1
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Gibaut QR, Bush JA, Tong Y, Baisden JT, Taghavi A, Olafson H, Yao X, Childs-Disney JL, Wang ET, Disney MD. Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG) exp Degrader in Myotonic Dystrophy. ACS CENTRAL SCIENCE 2023; 9:1342-1353. [PMID: 37521782 PMCID: PMC10375898 DOI: 10.1021/acscentsci.2c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 08/01/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is caused by a highly structured RNA repeat expansion, r(CUG)exp, harbored in the 3' untranslated region (3' UTR) of dystrophia myotonica protein kinase (DMPK) mRNA and drives disease through a gain-of-function mechanism. A panel of low-molecular-weight fragments capable of reacting with RNA upon UV irradiation was studied for cross-linking to r(CUG)expin vitro, affording perimidin-2-amine diazirine (1) that bound to r(CUG)exp. The interactions between the small molecule and RNA were further studied by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Binding of 1 in DM1 myotubes was profiled transcriptome-wide, identifying 12 transcripts including DMPK that were bound by 1. Augmenting the functionality of 1 with cleaving capability created a chimeric degrader that specifically targets r(CUG)exp for elimination. The degrader broadly improved DM1-associated defects as assessed by RNA-seq, while having limited effects on healthy myotubes. This study (i) provides a platform to investigate molecular recognition of ligands directly in disease-affected cells; (ii) illustrates that RNA degraders can be more specific than the binders from which they are derived; and (iii) suggests that repeating transcripts can be selectively degraded due to the presence of multiple ligand binding sites.
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Affiliation(s)
- Quentin
M. R. Gibaut
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jared T. Baisden
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hailey Olafson
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Xiyuan Yao
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Eric T. Wang
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Matthew D. Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
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2
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Porquet F, Weidong L, Jehasse K, Gazon H, Kondili M, Blacher S, Massotte L, Di Valentin E, Furling D, Gillet NA, Klein AF, Seutin V, Willems L. Specific DMPK-promoter targeting by CRISPRi reverses myotonic dystrophy type 1-associated defects in patient muscle cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:857-871. [PMID: 37273786 PMCID: PMC10238591 DOI: 10.1016/j.omtn.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 06/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a neuromuscular disease that originates from an expansion of CTG microsatellites in the 3' untranslated region of the DMPK gene, thus leading to the expression of transcripts containing expanded CUG repeats (CUGexp). The pathophysiology is explained by a toxic RNA gain of function where CUGexp RNAs form nuclear aggregates that sequester and alter the function of MBNL splicing factors, triggering splicing misregulation linked to the DM1 symptoms. There is currently no cure for DM1, and most therapeutic strategies aim at eliminating CUGexp-DMPK transcripts. Here, we investigate a DMPK-promoter silencing strategy using CRISPR interference as a new alternative approach. Different sgRNAs targeting the DMPK promoter are evaluated in DM1 patient muscle cells. The most effective guides allowed us to reduce the level of DMPK transcripts and CUGexp-RNA aggregates up to 80%. The CUGexp-DMPK repression corrects the overall transcriptome, including spliceopathy, and reverses a physiological parameter in DM1 muscle cells. Its action is specific and restricted to the DMPK gene, as confirmed by genome-wide expression analysis. Altogether, our findings highlight DMPK-promoter silencing by CRISPRi as a promising therapeutic approach for DM1.
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Affiliation(s)
- Florent Porquet
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Lin Weidong
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Kévin Jehasse
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | - Hélène Gazon
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Maria Kondili
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Silvia Blacher
- Laboratory of Biology of Tumor and Development, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Laurent Massotte
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | | | - Denis Furling
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Nicolas Albert Gillet
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, 5000 Namur, Belgium
| | - Arnaud François Klein
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Vincent Seutin
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | - Luc Willems
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
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3
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El Boujnouni N, van der Bent ML, Willemse M, ’t Hoen PA, Brock R, Wansink DG. Block or degrade? Balancing on- and off-target effects of antisense strategies against transcripts with expanded triplet repeats in DM1. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:622-636. [PMID: 37200862 PMCID: PMC10185704 DOI: 10.1016/j.omtn.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/13/2023] [Indexed: 05/20/2023]
Abstract
Antisense oligonucleotide (ASO) therapies for myotonic dystrophy type 1 (DM1) are based on elimination of transcripts containing an expanded repeat or inhibition of sequestration of RNA-binding proteins. This activity is achievable by both degradation of expanded transcripts and steric hindrance, although it is unknown which approach is superior. We compared blocking ASOs with RNase H-recruiting gapmers of equivalent chemistries. Two DMPK target sequences were selected: the triplet repeat and a unique sequence upstream thereof. We assessed ASO effects on transcript levels, ribonucleoprotein foci and disease-associated missplicing, and performed RNA sequencing to investigate on- and off-target effects. Both gapmers and the repeat blocker led to significant DMPK knockdown and a reduction in (CUG)exp foci. However, the repeat blocker was more effective in MBNL1 protein displacement and had superior efficiency in splicing correction at the tested dose of 100 nM. By comparison, on a transcriptome level, the blocking ASO had the fewest off-target effects. In particular, the off-target profile of the repeat gapmer asks for cautious consideration in further therapeutic development. Altogether, our study demonstrates the importance of evaluating both on-target and downstream effects of ASOs in a DM1 context, and provides guiding principles for safe and effective targeting of toxic transcripts.
