSC-derived cardiomyocytes from DM1 but not DM2 had aberrant splicing of known target genes and MBNL sequestration. High-resolution imaging revealed tight association between MBNL clusters and RNA foci in DM1. Ca2+ transients differed between DM1- and DM2 iPSC-derived cardiomyocytes, and each differed from healthy control cells. RNA-sequencing from DM1- and DM2 iPSC-derived cardiomyocytes revealed distinct misregulation of gene expression, as well as differential aberrant splicing patterns. Together, these data support that DM1 and DM2, despite some shared clinical and molecular features, have distinct pathological signatures.
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Affiliation(s)
- Ellis Y Kim
- Molecular Pathogenesis and Molecular Medicine, The University of Chicago, Chicago, Illinois, USA
| | - David Y Barefield
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Andy H Vo
- Committee on Development, Regeneration, and Stem Cell Biology, The University of Chicago, Chicago, Illinois, USA
| | - Anthony M Gacita
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Emma J Schuster
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Eugene J Wyatt
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Biqin Dong
- Department of Biomedical Engineering and.,Department of Mechanical Engineering, Northwestern University, Evanston, Illinois, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois, USA
| | - Patrick Page
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lisa Dellefave-Castillo
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alexis Demonbreun
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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129
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Musolf AM, Simpson CL, Alexander TA, Portas L, Murgia F, Ciner EB, Stambolian D, Bailey-Wilson JE. Genome-wide scans of myopia in Pennsylvania Amish families reveal significant linkage to 12q15, 8q21.3 and 5p15.33. Hum Genet 2019; 138:339-354. [PMID: 30826882 DOI: 10.1007/s00439-019-01991-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022]
Abstract
Myopia is one of the most common ocular disorders in the world, yet the genetic etiology of the disease remains poorly understood. Specialized founder populations, such as the Pennsylvania Amish, provide the opportunity to utilize exclusive genomic architecture, like unique haplotypes, to better understand the genetic causes of myopia. We perform genetic linkage analysis on Pennsylvania Amish families that have a strong familial history of myopia to map any potential causal variants and genes for the disease. 293 individuals from 25 extended families were genotyped on the Illumina ExomePlus array and merged with previous microsatellite data. We coded myopia affection as a binary phenotype; myopia was defined as having a mean spherical equivalent (MSE) of less than or equal to - 1 D (diopters). Two-point and multipoint parametric linkage analyses were performed under an autosomal dominant model. When allowing for locus heterogeneity, we identified two novel genome-wide significantly linked variants at 12q15 (heterogeneity LOD, HLOD = 3.77) in PTPRB and at 8q21.3 (HLOD = 3.35) in CNGB3. We identified further three genome-wide significant variants within a single family. These three variants were located in exons of SLC6A18 at 5p15.33 (LODs ranged from 3.51 to 3.37). Multipoint analysis confirmed the significant signal at 5p15.33 with six genome-wide significant variants (LODs ranged from 3.6 to 3.3). Further suggestive evidence of linkage was observed in several other regions of the genome. All three novel linked regions contain strong candidate genes, especially CNGB3 on 8q21.3, which has been shown to affect photoreceptors and cause complete color blindness. Whole genome sequencing on these regions is planned to conclusively elucidate the causal variants.
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Affiliation(s)
- Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Claire L Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA.,Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Theresa A Alexander
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Laura Portas
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Federico Murgia
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Elise B Ciner
- The Pennsylvania College of Optometry at Salus University, Elkins Park, PA, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA.
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130
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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131
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Maury Y, Poydenot P, Brinon B, Lesueur L, Gide J, Roquevière S, Côme J, Polvèche H, Auboeuf D, Alexandre Denis J, Pietu G, Furling D, Lechuga M, Baghdoyan S, Peschanski M, Martinat C. Pluripotent Stem Cell-Based Drug Screening Reveals Cardiac Glycosides as Modulators of Myotonic Dystrophy Type 1. iScience 2019; 11:258-271. [PMID: 30639849 PMCID: PMC6327858 DOI: 10.1016/j.isci.2018.12.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/14/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
There is currently no treatment for myotonic dystrophy type 1 (DM1), the most frequent myopathy of genetic origin. This progressive neuromuscular disease is caused by nuclear-retained RNAs containing expanded CUG repeats. These toxic RNAs alter the activities of RNA splicing factors, resulting in alternative splicing misregulation. By combining human mutated pluripotent stem cells and phenotypic drug screening, we revealed that cardiac glycosides act as modulators for both upstream nuclear aggregations of DMPK mRNAs and several downstream alternative mRNA splicing defects. However, these occurred at different drug concentration ranges. Similar biological effects were recorded in a DM1 mouse model. At the mechanistic level, we demonstrated that this effect was calcium dependent and was synergic with inhibition of the ERK pathway. These results further underscore the value of stem-cell-based assays for drug discovery in monogenic diseases. Myotonic dystrophy type 1 hPSCs were adapted for high content screening FDA-approved cardiac glycosides normalize in vitro and in vivo DM1 biological markers Cardiac glycosides synergize with the ERK pathway to normalize DM1 biomarkers This study emphasizes the value of human pluripotent stem cells for drug discovery
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Affiliation(s)
- Yves Maury
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | | | | | - Lea Lesueur
- INSERM, UMR 861, UEVE, ISTEM, AFM, 91100 Corbeil-Essonnes, France
| | | | | | - Julien Côme
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | | | | | | | - Geneviève Pietu
- INSERM, UMR 861, UEVE, ISTEM, AFM, 91100 Corbeil-Essonnes, France
| | - Denis Furling
- Sorbonne Universités UPMC Univ Paris 06, INSERM, Centre de Recherche en Myologie - UMRS974, Institut de Myologie, 75013 Paris, France
| | - Marc Lechuga
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | | | - Marc Peschanski
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France; INSERM, UMR 861, UEVE, ISTEM, AFM, 91100 Corbeil-Essonnes, France
| | - Cécile Martinat
- INSERM, UMR 861, UEVE, ISTEM, AFM, 91100 Corbeil-Essonnes, France.
