1
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Ellis JA, Hale MA, Cleary JD, Wang E, Andrew Berglund J. Alternative splicing outcomes across an RNA-binding protein concentration gradient. J Mol Biol 2023:168156. [PMID: 37230319 DOI: 10.1016/j.jmb.2023.168156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/18/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
Alternative splicing (AS) is a dynamic RNA processing step that produces multiple RNA isoforms from a single pre-mRNA transcript and contributes to the complexity of the cellular transcriptome and proteome. This process is regulated through a network of cis-regulatory sequence elements and trans-acting factors, most-notably RNA binding proteins (RBPs). The muscleblind-like (MBNL) and RNA binding fox-1 homolog (RBFOX) are two well characterized families of RBPs that regulate fetal to adult AS transitions critical for proper muscle, heart, and central nervous system development. To better understand how the concentration of these RBPs influences AS transcriptome wide, we engineered a MBNL1 and RBFOX1 inducible HEK-293 cell line. Modest induction of exogenous RBFOX1 in this cell line modulated MBNL1-dependent AS outcomes in 3 skipped exon events, despite significant levels of endogenous RBFOX1 and RBFOX2. Due to background RBFOX levels, we conducted a focused analysis of dose-dependent MBNL1 skipped exon AS outcomes and generated transcriptome wide dose-response curves. Analysis of this data demonstrates that MBNL1-regulated exclusion events may require higher concentrations of MBNL1 protein to properly regulate AS outcomes compared to inclusion events and that multiple arrangements of YGCY motifs can produce similar splicing outcomes. These results suggest that rather than a simple relationship between the organization of RBP binding sites and a specific splicing outcome, that complex interaction networks govern both AS inclusion and exclusion events across a RBP gradient.
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Affiliation(s)
- Joseph A Ellis
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Melissa A Hale
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; Department of Neurology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - John D Cleary
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Eric Wang
- Department of Microbiology and Molecular Genetics & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - J Andrew Berglund
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; Department of Biological Sciences, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; RNA Institute, State University of New York at Albany, LSRB-2033, 1400 Washington Avenue, Albany, New York, 12222.
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2
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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3
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Gibaut QMR, Akahori Y, Bush JA, Taghavi A, Tanaka T, Aikawa H, Ryan LS, Paegel BM, Disney MD. Study of an RNA-Focused DNA-Encoded Library Informs Design of a Degrader of a r(CUG) Repeat Expansion. J Am Chem Soc 2022; 144:21972-21979. [PMID: 36399603 PMCID: PMC9878440 DOI: 10.1021/jacs.2c08883] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A solid-phase DNA-encoded library (DEL) was studied for binding the RNA repeat expansion r(CUG)exp, the causative agent of the most common form of adult-onset muscular dystrophy, myotonic dystrophy type 1 (DM1). A variety of uncharged and novel RNA binders were identified to selectively bind r(CUG)exp by using a two-color flow cytometry screen. The cellular activity of one binder was augmented by attaching it with a module that directly cleaves r(CUG)exp. In DM1 patient-derived muscle cells, the compound specifically bound r(CUG)exp and allele-specifically eliminated r(CUG)exp, improving disease-associated defects. The approaches herein can be used to identify and optimize ligands and bind RNA that can be further augmented for functionality including degradation.
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Affiliation(s)
- Quentin M. R. Gibaut
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yoshihiro Akahori
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Toru Tanaka
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Haruo Aikawa
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Lucas S. Ryan
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States; Department of Chemistry and Pharmaceutical Sciences, University of California, Irvine, California 92617, United States
| | - Matthew D. Disney
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
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Childs-Disney JL, Yang X, Gibaut QMR, Tong Y, Batey RT, Disney MD. Targeting RNA structures with small molecules. Nat Rev Drug Discov 2022; 21:736-762. [PMID: 35941229 PMCID: PMC9360655 DOI: 10.1038/s41573-022-00521-4] [Citation(s) in RCA: 159] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
RNA adopts 3D structures that confer varied functional roles in human biology and dysfunction in disease. Approaches to therapeutically target RNA structures with small molecules are being actively pursued, aided by key advances in the field including the development of computational tools that predict evolutionarily conserved RNA structures, as well as strategies that expand mode of action and facilitate interactions with cellular machinery. Existing RNA-targeted small molecules use a range of mechanisms including directing splicing - by acting as molecular glues with cellular proteins (such as branaplam and the FDA-approved risdiplam), inhibition of translation of undruggable proteins and deactivation of functional structures in noncoding RNAs. Here, we describe strategies to identify, validate and optimize small molecules that target the functional transcriptome, laying out a roadmap to advance these agents into the next decade.
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Affiliation(s)
| | - Xueyi Yang
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | | | - Yuquan Tong
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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5
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Krueger SB, Lanzendorf AN, Jeon HH, Zimmerman SC. Selective and Reversible Ligand Assembly on the DNA and RNA Repeat Sequences in Myotonic Dystrophy. Chembiochem 2022; 23:e202200260. [PMID: 35790065 PMCID: PMC9733911 DOI: 10.1002/cbic.202200260] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/03/2022] [Indexed: 02/06/2023]
Abstract
Small molecule targeting of DNA and RNA sequences has come into focus as a therapeutic strategy for diseases such as myotonic dystrophy type 1 (DM1), a trinucleotide repeat disease characterized by RNA gain-of-function. Herein, we report a novel template-selected, reversible assembly of therapeutic agents in situ via aldehyde-amine condensation. Rationally designed small molecule targeting agents functionalized with either an aldehyde or an amine were synthesized and screened against the target nucleic acid sequence. The assembly of fragments was confirmed by MALDI-MS in the presence of DM1-relevant nucleic acid sequences. The resulting hit combinations of aldehyde and amine inhibited the formation of r(CUG)exp in vitro in a cooperative manner at low micromolar levels and rescued mis-splicing defects in DM1 model cells. This reversible template-selected assembly is a promising approach to achieve cell permeable and multivalent targeting via in situ synthesis and could be applied to other nucleic acid targets.