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Affiliation(s)
- Najoua El Boujnouni
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - M. Leontien van der Bent
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Marieke Willemse
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Peter A.C. ’t Hoen
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Roland Brock
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 293, Bahrain
- Corresponding author Roland Brock, Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
| | - Derick G. Wansink
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Corresponding author Derick G. Wansink, Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
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4
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De Serres-Bérard T, Ait Benichou S, Jauvin D, Boutjdir M, Puymirat J, Chahine M. Recent Progress and Challenges in the Development of Antisense Therapies for Myotonic Dystrophy Type 1. Int J Mol Sci 2022; 23:13359. [PMID: 36362145 PMCID: PMC9657934 DOI: 10.3390/ijms232113359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 08/01/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a dominant genetic disease in which the expansion of long CTG trinucleotides in the 3' UTR of the myotonic dystrophy protein kinase (DMPK) gene results in toxic RNA gain-of-function and gene mis-splicing affecting mainly the muscles, the heart, and the brain. The CUG-expanded transcripts are a suitable target for the development of antisense oligonucleotide (ASO) therapies. Various chemical modifications of the sugar-phosphate backbone have been reported to significantly enhance the affinity of ASOs for RNA and their resistance to nucleases, making it possible to reverse DM1-like symptoms following systemic administration in different transgenic mouse models. However, specific tissue delivery remains to be improved to achieve significant clinical outcomes in humans. Several strategies, including ASO conjugation to cell-penetrating peptides, fatty acids, or monoclonal antibodies, have recently been shown to improve potency in muscle and cardiac tissues in mice. Moreover, intrathecal administration of ASOs may be an advantageous complementary administration route to bypass the blood-brain barrier and correct defects of the central nervous system in DM1. This review describes the evolution of the chemical design of antisense oligonucleotides targeting CUG-expanded mRNAs and how recent advances in the field may be game-changing by forwarding laboratory findings into clinical research and treatments for DM1 and other microsatellite diseases.
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Affiliation(s)
- Thiéry De Serres-Bérard
- CERVO Research Center, Institut Universitaire en Santé Mentale de Québec, Quebec City, QC G1J 2G3, Canada
| | - Siham Ait Benichou
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, QC G1J 1Z4, Canada
| | - Dominic Jauvin
- CERVO Research Center, Institut Universitaire en Santé Mentale de Québec, Quebec City, QC G1J 2G3, Canada
| | - Mohamed Boutjdir
- Cardiovascular Research Program, VA New York Harbor Healthcare System, New York, NY 11209, USA
- Department of Medicine, Cell Biology and Pharmacology, State University of New York Downstate Health Science University, New York, NY 11203, USA
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Jack Puymirat
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, QC G1J 1Z4, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Mohamed Chahine
- CERVO Research Center, Institut Universitaire en Santé Mentale de Québec, Quebec City, QC G1J 2G3, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
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5
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Dincã DM, Lallemant L, González-Barriga A, Cresto N, Braz SO, Sicot G, Pillet LE, Polvèche H, Magneron P, Huguet-Lachon A, Benyamine H, Azotla-Vilchis CN, Agonizantes-Juárez LE, Tahraoui-Boris J, Martinat C, Hernández-Hernández O, Auboeuf D, Rouach N, Bourgeois CF, Gourdon G, Gomes-Pereira M. Myotonic dystrophy RNA toxicity alters morphology, adhesion and migration of mouse and human astrocytes. Nat Commun 2022; 13:3841. [PMID: 35789154 PMCID: PMC9253038 DOI: 10.1038/s41467-022-31594-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/21/2022] [Indexed: 11/24/2022] Open
Abstract
Brain dysfunction in myotonic dystrophy type 1 (DM1), the prototype of toxic RNA disorders, has been mainly attributed to neuronal RNA misprocessing, while little attention has been given to non-neuronal brain cells. Here, using a transgenic mouse model of DM1 that expresses mutant RNA in various brain cell types (neurons, astroglia, and oligodendroglia), we demonstrate that astrocytes exhibit impaired ramification and polarization in vivo and defects in adhesion, spreading, and migration. RNA-dependent toxicity and phenotypes are also found in human transfected glial cells. In line with the cell phenotypes, molecular analyses reveal extensive expression and accumulation of toxic RNA in astrocytes, which result in RNA spliceopathy that is more severe than in neurons. Astrocyte missplicing affects primarily transcripts that regulate cell adhesion, cytoskeleton, and morphogenesis, and it is confirmed in human brain tissue. Our findings demonstrate that DM1 impacts astrocyte cell biology, possibly compromising their support and regulation of synaptic function. Myotonic dystrophy type 1 (DM1) is characterized by debilitating neurological symptoms. Dinca et al. demonstrate the pronounced impact of DM1 on the morphology and RNA metabolism of astrocytes. Their findings suggest astroglial pathology in DM1 brain dysfunction.
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Affiliation(s)
- Diana M Dincã
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Louison Lallemant
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | | | - Noémie Cresto
- Neuroglial Interactions in Cerebral Physiology and Pathologies, Center for Interdisciplinary Research in Biology, Collège de France, CNRS, Inserm, Labex Memolife, 75005, Paris, France
| | - Sandra O Braz
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France.,Inserm UMR1163, Institut Imagine, Université Paris Cite, 75015, Paris, France
| | - Géraldine Sicot
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Laure-Elise Pillet
- Neuroglial Interactions in Cerebral Physiology and Pathologies, Center for Interdisciplinary Research in Biology, Collège de France, CNRS, Inserm, Labex Memolife, 75005, Paris, France.,Doctoral School N°562, Paris Descartes University, Paris, 75006, France
| | - Hélène Polvèche
- Inserm/UEVE UMR861, Université Paris Saclay I-STEM, 91110, Corbeil-Essonnes, France
| | - Paul Magneron
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Aline Huguet-Lachon
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Hélène Benyamine
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France
| | - Cuauhtli N Azotla-Vilchis
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City, Mexico
| | - Luis E Agonizantes-Juárez
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City, Mexico
| | - Julie Tahraoui-Boris
- Inserm/UEVE UMR861, Université Paris Saclay I-STEM, 91110, Corbeil-Essonnes, France
| | - Cécile Martinat
- Inserm/UEVE UMR861, Université Paris Saclay I-STEM, 91110, Corbeil-Essonnes, France
| | - Oscar Hernández-Hernández
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City, Mexico
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allée d'Italie, 69364, Lyon, France
| | - Nathalie Rouach
- Neuroglial Interactions in Cerebral Physiology and Pathologies, Center for Interdisciplinary Research in Biology, Collège de France, CNRS, Inserm, Labex Memolife, 75005, Paris, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allée d'Italie, 69364, Lyon, France
| | - Geneviève Gourdon
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France.
| | - Mário Gomes-Pereira
- Sorbonne Université, Inserm, Centre de Recherche en Myologie, 75013, Paris, France.