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132
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Hinkle ER, Wiedner HJ, Black AJ, Giudice J. RNA processing in skeletal muscle biology and disease. Transcription 2019; 10:1-20. [PMID: 30556762 DOI: 10.1080/21541264.2018.1558677] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing.
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Affiliation(s)
- Emma R Hinkle
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Hannah J Wiedner
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Adam J Black
- b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Jimena Giudice
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA.,c McAllister Heart Institute , University of North Carolina , Chapel Hill , USA
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133
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Myotonic Dystrophy: an RNA Toxic Gain of Function Tauopathy? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1184:207-216. [PMID: 32096040 DOI: 10.1007/978-981-32-9358-8_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Myotonic dystrophies (DM) are rare inherited neuromuscular disorders linked to microsatellite unstable expansions in non-coding regions of ubiquitously expressed genes. The DMPK and ZNF9/CNBP genes which mutations are responsible for DM1 and DM2 respectively. DM are multisystemic disorders with brain affection and cognitive deficits. Brain lesions consisting of neurofibrillary tangles are often observed in DM1 and DM2 brain. Neurofibrillary tangles (NFT) made of aggregates of hyper and abnormally phosphorylated isoforms of Tau proteins are neuropathological lesions common to more than 20 neurological disorders globally referred to as Tauopathies. Although NFT are observed in DM1 and DM2 brain, the question of whether DM1 and DM2 are Tauopathies remains a matter of debate. In the present review, several pathophysiological processes including, missplicing, nucleocytoplasmic transport disruption, RAN translation which are common mechanisms implicated in neurodegenerative diseases will be described. Together, these processes including the missplicing of Tau are providing evidence that DM1 and DM2 are not solely muscular diseases but that their brain affection component share many similarities with Tauopathies and other neurodegenerative diseases. Understanding DM1 and DM2 pathophysiology is therefore valuable to more globally understand other neurodegenerative diseases such as Tauopathies but also frontotemporal lobar neurodegeneration and amyotrophic lateral sclerosis.
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135
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Neueder A. RNA-Mediated Disease Mechanisms in Neurodegenerative Disorders. J Mol Biol 2018; 431:1780-1791. [PMID: 30597161 DOI: 10.1016/j.jmb.2018.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 12/16/2022]
Abstract
RNA is accurately entangled in virtually all pathways that maintain cellular homeostasis. To name but a few, RNA is the "messenger" between DNA encoded information and the resulting proteins. Furthermore, RNAs regulate diverse processes by forming DNA::RNA or RNA::RNA interactions. Finally, RNA itself can be the scaffold for ribonucleoprotein complexes, for example, ribosomes or cellular bodies. Consequently, disruption of any of these processes can lead to disease. This review describes known and emerging RNA-based disease mechanisms like interference with regular splicing, the anomalous appearance of RNA-protein complexes and uncommon RNA species, as well as non-canonical translation. Due to the complexity and entanglement of the above-mentioned pathways, only few drugs are available that target RNA-based disease mechanisms. However, advances in our understanding how RNA is involved in and modulates cellular homeostasis might pave the way to novel treatments.
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Affiliation(s)
- Andreas Neueder
- Experimental Neurology, Department of Neurology, Ulm University, 89081 Ulm, Germany.
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136
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Souidi A, Zmojdzian M, Jagla K. Dissecting Pathogenetic Mechanisms and Therapeutic Strategies in Drosophila Models of Myotonic Dystrophy Type 1. Int J Mol Sci 2018; 19:E4104. [PMID: 30567354 PMCID: PMC6321436 DOI: 10.3390/ijms19124104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/08/2018] [Accepted: 12/13/2018] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1), the most common cause of adult-onset muscular dystrophy, is autosomal dominant, multisystemic disease with characteristic symptoms including myotonia, heart defects, cataracts and testicular atrophy. DM1 disease is being successfully modelled in Drosophila allowing to identify and validate new pathogenic mechanisms and potential therapeutic strategies. Here we provide an overview of insights gained from fruit fly DM1 models, either: (i) fundamental with particular focus on newly identified gene deregulations and their link with DM1 symptoms; or (ii) applied via genetic modifiers and drug screens to identify promising therapeutic targets.