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Affiliation(s)
- Sarah B Krueger
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Amie N Lanzendorf
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Hyoeun Heather Jeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
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Li K, Krueger SB, Zimmerman SC. A Novel Minor Groove Binder as a Potential Therapeutic Agent for Myotonic Dystrophy Type 1. ChemMedChem 2021; 16:2638-2644. [PMID: 34114350 DOI: 10.1002/cmdc.202100243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Indexed: 11/10/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic neuromuscular disorder that is inherited in an autosomal dominant manner. DM1 originates in a (CTG⋅CAG) repeat expansion in the 3'-UTR of the dystrophia myotonic protein kinase (DMPK) gene on chromosome 19. One of the transcripts, r(CUG)exp , is toxic in various ways. Herein we report a rationally designed small molecule with a thiazole peptidomimetic unit that can serve as a minor groove binder for the nucleic acid targets. This peptide unit linked to two triaminotriazine recognition units selectively binds to d(CTG)exp to inhibit the transcription process, and also targets r(CUG)exp selectively to improve representative DM1 pathological molecular features, including foci formation and pre-mRNA splicing defects in DM1 model cells. As such, it represents a new structure type that might serve as a lead compound for future structure-activity optimization.
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Affiliation(s)
- Ke Li
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, 61801, Urbana, IL, USA
| | - Sarah B Krueger
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, 61801, Urbana, IL, USA
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, 61801, Urbana, IL, USA
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7
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Intrinsically cell-penetrating multivalent and multitargeting ligands for myotonic dystrophy type 1. Proc Natl Acad Sci U S A 2019; 116:8709-8714. [PMID: 30975744 DOI: 10.1073/pnas.1820827116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Developing highly active, multivalent ligands as therapeutic agents is challenging because of delivery issues, limited cell permeability, and toxicity. Here, we report intrinsically cell-penetrating multivalent ligands that target the trinucleotide repeat DNA and RNA in myotonic dystrophy type 1 (DM1), interrupting the disease progression in two ways. The oligomeric ligands are designed based on the repetitive structure of the target with recognition moieties alternating with bisamidinium groove binders to provide an amphiphilic and polycationic structure, mimicking cell-penetrating peptides. Multiple biological studies suggested the success of our multivalency strategy. The designed oligomers maintained cell permeability and exhibited no apparent toxicity both in cells and in mice at working concentrations. Furthermore, the oligomers showed important activities in DM1 cells and in a DM1 liver mouse model, reducing or eliminating prominent DM1 features. Phenotypic recovery of the climbing defect in adult DM1 Drosophila was also observed. This design strategy should be applicable to other repeat expansion diseases and more generally to DNA/RNA-targeted therapeutics.
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8
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Manta A, Stouth DW, Xhuti D, Chi L, Rebalka IA, Kalmar JM, Hawke TJ, Ljubicic V. Chronic exercise mitigates disease mechanisms and improves muscle function in myotonic dystrophy type 1 mice. J Physiol 2019; 597:1361-1381. [PMID: 30628727 DOI: 10.1113/jp277123] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
KEY POINTS Myotonic dystrophy type 1 (DM1), the second most common muscular dystrophy and most prevalent adult form of muscular dystrophy, is characterized by muscle weakness, wasting and myotonia. A microsatellite repeat expansion mutation results in RNA toxicity and dysregulation of mRNA processing, which are the primary downstream causes of the disorder. Recent studies with DM1 participants demonstrate that exercise is safe, enjoyable and elicits benefits in muscle strength and function; however, the molecular mechanisms of exercise adaptation in DM1 are undefined. Our results demonstrate that 7 weeks of volitional running wheel exercise in a pre-clinical DM1 mouse model resulted in significantly improved motor performance, muscle strength and endurance, as well as reduced myotonia. At the cellular level, chronic physical activity attenuated RNA toxicity, liberated Muscleblind-like 1 protein from myonuclear foci and improved mRNA alternative splicing. ABSTRACT Myotonic dystrophy type 1 (DM1) is a trinucleotide repeat expansion neuromuscular disorder that is most prominently characterized by skeletal muscle weakness, wasting and myotonia. Chronic physical activity is safe and satisfying, and can elicit functional benefits such as improved strength and endurance in DM1 patients, but the underlying cellular basis of exercise adaptation is undefined. Our purpose was to examine the mechanisms of exercise biology in DM1. Healthy, sedentary wild-type (SED-WT) mice, as well as sedentary human skeletal actin-long repeat animals, a murine model of DM1 myopathy (SED-DM1), and DM1 mice with volitional access to a running wheel for 7 weeks (EX-DM1), were utilized. Chronic exercise augmented strength and endurance in vivo and in situ in DM1 mice. These alterations coincided with normalized measures of myopathy, as well as increased mitochondrial content. Electromyography revealed a 70-85% decrease in the duration of myotonic discharges in muscles from EX-DM1 compared to SED-DM1 animals. The exercise-induced enhancements in muscle function corresponded at the molecular level with mitigated spliceopathy, specifically the processing of bridging integrator 1 and muscle-specific chloride channel (CLC-1) transcripts. CLC-1 protein content and sarcolemmal expression were lower in SED-DM1 versus SED-WT animals, but they were similar between SED-WT and EX-DM1 groups. Chronic exercise also attenuated RNA toxicity, as indicated by reduced (CUG)n foci-positive myonuclei and sequestered Muscleblind-like 1 (MBNL1). Our data indicate that chronic exercise-induced physiological improvements in DM1 occur in concert with mitigated primary downstream disease mechanisms, including RNA toxicity, MBNL1 loss-of-function, and alternative mRNA splicing.