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6
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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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7
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Koscianska E, Kozlowska E, Fiszer A. Regulatory Potential of Competing Endogenous RNAs in Myotonic Dystrophies. Int J Mol Sci 2021; 22:ijms22116089. [PMID: 34200099 PMCID: PMC8201210 DOI: 10.3390/ijms22116089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have been reported to be implicated in cell fate determination and various human diseases. All ncRNA molecules are emerging as key regulators of diverse cellular processes; however, little is known about the regulatory interaction among these various classes of RNAs. It has been proposed that the large-scale regulatory network across the whole transcriptome is mediated by competing endogenous RNA (ceRNA) activity attributed to both protein-coding and ncRNAs. ceRNAs are considered to be natural sponges of miRNAs that can influence the expression and availability of multiple miRNAs and, consequently, the global mRNA and protein levels. In this review, we summarize the current understanding of the role of ncRNAs in two neuromuscular diseases, myotonic dystrophy type 1 and 2 (DM1 and DM2), and the involvement of expanded CUG and CCUG repeat-containing transcripts in miRNA-mediated RNA crosstalk. More specifically, we discuss the possibility that long repeat tracts present in mutant transcripts can be potent miRNA sponges and may affect ceRNA crosstalk in these diseases. Moreover, we highlight practical information related to innovative disease modelling and studying RNA regulatory networks in cells. Extending knowledge of gene regulation by ncRNAs, and of complex regulatory ceRNA networks in DM1 and DM2, will help to address many questions pertinent to pathogenesis and treatment of these disorders; it may also help to better understand general rules of gene expression and to discover new rules of gene control.
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8
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Tanner MK, Tang Z, Thornton CA. Targeted splice sequencing reveals RNA toxicity and therapeutic response in myotonic dystrophy. Nucleic Acids Res 2021; 49:2240-2254. [PMID: 33503262 PMCID: PMC7913682 DOI: 10.1093/nar/gkab022] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/03/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
Biomarker-driven trials hold promise for therapeutic development in chronic diseases, such as muscular dystrophy. Myotonic dystrophy type 1 (DM1) involves RNA toxicity, where transcripts containing expanded CUG-repeats (CUGexp) accumulate in nuclear foci and sequester splicing factors in the Muscleblind-like (Mbnl) family. Oligonucleotide therapies to mitigate RNA toxicity have emerged but reliable measures of target engagement are needed. Here we examined muscle transcriptomes in mouse models of DM1 and found that CUGexp expression or Mbnl gene deletion cause similar dysregulation of alternative splicing. We selected 35 dysregulated exons for further study by targeted RNA sequencing. Across a spectrum of mouse models, the individual splice events and a composite index derived from all events showed a graded response to decrements of Mbnl or increments of CUGexp. Antisense oligonucleotides caused prompt reduction of CUGexp RNA and parallel correction of the splicing index, followed by subsequent elimination of myotonia. These results suggest that targeted splice sequencing may provide a sensitive and reliable way to assess therapeutic impact in DM1.
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Affiliation(s)
- Matthew K Tanner
- Medical Scientist Training Program, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Zhenzhi Tang
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
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9
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Chu Y, Hu J, Liang H, Kanchwala M, Xing C, Beebe W, Bowman CB, Gong X, Corey DR, Mootha VV. Analyzing pre-symptomatic tissue to gain insights into the molecular and mechanistic origins of late-onset degenerative trinucleotide repeat disease. Nucleic Acids Res 2020; 48:6740-6758. [PMID: 32463444 PMCID: PMC7337964 DOI: 10.1093/nar/gkaa422] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/02/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022] Open
Abstract
How genetic defects trigger the molecular changes that cause late-onset disease is important for understanding disease progression and therapeutic development. Fuchs' endothelial corneal dystrophy (FECD) is an RNA-mediated disease caused by a trinucleotide CTG expansion in an intron within the TCF4 gene. The mutant intronic CUG RNA is present at one-two copies per cell, posing a challenge to understand how a rare RNA can cause disease. Late-onset FECD is a uniquely advantageous model for studying how RNA triggers disease because: (i) Affected tissue is routinely removed during surgery; (ii) The expanded CTG mutation is one of the most prevalent disease-causing mutations, making it possible to obtain pre-symptomatic tissue from eye bank donors to probe how gene expression changes precede disease; and (iii) The affected tissue is a homogeneous single cell monolayer, facilitating accurate transcriptome analysis. Here, we use RNA sequencing (RNAseq) to compare tissue from individuals who are pre-symptomatic (Pre_S) to tissue from patients with late stage FECD (FECD_REP). The abundance of mutant repeat intronic RNA in Pre_S and FECD_REP tissue is elevated due to increased half-life in a corneal cells. In Pre_S tissue, changes in splicing and extracellular matrix gene expression foreshadow the changes observed in advanced disease and predict the activation of the fibrosis pathway and immune system seen in late-stage patients. The absolute magnitude of splicing changes is similar in pre-symptomatic and late stage tissue. Our data identify gene candidates for early drivers of disease and biomarkers that may represent diagnostic and therapeutic targets for FECD. We conclude that changes in alternative splicing and gene expression are observable decades prior to the diagnosis of late-onset trinucleotide repeat disease.
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Affiliation(s)
- Yongjun Chu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiaxin Hu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hanquan Liang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Xin Gong
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9057, USA
| | - David R Corey
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - V Vinod Mootha
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9057, USA
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Al-Khalili Szigyarto C. Duchenne Muscular Dystrophy: recent advances in protein biomarkers and the clinical application. Expert Rev Proteomics 2020; 17:365-375. [PMID: 32713262 DOI: 10.1080/14789450.2020.1773806] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Early biomarker discovery studies have praised the value of their emerging results, predicting an unprecedented impact on health care. Biomarkers are expected to provide tests with increased specificity and sensitivity compared to existing measures, improve the decision-making process, and accelerate the development of therapies. For rare disorders, like Duchenne Muscular Dystrophy (DMD) such biomarkers can assist the development of therapies, therefore also helping to find a cure for the disease. AREA COVERED State-of-the-art technologies have been used to identify blood biomarkers for DMD and efforts have been coordinated to develop and promote translation of biomarkers for clinical practice. Biomarker translation to clinical practice is however, adjoined by challenges related to the complexity of the disease, involving numerous biological processes, and the limited sample resources. This review highlights the current progress on the development of biomarkers, describing the proteomics technologies used, the most promising findings and the challenges encountered. EXPERT OPINION Strategies for effective use of samples combined with orthogonal proteomics methods for protein quantification are essential for translating biomarkers to the patient's bed side. Progress is achieved only if strong evidence is provided that the biomarker constitutes a reliable indicator of the patient's health status for a specific context of use.
