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Bouton L, Ecoutin A, Malard F, Campagne S. Small molecules modulating RNA splicing: a review of targets and future perspectives. RSC Med Chem 2024; 15:1109-1126. [PMID: 38665842 PMCID: PMC11042171 DOI: 10.1039/d3md00685a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 04/28/2024] Open
Abstract
In eukaryotic cells, RNA splicing is crucial for gene expression. Dysregulation of this process can result in incorrect mRNA processing, leading to aberrant gene expression patterns. Such abnormalities are implicated in many inherited diseases and cancers. Historically, antisense oligonucleotides, which bind to specific RNA targets, have been used to correct these splicing abnormalities. Despite their high specificity of action, these oligonucleotides have drawbacks, such as lack of oral bioavailability and the need for chemical modifications to enhance cellular uptake and stability. As a result, recent efforts focused on the development of small organic molecules that can correct abnormal RNA splicing event under disease conditions. This review discusses known and potential targets of these molecules, including RNA structures, trans-acting splicing factors, and the spliceosome - the macromolecular complex responsible for RNA splicing. We also rely on recent advances to discuss therapeutic applications of RNA-targeting small molecules in splicing correction. Overall, this review presents an update on strategies for RNA splicing modulation, emphasizing the therapeutic promise of small molecules.
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Affiliation(s)
- Léa Bouton
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Agathe Ecoutin
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
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2
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Ohara H, Hosokawa M, Awaya T, Hagiwara A, Kurosawa R, Sako Y, Ogawa M, Ogasawara M, Noguchi S, Goto Y, Takahashi R, Nishino I, Hagiwara M. Branchpoints as potential targets of exon-skipping therapies for genetic disorders. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:404-412. [PMID: 37547287 PMCID: PMC10403725 DOI: 10.1016/j.omtn.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Fukutin (FKTN) c.647+2084G>T creates a pseudo-exon with a premature stop codon, which causes Fukuyama congenital muscular dystrophy (FCMD). We aimed to ameliorate aberrant splicing of FKTN caused by this variant. We screened compounds focusing on splicing regulation using the c.647+2084G>T splicing reporter and discovered that the branchpoint, which is essential for splicing reactions, could be a potential therapeutic target. To confirm the effectiveness of branchpoints as targets for exon skipping, we designed branchpoint-targeted antisense oligonucleotides (BP-AONs). This restored normal FKTN mRNA and protein production in FCMD patient myotubes. We identified a functional BP by detecting splicing intermediates and creating BP mutations in the FKTN reporter gene; this BP was non-redundant and sufficiently blocked by BP-AONs. Next, a BP-AON was designed for a different FCMD-causing variant, which induces pathogenic exon trapping by a common SINE-VNTR-Alu-type retrotransposon. Notably, this BP-AON also restored normal FKTN mRNA and protein production in FCMD patient myotubes. Our findings suggest that BPs could be potential targets in exon-skipping therapeutic strategies for genetic disorders.
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Affiliation(s)
- Hiroaki Ohara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
- Department of Drug Discovery for Intractable Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Motoyasu Hosokawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Tumor Microenvironment and Immunity, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Atsuko Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yukiya Sako
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Megumu Ogawa
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Masashi Ogasawara
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Yuichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neurology, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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3
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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4
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Song M, Pang L, Zhang M, Qu Y, Laster KV, Dong Z. Cdc2-like kinases: structure, biological function, and therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:148. [PMID: 37029108 PMCID: PMC10082069 DOI: 10.1038/s41392-023-01409-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023] Open
Abstract
The CLKs (Cdc2-like kinases) belong to the dual-specificity protein kinase family and play crucial roles in regulating transcript splicing via the phosphorylation of SR proteins (SRSF1-12), catalyzing spliceosome molecular machinery, and modulating the activities or expression of non-splicing proteins. The dysregulation of these processes is linked with various diseases, including neurodegenerative diseases, Duchenne muscular dystrophy, inflammatory diseases, viral replication, and cancer. Thus, CLKs have been considered as potential therapeutic targets, and significant efforts have been exerted to discover potent CLKs inhibitors. In particular, clinical trials aiming to assess the activities of the small molecules Lorecivivint on knee Osteoarthritis patients, and Cirtuvivint and Silmitasertib in different advanced tumors have been investigated for therapeutic usage. In this review, we comprehensively documented the structure and biological functions of CLKs in various human diseases and summarized the significance of related inhibitors in therapeutics. Our discussion highlights the most recent CLKs research, paving the way for the clinical treatment of various human diseases.
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Affiliation(s)
- Mengqiu Song
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
| | - Luping Pang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Mengmeng Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yingzi Qu
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Kyle Vaughn Laster
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China.
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
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5
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Abstract
Alternative splicing (AS) of mRNAs is an essential regulatory mechanism in eukaryotic gene expression. AS misregulation, caused by either dysregulation or mutation of splicing factors, has been shown to be involved in cancer development and progression, making splicing factors suitable targets for cancer therapy. In recent years, various types of pharmacological modulators, such as small molecules and oligonucleotides, targeting distinct components of the splicing machinery, have been under development to treat multiple disorders. Although these approaches have promise, targeting the core spliceosome components disrupts the early stages of spliceosome assembly and can lead to nonspecific and toxic effects. New research directions have been focused on targeting specific splicing factors for a more precise effect. In this Perspective, we will highlight several approaches for targeting splicing factors and their functions and suggest ways to improve their specificity.
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Affiliation(s)
- Ariel Bashari
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
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ElHady AK, El-Gamil DS, Abadi AH, Abdel-Halim M, Engel M. An overview of cdc2-like kinase 1 (Clk1) inhibitors and their therapeutic indications. Med Res Rev 2023; 43:343-398. [PMID: 36262046 DOI: 10.1002/med.21928] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/07/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Over the past decade, Clk1 has been identified as a promising target for the treatment of various diseases, in which deregulated alternative splicing plays a role. First small molecules targeting Clk1 are in clinical trials for the treatment of solid cancer, where variants of oncogenic proteins derived from alternative splicing promote tumor progression. Since many infectious pathogens hi-jack the host cell's splicing machinery to ensure efficient replication, further indications in this area are under investigation, such as Influenza A, HIV-1 virus, and Trypanosoma infections, and more will likely be discovered in the future. In addition, Clk1 was found to contribute to the progression of Alzheimer's disease through causing an imbalance of tau splicing products. Interestingly, homozygous Clk1 knockout mice showed a rather mild phenotype, opposed to what might be expected in view of the profound role of Clk1 in alternative splicing. A major drawback of most Clk1 inhibitors is their insufficient selectivity; in particular, Dyrk kinases and haspin were frequently identified as off-targets, besides the other Clk isoforms. Only few inhibitors were shown to be selective over Dyrk1A and haspin, whereas no Clk1 inhibitor so far achieved selectivity over the Clk4 isoform. In this review, we carefully compiled all Clk1 inhibitors from the scientific literature and summarized their structure-activity relationships (SAR). In addition, we critically discuss the available selectivity data and describe the inhibitor's efficacy in cellular models, if reported. Thus, we provide a comprehensive overview on the current state of Clk1 drug discovery and highlight the most promising chemotypes.
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Affiliation(s)
- Ahmed K ElHady
- Department of Organic and Pharmaceutical Chemistry, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Dalia S El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.,Department of Chemistry, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Matthias Engel
- Department of Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
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7
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Matsushima S, Ajiro M, Iida K, Chamoto K, Honjo T, Hagiwara M. Chemical induction of splice-neoantigens attenuates tumor growth in a preclinical model of colorectal cancer. Sci Transl Med 2022; 14:eabn6056. [PMID: 36449604 DOI: 10.1126/scitranslmed.abn6056] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Neoantigen production is a determinant of cancer immunotherapy. However, the expansion of neoantigen abundance for cancer therapeutics is technically challenging. Here, we report that the synthetic compound RECTAS can induce the production of splice-neoantigens that could be used to boost antitumor immune responses. RECTAS suppressed tumor growth in a CD8+ T cell- and tumor major histocompatibility complex class I-dependent manner and enhanced immune checkpoint blockade efficacy. Subsequent transcriptome analysis and validation for immunogenicity identified six splice-neoantigen candidates whose expression was induced by RECTAS treatment. Vaccination of the identified neoepitopes elicited T cell responses capable of killing cancer cells in vitro, in addition to suppression of tumor growth in vivo upon sensitization with RECTAS. Collectively, these results provide support for the further development of splice variant-inducing treatments for cancer immunotherapy.
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Affiliation(s)
- Shingo Matsushima
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan.,Pharmacology Research Laboratories, Watarase Research Center, Kyorin Pharmaceutical Co. Ltd, Tochigi 329-0114, Japan
| | - Masahiko Ajiro
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Faculty of Science and Engineering, Kindai University, Osaka 577-8502, Japan
| | - Kenji Chamoto
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
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8
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Lebecque B, Bourgne C, Munje C, Berger J, Tassin T, Cony-Makhoul P, Guerci-Bresler A, Johnson-Ansah H, Liu W, Saugues S, Tchirkov A, Vetrie D, Copland M, Berger MG. The Spliceosome: A New Therapeutic Target in Chronic Myeloid Leukaemia. Cancers (Basel) 2022; 14:4695. [PMID: 36230624 PMCID: PMC9563771 DOI: 10.3390/cancers14194695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022] Open
Abstract
RNA splicing factors are frequently altered in cancer and can act as both oncoproteins and tumour suppressors. They have been found mutated or deregulated, justifying the growing interest in the targeting of splicing catalysis, splicing regulatory proteins, and/or specific, key altered splicing events. We recently showed that the DNA methylation alterations of CD34+CD15- chronic myeloid leukaemia (CML) cells affect, among others, alternative splicing genes, suggesting that spliceosome actors might be altered in chronic-phase (CP)-CML. We investigated the expression of 12 spliceosome genes known to be oncogenes or tumour suppressor genes in primary CP-CML CD34+ cells at diagnosis (n = 15). We found that CP-CML CD34+ cells had a distinct splicing signature profile as compared with healthy donor CD34+ cells or whole CP-CML cells, suggesting: (i) a spliceosome deregulation from the diagnosis time and (ii) an intraclonal heterogeneity. We could identify three profile types, but there was no relationship with a patient's characteristics. By incubating cells with TKI and/or a spliceosome-targeted drug (TG003), we showed that CP-CML CD34+ cells are both BCR::ABL and spliceosome dependent, with the combination of the two drugs showing an additive effect while sparing healthy donors cells. Our results suggest that the spliceosome may be a new potential target for the treatment of CML.