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Affiliation(s)
- Alexander Manta
- Department of Kinesiology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | - Derek W Stouth
- Department of Kinesiology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | - Donald Xhuti
- Department of Kinesiology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | - Leon Chi
- Department of Kinesiology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | - Irena A Rebalka
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | - Jayne M Kalmar
- Department of Kinesiology & Physical Education, Wilfred Laurier University, Waterloo, ON, Canada, N2L 3C5
| | - Thomas J Hawke
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | - Vladimir Ljubicic
- Department of Kinesiology, McMaster University, Hamilton, ON, Canada, L8S 4K1
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9
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Neueder A. RNA-Mediated Disease Mechanisms in Neurodegenerative Disorders. J Mol Biol 2018; 431:1780-1791. [PMID: 30597161 DOI: 10.1016/j.jmb.2018.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 12/16/2022]
Abstract
RNA is accurately entangled in virtually all pathways that maintain cellular homeostasis. To name but a few, RNA is the "messenger" between DNA encoded information and the resulting proteins. Furthermore, RNAs regulate diverse processes by forming DNA::RNA or RNA::RNA interactions. Finally, RNA itself can be the scaffold for ribonucleoprotein complexes, for example, ribosomes or cellular bodies. Consequently, disruption of any of these processes can lead to disease. This review describes known and emerging RNA-based disease mechanisms like interference with regular splicing, the anomalous appearance of RNA-protein complexes and uncommon RNA species, as well as non-canonical translation. Due to the complexity and entanglement of the above-mentioned pathways, only few drugs are available that target RNA-based disease mechanisms. However, advances in our understanding how RNA is involved in and modulates cellular homeostasis might pave the way to novel treatments.
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Affiliation(s)
- Andreas Neueder
- Experimental Neurology, Department of Neurology, Ulm University, 89081 Ulm, Germany.
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10
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Neueder A, Bates GP. RNA Related Pathology in Huntington's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1049:85-101. [PMID: 29427099 DOI: 10.1007/978-3-319-71779-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This chapter summarises research investigating the expression of huntingtin sense and anti-sense transcripts, the effect of the mutation on huntingtin processing as well as the more global effect of the mutation on the coding and non-coding transcriptomes. The huntingtin gene is ubiquitously expressed, although expression levels vary between tissues and cell types. A SNP that affects NF-ĸB binding in the huntingtin promoter modulates the expression level of huntingtin transcripts and is associated with the age of disease onset. Incomplete splicing between exon 1 and exon 2 has been shown to result in the expression of a small polyadenylated mRNA that encodes the highly pathogenic exon 1 huntingtin protein. This occurs in a CAG-repeat length dependent manner in all full-length mouse models of HD as well as HD patient post-mortem brains and fibroblasts. An antisense transcript to huntingtin is generated that contains a CUG repeat that is expanded in HD patients. In myotonic dystrophy, expanded CUG repeats form RNA foci in cell nuclei that bind specific proteins (e.g. MBL1). Short, pure CAG RNAs of approximately 21 nucleotides that have been processed by DICER can inhibit the translation of other CAG repeat containing mRNAs. The HD mutation affects the transcriptome at the level of mRNA expression, splicing and the expression of non-coding RNAs. Finally, expanded repetitive stretched of nucleotides can lead to RAN translation, in which the ribosome translates from the expanded repeat in all possible reading frames, producing proteins with various poly-amino acid tracts. The extent to which these events contribute to HD pathogenesis is largely unknown.
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Affiliation(s)
- Andreas Neueder
- Sobell Department of Motor Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Gillian P Bates
- Sobell Department of Motor Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
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11
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Konieczny P, Stepniak-Konieczna E, Taylor K, Sznajder LJ, Sobczak K. Autoregulation of MBNL1 function by exon 1 exclusion from MBNL1 transcript. Nucleic Acids Res 2017; 45:1760-1775. [PMID: 27903900 PMCID: PMC5389549 DOI: 10.1093/nar/gkw1158] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 11/07/2016] [Indexed: 01/14/2023] Open
Abstract
Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed that MBNL1 binds to MBNL1 exon 1 (e1) encoding both the major part of 5΄UTR and an amino-terminal region of MBNL1 protein. We tested several hypotheses regarding the possible autoregulatory function of MBNL1 binding to its own transcript. Our data indicate that MBNLs induce skipping of e1 from precursor MBNL1 mRNA and that e1 exclusion may impact transcript association with polysomes and translation. Furthermore, e1-deficient protein isoform lacking the first two zinc fingers is highly unstable and its EGFP fusion protein has severely compromised splicing activity. We also show that MBNL1 can be transcribed from three different promoters and that the transcription initiation site determines the mode of e1 regulation. Taken together, we demonstrate that MBNL proteins control steady-state levels of MBNL1 through an interaction with e1 in its precursor mRNA. Insights from our study open a new avenue in therapies against DM based on manipulation of the transcription initiation site and e1 splicing of MBNL1 mRNA.
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Affiliation(s)
- Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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12
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Gourdon G, Meola G. Myotonic Dystrophies: State of the Art of New Therapeutic Developments for the CNS. Front Cell Neurosci 2017; 11:101. [PMID: 28473756 PMCID: PMC5397409 DOI: 10.3389/fncel.2017.00101] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/27/2017] [Indexed: 12/12/2022] Open
Abstract
Myotonic dystrophies are multisystemic diseases characterized not only by muscle and heart dysfunction but also by CNS alteration. They are now recognized as brain diseases affecting newborns and children for myotonic dystrophy type 1 and adults for both myotonic dystrophy type 1 and type 2. In the past two decades, much progress has been made in understanding the mechanisms underlying the DM symptoms allowing development of new molecular therapeutic tools with the ultimate aim of curing the disease. This review describes the state of the art for the characterization of CNS related symptoms, the development of molecular strategies to target the CNS as well as the available tools for screening and testing new possible treatments.
