1
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Molecular Therapies for Myotonic Dystrophy Type 1: From Small Drugs to Gene Editing. Int J Mol Sci 2022; 23:ijms23094622. [PMID: 35563013 PMCID: PMC9101876 DOI: 10.3390/ijms23094622] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy affecting many different body tissues, predominantly skeletal and cardiac muscles and the central nervous system. The expansion of CTG repeats in the DM1 protein-kinase (DMPK) gene is the genetic cause of the disease. The pathogenetic mechanisms are mainly mediated by the production of a toxic expanded CUG transcript from the DMPK gene. With the availability of new knowledge, disease models, and technical tools, much progress has been made in the discovery of altered pathways and in the potential of therapeutic intervention, making the path to the clinic a closer reality. In this review, we describe and discuss the molecular therapeutic strategies for DM1, which are designed to directly target the CTG genomic tract, the expanded CUG transcript or downstream signaling molecules.
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2
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Disrupting the Molecular Pathway in Myotonic Dystrophy. Int J Mol Sci 2021; 22:ijms222413225. [PMID: 34948025 PMCID: PMC8708683 DOI: 10.3390/ijms222413225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 01/26/2023] Open
Abstract
Myotonic dystrophy is the most common muscular dystrophy in adults. It consists of two forms: type 1 (DM1) and type 2 (DM2). DM1 is associated with a trinucleotide repeat expansion mutation, which is transcribed but not translated into protein. The mutant RNA remains in the nucleus, which leads to a series of downstream abnormalities. DM1 is widely considered to be an RNA-based disorder. Thus, we consider three areas of the RNA pathway that may offer targeting opportunities to disrupt the production, stability, and degradation of the mutant RNA.
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3
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Liu J, Guo ZN, Yan XL, Yang Y, Huang S. Brain Pathogenesis and Potential Therapeutic Strategies in Myotonic Dystrophy Type 1. Front Aging Neurosci 2021; 13:755392. [PMID: 34867280 PMCID: PMC8634727 DOI: 10.3389/fnagi.2021.755392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/20/2021] [Indexed: 12/17/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy that affects multiple systems including the muscle and heart. The mutant CTG expansion at the 3′-UTR of the DMPK gene causes the expression of toxic RNA that aggregate as nuclear foci. The foci then interfere with RNA-binding proteins, affecting hundreds of mis-spliced effector genes, leading to aberrant alternative splicing and loss of effector gene product functions, ultimately resulting in systemic disorders. In recent years, increasing clinical, imaging, and pathological evidence have indicated that DM1, though to a lesser extent, could also be recognized as true brain diseases, with more and more researchers dedicating to develop novel therapeutic tools dealing with it. In this review, we summarize the current advances in the pathogenesis and pathology of central nervous system (CNS) deficits in DM1, intervention measures currently being investigated are also highlighted, aiming to promote novel and cutting-edge therapeutic investigations.
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Affiliation(s)
- Jie Liu
- Department of Neurology, Stroke Center & Clinical Trial and Research Center for Stroke, The First Hospital of Jilin University, Changchun, China
- China National Comprehensive Stroke Center, Changchun, China
- Jilin Provincial Key Laboratory of Cerebrovascular Disease, Changchun, China
| | - Zhen-Ni Guo
- Department of Neurology, Stroke Center & Clinical Trial and Research Center for Stroke, The First Hospital of Jilin University, Changchun, China
- China National Comprehensive Stroke Center, Changchun, China
- Jilin Provincial Key Laboratory of Cerebrovascular Disease, Changchun, China
| | - Xiu-Li Yan
- Department of Neurology, Stroke Center & Clinical Trial and Research Center for Stroke, The First Hospital of Jilin University, Changchun, China
| | - Yi Yang
- Department of Neurology, Stroke Center & Clinical Trial and Research Center for Stroke, The First Hospital of Jilin University, Changchun, China
- China National Comprehensive Stroke Center, Changchun, China
- Jilin Provincial Key Laboratory of Cerebrovascular Disease, Changchun, China
| | - Shuo Huang
- Department of Neurology, Stroke Center & Clinical Trial and Research Center for Stroke, The First Hospital of Jilin University, Changchun, China
- China National Comprehensive Stroke Center, Changchun, China
- Jilin Provincial Key Laboratory of Cerebrovascular Disease, Changchun, China
- *Correspondence: Shuo Huang,
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4
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Neault N, O’Reilly S, Baig AT, Plaza-Diaz J, Azimi M, Farooq F, Baird SD, MacKenzie A. High-throughput kinome-RNAi screen identifies protein kinase R activator (PACT) as a novel genetic modifier of CUG foci integrity in myotonic dystrophy type 1 (DM1). PLoS One 2021; 16:e0256276. [PMID: 34520479 PMCID: PMC8439471 DOI: 10.1371/journal.pone.0256276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 08/03/2021] [Indexed: 11/24/2022] Open
Abstract
Myotonic Dystrophy Type 1 (DM1) is the most common form of adult muscular dystrophy (~1:8000). In DM1, expansion of CTG trinucleotide repeats in the 3' untranslated region of the dystrophia myotonica protein kinase (DMPK) gene results in DMPK mRNA hairpin structures which aggregate as insoluble ribonuclear foci and sequester several RNA-binding proteins. The resulting sequestration and misregulation of important splicing factors, such as muscleblind-like 1 (MBNL1), causes the aberrant expression of fetal transcripts for several genes that contribute to the disease phenotype. Previous work has shown that antisense oligonucleotide-mediated disaggregation of the intranuclear foci has the potential to reverse downstream anomalies. To explore whether the nuclear foci are, to some extent, controlled by cell signalling pathways, we have performed a screen using a small interfering RNA (siRNA) library targeting 518 protein kinases to look at kinomic modulation of foci integrity. RNA foci were visualized by in situ hybridization of a fluorescent-tagged (CAG)10 probe directed towards the expanded DMPK mRNA and the cross-sectional area and number of foci per nuclei were recorded. From our screen, we have identified PACT (protein kinase R (PKR) activator) as a novel modulator of foci integrity and have shown that PACT knockdown can both increase MBNL1 protein levels; however, these changes are not suffcient for significant correction of downstream spliceopathies.
