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Ptok J, Müller L, Theiss S, Schaal H. Context matters: Regulation of splice donor usage. Biochim Biophys Acta Gene Regul Mech 2019; 1862:194391. [PMID: 31202784 DOI: 10.1016/j.bbagrm.2019.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 11/16/2022]
Abstract
Elaborate research on splicing, starting in the late seventies, evolved from the discovery that 5' splice sites are recognized by their complementarity to U1 snRNA towards the realization that RNA duplex formation cannot be the sole basis for 5'ss selection. Rather, their recognition is highly influenced by a number of context factors including transcript architecture as well as splicing regulatory elements (SREs) in the splice site neighborhood. In particular, proximal binding of splicing regulatory proteins highly influences splicing outcome. The importance of SRE integrity especially becomes evident in the light of human pathogenic mutations where single nucleotide changes in SREs can severely affect the resulting transcripts. Bioinformatics tools nowadays greatly assist in the computational evaluation of 5'ss, their neighborhood and the impact of pathogenic mutations. Although predictions are already quite robust, computational evaluation of the splicing regulatory landscape still faces challenges to increase future reliability. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/29/2019] [Indexed: 01/23/2023]
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3
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Tuffery-giraud S, Miro J, Koenig M, Claustres M. Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 2017; 136:1155-72. [DOI: 10.1007/s00439-017-1820-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
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Brinkmeyer-Langford C, Balog-Alvarez C, Cai JJ, Davis BW, Kornegay JN. Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy. BMC Genomics 2016; 17:665. [PMID: 27549615 PMCID: PMC4994242 DOI: 10.1186/s12864-016-2948-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 07/18/2016] [Indexed: 12/17/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) causes progressive muscle degeneration, cardiomyopathy and respiratory failure in approximately 1/5,000 boys. Golden Retriever muscular dystrophy (GRMD) resembles DMD both clinically and pathologically. Like DMD, GRMD exhibits remarkable phenotypic variation among affected dogs, suggesting the influence of modifiers. Understanding the role(s) of genetic modifiers of GRMD may identify genes and pathways that also modify phenotypes in DMD and reveal novel therapies. Therefore, our objective in this study was to identify genetic modifiers that affect discrete GRMD phenotypes. Results We performed a linear mixed-model (LMM) analysis using 16 variably-affected dogs from our GRMD colony (8 dystrophic, 8 non-dystrophic). All of these dogs were either full or half-siblings, and phenotyped for 19 objective, quantitative biomarkers at ages 6 and 12 months. Each biomarker was individually assessed. Gene expression profiles of 59 possible candidate genes were generated for two muscle types: the cranial tibialis and medial head of the gastrocnemius. SNPs significantly associated with GRMD biomarkers were identified on multiple chromosomes (including the X chromosome). Gene expression levels for candidate genes located near these SNPs correlated with biomarker values, suggesting possible roles as GRMD modifiers. Conclusions The results of this study enhance our understanding of GRMD pathology and represent a first step toward the characterization of GRMD modifiers that may be relevant to DMD pathology. Such modifiers are likely to be useful for DMD treatment development based on their relationships to GRMD phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2948-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Cynthia Balog-Alvarez
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Brian W Davis
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joe N Kornegay
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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Zamani GR, Karami F, Mehdizadeh M, Movafagh A, Nilipour Y, Zamani M. Analysis of dystrophin gene in Iranian Duchenne and Becker muscular dystrophies patients and identification of a novel mutation. Neurol Sci 2015; 36:2011-7. [DOI: 10.1007/s10072-015-2290-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
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6
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Miro J, Laaref AM, Rofidal V, Lagrafeuille R, Hem S, Thorel D, Méchin D, Mamchaoui K, Mouly V, Claustres M, Tuffery-Giraud S. FUBP1: a new protagonist in splicing regulation of the DMD gene. Nucleic Acids Res 2015; 43:2378-89. [PMID: 25662218 PMCID: PMC4344520 DOI: 10.1093/nar/gkv086] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We investigated the molecular mechanisms for in-frame skipping of DMD exon 39 caused by the nonsense c.5480T>A mutation in a patient with Becker muscular dystrophy. RNase-assisted pull down assay coupled with mass spectrometry revealed that the mutant RNA probe specifically recruits hnRNPA1, hnRNPA2/B1 and DAZAP1. Functional studies in a human myoblast cell line transfected with DMD minigenes confirmed the splicing inhibitory activity of hnRNPA1 and hnRNPA2/B1, and showed that DAZAP1, also known to activate splicing, acts negatively in the context of the mutated exon 39. Furthermore, we uncovered that recognition of endogenous DMD exon 39 in muscle cells is promoted by FUSE binding protein 1 (FUBP1), a multifunctional DNA- and RNA-binding protein whose role in splicing is largely unknown. By serial deletion and mutagenesis studies in minigenes, we delineated a functional intronic splicing enhancer (ISE) in intron 38. FUBP1 recruitment to the RNA sequence containing the ISE was established by RNA pull down and RNA EMSA, and further confirmed by RNA-ChIP on endogenous DMD pre-mRNA. This study provides new insights about the splicing regulation of DMD exon 39, highlighting the emerging role of FUBP1 in splicing and describing the first ISE for constitutive exon inclusion in the mature DMD transcript.