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Affiliation(s)
- Anissa Souidi
- GReD, INSERM U1103, CNRS, UMR6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Monika Zmojdzian
- GReD, INSERM U1103, CNRS, UMR6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Krzysztof Jagla
- GReD, INSERM U1103, CNRS, UMR6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
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137
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Non-invasive monitoring of alternative splicing outcomes to identify candidate therapies for myotonic dystrophy type 1. Nat Commun 2018; 9:5227. [PMID: 30531949 PMCID: PMC6286378 DOI: 10.1038/s41467-018-07517-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/07/2018] [Indexed: 01/16/2023] Open
Abstract
During drug development, tissue samples serve as indicators of disease activity and pharmacodynamic responses. Reliable non-invasive measures of drug target engagement will facilitate identification of promising new treatments. Here we develop and validate a novel bi-transgenic mouse model of myotonic dystrophy type 1 (DM1) in which expression of either DsRed or GFP is determined by alternative splicing of an upstream minigene that is mis-regulated in DM1. Using a novel in vivo fluorescence spectroscopy system, we show that quantitation of the DsRed/GFP ratio provides an accurate estimation of splicing outcomes in muscle tissue of live mice that nearly doubles throughput over conventional fluorescence imaging techniques. Serial in vivo spectroscopy measurements in mice treated with a C16 fatty acid ligand conjugated antisense (LICA) oligonucleotide reveal a dose-dependent therapeutic response within seven days, confirm a several-week duration of action, and demonstrate a two-fold greater target engagement as compared to the unconjugated parent oligonucleotide.
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138
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Antoury L, Hu N, Balaj L, Das S, Georghiou S, Darras B, Clark T, Breakefield XO, Wheeler TM. Analysis of extracellular mRNA in human urine reveals splice variant biomarkers of muscular dystrophies. Nat Commun 2018; 9:3906. [PMID: 30254196 PMCID: PMC6156576 DOI: 10.1038/s41467-018-06206-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 08/22/2018] [Indexed: 12/18/2022] Open
Abstract
Urine contains extracellular RNA (exRNA) markers of urogenital cancers. However, the capacity of genetic material in urine to identify systemic diseases is unknown. Here we describe exRNA splice products in human urine as a source of biomarkers for the two most common forms of muscular dystrophies, myotonic dystrophy (DM) and Duchenne muscular dystrophy (DMD). Using a training set, RT-PCR, droplet digital PCR, and principal component regression, we identify ten transcripts that are spliced differently in urine exRNA from patients with DM type 1 (DM1) as compared to unaffected or disease controls, form a composite biomarker, and develop a predictive model that is 100% accurate in our independent validation set. Urine also contains mutation-specific DMD mRNAs that confirm exon-skipping activity of the antisense oligonucleotide drug eteplirsen. Our results establish that urine mRNA splice variants can be used to monitor systemic diseases with minimal or no clinical effect on the urinary tract.
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Affiliation(s)
- Layal Antoury
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ningyan Hu
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sofia Georghiou
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Basil Darras
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Tim Clark
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Xandra O Breakefield
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Thurman M Wheeler
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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139
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Jenquin JR, Coonrod LA, Silverglate QA, Pellitier NA, Hale MA, Xia G, Nakamori M, Berglund JA. Furamidine Rescues Myotonic Dystrophy Type I Associated Mis-Splicing through Multiple Mechanisms. ACS Chem Biol 2018; 13:2708-2718. [PMID: 30118588 DOI: 10.1021/acschembio.8b00646] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is an autosomal dominant, CTG•CAG microsatellite expansion disease. Expanded CUG repeat RNA sequester the muscleblind-like (MBNL) family of RNA-binding proteins, thereby disrupting their normal cellular function which leads to global mis-regulation of RNA processing. Previously, the small molecule furamidine was shown to reduce CUG foci and rescue mis-splicing in a DM1 HeLa cell model and to rescue mis-splicing in the HSALR DM1 mouse model, but furamidine's mechanism of action was not explored. Here we use a combination of biochemical, cell toxicity, and genomic studies in DM1 patient-derived myotubes and the HSALR DM1 mouse model to investigate furamidine's mechanism of action. Mis-splicing rescue was observed in DM1 myotubes and the HSALR DM1 mouse with furamidine treatment. Interestingly, while furamidine was found to bind CTG•CAG repeat DNA with nanomolar affinity, a reduction in expanded CUG repeat transcript levels was observed in the HSALR DM1 mouse but not DM1 patient-derived myotubes. Further investigation in these cells revealed that furamidine treatment at nanomolar concentrations led to up-regulation of MBNL1 and MBNL2 protein levels and a reduction of ribonuclear foci. Additionally, furamidine was shown to bind CUG RNA with nanomolar affinity and disrupted the MBNL1 -CUG RNA complex in vitro at micromolar concentrations. Furamidine's likely promiscuous interactions in vitro and in vivo appear to affect multiple pathways in the DM1 mechanism to rescue mis-splicing, yet surprisingly furamidine was shown globally to rescue many mis-splicing events with only modest off-target effects on gene expression in the HSALR DM1 mouse model. Importantly, over 20% of the differentially expressed genes were shown to be returned, to varying degrees, to wild-type expression levels.