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Affiliation(s)
- Nafisa Neault
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Sean O’Reilly
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Aiman Tariq Baig
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Julio Plaza-Diaz
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Mehrdad Azimi
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Faraz Farooq
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Stephen D. Baird
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Alex MacKenzie
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
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5
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An Overview of Alternative Splicing Defects Implicated in Myotonic Dystrophy Type I. Genes (Basel) 2020; 11:genes11091109. [PMID: 32971903 PMCID: PMC7564762 DOI: 10.3390/genes11091109] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 01/02/2023] Open
Abstract
Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy, caused by expansion of a CTG triplet repeat in the 3′ untranslated region (3′UTR) of the myotonic dystrophy protein kinase (DMPK) gene. The pathological CTG repeats result in protein trapping by expanded transcripts, a decreased DMPK translation and the disruption of the chromatin structure, affecting neighboring genes expression. The muscleblind-like (MBNL) and CUG-BP and ETR-3-like factors (CELF) are two families of tissue-specific regulators of developmentally programmed alternative splicing that act as antagonist regulators of several pre-mRNA targets, including troponin 2 (TNNT2), insulin receptor (INSR), chloride channel 1 (CLCN1) and MBNL2. Sequestration of MBNL proteins and up-regulation of CELF1 are key to DM1 pathology, inducing a spliceopathy that leads to a developmental remodelling of the transcriptome due to an adult-to-foetal splicing switch, which results in the loss of cell function and viability. Moreover, recent studies indicate that additional pathogenic mechanisms may also contribute to disease pathology, including a misregulation of cellular mRNA translation, localization and stability. This review focuses on the cause and effects of MBNL and CELF1 deregulation in DM1, describing the molecular mechanisms underlying alternative splicing misregulation for a deeper understanding of DM1 complexity. To contribute to this analysis, we have prepared a comprehensive list of transcript alterations involved in DM1 pathogenesis, as well as other deregulated mRNA processing pathways implications.
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6
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An Overview of Circular RNAs and Their Implications in Myotonic Dystrophy. Int J Mol Sci 2019; 20:ijms20184385. [PMID: 31500099 PMCID: PMC6769675 DOI: 10.3390/ijms20184385] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded covalently closed RNA rings. Biogenesis of circRNAs, which may occur co-transcriptionally and post-transcriptionally via a back-splicing mechanism, requires the presence of complementary and/or inverted repeat sequences in introns flanking back-spliced exons and is facilitated by RNA-binding proteins. CircRNAs are abundant across eukaryotes; however, their biological functions remain largely speculative. Recently, they have been emerging as new members of a gene regulatory network and contributing factors in various human diseases including cancer, neurological, muscular and cardiovascular disorders. In this review, we present an overview of the current knowledge about circRNAs biogenesis and their aberrant expression in various human disorders. In particular, we focus on the latest discovery of circRNAs global upregulation in myotonic dystrophy type 1 (DM1) skeletal muscles and the role these prospective biomarkers might have for prognosis and therapeutic response in DM1.