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Affiliation(s)
- Julie Miro
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France
| | - Abdelhamid Mahdi Laaref
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France
| | - Valérie Rofidal
- UR1199 Laboratoire de Protéomique Fonctionnelle, INRA, 34060 Montpellier cedex, France
| | - Rosyne Lagrafeuille
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France
| | - Sonia Hem
- UR1199 Laboratoire de Protéomique Fonctionnelle, INRA, 34060 Montpellier cedex, France
| | - Delphine Thorel
- CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, F-34000 Montpellier, France
| | - Déborah Méchin
- CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, F-34000 Montpellier, France
| | - Kamel Mamchaoui
- Institut de Myologie, UM76 Université Pierre et Marie Curie (UPMC), Paris, France INSERM U 974, Paris, France CNRS UMR 7215, Paris, France
| | - Vincent Mouly
- Institut de Myologie, UM76 Université Pierre et Marie Curie (UPMC), Paris, France INSERM U 974, Paris, France CNRS UMR 7215, Paris, France
| | - Mireille Claustres
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, F-34000 Montpellier, France
| | - Sylvie Tuffery-Giraud
- Université Montpellier, UFR de Médecine, Montpellier F-34000, France Inserm U827, Laboratoire de Génétique de Maladies Rares, F-34000 Montpellier, France
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Tran VK, Ta VT, Vu DC, Nguyen STB, Do HN, Ta MH, Tran TH, Matsuo M. Exon Deletion Patterns of the Dystrophin Gene in 82 Vietnamese Duchenne/Becker Muscular Dystrophy Patients. J Neurogenet 2013; 27:170-5. [DOI: 10.3109/01677063.2013.830616] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Nakagawa T, Takeuchi A, Kakiuchi R, Lee T, Yagi M, Awano H, Iijima K, Takeshima Y, Urade Y, Matsuo M. A prostaglandin D2 metabolite is elevated in the urine of Duchenne muscular dystrophy patients and increases further from 8years old. Clin Chim Acta 2013; 423:10-4. [DOI: 10.1016/j.cca.2013.03.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 11/26/2022]
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9
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Juan-Mateu J, González-Quereda L, Rodríguez MJ, Verdura E, Lázaro K, Jou C, Nascimento A, Jiménez-Mallebrera C, Colomer J, Monges S, Lubieniecki F, Foncuberta ME, Pascual-Pascual SI, Molano J, Baiget M, Gallano P. Interplay between DMD point mutations and splicing signals in Dystrophinopathy phenotypes. PLoS One 2013; 8:e59916. [PMID: 23536893 PMCID: PMC3607557 DOI: 10.1371/journal.pone.0059916] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/19/2013] [Indexed: 12/12/2022] Open
Abstract
DMD nonsense and frameshift mutations lead to severe Duchenne muscular dystrophy while in-frame mutations lead to milder Becker muscular dystrophy. Exceptions are found in 10% of cases and the production of alternatively spliced transcripts is considered a key modifier of disease severity. Several exonic mutations have been shown to induce exon-skipping, while splice site mutations result in exon-skipping or activation of cryptic splice sites. However, factors determining the splicing pathway are still unclear. Point mutations provide valuable information regarding the regulation of pre-mRNA splicing and elements defining exon identity in the DMD gene. Here we provide a comprehensive analysis of 98 point mutations related to clinical phenotype and their effect on muscle mRNA and dystrophin expression. Aberrant splicing was found in 27 mutations due to alteration of splice sites or splicing regulatory elements. Bioinformatics analysis was performed to test the ability of the available algorithms to predict consequences on mRNA and to investigate the major factors that determine the splicing pathway in mutations affecting splicing signals. Our findings suggest that the splicing pathway is highly dependent on the interplay between splice site strength and density of regulatory elements.