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Affiliation(s)
- Benjamin Lebecque
- Hématologie Biologique, CHU Estaing, 63000 Clermont-Ferrand, France
- Equipe d’Accueil 7453 CHELTER, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Celine Bourgne
- Hématologie Biologique, CHU Estaing, 63000 Clermont-Ferrand, France
- Equipe d’Accueil 7453 CHELTER, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Chinmay Munje
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Juliette Berger
- Hématologie Biologique, CHU Estaing, 63000 Clermont-Ferrand, France
- Equipe d’Accueil 7453 CHELTER, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Thomas Tassin
- Hématologie Biologique, CHU Estaing, 63000 Clermont-Ferrand, France
- Equipe d’Accueil 7453 CHELTER, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Pascale Cony-Makhoul
- CH Annecy-Genevois, 74374 Pringy, France
- Groupe Fi-LMC, Centre Léon Bérard, 69008 Lyon, France
| | - Agnès Guerci-Bresler
- Groupe Fi-LMC, Centre Léon Bérard, 69008 Lyon, France
- Hématologie Clinique, CHRU Brabois, 54500 Vandoeuvre-lès-Nancy, France
| | - Hyacinthe Johnson-Ansah
- Groupe Fi-LMC, Centre Léon Bérard, 69008 Lyon, France
- Institut d’Hématologie de Basse Normandie, CHU, 14033 Caen, France
| | - Wei Liu
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sandrine Saugues
- Hématologie Biologique, CHU Estaing, 63000 Clermont-Ferrand, France
- Equipe d’Accueil 7453 CHELTER, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Andrei Tchirkov
- Equipe d’Accueil 7453 CHELTER, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, 63000 Clermont-Ferrand, France
| | - David Vetrie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Mhairi Copland
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Marc G. Berger
- Hématologie Biologique, CHU Estaing, 63000 Clermont-Ferrand, France
- Equipe d’Accueil 7453 CHELTER, Université Clermont Auvergne, 63001 Clermont-Ferrand, France
- Groupe Fi-LMC, Centre Léon Bérard, 69008 Lyon, France
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Abe I, Tanaka T, Ohe K, Fujii H, Nagata M, Ochi K, Senda Y, Takeshita K, Koga M, Kudo T, Enjoji M, Yanase T, Kobayashi K. Inhibition of NR5A1 phosphorylation alleviates a transcriptional suppression defect caused by a novel NR0B1 mutation. J Endocr Soc 2022; 6:bvac068. [PMID: 35592512 PMCID: PMC9113462 DOI: 10.1210/jendso/bvac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 11/19/2022] Open
Abstract
Context Mutations in the NR0B1 gene, also well-known as the DAX1 gene, are known to cause congenital adrenal hypoplasia associated with hypogonadotropic hypogonadism. The abnormal NR0B1 protein fails to suppress the transcription of promoters of steroidogenic enzymes, which are also targets of NR5A1 protein, also well-known as Ad4BP/SF-1 protein. Since NR5A1 and NR0B1 have antagonistic effects on steroidogenesis, the loss of function due to NR0B1 mutations may be compensated by inducing loss of function of NR5A1 protein. Patient A middle-aged man was diagnosed with congenital adrenal hypoplasia associated with hypogonadotropic hypogonadism and genetic analysis revealed him to have a novel NR0B1 mutation, c.1222C>T(p.Gln408Ter). Methods NR0B1 activity was evaluated in CLK1/4 inhibitor-treated 293T cells via immunoblotting and luciferase assays of the STAR promoter. Results TG003 treatment suppressed NR5A1 protein function to compensate for the mutant NR0B1 showing inhibited suppression of transcription. Immunoblotting analyses showed that the phosphorylation status of NR5A1 at Ser203 was attenuated by the CLK1/4 inhibitor. Conclusion The specific reduction of NR5A1 phosphorylation by a CLK1/4 inhibitor may alleviate developmental defects in patients with NR0B1 mutations.
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Affiliation(s)
- Ichiro Abe
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
| | - Tomoko Tanaka
- Department of Regenerative Medicine and Transplantation, Fukuoka University, Nanakuma Jonan-ku, Fukuoka, Japan
| | - Kenji Ohe
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Nanakuma, Jonan-ku, Fukuoka, Japan
| | - Hideyuki Fujii
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
| | - Mai Nagata
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
| | - Kentaro Ochi
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
| | - Yuki Senda
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
| | - Kaori Takeshita
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
| | - Midori Koga
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
| | - Tadachika Kudo
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
| | - Munechika Enjoji
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Nanakuma, Jonan-ku, Fukuoka, Japan
| | | | - Kunihisa Kobayashi
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Zokumyoin, Chikushino, Fukuoka, Japan
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10
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Sarasati SA, Iskandar K, Septianastiti MA, Malueka RG, Dwianingsih EK. Diagnostic Value of Dystrophin Immunostaining in the Diagnosis of Duchenne and Becker Muscular Dystrophy Patients. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.7612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background: Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive muscular disorders caused by the absence or reduction of the muscle cytoskeletal protein dystrophin. Standard procedures to detect deletion and duplication of the DMD gene use Multiplex Ligation-Dependent Probe Amplification (MLPA). However, genetic testing, such as MLPA, is not covered by the national insurance scheme in Indonesia. Immunohistochemical (IHC) staining of dystrophin from muscle biopsy in the form of Formalin-Fixed Paraffin-Embedded (FFPE) specimens can be an alternative method to detect dystrophin expression in protein levels to establish the diagnosis of DMD or BMD.
Objectives: To determinate sensitivity, specificity and accuracy of IHC analysis of dystrophin in DMD/BMD patient in comparison with the standard genetic testing, MLPA.
Methods: Twenty-six patients enrolled in this study were clinically diagnosed as DMD/BMD in Dr. Sardjito Hospital and Universitas Gadjah Mada Academic Hospital. Genomic DNA was isolated from 3 mL of EDTA-peripheral whole blood samples. The deletion and duplication of DMD genes were detected by MLPA. IHC examination was performed using a specific antibody dystrophin (DYS2). Complete loss of dystrophin staining indicated DMD, while partial loss of dystrophin staining indicated BMD. MLPA result was used as the gold standard to determine sensitivity, specificity, and accuracy of IHC technique using a 2x2 table.
Results: MLPA results revealed 18 (18/26; 69.3%) patients with deletion and 3 (3/26; 11.5%) patients with duplication. Five (5/26; 19.2%) patients who showed no deletion nor duplication were excluded from the analysis. Among 21 patients with deletion or duplication, 18 (18/21; 85.7%) patients were out-of-frame (DMD) and 3 (3/21; 14.3%) patients were in-frame (BMD). Six patients showed a discrepancy between the IHC and MLPA results with 9.5% (2/21) false positive and 19% (4/21) false negative. The sensitivity of dystrophin IHC was 77.78%, specificity 33.33%, positive predictive value 87.5%, negative predictive value 20%, and accuracy 71.43%.
Conclusion: Muscle biopsy followed by IHC can be one of the diagnostic tools to diagnose BMD or DMD, with high sensitivity. The protein-based strategy is probably the most efficient way to approach the diagnosis of Duchenne and Becker muscular dystrophy in limited health care settings.
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11
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Niba ETE, Awano H, Lee T, Takeshima Y, Shinohara M, Nishio H, Matsuo M. Dystrophin Dp71 Subisoforms Localize to the Mitochondria of Human Cells. Life (Basel) 2021; 11:life11090978. [PMID: 34575126 PMCID: PMC8468555 DOI: 10.3390/life11090978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease caused by deficiency in dystrophin, a protein product encoded by the DMD gene. Mitochondrial dysfunction is now attracting much attention as a central player in DMD pathology. However, dystrophin has never been explored in human mitochondria. Here, we analyzed dystrophin in cDNAs and mitochondrial fractions of human cells. Mitochondrial fraction was obtained using a magnetic-associated cell sorting (MACS) technology. Dystrophin was analyzed by reverse transcription (RT)-PCR and western blotting using an antibody against the dystrophin C-terminal. In isolated mitochondrial fraction from HEK293 cells, dystrophin was revealed as a band corresponding to Dp71b and Dp71ab subisoforms. Additionally, in mitochondria from HeLa, SH-SY5Y, CCL-136 and HepG2 cells, signals for Dp71b and Dp71ab were revealed as well. Concomitantly, dystrophin mRNAs encoding Dp71b and Dp71ab were disclosed by RT-PCR in these cells. Primary cultured myocytes from three dystrophinopathy patients showed various levels of mitochondrial Dp71 expression. Coherently, levels of mRNA were different in all cells reflecting the protein content, which indicated predominant accumulation of Dp71. Dystrophin was demonstrated to be localized to human mitochondrial fraction, specifically as Dp71 subisoforms. Myocytes derived from dystrophinopathy patients manifested different levels of mitochondrial Dp71, with higher expression revealed in myocytes from Becker muscular dystrophy (BMD) patient-derived myocytes.
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Affiliation(s)
- Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
- Correspondence: ; Tel.: +81-78-382-5543
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 663-8501, Japan; (T.L.); (Y.T.)