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Affiliation(s)
- Cristina Al-Khalili Szigyarto
- Science for Life Laboratory, KTH - Royal Institute of Technology , Solna, Sweden.,School of Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology , Stockholm, Sweden
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Ballester-Lopez A, Núñez-Manchón J, Koehorst E, Linares-Pardo I, Almendrote M, Lucente G, Guanyabens N, Lopez-Osias M, Suárez-Mesa A, Hanick SA, Chojnacki J, Lucia A, Pintos-Morell G, Coll-Cantí J, Martínez-Piñeiro A, Ramos-Fransi A, Nogales-Gadea G. Three-dimensional imaging in myotonic dystrophy type 1: Linking molecular alterations with disease phenotype. NEUROLOGY-GENETICS 2020; 6:e484. [PMID: 32802949 PMCID: PMC7413607 DOI: 10.1212/nxg.0000000000000484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/05/2020] [Indexed: 12/31/2022]
Abstract
Objective We aimed to determine whether 3D imaging reconstruction allows identifying molecular:clinical associations in myotonic dystrophy type 1 (DM1). Methods We obtained myoblasts from 6 patients with DM1 and 6 controls. We measured cytosine-thymine-guanine (CTG) expansion and detected RNA foci and muscleblind like 1 (MBNL1) through 3D reconstruction. We studied dystrophia myotonica protein kinase (DMPK) expression and splicing alterations of MBNL1, insulin receptor, and sarcoplasmic reticulum Ca(2+)-ATPase 1. Results Three-dimensional analysis showed that RNA foci (nuclear and/or cytoplasmic) were present in 45%-100% of DM1-derived myoblasts we studied (range: 0-6 foci per cell). RNA foci represented <0.6% of the total myoblast nuclear volume. CTG expansion size was associated with the number of RNA foci per myoblast (r = 0.876 [95% confidence interval 0.222-0.986]) as well as with the number of cytoplasmic RNA foci (r = 0.943 [0.559-0.994]). Although MBNL1 colocalized with RNA foci in all DM1 myoblast cell lines, colocalization only accounted for 1% of total MBNL1 expression, with the absence of DM1 alternative splicing patterns. The number of RNA foci was associated with DMPK expression (r = 0.967 [0.079-0.999]). On the other hand, the number of cytoplasmic RNA foci was correlated with the age at disease onset (r = -0.818 [-0.979 to 0.019]). Conclusions CTG expansion size modulates RNA foci number in myoblasts derived from patients with DM1. MBNL1 sequestration plays only a minor role in the pathobiology of the disease in these cells. Higher number of cytoplasmic RNA foci is related to an early onset of the disease, a finding that should be corroborated in future studies.
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Affiliation(s)
- Alfonsina Ballester-Lopez
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Judit Núñez-Manchón
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Emma Koehorst
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Ian Linares-Pardo
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Miriam Almendrote
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Giuseppe Lucente
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Nicolau Guanyabens
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Marta Lopez-Osias
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Adrián Suárez-Mesa
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Shaliza Ann Hanick
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Jakub Chojnacki
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Alejandro Lucia
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Guillem Pintos-Morell
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Jaume Coll-Cantí
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Alicia Martínez-Piñeiro
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Alba Ramos-Fransi
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
| | - Gisela Nogales-Gadea
- Neuromuscular and Neuropediatric Research Group (A.B.-L., J.N.-M., E.K., I.L.-P., M.A., G.L., M.L.-O., A.S.-M., S.A.H., G.P.-M., J.C.-C., A.M.-P., A.R.-F., G.N.-G.), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Campus Can Ruti, Universitat Autònoma de Barcelona, Badalona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) (A.B.-L., G.P.-M., J.C.-C., G.N.-G.), Instituto de Salud Carlos III, Madrid; Neuromuscular Pathology Unit. Neurology Service. Neuroscience department (M.A., G.L., N.G., J.C.-C., A.M.-P., A.R.-F.), Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona; IrsiCaixa AIDS Research Institute (J.C.), Badalona, Spain; Faculty of Sport Sciences (A.L.), Universidad Europea de Madrid; Instituto de Investigación Hospital 12 de Octubre (i+12) (A.L.), Madrid; and Division of Rare Diseases. University Hospital Vall d'Hebron (G.P.-M.), Barcelona, Spain
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Wansink DG, Gourdon G, van Engelen BGM, Schoser B. 248th ENMC International Workshop: Myotonic dystrophies: Molecular approaches for clinical purposes, framing a European molecular research network, Hoofddorp, the Netherlands, 11-13 October 2019. Neuromuscul Disord 2020; 30:521-531. [PMID: 32417002 DOI: 10.1016/j.nmd.2020.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Derick G Wansink
- Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Geneviève Gourdon
- Inserm UMR 974, Sorbonne Université, Centre de Recherche en Myologie, Association Institut de Myologie, 75013 Paris, France
| | - Baziel G M van Engelen
- Donders Institute for Brain, Cognition and Behaviour, Department of Neurology, Radboud University Medical Center, 6525 GC Nijmegen, the Netherlands
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich, Germany.