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7
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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: 2.8] [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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8
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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: 4.6] [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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9
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Czubak K, Taylor K, Piasecka A, Sobczak K, Kozlowska K, Philips A, Sedehizadeh S, Brook JD, Wojciechowska M, Kozlowski P. Global Increase in Circular RNA Levels in Myotonic Dystrophy. Front Genet 2019; 10:649. [PMID: 31428124 PMCID: PMC6689976 DOI: 10.3389/fgene.2019.00649] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/19/2019] [Indexed: 12/24/2022] Open
Abstract
Splicing aberrations induced as a consequence of the sequestration of muscleblind-like splicing factors on the dystrophia myotonica protein kinase transcript, which contains expanded CUG repeats, present a major pathomechanism of myotonic dystrophy type 1 (DM1). As muscleblind-like factors may also be important factors involved in the biogenesis of circular RNAs (circRNAs), we hypothesized that the level of circRNAs would be decreased in DM1. To test this hypothesis, we selected 20 well-validated circRNAs and analyzed their levels in several experimental systems (e.g., cell lines, DM muscle tissues, and a mouse model of DM1) using droplet digital PCR assays. We also explored the global level of circRNAs using two RNA-Seq datasets of DM1 muscle samples. Contrary to our original hypothesis, our results consistently showed a global increase in circRNA levels in DM1, and we identified numerous circRNAs that were increased in DM1. We also identified many genes (including muscle-specific genes) giving rise to numerous (>10) circRNAs. Thus, this study is the first to show an increase in global circRNA levels in DM1. We also provided preliminary results showing the association of circRNA level with muscle weakness and alternative splicing changes that are biomarkers of DM1 severity.
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Affiliation(s)
- Karol Czubak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Taylor
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Agnieszka Piasecka
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Katarzyna Kozlowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Saam Sedehizadeh
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - J. David Brook
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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10
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Li J, Nakamori M, Matsumoto J, Murata A, Dohno C, Kiliszek A, Taylor K, Sobczak K, Nakatani K. A Dimeric 2,9‐Diamino‐1,10‐phenanthroline Derivative Improves Alternative Splicing in Myotonic Dystrophy Type 1 Cell and Mouse Models. Chemistry 2018; 24:18115-18122. [DOI: 10.1002/chem.201804368] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/05/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Jinxing Li
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Masayuki Nakamori
- Department of NeurologyGraduate School of MedicineOsaka University 2-2 Yamadaoka Suita 565-0871 Japan
| | - Jun Matsumoto
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Asako Murata
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Agnieszka Kiliszek
- Department of Structure and Function of BiomoleculesThe Institute of Bioorganic ChemistryPolish Academy of Sciences Z. Noskowskiego 12/14 61-704 Poznan Poland
| | - Katarzyna Taylor
- Department of Gene ExpressionLaboratory of Gene TherapyInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz University Umultowska 89 61-614 Poznań Poland
| | - Krzysztof Sobczak
- Department of Gene ExpressionLaboratory of Gene TherapyInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz University Umultowska 89 61-614 Poznań Poland
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
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11
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López-Morató M, Brook JD, Wojciechowska M. Small Molecules Which Improve Pathogenesis of Myotonic Dystrophy Type 1. Front Neurol 2018; 9:349. [PMID: 29867749 PMCID: PMC5968088 DOI: 10.3389/fneur.2018.00349] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/30/2018] [Indexed: 12/30/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy in adults for which there is currently no treatment. The pathogenesis of this autosomal dominant disorder is associated with the expansion of CTG repeats in the 3'-UTR of the DMPK gene. DMPK transcripts with expanded CUG repeats (CUGexpDMPK) are retained in the nucleus forming multiple discrete foci, and their presence triggers a cascade of toxic events. Thus far, most research emphasis has been on interactions of CUGexpDMPK with the muscleblind-like (MBNL) family of splicing factors. These proteins are sequestered by the expanded CUG repeats of DMPK RNA leading to their functional depletion. As a consequence, abnormalities in many pathways of RNA metabolism, including alternative splicing, are detected in DM1. To date, in vitro and in vivo efforts to develop therapeutic strategies for DM1 have mostly been focused on targeting CUGexpDMPK via reducing their expression and/or preventing interactions with MBNL1. Antisense oligonucleotides targeted to the CUG repeats in the DMPK transcripts are of particular interest due to their potential capacity to discriminate between mutant and normal transcripts. However, a growing number of reports describe alternative strategies using small molecule chemicals acting independently of a direct interaction with CUGexpDMPK. In this review, we summarize current knowledge about these chemicals and we describe the beneficial effects they caused in different DM1 experimental models. We also present potential mechanisms of action of these compounds and pathways they affect which could be considered for future therapeutic interventions in DM1.