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 663-8501, Japan; (T.L.); (Y.T.)
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
| | - Hisahide Nishio
- Department of Occupational Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 651-2180, Japan;
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 651-2180, Japan;
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12
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Ajiro M, Awaya T, Kim YJ, Iida K, Denawa M, Tanaka N, Kurosawa R, Matsushima S, Shibata S, Sakamoto T, Studer R, Krainer AR, Hagiwara M. Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia. Nat Commun 2021; 12:4507. [PMID: 34301951 PMCID: PMC8302731 DOI: 10.1038/s41467-021-24705-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/21/2021] [Indexed: 01/10/2023] Open
Abstract
Approximately half of genetic disease-associated mutations cause aberrant splicing. However, a widely applicable therapeutic strategy to splicing diseases is yet to be developed. Here, we analyze the mechanism whereby IKBKAP-familial dysautonomia (FD) exon 20 inclusion is specifically promoted by a small molecule splice modulator, RECTAS, even though IKBKAP-FD exon 20 has a suboptimal 5' splice site due to the IVS20 + 6 T > C mutation. Knockdown experiments reveal that exon 20 inclusion is suppressed in the absence of serine/arginine-rich splicing factor 6 (SRSF6) binding to an intronic splicing enhancer in intron 20. We show that RECTAS directly interacts with CDC-like kinases (CLKs) and enhances SRSF6 phosphorylation. Consistently, exon 20 splicing is bidirectionally manipulated by targeting cellular CLK activity with RECTAS versus CLK inhibitors. The therapeutic potential of RECTAS is validated in multiple FD disease models. Our study indicates that small synthetic molecules affecting phosphorylation state of SRSFs is available as a new therapeutic modality for mechanism-oriented precision medicine of splicing diseases.
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Affiliation(s)
- Masahiko Ajiro
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masatsugu Denawa
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nobuo Tanaka
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shingo Matsushima
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Saiko Shibata
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tetsunori Sakamoto
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Rolenz Studer
- Center for Stem Cell Biology, Sloan Kettering Institute, New York, NY, USA
| | | | - Masatoshi Hagiwara
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan. .,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
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13
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Nakura T, Ozoe A, Narita Y, Matsuo M, Hakuno F, Kataoka N, Takahashi SI. Rbfox2 mediates exon 11 inclusion in insulin receptor pre-mRNA splicing in hepatoma cells. Biochimie 2021; 187:25-32. [PMID: 34022289 DOI: 10.1016/j.biochi.2021.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 11/27/2022]
Abstract
Insulin receptor (IR) pre-mRNA undergoes alternative splicing that produces two isoforms, IR-A and IR-B. The ratio of IR-A to IR-B varies among tissues, which strongly suggests that IR mRNA alternative splicing is regulated in a tissue-specific manner. However, the precise molecular mechanism for IR alternative splicing remains to be elucidated, especially in liver. In this study, we have analyzed IR alternative splicing mechanism by preparing a mini-gene splicing reporter with rat genomic DNA. The splicing reporter that contains exon 11 and its flanking intronic sequences could reproduce alternative splicing pattern in rat hepatoma H4IIE cells. Introducing several deletions in introns of the reporter revealed that intron 11 contains the region near exon 11 essential to promote exon 11 inclusion. This region contains an UGCAUG sequence, a specific binding site for the Rbfox splicing regulator, and mutation in this sequence results in exon 11 skipping. Furthermore, RbFox2 knockdown in H4IIE cells enhanced exon 11 skipping of endogenous IR pre-mRNA. Lastly mutations in the SRSF3 binding site of exon11 together with the Rbfox2 binding site completely abolished exon 11 inclusion with a mini-gene reporter pre-mRNA. Our results indicate that RbFox2 and SRSF3 proteins mediate exon 11 inclusion in rat hepatoma cells.
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Affiliation(s)
- Takahito Nakura
- Laboratory of Cell Regulation, Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsufumi Ozoe
- Laboratory of Cell Regulation, Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuka Narita
- Laboratory of Cell Regulation, Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - Fumihiko Hakuno
- Laboratory of Cell Regulation, Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoyuki Kataoka
- Laboratory of Cell Regulation, Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan; Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Japan.
| | - Shin-Ichiro Takahashi
- Laboratory of Cell Regulation, Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan.
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14
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Natua S, Ashok C, Shukla S. Hypoxia-induced alternative splicing in human diseases: the pledge, the turn, and the prestige. Cell Mol Life Sci 2021; 78:2729-2747. [PMID: 33386889 PMCID: PMC11072330 DOI: 10.1007/s00018-020-03727-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 12/30/2022]
Abstract
Maintenance of oxygen homeostasis is an indispensable criterion for the existence of multicellular life-forms. Disruption of this homeostasis due to inadequate oxygenation of the respiring tissues leads to pathological hypoxia, which acts as a significant stressor in several pathophysiological conditions including cancer, cardiovascular defects, bacterial infections, and neurological disorders. Consequently, the hypoxic tissues develop necessary adaptations both at the tissue and cellular level. The cellular adaptations involve a dramatic alteration in gene expression, post-transcriptional and post-translational modification of gene products, bioenergetics, and metabolism. Among the key responses to oxygen-deprivation is the skewing of cellular alternative splicing program. Herein, we discuss the current concepts of oxygen tension-dependent alternative splicing relevant to various pathophysiological conditions. Following a brief description of cellular response to hypoxia and the pre-mRNA splicing mechanism, we outline the impressive number of hypoxia-elicited alternative splicing events associated with maladies like cancer, cardiovascular diseases, and neurological disorders. Furthermore, we discuss how manipulation of hypoxia-induced alternative splicing may pose promising strategies for novel translational diagnosis and therapeutic interventions.
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Affiliation(s)
- Subhashis Natua
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Cheemala Ashok
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India.
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15
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Sasaki E, Hayashi Y, Kimura Y, Sashida S, Hamano N, Nirasawa K, Hamada K, Katagiri F, Kikkawa Y, Sakai T, Yoshida A, Kawada M, Hirashima SI, Miura T, Endo-Takahashi Y, Nomizu M, Negishi Y. Alpha-dystroglycan binding peptide A2G80-modified stealth liposomes as a muscle-targeting carrier for Duchenne muscular dystrophy. J Control Release 2021; 329:1037-1045. [PMID: 33080271 DOI: 10.1016/j.jconrel.2020.10.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 01/16/2023]
Abstract
Safe and efficient gene therapy for the treatment of Duchenne muscular dystrophy (DMD), a genetic disorder, is required. For this, the muscle-targeting delivery system of genes and nucleic acids is ideal. In this study, we focused on the A2G80 peptide, which has an affinity for α-dystroglycan expressed on muscle cell membranes, as a muscle targeted nanocarrier for DMD and developed A2G80-modified liposomes. We also prepared A2G80-modified liposomes coated with long- and short-chain PEG, called A2G80-LSP-Lip, to improve the blood circulation of liposomes using microfluidics. The liposomes had a particle size of approximately 80 nm. A2G80-LSP-Lip showed an affinity for the muscle tissue section of mice by overlay assay. When the liposomes were administered to DMD model mice (mdx mice) via the tail vein, A2G80-LSP-Lip accumulated efficiently in muscle tissue compared to control liposomes. These results suggest that A2G80-LSP-Lip can function as a muscle-targeting liposome for DMD via systemic administration, and may be a useful tool for DMD treatment.
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Affiliation(s)
- Eri Sasaki
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yoshihiro Hayashi
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yuka Kimura
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Sanae Sashida
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Nobuhito Hamano
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kei Nirasawa
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Keisuke Hamada
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Fumihiko Katagiri
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Yamato Kikkawa
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Takaaki Sakai
- Department of Pharmaceutical Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiro Yoshida
- Department of Pharmaceutical Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Masahiro Kawada
- Department of Pharmaceutical Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Shin-Ichi Hirashima
- Department of Pharmaceutical Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Tsuyoshi Miura
- Department of Pharmaceutical Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yoko Endo-Takahashi
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Motoyoshi Nomizu
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Yoichi Negishi
- Department of Drug Delivery and Molecular Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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16
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Shibata S, Ajiro M, Hagiwara M. Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion. Cell Chem Biol 2020; 27:1472-1482.e6. [DOI: 10.1016/j.chembiol.2020.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/29/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
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17
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Fukushima S, Farea M, Maeta K, Rani AQM, Fujioka K, Nishio H, Matsuo M. Dual Fluorescence Splicing Reporter Minigene Identifies an Antisense Oligonucleotide to Skip Exon v8 of the CD44 Gene. Int J Mol Sci 2020; 21:ijms21239136. [PMID: 33266296 PMCID: PMC7729581 DOI: 10.3390/ijms21239136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 12/14/2022] Open
Abstract
Splicing reporter minigenes are used in cell-based in vitro splicing studies. Exon skippable antisense oligonucleotide (ASO) has been identified using minigene splicing assays, but these assays include a time- and cost-consuming step of reverse transcription PCR amplification. To make in vitro splicing assay easier, a ready-made minigene (FMv2) amenable to quantitative splicing analysis by fluorescence microscopy was constructed. FMv2 was designed to encode two fluorescence proteins namely, mCherry, a transfection marker and split eGFP, a marker of splicing reaction. The split eGFP was intervened by an artificial intron containing a multicloning site sequence. Expectedly, FMv2 transfected HeLa cells produced not only red mCherry but also green eGFP signals. Transfection of FMv2CD44v8, a modified clone of FMv2 carrying an insertion of CD44 exon v8 in the multicloning site, that was applied to screen exon v8 skippable ASO, produced only red signals. Among seven different ASOs tested against exon v8, ASO#14 produced the highest index of green signal positive cells. Hence, ASO#14 was the most efficient exon v8 skippable ASO. Notably, the well containing ASO#14 was clearly identified among the 96 wells containing randomly added ASOs, enabling high throughput screening. A ready-made FMv2 is expected to contribute to identify exon skippable ASOs.