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Recovery in the Myogenic Program of Congenital Myotonic Dystrophy Myoblasts after Excision of the Expanded (CTG) n Repeat. Int J Mol Sci 2019; 20:ijms20225685. [PMID: 31766224 PMCID: PMC6888582 DOI: 10.3390/ijms20225685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022] Open
Abstract
The congenital form of myotonic dystrophy type 1 (cDM) is caused by the large-scale expansion of a (CTG•CAG)n repeat in DMPK and DM1-AS. The production of toxic transcripts with long trinucleotide tracts from these genes results in impairment of the myogenic differentiation capacity as cDM’s most prominent morpho-phenotypic hallmark. In the current in vitro study, we compared the early differentiation programs of isogenic cDM myoblasts with and without a (CTG)2600 repeat obtained by gene editing. We found that excision of the repeat restored the ability of cDM myoblasts to engage in myogenic fusion, preventing the ensuing myotubes from remaining immature. Although the cDM-typical epigenetic status of the DM1 locus and the expression of genes therein were not altered upon removal of the repeat, analyses at the transcriptome and proteome level revealed that early abnormalities in the temporal expression of differentiation regulators, myogenic progression markers, and alternative splicing patterns before and immediately after the onset of differentiation became normalized. Our observation that molecular and cellular features of cDM are reversible in vitro and can be corrected by repeat-directed genome editing in muscle progenitors, when already committed and poised for myogenic differentiation, is important information for the future development of gene therapy for different forms of myotonic dystrophy type 1 (DM1).
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Ausems CRM, Raaijmakers RHL, van den Broek WJAA, Willemse M, van Engelen BGM, Wansink DG, van Bokhoven H. Intrinsic Myogenic Potential of Skeletal Muscle-Derived Pericytes from Patients with Myotonic Dystrophy Type 1. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 15:120-132. [PMID: 31649961 PMCID: PMC6804802 DOI: 10.1016/j.omtm.2019.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/04/2019] [Indexed: 12/21/2022]
Abstract
Pericytes are multipotent, vessel-associated progenitors that exhibit high proliferative capacity, can cross the blood-muscle barrier, and have the ability to home to muscle tissue and contribute to myogenesis. Consequently, pericyte-based therapies hold great promise for muscular dystrophies. A complex multi-system disorder exhibiting muscular dystrophy for which pericytes might be a valuable cell source is myotonic dystrophy type 1 (DM1). DM1 is caused by an unstable (CTG)n repeat in the DMPK gene and characterized by skeletal muscle weakness, muscle wasting, and myotonia. We have successfully isolated alkaline phosphatase-positive pericytes from skeletal muscle of DM1 patients and a transgenic mouse model. Intranuclear (CUG)n RNA foci, a pathogenic DM1 hallmark, were identified in human and mouse pericytes. Notably, pericytes from DM1 patients maintained similar growth parameters and innate myogenic characteristics in vitro compared to cells from unaffected controls. Our in vitro results thus demonstrate the potential of pericytes to ameliorate muscle features in DM1 in a therapeutic setting.
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Affiliation(s)
- Cornelia Rosanne Maria Ausems
- Department of Human Genetics, Radboud University Medical Center, Donders lnstitute for Brain Cognition and Behavior, 6525 GA Nijmegen, the Netherlands.,Department of Neurology, Radboud University Medical Center, Donders lnstitute for Brain Cognition and Behavior, 6500 HB Nijmegen, the Netherlands.,Department of Cell Biology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, the Netherlands
| | - Renée Henrica Lamberta Raaijmakers
- Department of Human Genetics, Radboud University Medical Center, Donders lnstitute for Brain Cognition and Behavior, 6525 GA Nijmegen, the Netherlands.,Department of Neurology, Radboud University Medical Center, Donders lnstitute for Brain Cognition and Behavior, 6500 HB Nijmegen, the Netherlands.,Department of Cell Biology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, the Netherlands
| | | | - Marieke Willemse
- Department of Cell Biology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, the Netherlands
| | - Baziel Gerardus Maria van Engelen
- Department of Neurology, Radboud University Medical Center, Donders lnstitute for Brain Cognition and Behavior, 6500 HB Nijmegen, the Netherlands
| | - Derick Gert Wansink
- Department of Cell Biology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Donders lnstitute for Brain Cognition and Behavior, 6525 GA Nijmegen, the Netherlands
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15
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Rong Z, Hu J, Corey DR, Mootha VV. Quantitative Studies of Muscleblind Proteins and Their Interaction With TCF4 RNA Foci Support Involvement in the Mechanism of Fuchs' Dystrophy. Invest Ophthalmol Vis Sci 2019; 60:3980-3991. [PMID: 31560764 PMCID: PMC6779288 DOI: 10.1167/iovs.19-27641] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023] Open
Abstract
Purpose Fuchs' endothelial corneal dystrophy (FECD) is a major cause of vision loss and the most common nucleotide repeat disorder, affecting 4% of United States population greater than 40 years of age. Seventy percent of FECD cases are due to an intronic CTG expansion within the TCF4 gene, resulting in accumulation of CUG repeat RNA nuclear foci in corneal endothelium. Each endothelial cell has approximately two sense foci, and each focus is a single RNA molecule. This study aimed to obtain a better understanding of how rare repeat RNA species lead to disease. Methods We quantitatively examined muscleblind-like (MBNL) proteins and their interaction with foci in both patient-derived corneal endothelial cell lines and human corneal endothelial tissue. Results Using fluorescent in situ hybridization and immunofluorescence, we found that depletion of both MBNL1 and MBNL2 reduces nuclear RNA foci formed by the repeat, suggesting that both are necessary for foci. Quantitative studies of RNA and protein copy number revealed MBNLs to be abundant in the total cellular pool in endothelial cell lines but are much lower in human corneal endothelial tissue. Studies using human tissue nuclear and cytoplasmic fractions indicate that most MBNL proteins are localized to the cytoplasm. Conclusions The low levels of MBNL1/2 in corneal tissue, in combination with the small fraction of protein in the nucleus, may make corneal endothelial cells especially susceptible to sequestration of MBNL1/2 by CUG repeat RNA. These observations may explain how a limited number of RNA molecules can cause widespread alteration of splicing and late-onset degenerative FECD.