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Affiliation(s)
- Marta López-Morató
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - John David Brook
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Marzena Wojciechowska
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Polish Academy of Sciences, Department of Molecular Genetics, Institute of Bioorganic Chemistry, Poznan, Poland
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12
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Wojciechowska M, Sobczak K, Kozlowski P, Sedehizadeh S, Wojtkowiak-Szlachcic A, Czubak K, Markus R, Lusakowska A, Kaminska A, Brook JD. Quantitative Methods to Monitor RNA Biomarkers in Myotonic Dystrophy. Sci Rep 2018; 8:5885. [PMID: 29651162 PMCID: PMC5897446 DOI: 10.1038/s41598-018-24156-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/22/2018] [Indexed: 12/18/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are human neuromuscular disorders associated with mutations of simple repetitive sequences in affected genes. The abnormal expansion of CTG repeats in the 3'-UTR of the DMPK gene elicits DM1, whereas elongated CCTG repeats in intron 1 of ZNF9/CNBP triggers DM2. Pathogenesis of both disorders is manifested by nuclear retention of expanded repeat-containing RNAs and aberrant alternative splicing. The precise determination of absolute numbers of mutant RNA molecules is important for a better understanding of disease complexity and for accurate evaluation of the efficacy of therapeutic drugs. We present two quantitative methods, Multiplex Ligation-Dependent Probe Amplification and droplet digital PCR, for studying the mutant DMPK transcript (DMPKexpRNA) and the aberrant alternative splicing in DM1 and DM2 human tissues and cells. We demonstrate that in DM1, the DMPKexpRNA is detected in higher copy number than its normal counterpart. Moreover, the absolute number of the mutant transcript indicates its low abundance with only a few copies per cell in DM1 fibroblasts. Most importantly, in conjunction with fluorescence in-situ hybridization experiments, our results suggest that in DM1 fibroblasts, the vast majority of nuclear RNA foci consist of a few molecules of DMPKexpRNA.
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Affiliation(s)
- Marzena Wojciechowska
- University of Nottingham, Queen's Medical Centre, School of Life Sciences, Nottingham, NG7 2UH, United Kingdom. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Department of Molecular Genetics, Poznan, 61-704, Poland.
| | - Krzysztof Sobczak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Department of Gene Expression, Poznan, 60-614, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Department of Molecular Genetics, Poznan, 61-704, Poland
| | - Saam Sedehizadeh
- University of Nottingham, Queen's Medical Centre, School of Life Sciences, Nottingham, NG7 2UH, United Kingdom
| | - Agnieszka Wojtkowiak-Szlachcic
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Department of Gene Expression, Poznan, 60-614, Poland
| | - Karol Czubak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Department of Molecular Genetics, Poznan, 61-704, Poland
| | - Robert Markus
- University of Nottingham, Queen's Medical Centre, School of Life Sciences, Nottingham, NG7 2UH, United Kingdom
| | - Anna Lusakowska
- Medical University of Warsaw, Department of Neurology, Warsaw, 02-097, Poland
| | - Anna Kaminska
- Medical University of Warsaw, Department of Neurology, Warsaw, 02-097, Poland
| | - J David Brook
- University of Nottingham, Queen's Medical Centre, School of Life Sciences, Nottingham, NG7 2UH, United Kingdom.
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13
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Zhang F, Bodycombe NE, Haskell KM, Sun YL, Wang ET, Morris CA, Jones LH, Wood LD, Pletcher MT. A flow cytometry-based screen identifies MBNL1 modulators that rescue splicing defects in myotonic dystrophy type I. Hum Mol Genet 2018; 26:3056-3068. [PMID: 28535287 PMCID: PMC5886090 DOI: 10.1093/hmg/ddx190] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 05/08/2017] [Indexed: 11/17/2022] Open
Abstract
Myotonic dystrophy Type 1 (DM1) is a rare genetic disease caused by the expansion of CTG trinucleotide repeats ((CTG)exp) in the 3' untranslated region of the DMPK gene. The repeat transcripts sequester the RNA binding protein Muscleblind-like protein 1 (MBNL1) and hamper its normal function in pre-mRNA splicing. Overexpressing exogenous MBNL1 in the DM1 mouse model has been shown to rescue the splicing defects and reverse myotonia. Although a viable therapeutic strategy, pharmacological modulators of MBNL1 expression have not been identified. Here, we engineered a ZsGreen tag into the endogenous MBNL1 locus in HeLa cells and established a flow cytometry-based screening system to identify compounds that increase MBNL1 level. The initial screen of small molecule compound libraries identified more than thirty hits that increased MBNL1 expression greater than double the baseline levels. Further characterization of two hits revealed that the small molecule HDAC inhibitors, ISOX and vorinostat, increased MBNL1 expression in DM1 patient-derived fibroblasts and partially rescued the splicing defect caused by (CUG)exp repeats in these cells. These findings demonstrate the feasibility of this flow-based cytometry screen to identify both small molecule compounds and druggable targets for MBNL1 upregulation.