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Affiliation(s)
- Sachiyo Fukushima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (S.F.); (K.F.)
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe 651-2180, Japan; (M.F.); (K.M.); (A.Q.M.R.); (H.N.)
| | - Manal Farea
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe 651-2180, Japan; (M.F.); (K.M.); (A.Q.M.R.); (H.N.)
| | - Kazuhiro Maeta
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe 651-2180, Japan; (M.F.); (K.M.); (A.Q.M.R.); (H.N.)
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 651-2180, Japan
| | - Abdul Qawee Mahyoob Rani
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe 651-2180, Japan; (M.F.); (K.M.); (A.Q.M.R.); (H.N.)
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 651-2180, Japan
| | - Kazumichi Fujioka
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (S.F.); (K.F.)
| | - Hisahide Nishio
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe 651-2180, Japan; (M.F.); (K.M.); (A.Q.M.R.); (H.N.)
- Department of Occupational Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 651-2180, Japan
| | - Masafumi Matsuo
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe 651-2180, Japan; (M.F.); (K.M.); (A.Q.M.R.); (H.N.)
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 651-2180, Japan
- Correspondence: ; Tel.: +81-78-974-6194
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18
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Dystrophin Dp71ab is monoclonally expressed in human satellite cells and enhances proliferation of myoblast cells. Sci Rep 2020; 10:17123. [PMID: 33051488 PMCID: PMC7553993 DOI: 10.1038/s41598-020-74157-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Dystrophin Dp71 is the smallest isoform of the DMD gene, mutations in which cause Duchenne muscular dystrophy (DMD). Dp71 has also been shown to have roles in various cellular processes. Stem cell-based therapy may be effective in treating DMD, but the inability to generate a sufficient number of stem cells remains a significant obstacle. Although Dp71 is comprised of many variants, Dp71 in satellite cells has not yet been studied. Here, the full-length Dp71 consisting of 18 exons from exons G1 to 79 was amplified by reverse transcription-PCR from total RNA of human satellite cells. The amplified product showed deletion of both exons 71 and 78 in all sequenced clones, indicating monoclonal expression of Dp71ab. Western blotting of the satellite cell lysate showed a band corresponding to over-expressed Dp71ab. Transfection of a plasmid expressing Dp71ab into human myoblasts significantly enhanced cell proliferation when compared to the cells transfected with the mock plasmid. However, transfection of the Dp71 expression plasmid encoding all 18 exons did not enhance myoblast proliferation. These findings indicated that Dp71ab, but not Dp71, is a molecular enhancer of myoblast proliferation and that transfection with Dp71ab may generate a high yield of stem cells for DMD treatment.
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Exon skipping induced by nonsense/frameshift mutations in DMD gene results in Becker muscular dystrophy. Hum Genet 2020; 139:247-255. [PMID: 31919629 PMCID: PMC6981323 DOI: 10.1007/s00439-019-02107-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/27/2019] [Indexed: 01/13/2023]
Abstract
Duchenne muscular dystrophy (DMD) is caused by a nonsense or frameshift mutation in the DMD gene, while its milder form, Becker muscular dystrophy (BMD) is caused by an in-frame deletion/duplication or a missense mutation. Interestingly, however, some patients with a nonsense mutation exhibit BMD phenotype, which is mostly attributed to the skipping of the exon containing the nonsense mutation, resulting in in-frame deletion. This study aims to find BMD cases with nonsense/frameshift mutations in DMD and to investigate the exon skipping rate of those nonsense/frameshift mutations. We searched for BMD cases with nonsense/frameshift mutations in DMD in the Japanese Registry of Muscular Dystrophy. For each DMD mutation identified, we constructed minigene plasmids containing one exon with/without a mutation and its flanking intronic sequence. We then introduced them into HeLa cells and measured the skipping rate of transcripts of the minigene by RT-qPCR. We found 363 cases with a nonsense/frameshift mutation in DMD gene from a total of 1497 dystrophinopathy cases in the registry. Among them, 14 had BMD phenotype. Exon skipping rates were well correlated with presence or absence of dystrophin, suggesting that 5% exon skipping rate is critical for the presence of dystrophin in the sarcolemma, leading to milder phenotypes. Accurate quantification of the skipping rate is important in understanding the exact functions of the nonsense/frameshift mutations in DMD and for interpreting the phenotypes of the BMD patients.
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20
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More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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21
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Zhu Y, Deng H, Chen X, Li H, Yang C, Li S, Pan X, Tian S, Feng S, Tan X, Matsuo M, Zhang Z. Skipping of an exon with a nonsense mutation in the DMD gene is induced by the conversion of a splicing enhancer to a splicing silencer. Hum Genet 2019; 138:771-785. [DOI: 10.1007/s00439-019-02036-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/29/2019] [Indexed: 01/23/2023]
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22
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Verification and rectification of cell type-specific splicing of a Seckel syndrome-associated ATR mutation using iPS cell model. J Hum Genet 2019; 64:445-458. [PMID: 30846821 PMCID: PMC8075875 DOI: 10.1038/s10038-019-0574-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/25/2018] [Accepted: 01/18/2019] [Indexed: 11/08/2022]
Abstract
Seckel syndrome (SS) is a rare spectrum of congenital severe microcephaly and dwarfism. One SS-causative gene is Ataxia Telangiectasia and Rad3-Related Protein (ATR), and ATR (c.2101 A>G) mutation causes skipping of exon 9, resulting in a hypomorphic ATR defect. This mutation is considered the cause of an impaired response to DNA replication stress, the main function of ATR, contributing to the pathogenesis of microcephaly. However, the precise behavior and impact of this splicing defect in human neural progenitor cells (NPCs) is unclear. To address this, we established induced pluripotent stem cells (iPSCs) from fibroblasts carrying the ATR mutation and an isogenic ATR-corrected counterpart iPSC clone. SS-patient-derived iPSCs (SS-iPSCs) exhibited cell type-specific splicing; exon 9 was dominantly skipped in fibroblasts and iPSC-derived NPCs, but it was included in undifferentiated iPSCs and definitive endodermal cells. SS-iPSC-derived NPCs (SS-NPCs) showed distinct expression profiles from ATR non-mutated NPCs with negative enrichment of neuronal genesis-related gene sets. In SS-NPCs, abnormal mitotic spindles occurred more frequently than in gene-corrected counterparts, and the alignment of NPCs in the surface of the neurospheres was perturbed. Finally, we tested several splicing-modifying compounds and found that TG003, a CLK1 inhibitor, could pharmacologically rescue the exon 9 skipping in SS-NPCs. Treatment with TG003 restored the ATR kinase activity in SS-NPCs and decreased the frequency of abnormal mitotic events. In conclusion, our iPSC model revealed a novel effect of the ATR mutation in mitotic processes of NPCs and NPC-specific missplicing, accompanied by the recovery of neuronal defects using a splicing rectifier.
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Rani AQM, Farea M, Maeta K, Kawaguchi T, Awano H, Nagai M, Nishio H, Matsuo M. Identification of the shortest splice variant of Dp71, together with five known variants, in glioblastoma cells. Biochem Biophys Res Commun 2019; 508:640-645. [DOI: 10.1016/j.bbrc.2018.11.168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022]
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Boisson B, Honda Y, Ajiro M, Bustamante J, Bendavid M, Gennery AR, Kawasaki Y, Ichishima J, Osawa M, Nihira H, Shiba T, Tanaka T, Chrabieh M, Bigio B, Hur H, Itan Y, Liang Y, Okada S, Izawa K, Nishikomori R, Ohara O, Heike T, Abel L, Puel A, Saito MK, Casanova JL, Hagiwara M, Yasumi T. Rescue of recurrent deep intronic mutation underlying cell type-dependent quantitative NEMO deficiency. J Clin Invest 2018; 129:583-597. [PMID: 30422821 DOI: 10.1172/jci124011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/08/2018] [Indexed: 12/20/2022] Open
Abstract
X-linked dominant incontinentia pigmenti (IP) and X-linked recessive anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) are caused by loss-of-function and hypomorphic IKBKG (also known as NEMO) mutations, respectively. We describe a European mother with mild IP and a Japanese mother without IP, whose 3 boys with EDA-ID died from ID. We identify the same private variant in an intron of IKBKG, IVS4+866 C>T, which was inherited from and occurred de novo in the European mother and Japanese mother, respectively. This mutation creates a new splicing donor site, giving rise to a 44-nucleotide pseudoexon (PE) generating a frameshift. Its leakiness accounts for NF-κB activation being impaired but not abolished in the boys' cells. However, aberrant splicing rates differ between cell types, with WT NEMO mRNA and protein levels ranging from barely detectable in leukocytes to residual amounts in induced pluripotent stem cell-derived (iPSC-derived) macrophages, and higher levels in fibroblasts and iPSC-derived neuronal precursor cells. Finally, SRSF6 binds to the PE, facilitating its inclusion. Moreover, SRSF6 knockdown or CLK inhibition restores WT NEMO expression and function in mutant cells. A recurrent deep intronic splicing mutation in IKBKG underlies a purely quantitative NEMO defect in males that is most severe in leukocytes and can be rescued by the inhibition of SRSF6 or CLK.