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Affiliation(s)
- Jana R. Jenquin
- Department of Biochemistry & Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Leslie A. Coonrod
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - Quinn A. Silverglate
- Department of Biochemistry & Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Natalie A. Pellitier
- Department of Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Melissa A. Hale
- Department of Biochemistry & Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Guangbin Xia
- Department of Neurology and Neuroscience, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131, United States
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - J. Andrew Berglund
- Department of Biochemistry & Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
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140
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Dastidar S, Ardui S, Singh K, Majumdar D, Nair N, Fu Y, Reyon D, Samara E, Gerli MF, Klein AF, De Schrijver W, Tipanee J, Seneca S, Tulalamba W, Wang H, Chai Y, In’t Veld P, Furling D, Tedesco F, Vermeesch JR, Joung JK, Chuah MK, VandenDriessche T. Efficient CRISPR/Cas9-mediated editing of trinucleotide repeat expansion in myotonic dystrophy patient-derived iPS and myogenic cells. Nucleic Acids Res 2018; 46:8275-8298. [PMID: 29947794 PMCID: PMC6144820 DOI: 10.1093/nar/gky548] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/17/2022] Open
Abstract
CRISPR/Cas9 is an attractive platform to potentially correct dominant genetic diseases by gene editing with unprecedented precision. In the current proof-of-principle study, we explored the use of CRISPR/Cas9 for gene-editing in myotonic dystrophy type-1 (DM1), an autosomal-dominant muscle disorder, by excising the CTG-repeat expansion in the 3'-untranslated-region (UTR) of the human myotonic dystrophy protein kinase (DMPK) gene in DM1 patient-specific induced pluripotent stem cells (DM1-iPSC), DM1-iPSC-derived myogenic cells and DM1 patient-specific myoblasts. To eliminate the pathogenic gain-of-function mutant DMPK transcript, we designed a dual guide RNA based strategy that excises the CTG-repeat expansion with high efficiency, as confirmed by Southern blot and single molecule real-time (SMRT) sequencing. Correction efficiencies up to 90% could be attained in DM1-iPSC as confirmed at the clonal level, following ribonucleoprotein (RNP) transfection of CRISPR/Cas9 components without the need for selective enrichment. Expanded CTG repeat excision resulted in the disappearance of ribonuclear foci, a quintessential cellular phenotype of DM1, in the corrected DM1-iPSC, DM1-iPSC-derived myogenic cells and DM1 myoblasts. Consequently, the normal intracellular localization of the muscleblind-like splicing regulator 1 (MBNL1) was restored, resulting in the normalization of splicing pattern of SERCA1. This study validates the use of CRISPR/Cas9 for gene editing of repeat expansions.
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Affiliation(s)
- Sumitava Dastidar
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Simon Ardui
- Department of Human Genetics, University of Leuven, Leuven 3000, Belgium
| | - Kshitiz Singh
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Debanjana Majumdar
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Nisha Nair
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Yanfang Fu
- Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ermira Samara
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Mattia F M Gerli
- Department of Cell and Developmental Biology, University College London, London WC1E6DE, UK
| | - Arnaud F Klein
- Sorbonne Universités, INSERM, Association Institute de Myologie, Center de Recherche en Myologie, F-75013 , France
| | - Wito De Schrijver
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Jaitip Tipanee
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Sara Seneca
- Research Group Reproduction and Genetics (REGE), Center for Medical Genetics, UZ Brussels, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Warut Tulalamba
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Hui Wang
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Yoke Chin Chai
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Peter In’t Veld
- Department of Pathology, Vrije Universiteit Brussel, Brussels 1090, Belgium
| | - Denis Furling
- Sorbonne Universités, INSERM, Association Institute de Myologie, Center de Recherche en Myologie, F-75013 , France
| | | | - Joris R Vermeesch
- Department of Human Genetics, University of Leuven, Leuven 3000, Belgium
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Marinee K Chuah
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
- Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Thierry VandenDriessche
- Department of Gene Therapy & Regenerative Medicine, Vrije Universiteit Brussel, Brussels 1090, Belgium
- Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
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141
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Glineburg MR, Todd PK, Charlet-Berguerand N, Sellier C. Repeat-associated non-AUG (RAN) translation and other molecular mechanisms in Fragile X Tremor Ataxia Syndrome. Brain Res 2018; 1693:43-54. [PMID: 29453961 PMCID: PMC6010627 DOI: 10.1016/j.brainres.2018.02.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 11/11/2022]
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset inherited neurodegenerative disorder characterized by progressive intention tremor, gait ataxia and dementia associated with mild brain atrophy. The cause of FXTAS is a premutation expansion, of 55 to 200 CGG repeats localized within the 5'UTR of FMR1. These repeats are transcribed in the sense and antisense directions into mutants RNAs, which have increased expression in FXTAS. Furthermore, CGG sense and CCG antisense expanded repeats are translated into novel proteins despite their localization in putatively non-coding regions of the transcript. Here we focus on two proposed disease mechanisms for FXTAS: 1) RNA gain-of-function, whereby the mutant RNAs bind specific proteins and preclude their normal functions, and 2) repeat-associated non-AUG (RAN) translation, whereby translation through the CGG or CCG repeats leads to the production of toxic homopolypeptides, which in turn interfere with a variety of cellular functions. Here, we analyze the data generated to date on both of these potential molecular mechanisms and lay out a path forward for determining which factors drive FXTAS pathogenicity.