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Affiliation(s)
| | - Nicole E Bodycombe
- Medicine Design, Worldwide Research and Development, Pfizer, Cambridge, MA 02139, USA
| | - Keith M Haskell
- Pharmacokinetics, Dynamics and Metabolism - New Chemical Entities, Worldwide Research and Development, Pfizer, CT 06340, USA
| | | | - Eric T Wang
- Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA
| | | | - Lyn H Jones
- Medicine Design, Worldwide Research and Development, Pfizer, Cambridge, MA 02139, USA
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14
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Cywoniuk P, Taylor K, Sznajder ŁJ, Sobczak K. Hybrid splicing minigene and antisense oligonucleotides as efficient tools to determine functional protein/RNA interactions. Sci Rep 2017; 7:17587. [PMID: 29242583 PMCID: PMC5730568 DOI: 10.1038/s41598-017-17816-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing is a complex process that provides a high diversity of proteins from a limited number of protein-coding genes. It is governed by multiple regulatory factors, including RNA-binding proteins (RBPs), that bind to specific RNA sequences embedded in a specific structure. The ability to predict RNA-binding regions recognized by RBPs using whole-transcriptome approaches can deliver a multitude of data, including false-positive hits. Therefore, validation of the global results is indispensable. Here, we report the development of an efficient and rapid approach based on a modular hybrid minigene combined with antisense oligonucleotides to enable verification of functional RBP-binding sites within intronic and exonic sequences of regulated pre-mRNA. This approach also provides valuable information regarding the regulatory properties of pre-mRNA, including the RNA secondary structure context. We also show that the developed approach can be used to effectively identify or better characterize the inhibitory properties of potential therapeutic agents for myotonic dystrophy, which is caused by sequestration of specific RBPs, known as muscleblind-like proteins, by mutated RNA with expanded CUG repeats.
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Affiliation(s)
- Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland
| | - Łukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland.,Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida,, Gainesville, Florida, 32610-3610, USA
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland.
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15
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Konieczny P, Stepniak-Konieczna E, Taylor K, Sznajder LJ, Sobczak K. Autoregulation of MBNL1 function by exon 1 exclusion from MBNL1 transcript. Nucleic Acids Res 2017; 45:1760-1775. [PMID: 27903900 PMCID: PMC5389549 DOI: 10.1093/nar/gkw1158] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 11/07/2016] [Indexed: 01/14/2023] Open
Abstract
Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed that MBNL1 binds to MBNL1 exon 1 (e1) encoding both the major part of 5΄UTR and an amino-terminal region of MBNL1 protein. We tested several hypotheses regarding the possible autoregulatory function of MBNL1 binding to its own transcript. Our data indicate that MBNLs induce skipping of e1 from precursor MBNL1 mRNA and that e1 exclusion may impact transcript association with polysomes and translation. Furthermore, e1-deficient protein isoform lacking the first two zinc fingers is highly unstable and its EGFP fusion protein has severely compromised splicing activity. We also show that MBNL1 can be transcribed from three different promoters and that the transcription initiation site determines the mode of e1 regulation. Taken together, we demonstrate that MBNL proteins control steady-state levels of MBNL1 through an interaction with e1 in its precursor mRNA. Insights from our study open a new avenue in therapies against DM based on manipulation of the transcription initiation site and e1 splicing of MBNL1 mRNA.
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Affiliation(s)
- Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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16
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Konieczny P, Selma-Soriano E, Rapisarda AS, Fernandez-Costa JM, Perez-Alonso M, Artero R. Myotonic dystrophy: candidate small molecule therapeutics. Drug Discov Today 2017; 22:1740-1748. [PMID: 28780071 DOI: 10.1016/j.drudis.2017.07.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/14/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a rare multisystemic neuromuscular disorder caused by expansion of CTG trinucleotide repeats in the noncoding region of the DMPK gene. Mutant DMPK transcripts are toxic and alter gene expression at several levels. Chiefly, the secondary structure formed by CUGs has a strong propensity to capture and retain proteins, like those of the muscleblind-like (MBNL) family. Sequestered MBNL proteins cannot then fulfill their normal functions. Many therapeutic approaches have been explored to reverse these pathological consequences. Here, we review the myriad of small molecules that have been proposed for DM1, including examples obtained from computational rational design, HTS, drug repurposing, and therapeutic gene modulation.
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Affiliation(s)
- Piotr Konieczny
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Estela Selma-Soriano
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Anna S Rapisarda
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Juan M Fernandez-Costa
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Manuel Perez-Alonso
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Ruben Artero
- Department of Genetics and Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain.