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Affiliation(s)
- Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Yoshitaka Honda
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiko Ajiro
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Matthieu Bendavid
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Andrew R Gennery
- Institute of Cellular Medicine, Newcastle University and Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| | - Yuri Kawasaki
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Jose Ichishima
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Mitsujiro Osawa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Hiroshi Nihira
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeshi Shiba
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takayuki Tanaka
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Maya Chrabieh
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Hong Hur
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, USA
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,The Charles Bronfman Institute for Personalized Medicine, and.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yupu Liang
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, USA
| | - Satoshi Okada
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Kazushi Izawa
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Kazusa DNA Research Institute, Kisarazu, Japan
| | - Toshio Heike
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Megumu K Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France.,Howard Hughes Medical Institute (HHMI), New York, New York, USA
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Shiraishi Y, Kataoka K, Chiba K, Okada A, Kogure Y, Tanaka H, Ogawa S, Miyano S. A comprehensive characterization of cis-acting splicing-associated variants in human cancer. Genome Res 2018; 28:1111-1125. [PMID: 30012835 PMCID: PMC6071634 DOI: 10.1101/gr.231951.117] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 06/29/2018] [Indexed: 12/21/2022]
Abstract
Although many driver mutations are thought to promote carcinogenesis via abnormal splicing, the landscape of splicing-associated variants (SAVs) remains unknown due to the complexity of splicing abnormalities. Here, we developed a statistical framework to systematically identify SAVs disrupting or newly creating splice site motifs and applied it to matched whole-exome and transcriptome sequencing data from 8976 samples across 31 cancer types, generating a catalog of 14,438 SAVs. Such a large collection of SAVs enabled us to characterize their genomic features, underlying mutational processes, and influence on cancer driver genes. In fact, ∼50% of SAVs identified were those disrupting noncanonical splice sites (non-GT-AG dinucleotides), including the third and fifth intronic bases of donor sites, or newly creating splice sites. Mutation signature analysis revealed that tobacco smoking is more strongly associated with SAVs, whereas ultraviolet exposure has less impact. SAVs showed remarkable enrichment of cancer-related genes, and as many as 14.7% of samples harbored at least one SAVs affecting them, particularly in tumor suppressors. In addition to intron retention, whose association with tumor suppressor inactivation has been previously reported, exon skipping and alternative splice site usage caused by SAVs frequently affected tumor suppressors. Finally, we described high-resolution distributions of SAVs along the gene and their splicing outcomes in commonly disrupted genes, including TP53, PIK3R1, GATA3, and CDKN2A, which offers genetic clues for understanding their functional properties. Collectively, our findings delineate a comprehensive portrait of SAVs, novel insights into transcriptional de-regulation in cancer.
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Affiliation(s)
- Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Ai Okada
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasunori Kogure
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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Detection of Dystrophin Dp71 in Human Skeletal Muscle Using an Automated Capillary Western Assay System. Int J Mol Sci 2018; 19:ijms19061546. [PMID: 29789502 PMCID: PMC6032138 DOI: 10.3390/ijms19061546] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/26/2022] Open
Abstract
Background: Dystrophin Dp71 is one of the isoforms produced by the DMD gene which is mutated in patients with Duchenne muscular dystrophy (DMD). Although Dp71 is expressed ubiquitously, it has not been detected in normal skeletal muscle. This study was performed to assess the expression of Dp71 in human skeletal muscle. Methods: Human skeletal muscle RNA and tissues were obtained commercially. Mouse skeletal muscle was obtained from normal and DMDmdx mice. Dp71 mRNA and protein were determined by reverse-transcription PCR and an automated capillary Western assay system, the Simple Western, respectively. Dp71 was over-expressed or suppressed using a plasmid expressing Dp71 or antisense oligonucleotide, respectively. Results: Full-length Dp71 cDNA was PCR amplified as a single product from human skeletal muscle RNA. A ca. 70 kDa protein peak detected by the Simple Western was determined as Dp71 by over-expressing Dp71 in HEK293 cells, or suppressing Dp71 expression with antisense oligonucleotide in rhabdomyosarcoma cells. The Simple Western assay detected Dp71 in the skeletal muscles of both normal and DMD mice. In human skeletal muscle, Dp71 was also detected. The ratio of Dp71 to vinculin of human skeletal muscle samples varied widely, indicating various levels of Dp71 expression. Conclusions: Dp71 protein was detected in human skeletal muscle using a highly sensitive capillary Western blotting system.
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Schneider-Poetsch T, Yoshida M. Along the Central Dogma-Controlling Gene Expression with Small Molecules. Annu Rev Biochem 2018; 87:391-420. [PMID: 29727582 DOI: 10.1146/annurev-biochem-060614-033923] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The central dogma of molecular biology, that DNA is transcribed into RNA and RNA translated into protein, was coined in the early days of modern biology. Back in the 1950s and 1960s, bacterial genetics first opened the way toward understanding life as the genetically encoded interaction of macromolecules. As molecular biology progressed and our knowledge of gene control deepened, it became increasingly clear that expression relied on many more levels of regulation. In the process of dissecting mechanisms of gene expression, specific small-molecule inhibitors played an important role and became valuable tools of investigation. Small molecules offer significant advantages over genetic tools, as they allow inhibiting a process at any desired time point, whereas mutating or altering the gene of an important regulator would likely result in a dead organism. With the advent of modern sequencing technology, it has become possible to monitor global cellular effects of small-molecule treatment and thereby overcome the limitations of classical biochemistry, which usually looks at a biological system in isolation. This review focuses on several molecules, especially natural products, that have played an important role in dissecting gene expression and have opened up new fields of investigation as well as clinical venues for disease treatment.
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Affiliation(s)
- Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan;
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan; .,Department of Biotechnology, University of Tokyo, Tokyo 113-8657, Japan
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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. A Challenging Pie to Splice: Drugging the Spliceosome. Angew Chem Int Ed Engl 2017; 56:12052-12063. [PMID: 28371109 PMCID: PMC6311392 DOI: 10.1002/anie.201701065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 02/05/2023]
Abstract
Since its discovery in 1977, the study of alternative RNA splicing has revealed a plethora of mechanisms that had never before been documented in nature. Understanding these transitions and their outcome at the level of the cell and organism has become one of the great frontiers of modern chemical biology. Until 2007, this field remained in the hands of RNA biologists. However, the recent identification of natural product and synthetic modulators of RNA splicing has opened new access to this field, allowing for the first time a chemical-based interrogation of RNA splicing processes. Simultaneously, we have begun to understand the vital importance of splicing in disease, which offers a new platform for molecular discovery and therapy. As with many natural systems, gaining clear mechanistic detail at the molecular level is key towards understanding the operation of any biological machine. This minireview presents recent lessons learned in this emerging field of RNA splicing chemistry and chemical biology.
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Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - Warren C. Chan
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla CA, 92093-0820 (USA)
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500, Gilman Drive, La Jolla CA, 92093-0358 (USA) ,
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30
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León B, Kashyap MK, Chan WC, Krug KA, Castro JE, La Clair JJ, Burkart MD. Das Spliceosom als Angriffspunkt für Pharmaka. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brian León
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Manoj K. Kashyap
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - Warren C. Chan
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Kelsey A. Krug
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Januario E. Castro
- Moores Cancer Center and Department of Medicine; University of California, San Diego; La Jolla CA 92093-0820 USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
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Okubo M, Goto K, Komaki H, Nakamura H, Mori-Yoshimura M, Hayashi YK, Mitsuhashi S, Noguchi S, Kimura E, Nishino I. Comprehensive analysis for genetic diagnosis of Dystrophinopathies in Japan. Orphanet J Rare Dis 2017; 12:149. [PMID: 28859693 PMCID: PMC5580216 DOI: 10.1186/s13023-017-0703-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/23/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is the most common disease in children caused by mutations in the DMD gene, and DMD and Becker muscular dystrophy (BMD) are collectively called dystrophinopathies. Dystrophinopathies show a complex mutation spectrum. The importance of mutation databases, with clinical phenotypes and protein studies of patients, is increasingly recognized as a reference for genetic diagnosis and for the development of gene therapy. METHODS We used the data from the Japanese Registry of Muscular Dystrophy (Remudy) compiled during from July 2009 to March 2017, and reviewed 1497 patients with dystrophinopathies. RESULTS The spectrum of identified mutations contained exon deletions (61%), exon duplications (13%), nonsense mutations (13%), small deletions (5%), small insertions (3%), splice-site mutations (4%), and missense mutations (1%). Exon deletions were found most frequently in the central hot spot region between exons 45-52 (42%), and most duplications were detected in the proximal hot spot region between exons 3-25 (47%). In the 371 patients harboring a small mutation, 194 mutations were reported and 187 mutations were unreported. CONCLUSIONS We report the largest dystrophinopathies mutation dataset in Japan from a national patient registry, "Remudy". This dataset provides a useful reference to support the genetic diagnosis and treatment of dystrophinopathy.
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Affiliation(s)
- Mariko Okubo
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Pediatrics, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kanako Goto
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Genome Medicine Development, Medical Genome Center, NCNP, Tokyo, Japan
| | - Hirofumi Komaki
- Department of Child Neurology, National Center Hospital, NCNP, Tokyo, Japan
| | - Harumasa Nakamura
- Department of Neurology, National Center Hospital, NCNP, Tokyo, Japan
| | | | - Yukiko K Hayashi
- Department of Pathophysiology, Tokyo Medical University, Tokyo, Japan
| | - Satomi Mitsuhashi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Genome Medicine Development, Medical Genome Center, NCNP, Tokyo, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan
| | - En Kimura
- Department of Promoting Clinical Trial and Translational Medicine, Translational Medical Center, NCNP, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan. .,Department of Genome Medicine Development, Medical Genome Center, NCNP, Tokyo, Japan.