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Affiliation(s)
- Ziye Rong
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Jiaxin Hu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - David R. Corey
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - V. Vinod Mootha
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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16
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van der Bent ML, Paulino da Silva Filho O, Willemse M, Hällbrink M, Wansink DG, Brock R. The nuclear concentration required for antisense oligonucleotide activity in myotonic dystrophy cells. FASEB J 2019; 33:11314-11325. [PMID: 31311315 DOI: 10.1096/fj.201900263r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Antisense oligonucleotides (ASOs) are a promising class of therapeutics that are starting to emerge in the clinic. Determination of intracellular concentrations required for biologic effects and identification of effective delivery vehicles are crucial for understanding the mode of action and required dosing. Here, we investigated which nuclear oligonucleotide concentration is needed for a therapeutic effect for a triplet repeat-targeting ASO in a muscle cell model of myotonic dystrophy type 1 (DM1). For cellular delivery, ASOs were complexed into nanoparticles using the cationic cell-penetrating peptides nona-arginine and PepFect14 (PF14). Although both peptides facilitated uptake, only PF14 led to a dose-dependent correction of disease-typical abnormal splicing. In line with this observation, time-lapse confocal microscopy demonstrated that only PF14 mediated translocation of the ASOs to the nucleus, which is the main site of action. Through fluorescence lifetime imaging, we could distinguish intact oligonucleotide from free fluorophore, showing that PF14 also shielded the ASOs from degradation. Finally, we employed a combination of live-cell fluorescence correlation spectroscopy and immunofluorescence microscopy and demonstrated that intranuclear blocking-type oligonucleotide concentrations in the upper nanomolar range were required to dissolve nuclear muscleblind-like protein 1 foci, a hallmark of DM1. Our findings have important implications for the clinical use of ASOs in DM1 and provide a basis for further research on other types of ASOs.-Van der Bent, M. L., Paulino da Silva Filho, O., Willemse, M., Hällbrink, M., Wansink, D. G., Brock, R. The nuclear concentration required for antisense oligonucleotide activity in myotonic dystrophy cells.
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Affiliation(s)
- M Leontien van der Bent
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Omar Paulino da Silva Filho
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands.,Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - Marieke Willemse
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mattias Hällbrink
- Department of Neurochemistry, Stockholm University, Stockholm, Sweden
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
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17
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Sznajder ŁJ, Swanson MS. Short Tandem Repeat Expansions and RNA-Mediated Pathogenesis in Myotonic Dystrophy. Int J Mol Sci 2019; 20:ijms20133365. [PMID: 31323950 PMCID: PMC6651174 DOI: 10.3390/ijms20133365] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 12/23/2022] Open
Abstract
Short tandem repeat (STR) or microsatellite, expansions underlie more than 50 hereditary neurological, neuromuscular and other diseases, including myotonic dystrophy types 1 (DM1) and 2 (DM2). Current disease models for DM1 and DM2 propose a common pathomechanism, whereby the transcription of mutant DMPK (DM1) and CNBP (DM2) genes results in the synthesis of CUG and CCUG repeat expansion (CUGexp, CCUGexp) RNAs, respectively. These CUGexp and CCUGexp RNAs are toxic since they promote the assembly of ribonucleoprotein (RNP) complexes or RNA foci, leading to sequestration of Muscleblind-like (MBNL) proteins in the nucleus and global dysregulation of the processing, localization and stability of MBNL target RNAs. STR expansion RNAs also form phase-separated gel-like droplets both in vitro and in transiently transfected cells, implicating RNA-RNA multivalent interactions as drivers of RNA foci formation. Importantly, the nucleation and growth of these nuclear foci and transcript misprocessing are reversible processes and thus amenable to therapeutic intervention. In this review, we provide an overview of potential DM1 and DM2 pathomechanisms, followed by a discussion of MBNL functions in RNA processing and how multivalent interactions between expanded STR RNAs and RNA-binding proteins (RBPs) promote RNA foci assembly.
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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.
| | - 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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18
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Carrell ST, Tang Z, Mohr S, Lambowitz AM, Thornton CA. Detection of expanded RNA repeats using thermostable group II intron reverse transcriptase. Nucleic Acids Res 2019; 46:e1. [PMID: 29036654 PMCID: PMC5758912 DOI: 10.1093/nar/gkx867] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/27/2017] [Indexed: 12/15/2022] Open
Abstract
Cellular accumulation of repetitive RNA occurs in several dominantly-inherited genetic disorders. Expanded CUG, CCUG or GGGGCC repeats are expressed in myotonic dystrophy type 1 (DM1), myotonic dystrophy type 2 (DM2), or familial amyotrophic lateral sclerosis, respectively. Expanded repeat RNAs (ER-RNAs) exert a toxic gain-of-function and are prime therapeutic targets in these diseases. However, efforts to quantify ER-RNA levels or monitor knockdown are confounded by stable structure and heterogeneity of the ER-RNA tract and background signal from non-expanded repeats. Here, we used a thermostable group II intron reverse transcriptase (TGIRT-III) to convert ER-RNA to cDNA, followed by quantification on slot blots. We found that TGIRT-III was capable of reverse transcription (RTn) on enzymatically synthesized ER-RNAs. By using conditions that limit cDNA synthesis from off-target sequences, we observed hybridization signals on cDNA slot blots from DM1 and DM2 muscle samples but not from healthy controls. In transgenic mouse models of DM1 the cDNA slot blots accurately reflected the differences of ER-RNA expression across different transgenic lines, and showed therapeutic reductions in skeletal and cardiac muscle, accompanied by improvements of the DM1-associated splicing defects. TGIRT-III was also active on CCCCGG- and GGGGCC-repeats, suggesting that ER-RNA analysis is feasible for several repeat expansion disorders.