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17
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Yenigun VB, Sirito M, Amcheslavky A, Czernuszewicz T, Colonques-Bellmunt J, García-Alcover I, Wojciechowska M, Bolduc C, Chen Z, López Castel A, Krahe R, Bergmann A. (CCUG) n RNA toxicity in a Drosophila model of myotonic dystrophy type 2 (DM2) activates apoptosis. Dis Model Mech 2017. [PMID: 28623239 PMCID: PMC5560059 DOI: 10.1242/dmm.026179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The myotonic dystrophies are prototypic toxic RNA gain-of-function diseases. Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are caused by different unstable, noncoding microsatellite repeat expansions – (CTG)DM1 in DMPK and (CCTG)DM2 in CNBP. Although transcription of mutant repeats into (CUG)DM1 or (CCUG)DM2 appears to be necessary and sufficient to cause disease, their pathomechanisms remain incompletely understood. To study the mechanisms of (CCUG)DM2 toxicity and develop a convenient model for drug screening, we generated a transgenic DM2 model in the fruit fly Drosophila melanogaster with (CCUG)n repeats of variable length (n=16 and 106). Expression of noncoding (CCUG)106, but not (CCUG)16, in muscle and retinal cells led to the formation of ribonuclear foci and mis-splicing of genes implicated in DM pathology. Mis-splicing could be rescued by co-expression of human MBNL1, but not by CUGBP1 (CELF1) complementation. Flies with (CCUG)106 displayed strong disruption of external eye morphology and of the underlying retina. Furthermore, expression of (CCUG)106 in developing retinae caused a strong apoptotic response. Inhibition of apoptosis rescued the retinal disruption in (CCUG)106 flies. Finally, we tested two chemical compounds that have shown therapeutic potential in DM1 models. Whereas treatment of (CCUG)106 flies with pentamidine had no effect, treatment with a PKR inhibitor blocked both the formation of RNA foci and apoptosis in retinae of (CCUG)106 flies. Our data indicate that expression of expanded (CCUG)DM2 repeats is toxic, causing inappropriate cell death in affected fly eyes. Our Drosophila DM2 model might provide a convenient tool for in vivo drug screening. Summary: A Drosophila model of myotonic dystrophy type 2 (DM2) recapitulates several features of the human disease, identifies apoptosis as a contributing factor to DM2, and is likely to provide a convenient tool for drug screening.
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Affiliation(s)
- Vildan Betul Yenigun
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Graduate Programs in Genes & Development, University of Texas Graduate School in Biomedical Sciences at Houston, Houston, TX, USA
| | - Mario Sirito
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alla Amcheslavky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Tomek Czernuszewicz
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Marzena Wojciechowska
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clare Bolduc
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhihong Chen
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Ralf Krahe
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA .,Graduate Programs in Genes & Development, University of Texas Graduate School in Biomedical Sciences at Houston, Houston, TX, USA.,Graduate Programs in Human & Molecular Genetics, University of Texas Graduate School in Biomedical Sciences at Houston, Houston, Texas, USA
| | - Andreas Bergmann
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA .,Graduate Programs in Genes & Development, University of Texas Graduate School in Biomedical Sciences at Houston, Houston, TX, USA.,Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
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18
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Barage S, Kulkarni A, Pal JK, Joshi M. Unravelling the structural interactions between PKR kinase domain and its small molecule inhibitors using computational approaches. J Mol Graph Model 2017. [PMID: 28628858 DOI: 10.1016/j.jmgm.2017.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The RNA-dependent protein kinase (PKR), an eIF2α kinase plays an important role in anti-viral response, apoptosis and cell survival. It is also implicated to play a role in several cancers, metabolic and neurodegenerative disorders. A few ATP competitive inhibitors of the PKR have been reported in the literature with promising results in vitro and in vivo. The aim of this study was to unravel the structural interactions between these inhibitors and the PKR kinase domain using molecular simulations and docking. Our study reveals that the reported inhibitors bind in the adenine pocket and form hydrogen bonds with the hinge region and vdW interactions with non-polar residues in the binding site. The most potent inhibitor has several favorable interactions with the binding site and induces the P-loop to fold inward, creating a significant hydrophobic enclosure for itself. The computed binding free energies of these inhibitors are in accord with experimental data (IC50). Strategies to design potent and selective PKR inhibitors are discussed to overcome the reported promiscuity.
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Affiliation(s)
- Sagar Barage
- Bioinformatics Centre, S. P. Pune University, Pune 411007, India
| | | | - Jayanta K Pal
- Department of Biotechnology, S. P. Pune University, Pune 411007, India; Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune 411033, India
| | - Manali Joshi
- Bioinformatics Centre, S. P. Pune University, Pune 411007, India.