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Affiliation(s)
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Veteran's Affairs Medical Center, Ann Arbor, MI 48105, USA
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, University of Strasbourg, 67400 Illkirch, France
| | - Chantal Sellier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, University of Strasbourg, 67400 Illkirch, France.
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142
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Braz SO, Acquaire J, Gourdon G, Gomes-Pereira M. Of Mice and Men: Advances in the Understanding of Neuromuscular Aspects of Myotonic Dystrophy. Front Neurol 2018; 9:519. [PMID: 30050493 PMCID: PMC6050950 DOI: 10.3389/fneur.2018.00519] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 06/12/2018] [Indexed: 12/26/2022] Open
Abstract
Intensive effort has been directed toward the modeling of myotonic dystrophy (DM) in mice, in order to reproduce human disease and to provide useful tools to investigate molecular and cellular pathogenesis and test efficient therapies. Mouse models have contributed to dissect the multifaceted impact of the DM mutation in various tissues, cell types and in a pleiotropy of pathways, through the expression of toxic RNA transcripts. Changes in alternative splicing, transcription, translation, intracellular RNA localization, polyadenylation, miRNA metabolism and phosphorylation of disease intermediates have been described in different tissues. Some of these events have been directly associated with specific disease symptoms in the skeletal muscle and heart of mice, offering the molecular explanation for individual disease phenotypes. In the central nervous system (CNS), however, the situation is more complex. We still do not know how the molecular abnormalities described translate into CNS dysfunction, nor do we know if the correction of individual molecular events will provide significant therapeutic benefits. The variability in model design and phenotypes described so far requires a thorough and critical analysis. In this review we discuss the recent contributions of mouse models to the understanding of neuromuscular aspects of disease, therapy development, and we provide a reflective assessment of our current limitations and pressing questions that remain unanswered.
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Affiliation(s)
- Sandra O Braz
- Laboratory CTGDM, INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Julien Acquaire
- Laboratory CTGDM, INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Geneviève Gourdon
- Laboratory CTGDM, INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Mário Gomes-Pereira
- Laboratory CTGDM, INSERM UMR1163, Paris, France.,Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
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143
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Neueder A, Bates GP. RNA Related Pathology in Huntington's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1049:85-101. [PMID: 29427099 DOI: 10.1007/978-3-319-71779-1_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This chapter summarises research investigating the expression of huntingtin sense and anti-sense transcripts, the effect of the mutation on huntingtin processing as well as the more global effect of the mutation on the coding and non-coding transcriptomes. The huntingtin gene is ubiquitously expressed, although expression levels vary between tissues and cell types. A SNP that affects NF-ĸB binding in the huntingtin promoter modulates the expression level of huntingtin transcripts and is associated with the age of disease onset. Incomplete splicing between exon 1 and exon 2 has been shown to result in the expression of a small polyadenylated mRNA that encodes the highly pathogenic exon 1 huntingtin protein. This occurs in a CAG-repeat length dependent manner in all full-length mouse models of HD as well as HD patient post-mortem brains and fibroblasts. An antisense transcript to huntingtin is generated that contains a CUG repeat that is expanded in HD patients. In myotonic dystrophy, expanded CUG repeats form RNA foci in cell nuclei that bind specific proteins (e.g. MBL1). Short, pure CAG RNAs of approximately 21 nucleotides that have been processed by DICER can inhibit the translation of other CAG repeat containing mRNAs. The HD mutation affects the transcriptome at the level of mRNA expression, splicing and the expression of non-coding RNAs. Finally, expanded repetitive stretched of nucleotides can lead to RAN translation, in which the ribosome translates from the expanded repeat in all possible reading frames, producing proteins with various poly-amino acid tracts. The extent to which these events contribute to HD pathogenesis is largely unknown.