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Affiliation(s)
- Samuel T Carrell
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14611, USA
| | - Zhenzhi Tang
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14611, USA
| | - Sabine Mohr
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Alan M Lambowitz
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14611, USA
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19
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van Cruchten RTP, Wieringa B, Wansink DG. Expanded CUG repeats in DMPK transcripts adopt diverse hairpin conformations without influencing the structure of the flanking sequences. RNA (NEW YORK, N.Y.) 2019; 25:481-495. [PMID: 30700578 PMCID: PMC6426290 DOI: 10.1261/rna.068940.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a complex neuromuscular disorder caused by expansion of a CTG repeat in the 3'-untranslated region (UTR) of the DMPK gene. Mutant DMPK transcripts form aberrant structures and anomalously associate with RNA-binding proteins (RBPs). As a first step toward better understanding of the involvement of abnormal DMPK mRNA folding in DM1 manifestation, we used SHAPE, DMS, CMCT, and RNase T1 structure probing in vitro for modeling of the topology of the DMPK 3'-UTR with normal and pathogenic repeat lengths of up to 197 CUG triplets. The resulting structural information was validated by disruption of base-pairing with LNA antisense oligonucleotides (AONs) and used for prediction of therapeutic AON accessibility and verification of DMPK knockdown efficacy in cells. Our model for DMPK RNA structure demonstrates that the hairpin formed by the CUG repeat has length-dependent conformational plasticity, with a structure that is guided by and embedded in an otherwise rigid architecture of flanking regions in the DMPK 3'-UTR. Evidence is provided that long CUG repeats may form not only single asymmetrical hairpins but also exist as branched structures. These newly identified structures have implications for DM1 pathogenic mechanisms, like sequestration of RBPs and repeat-associated non-AUG (RAN) translation.
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Affiliation(s)
- Remco T P van Cruchten
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Bé Wieringa
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
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20
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Witkos TM, Krzyzosiak WJ, Fiszer A, Koscianska E. A potential role of extended simple sequence repeats in competing endogenous RNA crosstalk. RNA Biol 2018; 15:1399-1409. [PMID: 30381983 PMCID: PMC6284579 DOI: 10.1080/15476286.2018.1536593] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
MicroRNA (miRNA)-mediated crosstalk between coding and non-coding RNAs of various types is known as the competing endogenous RNA (ceRNA) concept. Here, we propose that there is a specific variant of the ceRNA language that takes advantage of simple sequence repeat (SSR) wording. We applied bioinformatics tools to identify human transcripts that may be regarded as repeat-associated ceRNAs (raceRNAs). Multiple protein-coding transcripts, transcribed pseudogenes, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) showing this potential were identified, and numerous miRNAs were predicted to bind to SSRs. We propose that simple repeats expanded in various hereditary neurological diseases may act as sponges for miRNAs containing complementary repeats that would affect raceRNA crosstalk. Based on the representation of specific SSRs in transcripts, expression data for SSR-binding miRNAs and expression profiling data from patients, we determined that raceRNA crosstalk is most likely to be perturbed in the case of myotonic dystrophy type 1 (DM1) and type 2 (DM2).
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Affiliation(s)
- Tomasz M Witkos
- a Department of Molecular Biomedicine , Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
| | - Wlodzimierz J Krzyzosiak
- a Department of Molecular Biomedicine , Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
| | - Agnieszka Fiszer
- a Department of Molecular Biomedicine , Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
| | - Edyta Koscianska
- a Department of Molecular Biomedicine , Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
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21
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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: 41] [Impact Index Per Article: 6.8] [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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22
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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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23
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Thomas JD, Oliveira R, Sznajder ŁJ, Swanson MS. Myotonic Dystrophy and Developmental Regulation of RNA Processing. Compr Physiol 2018; 8:509-553. [PMID: 29687899 DOI: 10.1002/cphy.c170002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Myotonic dystrophy (DM) is a multisystemic disorder caused by microsatellite expansion mutations in two unrelated genes leading to similar, yet distinct, diseases. DM disease presentation is highly variable and distinguished by differences in age-of-onset and symptom severity. In the most severe form, DM presents with congenital onset and profound developmental defects. At the molecular level, DM pathogenesis is characterized by a toxic RNA gain-of-function mechanism that involves the transcription of noncoding microsatellite expansions. These mutant RNAs disrupt key cellular pathways, including RNA processing, localization, and translation. In DM, these toxic RNA effects are predominantly mediated through the modulation of the muscleblind-like and CUGBP and ETR-3-like factor families of RNA binding proteins (RBPs). Dysfunction of these RBPs results in widespread RNA processing defects culminating in the expression of developmentally inappropriate protein isoforms in adult tissues. The tissue that is the focus of this review, skeletal muscle, is particularly sensitive to mutant RNA-responsive perturbations, as patients display a variety of developmental, structural, and functional defects in muscle. Here, we provide a comprehensive overview of DM1 and DM2 clinical presentation and pathology as well as the underlying cellular and molecular defects associated with DM disease onset and progression. Additionally, fundamental aspects of skeletal muscle development altered in DM are highlighted together with ongoing and potential therapeutic avenues to treat this muscular dystrophy. © 2018 American Physiological Society. Compr Physiol 8:509-553, 2018.
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Affiliation(s)
- James D Thomas
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Ruan Oliveira
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
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24
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Manning KS, Rao AN, Castro M, Cooper TA. BNA NC Gapmers Revert Splicing and Reduce RNA Foci with Low Toxicity in Myotonic Dystrophy Cells. ACS Chem Biol 2017; 12:2503-2509. [PMID: 28853853 DOI: 10.1021/acschembio.7b00416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic disease caused by an expanded CTG repeat in the 3' UTR of the dystrophia myotonica protein kinase (DMPK) gene. Short, DNA-based antisense oligonucleotides termed gapmers are a promising strategy to degrade toxic CUG expanded repeat (CUGexp) RNA. Nucleoside analogs are incorporated to increase gapmer affinity and stability; however, some analogs also exhibit toxicity. In this study, we demonstrate that the 2',4'-BNANC[NMe] (BNANC) modification is a promising nucleoside analog with high potency similar to 2',4'-LNA (LNA). BNANC gapmers targeting a nonrepetitive region of the DMPK 3' UTR show allele-specific knockdown of CUGexp RNA and revert characteristic DM1 molecular defects including mis-splicing and accumulation of RNA foci. Notably, the BNANC gapmers tested in this study did not induce caspase activation, in contrast to a sequence matched LNA gapmer. This study indicates that BNANC gapmers warrant further study as a promising RNA targeting therapeutic.