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19
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Urbanek MO, Fiszer A, Krzyzosiak WJ. Reduction of Huntington's Disease RNA Foci by CAG Repeat-Targeting Reagents. Front Cell Neurosci 2017; 11:82. [PMID: 28400719 PMCID: PMC5368221 DOI: 10.3389/fncel.2017.00082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/09/2017] [Indexed: 12/14/2022] Open
Abstract
In several human polyglutamine diseases caused by expansions of CAG repeats in the coding sequence of single genes, mutant transcripts are detained in nuclear RNA foci. In polyglutamine disorders, unlike other repeat-associated diseases, both RNA and proteins exert pathogenic effects; therefore, decreases of both RNA and protein toxicity need to be addressed in proposed treatments. A variety of oligonucleotide-based therapeutic approaches have been developed for polyglutamine diseases, but concomitant assays for RNA foci reduction are lacking. Here, we show that various types of oligonucleotide-based reagents affect RNA foci number in Huntington’s disease cells. We analyzed the effects of reagents targeting either CAG repeat tracts or specific HTT sequences in fibroblasts derived from patients. We tested reagents that either acted as translation blockers or triggered mRNA degradation via the RNA interference pathway or RNase H activation. We also analyzed the effect of chemical modifications of CAG repeat-targeting siRNAs on their efficiency in the foci decline. Our results suggest that the decrease of RNA foci number may be considered as a readout of treatment outcomes for oligonucleotide reagents.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
| | - Agnieszka Fiszer
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
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20
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Sznajder ŁJ, Michalak M, Taylor K, Cywoniuk P, Kabza M, Wojtkowiak-Szlachcic A, Matłoka M, Konieczny P, Sobczak K. Mechanistic determinants of MBNL activity. Nucleic Acids Res 2016; 44:10326-10342. [PMID: 27733504 PMCID: PMC5137450 DOI: 10.1093/nar/gkw915] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/05/2016] [Indexed: 11/13/2022] Open
Abstract
Muscleblind-like (MBNL) proteins are critical RNA processing factors in development. MBNL activity is disrupted in the neuromuscular disease myotonic dystrophy type 1 (DM1), due to the instability of a non-coding microsatellite in the DMPK gene and the expression of CUG expansion (CUGexp) RNAs. Pathogenic interactions between MBNL and CUGexp RNA lead to the formation of nuclear complexes termed foci and prevent MBNL function in pre-mRNA processing. The existence of multiple MBNL genes, as well as multiple protein isoforms, raises the question of whether different MBNL proteins possess unique or redundant functions. To address this question, we coexpressed three MBNL paralogs in cells at equivalent levels and characterized both specific and redundant roles of these proteins in alternative splicing and RNA foci dynamics. When coexpressed in the same cells, MBNL1, MBNL2 and MBNL3 bind the same RNA motifs with different affinities. While MBNL1 demonstrated the highest splicing activity, MBNL3 showed the lowest. When forming RNA foci, MBNL1 is the most mobile paralog, while MBNL3 is rather static and the most densely packed on CUGexp RNA. Therefore, our results demonstrate that MBNL paralogs and gene-specific isoforms possess inherent functional differences, an outcome that could be enlisted to improve therapeutic strategies for DM1.
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Affiliation(s)
- Łukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Michał Michalak
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Michał Kabza
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Agnieszka Wojtkowiak-Szlachcic
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Magdalena Matłoka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
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21
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Urbanek MO, Krzyzosiak WJ. RNA FISH for detecting expanded repeats in human diseases. Methods 2015; 98:115-123. [PMID: 26615955 DOI: 10.1016/j.ymeth.2015.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/18/2015] [Accepted: 11/21/2015] [Indexed: 12/14/2022] Open
Abstract
RNA fluorescence in situ hybridization (FISH) is a widely used technique for detecting transcripts in fixed cells and tissues. Many variants of RNA FISH have been proposed to increase signal strength, resolution and target specificity. The current variants of this technique facilitate the detection of the subcellular localization of transcripts at a single molecule level. Among the applications of RNA FISH are studies on nuclear RNA foci in diseases resulting from the expansion of tri-, tetra-, penta- and hexanucleotide repeats present in different single genes. The partial or complete retention of mutant transcripts forming RNA aggregates within the nucleoplasm has been shown in multiple cellular disease models and in the tissues of patients affected with these atypical mutations. Relevant diseases include, among others, myotonic dystrophy type 1 (DM1) with CUG repeats, Huntington's disease (HD) and spinocerebellar ataxia type 3 (SCA3) with CAG repeats, fragile X-associated tremor/ataxia syndrome (FXTAS) with CGG repeats, myotonic dystrophy type 2 (DM2) with CCUG repeats, amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) with GGGGCC repeats and spinocerebellar ataxia type 32 (SCA32) with GGCCUG. In this article, we summarize the results obtained with FISH to examine RNA nuclear inclusions. We provide a detailed protocol for detecting RNAs containing expanded CAG and CUG repeats in different cellular models, including fibroblasts, lymphoblasts, induced pluripotent stem cells and murine and human neuronal progenitors. We also present the results of the first single-molecule FISH application in a cellular model of polyglutamine disease.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
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22
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Koscianska E, Witkos TM, Kozlowska E, Wojciechowska M, Krzyzosiak WJ. Cooperation meets competition in microRNA-mediated DMPK transcript regulation. Nucleic Acids Res 2015; 43:9500-18. [PMID: 26304544 PMCID: PMC4627076 DOI: 10.1093/nar/gkv849] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 08/10/2015] [Indexed: 02/07/2023] Open
Abstract
The fundamental role of microRNAs (miRNAs) in the regulation of gene expression has been well-established, but many miRNA-driven regulatory mechanisms remain elusive. In the present study, we demonstrate that miRNAs regulate the expression of DMPK, the gene mutated in myotonic dystrophy type 1 (DM1), and we provide insight regarding the concerted effect of the miRNAs on the DMPK target. Specifically, we examined the binding of several miRNAs to the DMPK 3′ UTR using luciferase assays. We validated the interactions between the DMPK transcript and the conserved miR-206 and miR-148a. We suggest a possible cooperativity between these two miRNAs and discuss gene targeting by miRNA pairs that vary in distance between their binding sites and expression profiles. In the same luciferase reporter system, we showed miR-15b/16 binding to the non-conserved CUG repeat tract present in the DMPK transcript and that the CUG-repeat-binding miRNAs might also act cooperatively. Moreover, we detected miR-16 in cytoplasmic foci formed by exogenously expressed RNAs with expanded CUG repeats. Therefore, we propose that the expanded CUGs may serve as a target for concerted regulation by miRNAs and may also act as molecular sponges for natural miRNAs with CAG repeats in their seed regions, thereby affecting their physiological functions.