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Affiliation(s)
- Andreas Neueder
- Sobell Department of Motor Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Gillian P Bates
- Sobell Department of Motor Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
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144
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Zhang Y, Long C, Bassel-Duby R, Olson EN. Myoediting: Toward Prevention of Muscular Dystrophy by Therapeutic Genome Editing. Physiol Rev 2018; 98:1205-1240. [PMID: 29717930 PMCID: PMC6335101 DOI: 10.1152/physrev.00046.2017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/22/2017] [Accepted: 12/26/2017] [Indexed: 12/22/2022] Open
Abstract
Muscular dystrophies represent a large group of genetic disorders that significantly impair quality of life and often progress to premature death. There is no effective treatment for these debilitating diseases. Most therapies, developed to date, focus on alleviating the symptoms or targeting the secondary effects, while the underlying gene mutation is still present in the human genome. The discovery and application of programmable nucleases for site-specific DNA double-stranded breaks provides a powerful tool for precise genome engineering. In particular, the CRISPR/Cas system has revolutionized the genome editing field and is providing a new path for disease treatment by targeting the disease-causing genetic mutations. In this review, we provide a historical overview of genome-editing technologies, summarize the most recent advances, and discuss potential strategies and challenges for permanently correcting genetic mutations that cause muscular dystrophies.
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Affiliation(s)
- Yu Zhang
- Department of Molecular Biology, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center , Dallas, Texas
| | - Chengzu Long
- Department of Molecular Biology, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center , Dallas, Texas
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center , Dallas, Texas
| | - Eric N Olson
- Department of Molecular Biology, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center , Dallas, Texas
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145
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Jentsch TJ, Pusch M. CLC Chloride Channels and Transporters: Structure, Function, Physiology, and Disease. Physiol Rev 2018; 98:1493-1590. [DOI: 10.1152/physrev.00047.2017] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
CLC anion transporters are found in all phyla and form a gene family of eight members in mammals. Two CLC proteins, each of which completely contains an ion translocation parthway, assemble to homo- or heteromeric dimers that sometimes require accessory β-subunits for function. CLC proteins come in two flavors: anion channels and anion/proton exchangers. Structures of these two CLC protein classes are surprisingly similar. Extensive structure-function analysis identified residues involved in ion permeation, anion-proton coupling and gating and led to attractive biophysical models. In mammals, ClC-1, -2, -Ka/-Kb are plasma membrane Cl−channels, whereas ClC-3 through ClC-7 are 2Cl−/H+-exchangers in endolysosomal membranes. Biological roles of CLCs were mostly studied in mammals, but also in plants and model organisms like yeast and Caenorhabditis elegans. CLC Cl−channels have roles in the control of electrical excitability, extra- and intracellular ion homeostasis, and transepithelial transport, whereas anion/proton exchangers influence vesicular ion composition and impinge on endocytosis and lysosomal function. The surprisingly diverse roles of CLCs are highlighted by human and mouse disorders elicited by mutations in their genes. These pathologies include neurodegeneration, leukodystrophy, mental retardation, deafness, blindness, myotonia, hyperaldosteronism, renal salt loss, proteinuria, kidney stones, male infertility, and osteopetrosis. In this review, emphasis is laid on biophysical structure-function analysis and on the cell biological and organismal roles of mammalian CLCs and their role in disease.
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Affiliation(s)
- Thomas J. Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany; and Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Genova, Italy
| | - Michael Pusch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) and Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany; and Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Genova, Italy
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146
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Cappella M, Perfetti A, Cardinali B, Garcia-Manteiga JM, Carrara M, Provenzano C, Fuschi P, Cardani R, Renna LV, Meola G, Falcone G, Martelli F. High-throughput analysis of the RNA-induced silencing complex in myotonic dystrophy type 1 patients identifies the dysregulation of miR-29c and its target ASB2. Cell Death Dis 2018; 9:729. [PMID: 29955039 PMCID: PMC6023919 DOI: 10.1038/s41419-018-0769-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/01/2018] [Accepted: 06/08/2018] [Indexed: 01/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a multi-systemic disorder caused by abnormally expanded stretches of CTG DNA triplets in the DMPK gene, leading to mutated-transcript RNA-toxicity. MicroRNAs (miRNAs) are short non-coding RNAs that, after maturation, are loaded onto the RISC effector complex that destabilizes target mRNAs and represses their translation. In DM1 muscle biopsies not only the expression, but also the intracellular localization of specific miRNAs is disrupted, leading to the dysregulation of the relevant mRNA targets. To investigate the functional alterations of the miRNA/target interactions in DM1, we analyzed by RNA-sequencing the RISC-associated RNAs in skeletal muscle biopsies derived from DM1 patients and matched controls. The mRNAs found deregulated in DM1 biopsies were involved in pathways and functions relevant for the disease, such as energetic metabolism, calcium signaling, muscle contraction and p53-dependent apoptosis. Bioinformatic analysis of the miRNA/mRNA interactions based on the RISC enrichment profiles, identified 24 miRNA/mRNA correlations. Following validation in 21 independent samples, we focused on the couple miR-29c/ASB2 because of the role of miR-29c in fibrosis (a feature of late-stage DM1 patients) and of ASB2 in the regulation of muscle mass. Luciferase reporter assay confirmed the direct interaction between miR-29c and ASB2. Moreover, decreased miR-29c and increased ASB2 levels were verified also in immortalized myogenic cells and primary fibroblasts, derived from biopsies of DM1 patients and controls. CRISPR/Cas9-mediated deletion of CTG expansions rescued normal miR-29c and ASB2 levels, indicating a direct link between the mutant repeats and the miRNA/target expression. In conclusion, functionally relevant miRNA/mRNA interactions were identified in skeletal muscles of DM1 patients, highlighting the dysfunction of miR-29c and ASB2.