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Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 2017; 136:1155-1172. [DOI: 10.1007/s00439-017-1820-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
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33
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Sako Y, Ninomiya K, Okuno Y, Toyomoto M, Nishida A, Koike Y, Ohe K, Kii I, Yoshida S, Hashimoto N, Hosoya T, Matsuo M, Hagiwara M. Development of an orally available inhibitor of CLK1 for skipping a mutated dystrophin exon in Duchenne muscular dystrophy. Sci Rep 2017; 7:46126. [PMID: 28555643 PMCID: PMC5448077 DOI: 10.1038/srep46126] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 03/13/2017] [Indexed: 12/27/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal progressive muscle-wasting disease. Various attempts are underway to convert severe DMD to a milder phenotype by modulating the splicing of the dystrophin gene and restoring its expression. In our previous study, we reported TG003, an inhibitor of CDC2-like kinase 1 (CLK1), as a splice-modifying compound for exon-skipping therapy; however, its metabolically unstable feature hinders clinical application. Here, we show an orally available inhibitor of CLK1, named TG693, which promoted the skipping of the endogenous mutated exon 31 in DMD patient-derived cells and increased the production of the functional exon 31-skipped dystrophin protein. Oral administration of TG693 to mice inhibited the phosphorylation of serine/arginine-rich proteins, which are the substrates of CLK1, and modulated pre-mRNA splicing in the skeletal muscle. Thus, TG693 is a splicing modulator for the mutated exon 31 of the dystrophin gene in vivo, possibly possessing therapeutic potential for DMD patients.
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Affiliation(s)
- Yukiya Sako
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kensuke Ninomiya
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yukiko Okuno
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masayasu Toyomoto
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Atsushi Nishida
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
| | - Yuka Koike
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Ohe
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Isao Kii
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Suguru Yoshida
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Naohiro Hashimoto
- Department of Regenerative Medicine, National Center for Geriatrics and Gerontology, Oobu, Japan
| | - Takamitsu Hosoya
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masafumi Matsuo
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Niba ETE, Yamanaka R, Rani AQM, Awano H, Matsumoto M, Nishio H, Matsuo M. DMD transcripts in CRL-2061 rhabdomyosarcoma cells show high levels of intron retention by intron-specific PCR amplification. Cancer Cell Int 2017; 17:58. [PMID: 28546788 PMCID: PMC5442858 DOI: 10.1186/s12935-017-0428-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 05/16/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The DMD gene encoding dystrophin is mutated in Duchenne muscular dystrophy, a fatal progressive muscle wasting disease. DMD has also been shown to act as a tumor suppressor gene. Rhabdomyosarcoma (RMS) is a mesodermal sarcoma that shares characteristics of skeletal muscle precursors. Products of the DMD gene in RMS have not yet been fully clarified. Here, DMD products were analyzed in CRL-2061 cells established from alveolar RMS. METHODS The 14-kb long DMD cDNA was PCR amplified as 20 separated fragments, as were nine short intron regions. Dystrophin was analyzed by Western blotting using an antibody against the C-terminal region of dystrophin. RESULTS Sixteen of the 20 DMD cDNA fragments could be amplified from CRL-2061 cells as muscle cDNA. Three fragments included aberrant gene products, including one in which exon 71 was omitted and one each with retention of introns 40 and 58. In one fragment, extending from exon 70 to 79, no normally spliced product was obtained. Rather, six alternatively spliced products were identified, including a new product deleting exon 73, with the most abundant product showing deletion of exon 78. Although dystrophin expression was expected in CRL-2061 cells, western blotting of cell lysates showed no evidence of dystrophin, suggesting that translation of full-length DMD mRNA was inhibited by intron retention that generated a premature stop codon. Intron specific PCR amplification of nine short introns, showed retention of introns 40, 58, and 70, which constituted about 60, 25 and 9%, respectively, of the total PCR amplified products. The most abundant DMD transcript contained two abnormalities, intron 40 retention and exon 78 skipping. CONCLUSIONS Intron-specific PCR amplification showed that DMD transcripts contained high levels of introns 40, 58 and 70. Retention of these introns may have been responsible for the lack of dystrophin expression by CRL-2061 cells, thereby abolishing the tumor suppressor activity of dystrophin.
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Affiliation(s)
- Emma Tabe Eko Niba
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe, 6512180 Japan
| | - Ryo Yamanaka
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe, 6512180 Japan
| | - Abdul Qawee Mahyoob Rani
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe, 6512180 Japan.,Department of Pediatrics, Kobe University Graduate School of Medicine, Chuo, Kobe, 6500017 Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Chuo, Kobe, 6500017 Japan
| | - Masaaki Matsumoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Chuo, Kobe, 6500017 Japan
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Sciences, Kobe University Graduate School of Medicine, Chuo, Kobe, 6500017 Japan
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe, 6512180 Japan
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Kataoka N. Modulation of aberrant splicing in human RNA diseases by chemical compounds. Hum Genet 2017; 136:1237-1245. [PMID: 28364159 DOI: 10.1007/s00439-017-1789-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/25/2017] [Indexed: 01/09/2023]
Abstract
Pre-mRNA splicing is an essential step for gene expression in higher eukaryotes. Alternative splicing contributes to diversity of the expressed proteins from the limited number of genes. Disruption of splicing regulation often results in hereditary and sporadic diseases called as 'RNA diseases'. Modulation of splicing by small chemical compounds and nucleic acids has been tried to target aberrant splicing in those diseases. Several RNA diseases and splicing-target therapeutic approaches will be briefly introduced in this review. Accumulating knowledge about molecular mechanism of aberrant splicing and their correction by chemical compounds is important not only for RNA biologists, but also for clinicians who desire therapies for those diseases.
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Affiliation(s)
- Naoyuki Kataoka
- Laboratory of Cell Regulation, Departments of Applied Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan.
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Lim KRQ, Maruyama R, Yokota T. Eteplirsen in the treatment of Duchenne muscular dystrophy. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:533-545. [PMID: 28280301 PMCID: PMC5338848 DOI: 10.2147/dddt.s97635] [Citation(s) in RCA: 294] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Duchenne muscular dystrophy is a fatal neuromuscular disorder affecting around one in 3,500–5,000 male births that is characterized by progressive muscular deterioration. It is inherited in an X-linked recessive fashion and is caused by loss-of-function mutations in the DMD gene coding for dystrophin, a cytoskeletal protein that stabilizes the plasma membrane of muscle fibers. In September 2016, the US Food and Drug Administration granted accelerated approval for eteplirsen (or Exondys 51), a drug that acts to promote dystrophin production by restoring the translational reading frame of DMD through specific skipping of exon 51 in defective gene variants. Eteplirsen is applicable for approximately 14% of patients with DMD mutations. This article extensively reviews and discusses the available information on eteplirsen to date, focusing on pharmacological, efficacy, safety, and tolerability data from preclinical and clinical trials. Issues faced by eteplirsen, particularly those relating to its efficacy, will be identified. Finally, the place of eteplirsen and exon skipping as a general therapeutic strategy in Duchenne muscular dystrophy treatment will be discussed.
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Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta
| | - Rika Maruyama
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta; The Friends of Garrett Cumming Research & Muscular Dystrophy Canada, HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada
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Cryptic splice activation but not exon skipping is observed in minigene assays of dystrophin c.9361+1G>A mutation identified by NGS. J Hum Genet 2017; 62:531-537. [PMID: 28100912 DOI: 10.1038/jhg.2016.162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 12/01/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing (NGS) discloses nucleotide changes in the genome. Mutations at splicing regulatory elements are expected to cause splicing errors, such as exon skipping, cryptic splice site activation, partial exon loss or intron retention. In dystrophinopathy patients, prediction of splicing outcomes is essential to determine the phenotype: either severe Duchenne or mild Becker muscular dystrophy, based on the reading frame rule. In a Vietnamese patient, NGS identified a c.9361+1G>A mutation in the dystrophin gene and an additional DNA variation of A>G at +117 bases in intron 64. To ascertain the consequences of these DNA changes on dystrophin splicing, minigene constructs were prepared inserting dystrophin exon 64 plus various lengths of intron 64. Exon 64 skipping was observed in the minigene construct with 160 nucleotide (nt) of intron 64 sequence with both c.9361+1A and +117G. In contrast, minigene constructs with larger flanking intronic domains resulted in cryptic splice site activation rather than exon skipping. Meanwhile, the cryptic splice site activation was induced even in +117G when intron 64 was elongated to 272 nt and longer. It was expected that cryptic splice site activation is an in vivo splicing outcome.
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Ling Y, Alshareef S, Butt H, Lozano-Juste J, Li L, Galal AA, Moustafa A, Momin AA, Tashkandi M, Richardson DN, Fujii H, Arold S, Rodriguez PL, Duque P, Mahfouz MM. Pre-mRNA splicing repression triggers abiotic stress signaling in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:291-309. [PMID: 27664942 DOI: 10.1111/tpj.13383] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 05/24/2023]
Abstract
Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work has shown that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various inhibitors of AS. Here, we show that the macrolide pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA sequencing (RNA-seq) data revealed that PB mimics abiotic stress signals including salt, drought and abscisic acid (ABA). PB activates the abiotic stress- and ABA-responsive reporters RD29A::LUC and MAPKKK18::uidA in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2C phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling and post-transcriptional regulation in plants.