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Affiliation(s)
| | | | - Miguel Castro
- Bio-Synthesis, Inc., 612 East Main Street, Lewisville, Texas 75057, United States
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25
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Gudde AEEG, van Heeringen SJ, de Oude AI, van Kessel IDG, Estabrook J, Wang ET, Wieringa B, Wansink DG. Antisense transcription of the myotonic dystrophy locus yields low-abundant RNAs with and without (CAG)n repeat. RNA Biol 2017; 14:1374-1388. [PMID: 28102759 PMCID: PMC5711456 DOI: 10.1080/15476286.2017.1279787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/21/2016] [Accepted: 12/30/2016] [Indexed: 12/20/2022] Open
Abstract
The unstable (CTG·CAG)n trinucleotide repeat in the myotonic dystrophy type 1 (DM1) locus is bidirectionally transcribed from genes with terminal overlap. By transcription in the sense direction, the DMPK gene produces various alternatively spliced mRNAs with a (CUG)n repeat in their 3' UTR. Expression in opposite orientation reportedly yields (CAG)n-repeat containing RNA, but both structure and biologic significance of this antisense gene (DM1-AS) are largely unknown. Via a combinatorial approach of computational and experimental analyses of RNA from unaffected individuals and DM1 patients we discovered that DM1-AS spans >6 kb, contains alternative transcription start sites and uses alternative polyadenylation sites up- and downstream of the (CAG)n repeat. Moreover, its primary transcripts undergo alternative splicing, whereby the (CAG)n segment is removed as part of an intron. Thus, in patients a mixture of DM1-AS RNAs with and without expanded (CAG)n repeat are produced. DM1-AS expression appears upregulated in patients, but transcript abundance remains very low in all tissues analyzed. Our data suggest that DM1-AS transcripts belong to the class of long non-coding RNAs. These and other biologically relevant implications for how (CAG)n-expanded transcripts may contribute to DM1 pathology can now be explored experimentally.
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Affiliation(s)
- Anke E. E. G. Gudde
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Simon J. van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Amanda I. de Oude
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | | | - Joseph Estabrook
- Department of Molecular Genetics and Microbiology, Center for Neurogenetics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for Neurogenetics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Bé Wieringa
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G. Wansink
- Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
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26
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Rohilla KJ, Gagnon KT. RNA biology of disease-associated microsatellite repeat expansions. Acta Neuropathol Commun 2017; 5:63. [PMID: 28851463 PMCID: PMC5574247 DOI: 10.1186/s40478-017-0468-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.
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27
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Gudde AEEG, van Kessel IDG, André LM, Wieringa B, Wansink DG. Trinucleotide-repeat expanded and normal DMPK transcripts contain unusually long poly(A) tails despite differential nuclear residence. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:740-749. [PMID: 28435090 DOI: 10.1016/j.bbagrm.2017.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/26/2017] [Accepted: 04/14/2017] [Indexed: 12/29/2022]
Abstract
In yeast and higher eukaryotes nuclear retention of transcripts may serve in control over RNA decay, nucleocytoplasmic transport and premature cytoplasmic appearance of mRNAs. Hyperadenylation of RNA is known to be associated with nuclear retention, but the cause-consequence relationship between hyperadenylation and regulation of RNA nuclear export is still unclear. We compared polyadenylation status between normal and expanded DMPK transcripts in muscle cells and tissues derived from unaffected individuals and patients with myotonic dystrophy type 1 (DM1). DM1 is an autosomal dominant disorder caused by (CTG)n repeat expansion in the DMPK gene. DM1 etiology is characterized by an almost complete block of nuclear export of DMPK transcripts carrying a long (CUG)n repeat, including aberrant sequestration of RNA-binding proteins. We show here by use of cell fractionation, RNA size separation and analysis of poly(A) tail length that a considerable fraction of transcripts from the normal DMPK allele is also retained in the nucleus (~30%). They carry poly(A) tails with an unusually broad length distribution, ranging between a few dozen to >500 adenosine residues. Remarkably, expanded DMPK (CUG)n transcripts from the mutant allele, almost exclusively nuclear, carry equally long poly(A) tails. Our findings thus suggest that nuclear retention may be a common feature of regulation of DMPK RNA expression. The typical forced nuclear residence of expanded DMPK transcripts affects this regulation in tissues of DM1 patients, but not through hyperadenylation.
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Affiliation(s)
- Anke E E G Gudde
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Ingeborg D G van Kessel
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Laurène M André
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Bé Wieringa
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G Wansink
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Department of Cell Biology, Nijmegen, The Netherlands.
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28
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Urbanek MO, Michalak M, Krzyzosiak WJ. 2D and 3D FISH of expanded repeat RNAs in human lymphoblasts. Methods 2017; 120:49-57. [PMID: 28404480 DOI: 10.1016/j.ymeth.2017.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/09/2017] [Accepted: 04/05/2017] [Indexed: 12/18/2022] Open
Abstract
The first methods for visualizing RNAs within cells were designed for simple imaging of specific transcripts in cells or tissues and since then significant technical advances have been made in this field. Today, high-resolution images can be obtained, enabling visualization of single transcript molecules, quantitative analyses of images, and precise localization of RNAs within cells as well as co-localization of transcripts with specific proteins or other molecules. In addition, tracking of RNA dynamics within single cell has become possible. RNA imaging techniques have been utilized for investigating the role of mutant RNAs in a number of human disorders caused by simple microsatellite expansions. These diseases include myotonic dystrophy type 1 and 2, amyotrophic lateral sclerosis/frontotemporal dementia, fragile X-associated tremor/ataxia syndrome, and Huntington's disease. Mutant RNAs with expanded repeats tend to aggregate predominantly within cell nuclei, forming structures called RNA foci. In this study, we demonstrate methods for fluorescent visualization of RNAs in both fixed and living cells using the example of RNAs containing various expanded repeat tracts (CUG, CCUG, GGGGCC, CGG, and CAG) from experiment design to image analysis. We describe in detail 2D and 3D fluorescence in situ hybridization (FISH) protocols for imaging expanded repeats RNAs, and we review briefly live imaging techniques used to characterize RNA foci formed by mutant RNAs. These methods could be used to image the entire cellular pathway of RNAs, from transcription to degradation.
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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
| | - Michal Michalak
- 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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