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Affiliation(s)
- Genevieve Gourdon
- Institut National de la Santé et de la Recherche Médicale UMR1163Paris, France.,Laboratory CTGDM, Institut Imagine, Université Paris Descartes-Sorbonne Paris CitéParis, France
| | - Giovanni Meola
- Department of Biomedical Sciences for Health, Policlinico San Donato (IRCCS), University of MilanMilan, Italy
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13
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Sznajder ŁJ, Michalak M, Taylor K, Cywoniuk P, Kabza M, Wojtkowiak-Szlachcic A, Matłoka M, Konieczny P, Sobczak K. Mechanistic determinants of MBNL activity. Nucleic Acids Res 2016; 44:10326-10342. [PMID: 27733504 PMCID: PMC5137450 DOI: 10.1093/nar/gkw915] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/05/2016] [Indexed: 11/13/2022] Open
Abstract
Muscleblind-like (MBNL) proteins are critical RNA processing factors in development. MBNL activity is disrupted in the neuromuscular disease myotonic dystrophy type 1 (DM1), due to the instability of a non-coding microsatellite in the DMPK gene and the expression of CUG expansion (CUGexp) RNAs. Pathogenic interactions between MBNL and CUGexp RNA lead to the formation of nuclear complexes termed foci and prevent MBNL function in pre-mRNA processing. The existence of multiple MBNL genes, as well as multiple protein isoforms, raises the question of whether different MBNL proteins possess unique or redundant functions. To address this question, we coexpressed three MBNL paralogs in cells at equivalent levels and characterized both specific and redundant roles of these proteins in alternative splicing and RNA foci dynamics. When coexpressed in the same cells, MBNL1, MBNL2 and MBNL3 bind the same RNA motifs with different affinities. While MBNL1 demonstrated the highest splicing activity, MBNL3 showed the lowest. When forming RNA foci, MBNL1 is the most mobile paralog, while MBNL3 is rather static and the most densely packed on CUGexp RNA. Therefore, our results demonstrate that MBNL paralogs and gene-specific isoforms possess inherent functional differences, an outcome that could be enlisted to improve therapeutic strategies for DM1.
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Affiliation(s)
- Łukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Michał Michalak
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Michał Kabza
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Agnieszka Wojtkowiak-Szlachcic
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Magdalena Matłoka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
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Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy. PLoS Genet 2016; 12:e1006316. [PMID: 27681373 PMCID: PMC5082313 DOI: 10.1371/journal.pgen.1006316] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 08/23/2016] [Indexed: 01/23/2023] Open
Abstract
Alternative splicing is a regulated process that results in expression of
specific mRNA and protein isoforms. Alternative splicing factors determine the
relative abundance of each isoform. Here we focus on MBNL1, a splicing factor
misregulated in the disease myotonic dystrophy. By altering the concentration of
MBNL1 in cells across a broad dynamic range, we show that different splicing
events require different amounts of MBNL1 for half-maximal response, and respond
more or less steeply to MBNL1. Motifs around MBNL1 exon 5 were studied to assess
how cis-elements mediate the MBNL1 dose-dependent splicing
response. A framework was developed to estimate MBNL concentration using
splicing responses alone, validated in the cell-based model, and applied to
myotonic dystrophy patient muscle. Using this framework, we evaluated the
ability of individual and combinations of splicing events to predict functional
MBNL concentration in human biopsies, as well as their performance as biomarkers
to assay mild, moderate, and severe cases of DM. Our studies provide insight into the mechanisms of myotonic dystrophy, the most
common adult form of muscular dystrophy. In this disease, a family of RNA
binding proteins is sequestered by toxic RNA, which leads to mis-regulation and
disease symptoms. We have created a cellular model with one of these family
members to study how these RNA binding proteins function in the absence of the
toxic RNA. In parallel, we analyzed transcriptomic data from over 50 individuals
(44 affected by myotonic dystrophy) with a range of disease severity. The
results from the transcriptomic data provide a rational approach to select
biomarkers for clinical research and therapeutic trials.
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15
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Bai Y, Nguyen L, Song Z, Peng S, Lee J, Zheng N, Kapoor I, Hagler LD, Cai K, Cheng J, Chan HYE, Zimmerman SC. Integrating Display and Delivery Functionality with a Cell Penetrating Peptide Mimic as a Scaffold for Intracellular Multivalent Multitargeting. J Am Chem Soc 2016; 138:9498-507. [DOI: 10.1021/jacs.6b03697] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | - Shaohong Peng
- Laboratory
of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong SAR, China
| | | | | | | | | | | | | | - H. Y. Edwin Chan
- Laboratory
of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong SAR, China
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16
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Larsen M, Kress W, Schoser B, Hehr U, Müller CR, Rost S. Identification of variants in MBNL1 in patients with a myotonic dystrophy-like phenotype. Eur J Hum Genet 2016; 24:1467-72. [PMID: 27222292 DOI: 10.1038/ejhg.2016.41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 03/22/2016] [Accepted: 04/12/2016] [Indexed: 11/09/2022] Open
Abstract
The myotonic dystrophies (DMs) are the most common inherited muscular disorders in adults. In most of the cases, the disease is caused by (CTG)n/(CCTG)n repeat expansions (EXPs) in non-coding regions of the genes DMPK (dystrophia myotonica-protein kinase) and CNBP (CCHC-type zinc-finger nucleic acid-binding protein). The EXP is transcribed into mutant RNAs, which provoke a common pathomechanism that is characterized by misexpression and mis-splicing. In this study, we screened 138 patients with typical clinical features of DM being negative for EXP in the known genes. We sequenced DMPK and CNBP - associated with DM, as well as CELF1 (CUGBP, Elav-like family member 1) and MBNL1 (muscleblind-like splicing regulator 1) - associated with the pathomechanism of DM, for pathogenic variants, addressing the question whether defects in other genes could cause a DM-like phenotype. We identified variants in three unrelated patients in the MBNL1 gene, two of them were heterozygous missense mutations and one an in-frame deletion of three amino acids. The variants were located in different conserved regions of the protein. The missense mutations were classified as potentially pathogenic by prediction tools. Analysis of MBNL1 splice target genes was carried out for one of the patients using RNA from peripheral blood leukocytes (PBL). Analysis of six genes known to show mis-splicing in the skeletal muscle gave no informative results on the effect of this variant when tested in PBL. The association of these variants with the DM phenotype therefore remains unconfirmed, but we hope that in view of the key role of MBNL1 in DM pathogenesis our observations may foster further studies in this direction.