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Affiliation(s)
- Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Sahar Alshareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Jorge Lozano-Juste
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Lixin Li
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Aya A Galal
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Afaque A Momin
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Dale N Richardson
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Hiroaki Fujii
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Stefan Arold
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Pedro L Rodriguez
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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Nishida A, Oda A, Takeuchi A, Lee T, Awano H, Hashimoto N, Takeshima Y, Matsuo M. Staurosporine allows dystrophin expression by skipping of nonsense-encoding exon. Brain Dev 2016; 38:738-45. [PMID: 27021413 DOI: 10.1016/j.braindev.2016.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 03/13/2016] [Accepted: 03/17/2016] [Indexed: 01/16/2023]
Abstract
BACKGROUND Antisense oligonucleotides that induce exon skipping have been nominated as the most plausible treatment method for dystrophin expression in dystrophin-deficient Duchenne muscular dystrophy. Considering this therapeutic efficiency, small chemical compounds that can enable exon skipping have been highly awaited. In our previous report, a small chemical kinase inhibitor, TG003, was shown to enhance dystrophin expression by enhancing exon skipping. PURPOSE Staurosporine (STS), a small chemical broad kinase inhibitor, was examined for enhanced skipping of a nonsense-encoding dystrophin exon. METHODS STS was added to culture medium of HeLa cells transfected with minigenes expressing wild-type or mutated exon 31 with c.4303G>T (p.Glu1435X), and the resulting mRNAs were analyzed by RT-PCR amplification. Dystrophin mRNA and protein were analyzed in muscle cells treated with STS by RT-PCR and western blotting, respectively. RESULTS STS did not alter splicing of the wild-type minigene. In the mutated minigene, STS increased the exon 31-skipped product. A combination of STS and TG003 did not significantly increase the exon 31-skipped product. STS enhanced skipping of exon 4 of the CDC-like kinase 1 gene, whereas TG003 suppressed it. Two STS analogs with selective kinase inhibitory activity did not enhance the mutated exon 31 skipping. When immortalized muscle cells with c.4303G>T in the dystrophin gene were treated with STS, skipping of the mutated exon 31 and dystrophin expression was enhanced. CONCLUSIONS STS, a broad kinase inhibitor, was shown to enhance skipping of the mutated exon 31 and dystrophin expression, but selective kinase inhibitors did not.
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Affiliation(s)
- Atsushi Nishida
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Japan; Biopharmaceutical Innovation Research Department, Research Institute, Research Division, JCR Pharmaceuticals Co. Ltd., Japan
| | - Ayaka Oda
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Japan; Department of Clinical Pharmacology, Kobe Pharmaceutical University, Japan
| | - Atsuko Takeuchi
- Department of Clinical Pharmacology, Kobe Pharmaceutical University, Japan
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Japan
| | - Naohiro Hashimoto
- Department of Regenerative Medicine, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, Japan
| | | | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Japan.
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40
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Komatsu T, Virdee S. ICBS and ECBS Chemical Biology Meeting 2015 - Let Them Come to Berlin! ACS Chem Biol 2016; 11:1159-66. [PMID: 27198933 DOI: 10.1021/acschembio.6b00268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Toru Komatsu
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- JST PRESTO, Tokyo, Japan
| | - Satpal Virdee
- MRC
Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
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Nishida A, Yasuno S, Takeuchi A, Awano H, Lee T, Niba ETE, Fujimoto T, Itoh K, Takeshima Y, Nishio H, Matsuo M. HEK293 cells express dystrophin Dp71 with nucleus-specific localization of Dp71ab. Histochem Cell Biol 2016; 146:301-9. [PMID: 27109495 DOI: 10.1007/s00418-016-1439-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2016] [Indexed: 11/30/2022]
Abstract
The dystrophin gene consists of 79 exons and encodes tissue-specific isoforms. Mutations in the dystrophin gene cause Duchenne muscular dystrophy, of which a substantial proportion of cases are complicated by non-progressive mental retardation. Abnormalities of Dp71, an isoform transcribed from a promoter in intron 62, are a suspected cause of mental retardation. However, the roles of Dp71 in human brain have not been fully elucidated. Here, we characterized dystrophin in human HEK293 cells with the neuronal lineage. Reverse transcription-PCR amplification of the full-length dystrophin transcript revealed the absence of fragments covering the 5' part of the dystrophin cDNA. In contrast, fragments covering exons 64-79 were present. The Dp71 promoter-specific exon G1 was shown spliced to exon 63. We demonstrated that the Dp71 transcript comprised two subisoforms: one lacking exon 78 (Dp71b) and the other lacking both exons 71 and 78 (Dp71ab). Western blotting of cell lysates using an antibody against the dystrophin C-terminal region revealed two bands, corresponding to Dp71b and Dp71ab. Immunohistochemical examination with the dystrophin antibody revealed scattered punctate signals in the cytoplasm and the nucleus. Western blotting revealed one band corresponding to Dp71b in the cytoplasm and two bands corresponding to Dp71b and Dp71ab in the nucleus, with Dp71b being predominant. These results indicated that Dp71ab is a nucleus-specific subisoform. We concluded that Dp71, comprising Dp71b and Dp71ab, was expressed exclusively in HEK293 cells and that Dp71ab was specifically localized to the nucleus. Our findings suggest that Dp71ab in the nucleus contributes to the diverse functions of HEK293 cells.
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Affiliation(s)
- Atsushi Nishida
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe, 651-2180, Japan
| | - Sato Yasuno
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe, 651-2180, Japan.,Kobe Pharmaceutical University, Higashinada, Kobe, 658-8558, Japan
| | - Atsuko Takeuchi
- Kobe Pharmaceutical University, Higashinada, Kobe, 658-8558, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Chuo, Kobe, 650-0017, Japan
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Mukogawacho, Nishinomiya, 663-8501, Japan
| | - Emma Tabe Eko Niba
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe, 651-2180, Japan
| | - Takahiro Fujimoto
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Mukogawacho, Nishinomiya, 663-8501, Japan
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Graduate School of Medicine, Kobe University, Chuo, Kobe, 650-0017, Japan
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe, 651-2180, Japan.
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Matsuo M, Takeshima Y, Nishio H. Contributions of Japanese patients to development of antisense therapy for DMD. Brain Dev 2016; 38:4-9. [PMID: 26094594 DOI: 10.1016/j.braindev.2015.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/25/2015] [Accepted: 05/26/2015] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Duchenne muscular dystrophy (DMD) is a fatal progressive muscle wasting disease considered untreatable since its first description in 1868. In 1987, the dystrophin gene responsible for DMD was cloned. This paved the way for the development of therapies. Antisense oligonucleotide (AO)-mediated exon skipping therapy is now reaching the stage of marketing authorization. On the 20th anniversary of the proposal of AO-mediated exon skipping therapy for DMD, this review explores the contributions of Japanese patients. RESULTS In 1990, a Japanese DMD patient was reported as having a small deletion within dystrophin exon 19 and complicating exon 19 skipping in the absence of any mutation at the consensus splice sites. This led to identification of a splicing enhancer sequence within exon 19. Remarkably, AOs against this sequence were shown to induce exon skipping. This encouraged us to propose AO-mediated exon skipping therapy for DMD in 1995. The therapy's effectiveness was verified in a Japanese patient with a nonsense dystrophin mutation manifesting as Becker muscular dystrophy. The patient showed skipping of the nonsense mutation-encoding exon. Finally, a DMD patient carrying a deletion of exon 20 volunteered to undergo intravenous AO infusion, enabling us to obtain proof of concept. The findings from these three patients greatly facilitated studies on exon skipping therapy. As a result, more than 300 reports on AO-mediated exon skipping therapy for DMD have been published, including at least two a month during the last few years. CONCLUSION We greatly appreciate the important contributions of Japanese patients to development of the exon skipping therapy for DMD.
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Affiliation(s)
- Masafumi Matsuo
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobe Gakuin University, Japan.
| | | | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Japan
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Potentially Functional Polymorphisms in POU5F1 Gene Are Associated with the Risk of Lung Cancer in Han Chinese. BIOMED RESEARCH INTERNATIONAL 2015; 2015:851320. [PMID: 26824036 PMCID: PMC4707383 DOI: 10.1155/2015/851320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/28/2015] [Accepted: 12/06/2015] [Indexed: 01/06/2023]
Abstract
POU5F1 is a key regulator of self-renewal and differentiation in embryonic stem cells and may be associated with initiation, promotion, and progression in cancer. We hypothesized that functional polymorphisms in POU5F1 may play an important role in modifying the lung cancer risk. To test this hypothesis, we conducted a case-control study to explore the association between 17 potentially functional SNPs in POU5F1 gene and the lung cancer risk in 1,341 incident lung cancer cases and 1,982 healthy controls in a Chinese population. We found that variant alleles of rs887468 and rs3130457 were significantly associated with increased risk of lung cancer after multiple comparison (OR = 1.29, 95% CI: 1.11-1.51, P fdr = 0.017 for rs887468; OR = 1.29, 95% CI: 1.10-1.51, P fdr = 0.034 for rs3130457, resp.). In addition, we detected a significant interaction between rs887468 genotypes and smoking status on lung cancer risk (P = 0.017). Combined analysis of these 2 SNPs showed a significant allele-dosage association between the number of risk alleles and increased risk of lung cancer (P trend < 0.001). These findings indicate that potentially functional polymorphisms in POU5F1 gene may contribute to lung cancer susceptibility in a Chinese population.
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Sakuma M, Iida K, Hagiwara M. Deciphering targeting rules of splicing modulator compounds: case of TG003. BMC Mol Biol 2015; 16:16. [PMID: 26400733 PMCID: PMC4580995 DOI: 10.1186/s12867-015-0044-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 09/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the disease by altering the exon combination of transcripts to reduce the undesired effect of genetic mutations. However, the knowledge and tools to understand factors contributing to splicing modulator compound sensitivity have been lacking. Our goal was to establish a method to characterize sequence features found in compound sensitive exons. Results Here we developed a comparative transcriptomic approach to explore features that make an exon sensitive to a chemical compound. In this study, we chose TG003, a potential drug for Duchenne muscular dystrophy, and performed RNA-sequencing on samples from human and mouse skeletal muscle cells, with and without TG003 treatments. We compared TG003 responsiveness between homologous exon pairs and identified 21 pairs in which human exons were skip-enhanced but not mouse exons. We compared the sequence features; splice site scores, number of splicing factor binding sites, and properties of branch sequence and polypyrimidine tracts, and found that polypyrimidine tracts were stronger (longer stretches and richer content of consecutive polypyrimidine) in the mouse TG003 insensitive exons. We also compared the features between TG003 skip-enhanced and insensitive exons within the species, and discovered that human TG003 skip-enhanced exons were shorter and had less splicing factor binding sites than the group of human TG003 insensitive exons. Mouse insensitive exons homologous to human TG003 skip-enhanced exons shared these properties. Our results suggested that these features are prerequisites for TG003 skip-enhanced exons and weak polypyrimidine tracts are defining features, which were supported by a decision tree analysis on all cassette exons in human. Conclusions In this study we established a comparative transcriptomic approach, which shed lights on how small chemical compounds modulate RNA splicing. The results described here was the first attempt to decipher the targeting rules of a splicing modulator compound. We expect that this approach would contribute to the precise understanding of the mechanism of TG003-induced splicing modulation, expand target diseases of splicing modulators in general, as well as the development of new splicing modulators. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0044-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maki Sakuma
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan. .,Medical Research Support Center, Kyoto University Graduate School of Medicine, Konoecho Yoshida Sakyo-ku, Kyoto, 606-8501, Japan.