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Affiliation(s)
- Marisa Cappella
- Institute of Cell Biology and Neurobiology, National Research Council-Monterotondo, Rome, Italy
| | - Alessandra Perfetti
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council-Monterotondo, Rome, Italy
| | | | - Matteo Carrara
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Claudia Provenzano
- Institute of Cell Biology and Neurobiology, National Research Council-Monterotondo, Rome, Italy
| | - Paola Fuschi
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Rosanna Cardani
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Laura Valentina Renna
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
| | - Giovanni Meola
- Laboratory of Muscle Histopathology and Molecular Biology, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
- Department of Neurology, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Germana Falcone
- Institute of Cell Biology and Neurobiology, National Research Council-Monterotondo, Rome, Italy.
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, Milan, Italy.
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147
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Holdt LM, Kohlmaier A, Teupser D. Molecular functions and specific roles of circRNAs in the cardiovascular system. Noncoding RNA Res 2018; 3:75-98. [PMID: 30159442 PMCID: PMC6096412 DOI: 10.1016/j.ncrna.2018.05.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 12/25/2022] Open
Abstract
As part of the superfamily of long noncoding RNAs, circular RNAs (circRNAs) are emerging as a new type of regulatory molecules that partake in gene expression control. Here, we review the current knowledge about circRNAs in cardiovascular disease. CircRNAs are not only associated with different types of cardiovascular disease, but they have also been identified as intracellular effector molecules for pathophysiological changes in cardiovascular tissues, and as cardiovascular biomarkers. This evidence is put in the context of the current understanding of general circRNA biogenesis and of known interactions of circRNAs with DNA, RNA, and proteins.
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Affiliation(s)
- Lesca M. Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Germany
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148
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Corbett AH. Post-transcriptional regulation of gene expression and human disease. Curr Opin Cell Biol 2018; 52:96-104. [PMID: 29518673 PMCID: PMC5988930 DOI: 10.1016/j.ceb.2018.02.011] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 12/18/2022]
Abstract
A large number of mutations in genes that encode RNA binding proteins cause human disease. Many of these RNA binding proteins mediate key steps in post-transcriptional regulation of gene expression from mRNA processing to eventual decay in the cytoplasm. Surprisingly, these RNA binding proteins, which are ubiquitously expressed and play fundamental roles in gene expression, are often altered in tissue-specific disease. Mutations linked to disease impact nearly every post-transcriptional processing step and cause diverse disease phenotypes in a variety of specific tissues. This review summarizes steps in post-transcriptional regulation of gene expression that have been linked to disease providing specific examples of some of the many genes affected. Finally, recent advances that hold promise for treatment of some of these diseases are presented.
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Affiliation(s)
- Anita H Corbett
- Department of Biology, RRC 1021, Emory University, 1510 Clifton Road, NE, Atlanta 30322, GA, United States.
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149
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André LM, Ausems CRM, Wansink DG, Wieringa B. Abnormalities in Skeletal Muscle Myogenesis, Growth, and Regeneration in Myotonic Dystrophy. Front Neurol 2018; 9:368. [PMID: 29892259 PMCID: PMC5985300 DOI: 10.3389/fneur.2018.00368] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/07/2018] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) and 2 (DM2) are autosomal dominant degenerative neuromuscular disorders characterized by progressive skeletal muscle weakness, atrophy, and myotonia with progeroid features. Although both DM1 and DM2 are characterized by skeletal muscle dysfunction and also share other clinical features, the diseases differ in the muscle groups that are affected. In DM1, distal muscles are mainly affected, whereas in DM2 problems are mostly found in proximal muscles. In addition, manifestation in DM1 is generally more severe, with possible congenital or childhood-onset of disease and prominent CNS involvement. DM1 and DM2 are caused by expansion of (CTG•CAG)n and (CCTG•CAGG)n repeats in the 3' non-coding region of DMPK and in intron 1 of CNBP, respectively, and in overlapping antisense genes. This critical review will focus on the pleiotropic problems that occur during development, growth, regeneration, and aging of skeletal muscle in patients who inherited these expansions. The current best-accepted idea is that most muscle symptoms can be explained by pathomechanistic effects of repeat expansion on RNA-mediated pathways. However, aberrations in DNA replication and transcription of the DM loci or in protein translation and proteome homeostasis could also affect the control of proliferation and differentiation of muscle progenitor cells or the maintenance and physiological integrity of muscle fibers during a patient's lifetime. Here, we will discuss these molecular and cellular processes and summarize current knowledge about the role of embryonic and adult muscle-resident stem cells in growth, homeostasis, regeneration, and premature aging of healthy and diseased muscle tissue. Of particular interest is that also progenitor cells from extramuscular sources, such as pericytes and mesoangioblasts, can participate in myogenic differentiation. We will examine the potential of all these types of cells in the application of regenerative medicine for muscular dystrophies and evaluate new possibilities for their use in future therapy of DM.