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Affiliation(s)
- Mirjam Larsen
- Department of Human Genetics, Julius-Maximilians-University, Würzburg, Germany
| | - Wolfram Kress
- Department of Human Genetics, Julius-Maximilians-University, Würzburg, Germany
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich, Germany
| | - Ute Hehr
- Center for and Department of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Clemens R Müller
- Department of Human Genetics, Julius-Maximilians-University, Würzburg, Germany
| | - Simone Rost
- Department of Human Genetics, Julius-Maximilians-University, Würzburg, Germany
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17
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Genome Therapy of Myotonic Dystrophy Type 1 iPS Cells for Development of Autologous Stem Cell Therapy. Mol Ther 2016; 24:1378-87. [PMID: 27203440 DOI: 10.1038/mt.2016.97] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 04/26/2016] [Indexed: 12/11/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is caused by expanded Cytosine-Thymine-Guanine (CTG) repeats in the 3'-untranslated region (3' UTR) of the Dystrophia myotonica protein kinase (DMPK) gene, for which there is no effective therapy. The objective of this study is to develop genome therapy in human DM1 induced pluripotent stem (iPS) cells to eliminate mutant transcripts and reverse the phenotypes for developing autologous stem cell therapy. The general approach involves targeted insertion of polyA signals (PASs) upstream of DMPK CTG repeats, which will lead to premature termination of transcription and elimination of toxic mutant transcripts. Insertion of PASs was mediated by homologous recombination triggered by site-specific transcription activator-like effector nuclease (TALEN)-induced double-strand break. We found genome-treated DM1 iPS cells continue to maintain pluripotency. The insertion of PASs led to elimination of mutant transcripts and complete disappearance of nuclear RNA foci and reversal of aberrant splicing in linear-differentiated neural stem cells, cardiomyocytes, and teratoma tissues. In conclusion, genome therapy by insertion of PASs upstream of the expanded DMPK CTG repeats prevented the production of toxic mutant transcripts and reversal of phenotypes in DM1 iPS cells and their progeny. These genetically-treated iPS cells will have broad clinical application in developing autologous stem cell therapy for DM1.
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18
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Zhang BW, Cai HF, Wei XF, Sun JJ, Lan XY, Lei CZ, Lin FP, Qi XL, Plath M, Chen H. miR-30-5p Regulates Muscle Differentiation and Alternative Splicing of Muscle-Related Genes by Targeting MBNL. Int J Mol Sci 2016; 17:ijms17020182. [PMID: 26840300 PMCID: PMC4783916 DOI: 10.3390/ijms17020182] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/26/2015] [Accepted: 01/22/2016] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs), a class of single stranded, small (~22 nucleotides), non-coding RNAs, play an important role in muscle development. We focused on the role of the miR-30-5p family during bovine muscle development from previous high-throughput sequencing results and analyzed their expression profiles. MHC and MyoG mRNAs expression as well as their proteins were suppressed in differentiated C2C12 cells, suggesting the importance of miR-30-5p in muscle development. MBNL, the candidate target of miR-30-5p, is an alternative splicing regulation factor. MBNL1 and MBNL3 have opposite effects on muscle differentiation. Our results confirmed that miR-30a-5p and miR-30e-5p repress the expression of MBNL1, MBNL2 and MBNL3, whereas miR-30b-5p inhibits MBNL1 and MBNL2 expression. This provides direct evidence that MBNL expression can be flexibly regulated by miR-30-5p. Previous studies showed that MBNL1 promotes exon inclusion of two muscle-related genes (Trim55 and INSR). Through RNA splicing studies, we found that miR-30-5p had an effect on their alternative splicing, which means miR-30-5p via MBNL1 could be integrated into muscle signaling pathways in which INSR or Trim55 are located. In conclusion, miR-30-5p could inhibit muscle cell differentiation and regulate the alternative splicing of Trim55 and INSR by targeting MBNL. These results promote the understanding of the function of miRNAs in muscle development.