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Takarada T, Nishida A, Takeuchi A, Lee T, Takeshima Y, Matsuo M. Resveratrol enhances splicing of insulin receptor exon 11 in myotonic dystrophy type 1 fibroblasts. Brain Dev 2015; 37:661-8. [PMID: 25476247 DOI: 10.1016/j.braindev.2014.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Myotonic dystrophy type 1 (DM1) is characterized by splicing abnormalities caused by CUG expansion of the DMPK gene transcript. Splicing of exon 11 of the insulin receptor (IR) gene is deregulated to suppress exon 11 inclusion into mRNA in DM1. Consequently, the exon 11-deleted IR isoform that is less sensitive to insulin is predominantly produced, leading to glucose intolerance in DM1. Upregulation of exon 11 retaining full-length IR mRNA is a potential way to recover insulin sensitivity in DM1. METHODS We examined candidate chemicals for their ability to enhance inclusion of exon 11 of the IR gene in cultured cells by reverse transcription-PCR amplification of a fragment extending from exons 10 to 12 of IR mRNA. RESULTS We revealed that resveratrol (RES) enhanced the percentage of exon 11-containing IR mRNA among the total IR mRNA in HeLa cells. The RES-mediated enhancement of exon 11 inclusion was cell-specific and highest in fibroblasts. We tested RES on four fibroblast samples from three generations of one DM1 family. In each sample, RES treatment significantly upregulated the percentage of exon 11-containing IR mRNA to levels higher than that of the control, irrespective of the length of the sample's CTG repeat expansion. DISCUSSION A natural compound, RES, was shown for the first time to upregulate the full-length IR mRNA in fibroblasts from DM1 cases. Our results provide the justification of RES as a leading compound to improve glucose tolerance in DM1.
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Affiliation(s)
- Toru Takarada
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Nishi, Kobe 6512180, Japan; Kobe Pharmaceutical University, Higashinada, Kobe 6588558, Japan
| | - Atsushi Nishida
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Nishi, Kobe 6512180, Japan
| | - Atsuko Takeuchi
- Kobe Pharmaceutical University, Higashinada, Kobe 6588558, Japan
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638131, Japan
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638131, Japan
| | - Masafumi Matsuo
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Nishi, Kobe 6512180, Japan.
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Morooka S, Hoshina M, Kii I, Okabe T, Kojima H, Inoue N, Okuno Y, Denawa M, Yoshida S, Fukuhara J, Ninomiya K, Ikura T, Furuya T, Nagano T, Noda K, Ishida S, Hosoya T, Ito N, Yoshimura N, Hagiwara M. Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice. Mol Pharmacol 2015; 88:316-25. [PMID: 25993998 DOI: 10.1124/mol.114.097345] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/20/2015] [Indexed: 12/28/2022] Open
Abstract
Excessive angiogenesis contributes to numerous diseases, including cancer and blinding retinopathy. Antibodies against vascular endothelial growth factor (VEGF) have been approved and are widely used in clinical treatment. Our previous studies using SRPIN340, a small molecule inhibitor of SRPK1 (serine-arginine protein kinase 1), demonstrated that SRPK1 is a potential target for the development of antiangiogenic drugs. In this study, we solved the structure of SRPK1 bound to SRPIN340 by X-ray crystallography. Using pharmacophore docking models followed by in vitro kinase assays, we screened a large-scale chemical library, and thus identified a new inhibitor of SRPK1. This inhibitor, SRPIN803, prevented VEGF production more effectively than SRPIN340 owing to the dual inhibition of SRPK1 and CK2 (casein kinase 2). In a mouse model of age-related macular degeneration, topical administration of eye ointment containing SRPIN803 significantly inhibited choroidal neovascularization, suggesting a clinical potential of SRPIN803 as a topical ointment for ocular neovascularization. Thus SRPIN803 merits further investigation as a novel inhibitor of VEGF.
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Affiliation(s)
- Satoshi Morooka
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Mitsuteru Hoshina
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Isao Kii
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Takayoshi Okabe
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Hirotatsu Kojima
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Naoko Inoue
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Yukiko Okuno
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Masatsugu Denawa
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Suguru Yoshida
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Junichi Fukuhara
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Kensuke Ninomiya
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Teikichi Ikura
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Toshio Furuya
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Tetsuo Nagano
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Kousuke Noda
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Susumu Ishida
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Takamitsu Hosoya
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Nobutoshi Ito
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Masatoshi Hagiwara
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
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Ohe K, Hagiwara M. Modulation of alternative splicing with chemical compounds in new therapeutics for human diseases. ACS Chem Biol 2015; 10:914-24. [PMID: 25560473 DOI: 10.1021/cb500697f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alternative splicing is a critical step where a limited number of human genes generate a complex and diverse proteome. Various diseases, including inherited diseases with abnormalities in the "genome code," have been found to result in an aberrant mis-spliced "transcript code" with correlation to the resulting phenotype. Chemical compound-based and nucleic acid-based strategies are trying to target this mis-spliced "transcript code". We will briefly mention about how to obtain splicing-modifying-compounds by high-throughput screening and overview of what is known about compounds that modify splicing pathways. The main focus will be on RNA-binding protein kinase inhibitors. In the main text, we will refer to diseases where splicing-modifying-compounds have been intensively investigated, with comparison to nucleic acid-based strategies. The information on their involvement in mis-splicing as well as nonsplicing events will be helpful in finding better compounds with less off-target effects for future implications in mis-splicing therapy.
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Affiliation(s)
- Kenji Ohe
- †Department of Anatomy and Developmental Biology and ‡Training Program of Leaders for Integrated Medical System for Fruitful Healthy-Longevity Society (LIMS), Kyoto University Graduate School of Medicine, Kyoto 606-8315, Japan
| | - Masatoshi Hagiwara
- †Department of Anatomy and Developmental Biology and ‡Training Program of Leaders for Integrated Medical System for Fruitful Healthy-Longevity Society (LIMS), Kyoto University Graduate School of Medicine, Kyoto 606-8315, Japan
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Nishida A, Minegishi M, Takeuchi A, Niba ETE, Awano H, Lee T, Iijima K, Takeshima Y, Matsuo M. Tissue- and case-specific retention of intron 40 in mature dystrophin mRNA. J Hum Genet 2015; 60:327-33. [PMID: 25833469 DOI: 10.1038/jhg.2015.24] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 11/09/2022]
Abstract
The dystrophin gene, which is mutated in Duchenne muscular dystrophy (DMD), comprises 79 exons that show multiple alternative splicing events. Intron retention, a type of alternative splicing, may control gene expression. We examined intron retention in dystrophin introns by reverse-transcription PCR from skeletal muscle, focusing on the nine shortest (all <1000 bp), because these are more likely to be retained. Only one, intron 40, was retained in mRNA; sequencing revealed insertion of a complete intron 40 (851 nt) between exons 40 and 41. The intron 40 retention product accounted for 1.2% of the total product but had a premature stop codon at the fifth intronic codon. Intron 40 retention was most strongly observed in the kidney (36.6%) and was not obtained from the fetal liver, lung, spleen or placenta. This indicated that intron retention is a tissue-specific event whose level varies among tissues. In two DMD patients, intron 40 retention was observed in one patient but not in the other. Examination of splicing regulatory factors revealed that intron 40 had the highest guanine-cytosine content of all examined introns in a 30-nt segment at its 3' end. Further studies are needed to clarify the biological role of intron 40-retained dystrophin mRNA.
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Affiliation(s)
- Atsushi Nishida
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
| | - Maki Minegishi
- Department of Clinical Pharmacy, Kobe Pharmaceutical University, Kobe, Japan
| | - Atsuko Takeuchi
- Department of Clinical Pharmacy, Kobe Pharmaceutical University, Kobe, Japan
| | - Emma Tabe Eko Niba
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Kobe, Japan
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Kobe, Japan
| | | | - Masafumi Matsuo
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Kobe, Japan
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Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia. Proc Natl Acad Sci U S A 2015; 112:2764-9. [PMID: 25675486 DOI: 10.1073/pnas.1415525112] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Familial dysautonomia (FD), a hereditary sensory and autonomic neuropathy, is caused by missplicing of exon 20, resulting from an intronic mutation in the inhibitor of kappa light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene encoding IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1). A newly established splicing reporter assay allowed us to visualize pathogenic splicing in cells and to screen small chemicals for the ability to correct the aberrant splicing of IKBKAP. Using this splicing reporter, we screened our chemical libraries and identified a compound, rectifier of aberrant splicing (RECTAS), that rectifies the aberrant IKBKAP splicing in cells from patients with FD. Here, we found that the levels of modified uridine at the wobble position in cytoplasmic tRNAs are reduced in cells from patients with FD and that treatment with RECTAS increases the expression of IKAP and recovers the tRNA modifications. These findings suggest that the missplicing of IKBKAP results in reduced tRNA modifications in patients with FD and that RECTAS is a promising therapeutic drug candidate for FD.
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