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Affiliation(s)
- Jonàs Juan-Mateu
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Lidia González-Quereda
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Maria José Rodríguez
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Edgard Verdura
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Kira Lázaro
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Cristina Jou
- Servei d'Anatomia Patològica Hospital Sant Joan de Déu, Barcelona, Spain
| | - Andrés Nascimento
- Unitat de Patologia Neuromuscular, Servei de Neurologia, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Jaume Colomer
- Unitat de Patologia Neuromuscular, Servei de Neurologia, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Soledad Monges
- Servicio de Neuropediatría, Hospital Nacional Pediátrico Garrahan, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Servicio de Patología, Hospital Nacional Pediátrico Garrahan, Buenos Aires, Argentina
| | | | | | - Jesús Molano
- Unidad de Genética Molecular and CIBERER U753, Hospital Universitario Materno Infantil La Paz, Madrid, Spain
| | - Montserrat Baiget
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Pia Gallano
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
- * E-mail:
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Horn HF, Brownstein Z, Lenz DR, Shivatzki S, Dror AA, Dagan-Rosenfeld O, Friedman LM, Roux KJ, Kozlov S, Jeang KT, Frydman M, Burke B, Stewart CL, Avraham KB. The LINC complex is essential for hearing. J Clin Invest 2013; 123:740-50. [PMID: 23348741 DOI: 10.1172/jci66911] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/29/2012] [Indexed: 01/08/2023] Open
Abstract
Hereditary hearing loss is the most common sensory deficit. We determined that progressive high-frequency hearing loss in 2 families of Iraqi Jewish ancestry was due to homozygosity for the protein truncating mutation SYNE4 c.228delAT. SYNE4, a gene not previously associated with hearing loss, encodes nesprin-4 (NESP4), an outer nuclear membrane (ONM) protein expressed in the hair cells of the inner ear. The truncated NESP4 encoded by the families' mutation did not localize to the ONM. NESP4 and SUN domain-containing protein 1 (SUN1), which localizes to the inner nuclear membrane (INM), are part of the linker of nucleoskeleton and cytoskeleton (LINC) complex in the nuclear envelope. Mice lacking either Nesp4 or Sun1 were evaluated for hair cell defects and hearing loss. In both Nesp4-/- and Sun1-/- mice, OHCs formed normally, but degenerated as hearing matured, leading to progressive hearing loss. The nuclei of OHCs from mutant mice failed to maintain their basal localization, potentially affecting cell motility and hence the response to sound. These results demonstrate that the LINC complex is essential for viability and normal morphology of OHCs and suggest that the position of the nucleus in sensory epithelial cells is critical for maintenance of normal hearing.
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Malueka RG, Takaoka Y, Yagi M, Awano H, Lee T, Dwianingsih EK, Nishida A, Takeshima Y, Matsuo M. Categorization of 77 dystrophin exons into 5 groups by a decision tree using indexes of splicing regulatory factors as decision markers. BMC Genet 2012; 13:23. [PMID: 22462762 PMCID: PMC3350383 DOI: 10.1186/1471-2156-13-23] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 03/31/2012] [Indexed: 12/29/2022] Open
Abstract
Background Duchenne muscular dystrophy, a fatal muscle-wasting disease, is characterized by dystrophin deficiency caused by mutations in the dystrophin gene. Skipping of a target dystrophin exon during splicing with antisense oligonucleotides is attracting much attention as the most plausible way to express dystrophin in DMD. Antisense oligonucleotides have been designed against splicing regulatory sequences such as splicing enhancer sequences of target exons. Recently, we reported that a chemical kinase inhibitor specifically enhances the skipping of mutated dystrophin exon 31, indicating the existence of exon-specific splicing regulatory systems. However, the basis for such individual regulatory systems is largely unknown. Here, we categorized the dystrophin exons in terms of their splicing regulatory factors. Results Using a computer-based machine learning system, we first constructed a decision tree separating 77 authentic from 14 known cryptic exons using 25 indexes of splicing regulatory factors as decision markers. We evaluated the classification accuracy of a novel cryptic exon (exon 11a) identified in this study. However, the tree mislabeled exon 11a as a true exon. Therefore, we re-constructed the decision tree to separate all 15 cryptic exons. The revised decision tree categorized the 77 authentic exons into five groups. Furthermore, all nine disease-associated novel exons were successfully categorized as exons, validating the decision tree. One group, consisting of 30 exons, was characterized by a high density of exonic splicing enhancer sequences. This suggests that AOs targeting splicing enhancer sequences would efficiently induce skipping of exons belonging to this group. Conclusions The decision tree categorized the 77 authentic exons into five groups. Our classification may help to establish the strategy for exon skipping therapy for Duchenne muscular dystrophy.