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Affiliation(s)
- Bo-Wen Zhang
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Han-Fang Cai
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xue-Feng Wei
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jia-Jie Sun
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xian-Yong Lan
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chu-Zhao Lei
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Feng-Peng Lin
- Department of Animal Husbandry, Bureau of Biyang County of Henan province, Biyang 463700, Henan, China.
| | - Xing-Lei Qi
- Department of Animal Husbandry, Bureau of Biyang County of Henan province, Biyang 463700, Henan, China.
| | - Martin Plath
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Hong Chen
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
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19
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Siboni RB, Bodner MJ, Khalifa MM, Docter AG, Choi JY, Nakamori M, Haley MM, Berglund JA. Biological Efficacy and Toxicity of Diamidines in Myotonic Dystrophy Type 1 Models. J Med Chem 2015; 58:5770-80. [PMID: 26103061 PMCID: PMC4972181 DOI: 10.1021/acs.jmedchem.5b00356] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a disease characterized by errors in alternative splicing, or "mis-splicing". The causative agent of mis-splicing in DM1 is an inherited CTG repeat expansion located in the 3' untranslated region of the DM protein kinase gene. When transcribed, CUG repeat expansion RNA sequesters muscleblind-like (MBNL) proteins, which constitute an important family of alternative splicing regulators. Sequestration of MBNL proteins results in the mis-splicing of its regulated transcripts. Previous work has demonstrated that pentamidine, a diamidine which is currently FDA-approved as an antiparasitic agent, was able to partially reverse mis-splicing in multiple DM1 models, albeit at toxic concentrations. In this study, we characterized a series of pentamidine analogues to determine their ability to reverse mis-splicing and their toxicity in vivo. Experiments in cell and mouse models demonstrated that compound 13, also known as furamidine, effectively reversed mis-splicing with equal efficacy and reduced toxicity compared to pentamidine.
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Affiliation(s)
| | | | | | | | | | - Masayuki Nakamori
- §Department of Neurology, University of Osaka Graduate School of Medicine, Osaka 565-0871, Japan
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20
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Pettersson OJ, Aagaard L, Jensen TG, Damgaard CK. Molecular mechanisms in DM1 - a focus on foci. Nucleic Acids Res 2015; 43:2433-41. [PMID: 25605794 PMCID: PMC4344492 DOI: 10.1093/nar/gkv029] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/05/2015] [Accepted: 01/11/2015] [Indexed: 01/15/2023] Open
Abstract
Myotonic dystrophy type 1 is caused by abnormal expansion of a CTG-trinucleotide repeat in the gene encoding Dystrophia Myotonica Protein Kinase (DMPK), which in turn leads to global deregulation of gene expression in affected individuals. The transcribed mRNA contains a massive CUG-expansion in the 3' untranslated region (3'UTR) facilitating nucleation of several regulatory RNA-binding proteins, which are thus unable to perform their normal cellular function. These CUG-expanded mRNA-protein aggregates form distinct, primarily nuclear foci. In differentiated muscle cells, most of the CUG-expanded RNA remains in the nuclear compartment, while in dividing cells such as fibroblasts a considerable fraction of the mutant RNA reaches the cytoplasm, consistent with findings that both nuclear and cytoplasmic events are mis-regulated in DM1. Recent evidence suggests that the nuclear aggregates, or ribonuclear foci, are more dynamic than previously anticipated and regulated by several proteins, including RNA helicases. In this review, we focus on the homeostasis of DMPK mRNA foci and discuss how their dynamic regulation may affect disease-causing mechanisms in DM1.
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Affiliation(s)
- Olof Joakim Pettersson
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, Building 1240, DK-8000 Aarhus C, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, Building 1240, DK-8000 Aarhus C, Denmark
| | - Thomas Gryesten Jensen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, Building 1240, DK-8000 Aarhus C, Denmark
| | - Christian Kroun Damgaard
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
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21
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Konieczny P, Stepniak-Konieczna E, Sobczak K. MBNL proteins and their target RNAs, interaction and splicing regulation. Nucleic Acids Res 2014; 42:10873-87. [PMID: 25183524 PMCID: PMC4176163 DOI: 10.1093/nar/gku767] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Muscleblind-like (MBNL) proteins are key regulators of precursor and mature mRNA metabolism in mammals. Based on published and novel data, we explore models of tissue-specific MBNL interaction with RNA. We portray MBNL domains critical for RNA binding and splicing regulation, and the structure of MBNL's normal and pathogenic RNA targets, particularly in the context of myotonic dystrophy (DM), in which expanded CUG or CCUG repeat transcripts sequester several nuclear proteins including MBNLs. We also review the properties of MBNL/RNA complex, including recent data obtained from UV cross-linking and immunoprecipitation (CLIP-Seq), and discuss how this interaction shapes normal MBNL-dependent alternative splicing regulation. Finally, we review how this acquired knowledge about the pathogenic RNA structure and nature of MBNL sequestration can be translated into the design of therapeutic strategies against DM.
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Affiliation(s)
- Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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22
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Transcriptionally correlated subcellular dynamics of MBNL1 during lens development and their implication for the molecular pathology of myotonic dystrophy type 1. Biochem J 2014; 458:267-80. [PMID: 24354850 DOI: 10.1042/bj20130870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DM1 (myotonic dystrophy type 1) is caused by elongation of a CTG repeat in the DMPK (dystrophia myotonica-protein kinase) gene. mRNA transcripts containing these CUGexp (CUG expansion) repeats form accumulations, or foci, in the nucleus of the cell. The pathogenesis of DM1 is proposed to result from inappropriate patterns of alternative splicing caused by sequestration of the developmentally regulated alternative splicing factor MBNL1 (muscleblind-like 1) by these foci. Since eye lens cataract is a common feature of DM1 we have examined the distribution and dynamics of MBNL1 in lens epithelial cell lines derived from patients with DM1. The results of the present study demonstrate that only a small proportion of nuclear MBNL1 accumulates in CUGexp pre-mRNA foci. MBNL1 is, however, highly mobile and changes localization in response to altered transcription and splicing activity. Moreover, immunolocalization studies in lens sections suggest that a change in MBNL1 distribution is important during lens growth and differentiation. Although these data suggest that the loss of MBNL1 function due to accumulation in foci is an unlikely explanation for DM1 symptoms in the lens, they do demonstrate a strong relationship between the subcellular MBNL1 localization and pathways of cellular differentiation, providing an insight into the sensitivity of the lens to changes in MBNL1 distribution.