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Affiliation(s)
- Laurène M André
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - C Rosanne M Ausems
- Department of Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bé Wieringa
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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150
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Sellier C, Cerro-Herreros E, Blatter M, Freyermuth F, Gaucherot A, Ruffenach F, Sarkar P, Puymirat J, Udd B, Day JW, Meola G, Bassez G, Fujimura H, Takahashi MP, Schoser B, Furling D, Artero R, Allain FHT, Llamusi B, Charlet-Berguerand N. rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/type 2 differences. Nat Commun 2018; 9:2009. [PMID: 29789616 PMCID: PMC5964235 DOI: 10.1038/s41467-018-04370-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 04/26/2018] [Indexed: 12/30/2022] Open
Abstract
Myotonic dystrophy type 1 and type 2 (DM1, DM2) are caused by expansions of CTG and CCTG repeats, respectively. RNAs containing expanded CUG or CCUG repeats interfere with the metabolism of other RNAs through titration of the Muscleblind-like (MBNL) RNA binding proteins. DM2 follows a more favorable clinical course than DM1, suggesting that specific modifiers may modulate DM severity. Here, we report that the rbFOX1 RNA binding protein binds to expanded CCUG RNA repeats, but not to expanded CUG RNA repeats. Interestingly, rbFOX1 competes with MBNL1 for binding to CCUG expanded repeats and overexpression of rbFOX1 partly releases MBNL1 from sequestration within CCUG RNA foci in DM2 muscle cells. Furthermore, expression of rbFOX1 corrects alternative splicing alterations and rescues muscle atrophy, climbing and flying defects caused by expression of expanded CCUG repeats in a Drosophila model of DM2.
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Affiliation(s)
- Chantal Sellier
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France
| | - Estefanía Cerro-Herreros
- Translational Genomics Group, Interdisciplinary Research Structure for Biotechnology and Biomedicine BIOTECMED, University of Valencia, 46010, Valencia, Spain
- INCLIVA Health Research Institute, 46010, Valencia, Spain
| | - Markus Blatter
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH) Zurich, 8092, Zurich, Switzerland
| | - Fernande Freyermuth
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France
| | - Angeline Gaucherot
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France
| | - Frank Ruffenach
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France
| | - Partha Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jack Puymirat
- Human Genetics Research Unit, Laval University, CHUQ, Ste-Foy, Quebec, QC G1V 4G2, Canada
| | - Bjarne Udd
- Neuromuscular Research Center, Tampere University Hospital, 33521, Tampere, Finland
- Department of Medical Genetics, Folkhälsan Institute of Genetics, Helsinki University, 00290, Helsinki, Finland
- Department of Neurology, Vasa Central Hospital, 65130, Vaasa, Finland
| | - John W Day
- Department of Neurology, Stanford University, San Francisco, CA, 94305, USA
| | - Giovanni Meola
- Department of Biomedical Sciences for Health, University of Milan, 20097, Milan, Italy
- Neurology Unit, IRCCS Policlinico San Donato, San Donato Milanese, 20097, Milan, Italy
| | - Guillaume Bassez
- Sorbonne Université, Inserm, Association Institut de Myologie, Center of Research in Myology, 75013, Paris, France
| | - Harutoshi Fujimura
- Department of Neurology, Toneyama National Hospital, Toyonaka, 560-0045, Japan
| | - Masanori P Takahashi
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, Ludwig Maximilian University, 80539, Munich, Germany
| | - Denis Furling
- Sorbonne Université, Inserm, Association Institut de Myologie, Center of Research in Myology, 75013, Paris, France
| | - Ruben Artero
- Translational Genomics Group, Interdisciplinary Research Structure for Biotechnology and Biomedicine BIOTECMED, University of Valencia, 46010, Valencia, Spain
- INCLIVA Health Research Institute, 46010, Valencia, Spain
| | - Frédéric H T Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH) Zurich, 8092, Zurich, Switzerland
| | - Beatriz Llamusi
- Translational Genomics Group, Interdisciplinary Research Structure for Biotechnology and Biomedicine BIOTECMED, University of Valencia, 46010, Valencia, Spain.
- INCLIVA Health Research Institute, 46010, Valencia, Spain.
| | - Nicolas Charlet-Berguerand
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France.
- UMR7104, Centre National de la Recherche Scientifique, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
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