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Affiliation(s)
- Edyta Koscianska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Tomasz M Witkos
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Emilia Kozlowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marzena Wojciechowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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23
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Lipscombe D, Pan JQ, Schorge S. Tracks through the genome to physiological events. Exp Physiol 2015; 100:1429-40. [PMID: 26053180 PMCID: PMC5008151 DOI: 10.1113/ep085129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022]
Abstract
New Findings What is the topic of this review? We discuss tools available to access genome‐wide data sets that harbour cell‐specific, brain region‐specific and tissue‐specific information on exon usage for several species, including humans. In this Review, we demonstrate how to access this information in genome databases and its enormous value to physiology. What advances does it highlight? The sheer scale of protein diversity that is possible from complex genes, including those that encode voltage‐gated ion channels, is vast. But this choice is critical for a complete understanding of protein function in the most physiologically relevant context.
Many proteins of great interest to physiologists and neuroscientists are structurally complex and located in specialized subcellular domains, such as neuronal synapses and transverse tubules of muscle. Genes that encode these critical signalling molecules (receptors, ion channels, transporters, enzymes, cell adhesion molecules, cell–cell interaction proteins and cytoskeletal proteins) are similarly complex. Typically, these genes are large; human Dystrophin (DMD) encodes a cytoskeletal protein of muscle and it is the largest naturally occurring gene at a staggering 2.3 Mb. Large genes contain many non‐coding introns and coding exons; human Titin (TTN), which encodes a protein essential for the assembly and functioning of vertebrate striated muscles, has over 350 exons and consequently has an enormous capacity to generate different forms of Titin mRNAs that have unique exon combinations. Functional and pharmacological differences among protein isoforms originating from the same gene may be subtle but nonetheless of critical physiological significance. Standard functional, immunological and pharmacological approaches, so useful for characterizing proteins encoded by different genes, typically fail to discriminate among splice isoforms of individual genes. Tools are now available to access genome‐wide data sets that harbour cell‐specific, brain region‐specific and tissue‐specific information on exon usage for several species, including humans. In this Review, we demonstrate how to access this information in genome databases and its enormous value to physiology.
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Affiliation(s)
- Diane Lipscombe
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
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24
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Wojtkowiak-Szlachcic A, Taylor K, Stepniak-Konieczna E, Sznajder LJ, Mykowska A, Sroka J, Thornton CA, Sobczak K. Short antisense-locked nucleic acids (all-LNAs) correct alternative splicing abnormalities in myotonic dystrophy. Nucleic Acids Res 2015; 43:3318-31. [PMID: 25753670 PMCID: PMC4381072 DOI: 10.1093/nar/gkv163] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 02/19/2015] [Indexed: 12/22/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disorder caused by expansion of CTG triplet repeats in 3′-untranslated region of DMPK gene. The pathomechanism of DM1 is driven by accumulation of toxic transcripts containing expanded CUG repeats (CUGexp) in nuclear foci which sequester several factors regulating RNA metabolism, such as Muscleblind-like proteins (MBNLs). In this work, we utilized very short chemically modified antisense oligonucleotides composed exclusively of locked nucleic acids (all-LNAs) complementary to CUG repeats, as potential therapeutic agents against DM1. Our in vitro data demonstrated that very short, 8- or 10-unit all-LNAs effectively bound the CUG repeat RNA and prevented the formation of CUGexp/MBNL complexes. In proliferating DM1 cells as well as in skeletal muscles of DM1 mouse model the all-LNAs induced the reduction of the number and size of CUGexp foci and corrected MBNL-sensitive alternative splicing defects with high efficacy and specificity. The all-LNAs had low impact on the cellular level of CUGexp-containing transcripts and did not affect the expression of other transcripts with short CUG repeats. Our data strongly indicate that short all-LNAs complementary to CUG repeats are a promising therapeutic tool against DM1.
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Affiliation(s)
- Agnieszka Wojtkowiak-Szlachcic
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Agnieszka Mykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Joanna Sroka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Charles A Thornton
- Department of Neurology, Box 645, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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