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23
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Caillet-Boudin ML, Fernandez-Gomez FJ, Tran H, Dhaenens CM, Buee L, Sergeant N. Brain pathology in myotonic dystrophy: when tauopathy meets spliceopathy and RNAopathy. Front Mol Neurosci 2014; 6:57. [PMID: 24409116 PMCID: PMC3885824 DOI: 10.3389/fnmol.2013.00057] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 12/20/2013] [Indexed: 01/18/2023] Open
Abstract
Myotonic dystrophy (DM) of type 1 and 2 (DM1 and DM2) are inherited autosomal dominant diseases caused by dynamic and unstable expanded microsatellite sequences (CTG and CCTG, respectively) in the non-coding regions of the genes DMPK and ZNF9, respectively. These mutations result in the intranuclear accumulation of mutated transcripts and the mis-splicing of numerous transcripts. This so-called RNA gain of toxic function is the main feature of an emerging group of pathologies known as RNAopathies. Interestingly, in addition to these RNA inclusions, called foci, the presence of neurofibrillary tangles (NFT) in patient brains also distinguishes DM as a tauopathy. Tauopathies are a group of nearly 30 neurodegenerative diseases that are characterized by intraneuronal protein aggregates of the microtubule-associated protein Tau (MAPT) in patient brains. Furthermore, a number of neurodegenerative diseases involve the dysregulation of splicing regulating factors and have been characterized as spliceopathies. Thus, myotonic dystrophies are pathologies resulting from the interplay among RNAopathy, spliceopathy, and tauopathy. This review will describe how these processes contribute to neurodegeneration. We will first focus on the tauopathy associated with DM1, including clinical symptoms, brain histology, and molecular mechanisms. We will also discuss the features of DM1 that are shared by other tauopathies and, consequently, might participate in the development of a tauopathy. Moreover, we will discuss the determinants common to both RNAopathies and spliceopathies that could interfere with tau-related neurodegeneration.
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Affiliation(s)
- Marie-Laure Caillet-Boudin
- Alzheimer and Tauopathies, Faculty of Medicine, Jean-Pierre Aubert Research Centre, Institute of Predictive Medicine and Therapeutic Research, Inserm, UMR 837 Lille, France ; University of Lille Nord de France, UDSL Lille, France
| | - Francisco-Jose Fernandez-Gomez
- Alzheimer and Tauopathies, Faculty of Medicine, Jean-Pierre Aubert Research Centre, Institute of Predictive Medicine and Therapeutic Research, Inserm, UMR 837 Lille, France ; University of Lille Nord de France, UDSL Lille, France
| | - Hélène Tran
- Alzheimer and Tauopathies, Faculty of Medicine, Jean-Pierre Aubert Research Centre, Institute of Predictive Medicine and Therapeutic Research, Inserm, UMR 837 Lille, France ; University of Lille Nord de France, UDSL Lille, France
| | - Claire-Marie Dhaenens
- Alzheimer and Tauopathies, Faculty of Medicine, Jean-Pierre Aubert Research Centre, Institute of Predictive Medicine and Therapeutic Research, Inserm, UMR 837 Lille, France ; University of Lille Nord de France, UDSL Lille, France
| | - Luc Buee
- Alzheimer and Tauopathies, Faculty of Medicine, Jean-Pierre Aubert Research Centre, Institute of Predictive Medicine and Therapeutic Research, Inserm, UMR 837 Lille, France ; University of Lille Nord de France, UDSL Lille, France
| | - Nicolas Sergeant
- Alzheimer and Tauopathies, Faculty of Medicine, Jean-Pierre Aubert Research Centre, Institute of Predictive Medicine and Therapeutic Research, Inserm, UMR 837 Lille, France ; University of Lille Nord de France, UDSL Lille, France
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24
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Induction and reversal of myotonic dystrophy type 1 pre-mRNA splicing defects by small molecules. Nat Commun 2013; 4:2044. [PMID: 23806903 PMCID: PMC3710115 DOI: 10.1038/ncomms3044] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/23/2013] [Indexed: 02/06/2023] Open
Abstract
The ability to control pre-mRNA splicing with small molecules could facilitate the development of therapeutics or cell-based circuits that control gene function. Myotonic dystrophy type 1 (DM1) is caused by the dysregulation of alternative pre-mRNA splicing due to sequestration of muscleblind-like 1 protein (MBNL1) by expanded, non-coding r(CUG) repeats (r(CUG)exp). Here we report two small molecules that induce or ameliorate alternative splicing dysregulation. The thiophene-containing small molecule (1) inhibits the interaction of MBNL1 with its natural pre-mRNA substrates. Compound (2), a substituted naphthyridine, binds r(CUG)exp and displaces MBNL1. Structural models show that 1 binds MBNL1 in the Zn-finger domain and that 2 interacts with UU loops in r(CUG)exp. This study provides a structural framework for small molecules that target MBNL1 by mimicking r(CUG)exp and shows that targeting MBNL1 causes dysregulation of alternative splicing, suggesting that MBNL1 is thus not a suitable therapeutic target for the treatment of DM1.
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25
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Coonrod LA, Nakamori M, Wang W, Carrell S, Hilton CL, Bodner MJ, Siboni RB, Docter AG, Haley MM, Thornton CA, Berglund JA. Reducing levels of toxic RNA with small molecules. ACS Chem Biol 2013; 8:2528-37. [PMID: 24028068 DOI: 10.1021/cb400431f] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Myotonic dystrophy (DM) is one of the most common forms of muscular dystrophy. DM is an autosomal dominant disease caused by a toxic gain of function RNA. The toxic RNA is produced from expanded noncoding CTG/CCTG repeats, and these CUG/CCUG repeats sequester the Muscleblind-like (MBNL) family of RNA binding proteins. The MBNL proteins are regulators of alternative splicing, and their sequestration has been linked with mis-splicing events in DM. A previously reported screen for small molecules found that pentamidine was able to improve splicing defects associated with DM. Biochemical experiments and cell and mouse model studies of the disease indicate that pentamidine and related compounds may work through binding the CTG*CAG repeat DNA to inhibit transcription. Analysis of a series of methylene linker analogues of pentamidine revealed that heptamidine reverses splicing defects and rescues myotonia in a DM1 mouse model.
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Affiliation(s)
| | - Masayuki Nakamori
- Department
of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Wenli Wang
- Department
of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Samuel Carrell
- Department
of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | | | | | | | | | | | - Charles A. Thornton
- Department
of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
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26
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Rzuczek SG, Gao Y, Tang ZZ, Thornton CA, Kodadek T, Disney MD. Features of modularly assembled compounds that impart bioactivity against an RNA target. ACS Chem Biol 2013; 8:2312-21. [PMID: 24032410 DOI: 10.1021/cb400265y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transcriptomes provide a myriad of potential RNAs that could be the targets of therapeutics or chemical genetic probes of function. Cell-permeable small molecules, however, generally do not exploit these targets, owing to the difficulty in the design of high affinity, specific small molecules targeting RNA. As part of a general program to study RNA function using small molecules, we designed bioactive, modularly assembled small molecules that target the noncoding expanded RNA repeat that causes myotonic dystrophy type 1 (DM1), r(CUG)(exp). Herein, we present a rigorous study to elucidate features in modularly assembled compounds that afford bioactivity. Different modular assembly scaffolds were investigated, including polyamines, α-peptides, β-peptides, and peptide tertiary amides (PTAs). On the basis of activity as assessed by improvement of DM1-associated defects, stability against proteases, cellular permeability, and toxicity, we discovered that constrained backbones, namely, PTAs, are optimal. Notably, we determined that r(CUG)(exp) is the target of the optimal PTA in cellular models and that the optimal PTA improves DM1-associated defects in a mouse model. Biophysical analyses were employed to investigate potential sources of bioactivity. These investigations show that modularly assembled compounds have increased residence times on their targets and faster on rates than the RNA-binding modules from which they were derived. Moreover, they have faster on rates than the protein that binds r(CUG)(exp), the inactivation of which gives rise to DM1-associated defects. These studies provide information about features of small molecules that are programmable for targeting RNA, allowing for the facile optimization of therapeutics or chemical probes against other cellular RNA targets.
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Affiliation(s)
- Suzanne G. Rzuczek
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Yu Gao
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Zhen-Zhi Tang
- Department
of Neurology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Charles A. Thornton
- Department
of Neurology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Thomas Kodadek
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department
of Chemistry, The Scripps Research Institute, Scripps Florida, 130
Scripps Way #3A1, Jupiter, Florida 33458, United States
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27
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Mechanisms of RNA-induced toxicity in CAG repeat disorders. Cell Death Dis 2013; 4:e752. [PMID: 23907466 PMCID: PMC3763438 DOI: 10.1038/cddis.2013.276] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/21/2013] [Accepted: 06/28/2013] [Indexed: 01/27/2023]
Abstract
Several inherited neurodegenerative disorders are caused by CAG trinucleotide repeat expansions, which can be located either in the coding region or in the untranslated region (UTR) of the respective genes. Polyglutamine diseases (polyQ diseases) are caused by an expansion of a stretch of CAG repeats within the coding region, translating into a polyQ tract. The polyQ tract expansions result in conformational changes, eventually leading to aggregate formation. It is widely believed that the aggregation of polyQ proteins is linked with disease development. In addition, in the last couple of years, it has been shown that RNA-mediated mechanisms also have a profound role in neurotoxicity in both polyQ diseases and diseases caused by elongated CAG repeat motifs in their UTRs. Here, we review the different molecular mechanisms assigned to mRNAs with expanded CAG repeats. One aspect is the mRNA folding of CAG repeats. Furthermore, pathogenic mechanisms assigned to CAG repeat mRNAs are discussed. First, we discuss mechanisms that involve the sequestration of the diverse proteins to the expanded CAG repeat mRNA molecules. As a result of this, several cellular mechanisms are aberrantly regulated. These include the sequestration of MBNL1, leading to misregulated splicing; sequestration of nucleolin, leading to reduced cellular rRNA; and sequestration of proteins of the siRNA machinery, resulting in the production of short silencing RNAs that affect gene expression. Second, we discuss the effect of expanded CAG repeats on the subcellular localization, transcription and translation of the CAG repeat mRNA itself. Here we focus on the MID1 protein complex that triggers an increased translation of expanded CAG repeat mRNAs and a mechanism called repeat-associated non-ATG translation, which leads to proteins aberrantly translated from CAG repeat mRNAs. In addition, therapeutic approaches for CAG repeat disorders are discussed. Together, all the findings summarized here show that mutant mRNA has a fundamental role in the pathogenesis of CAG repeat diseases.
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Guan L, Disney MD. Covalent Small-Molecule-RNA Complex Formation Enables Cellular Profiling of Small-Molecule-RNA Interactions. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Guan L, Disney MD. Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions. Angew Chem Int Ed Engl 2013; 52:10010-3. [PMID: 23913698 DOI: 10.1002/anie.201301639] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 05/02/2013] [Indexed: 01/13/2023]
Abstract
Won't let you go! A strategy is described to design small molecules that react with their cellular RNA targets. This approach not only improves the activity of compounds targeting RNA in cell culture by a factor of about 2500 but also enables cell-wide profiling of its RNA targets.
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Affiliation(s)
- Lirui Guan
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, 3A1, Jupiter, FL 33458 (USA)
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