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Affiliation(s)
- Rusdy Ghazali Malueka
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Chuo, Kobe 6500017, Japan
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Flanigan KM, Dunn DM, von Niederhausern A, Soltanzadeh P, Howard MT, Sampson JB, Swoboda KJ, Bromberg MB, Mendell JR, Taylor LE, Anderson CB, Pestronk A, Florence JM, Connolly AM, Mathews KD, Wong B, Finkel RS, Bonnemann CG, Day JW, McDonald C, Weiss RB. Nonsense mutation-associated Becker muscular dystrophy: interplay between exon definition and splicing regulatory elements within the DMD gene. Hum Mutat 2012; 32:299-308. [PMID: 21972111 DOI: 10.1002/humu.21426] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nonsense mutations are usually predicted to function as null alleles due to premature termination of protein translation. However, nonsense mutations in the DMD gene, encoding the dystrophin protein, have been associated with both the severe Duchenne Muscular Dystrophy (DMD) and milder Becker Muscular Dystrophy (BMD) phenotypes. In a large survey, we identified 243 unique nonsense mutations in the DMD gene, and for 210 of these we could establish definitive phenotypes. We analyzed the reading frame predicted by exons flanking those in which nonsense mutations were found, and present evidence that nonsense mutations resulting in BMD likely do so by inducing exon skipping, confirming that exonic point mutations affecting exon definition have played a significant role in determining phenotype. We present a new model based on the combination of exon definition and intronic splicing regulatory elements for the selective association of BMD nonsense mutations with a subset of DMD exons prone to mutation-induced exon skipping.
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Affiliation(s)
- Kevin M Flanigan
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA.
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Nishida A, Kataoka N, Takeshima Y, Yagi M, Awano H, Ota M, Itoh K, Hagiwara M, Matsuo M. Chemical treatment enhances skipping of a mutated exon in the dystrophin gene. Nat Commun 2011; 2:308. [PMID: 21556062 DOI: 10.1038/ncomms1306] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 04/11/2011] [Indexed: 12/25/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease caused by a loss of the dystrophin protein. Control of dystrophin mRNA splicing to convert severe DMD to a milder phenotype is attracting much attention. Here we report a dystrophinopathy patient who has a point mutation in exon 31 of the dystrophin gene. Although the mutation generates a stop codon, a small amount of internally deleted, but functional, dystrophin protein is produced in the patient cells. An analysis of the mRNA reveals that the mutation promotes exon skipping and restores the open reading frame of dystrophin. Presumably, the mutation disrupts an exonic splicing enhancer and creates an exonic splicing silencer. Therefore, we searched for small chemicals that enhance exon skipping, and found that TG003 promotes the skipping of exon 31 in the endogenous dystrophin gene in a dose-dependent manner and increases the production of the dystrophin protein in the patient's cells. Duchenne muscular dystrophy is caused by a loss of the dystrophin gene, and control of dystrophin mRNA splicing could aid treatment of the disease. Nishida et al. show that a small molecule promotes skipping of exon 31 and increases production of a functional dystrophin protein in a patient.
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Ota M, Takeshima Y, Nishida A, Awano H, Lee T, Yagi M, Matsuo M. A G-to-T transversion at the splice acceptor site of dystrophin exon 14 shows multiple splicing outcomes that are not exemplified by transition mutations. Genet Test Mol Biomarkers 2011; 16:3-8. [PMID: 21854195 DOI: 10.1089/gtmb.2010.0276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations at splicing consensus sequences have been shown to induce splicing errors such as exon skipping or cryptic splice site activation. Here, we identified eight splicing products caused by a G-to-T transversion mutation at the splice acceptor site of exon 14 of the dystrophin gene (c.1603-1G>T). Unexpectedly, the most abundant product showed skipping of the two consecutive exons 14 and 15, and exon 14 skipping was observed as the second most abundant product. To examine the cause of this splicing multiplicity, minigenes containing dystrophin exons 14 and 15 with their flanking introns were constructed and subjected to in vitro splicing. Minigenes with the wild-type sequence or a G>A transition at position c.1603-1 produced only the mature mRNA. On the other hand, the minigenes with a G>T or G>C transversion mutation produced multiple splicing products. A time-course analysis of the in vitro splicing revealed that splicing of the middle intron, intron 14, was the first step in transcript maturation for all four minigene constructs. The identity of the mutant nucleotide, but not its position, is a factor leading to multiple splicing outcomes. Our results suggest that exon skipping therapy for Duchenne's muscular dystrophy should be carefully monitored for their splicing outcomes.
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Affiliation(s)
- Mitsunori Ota
- Department of Pediatrics, Graduate School of Medicine, Kobe University, Kobe, Japan
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Forrest S, Meloni PL, Muntoni F, Kim J, Fletcher S, Wilton SD. Personalized exon skipping strategies to address clustered non-deletion dystrophin mutations. Neuromuscul Disord 2011; 20:810-6. [PMID: 20817455 DOI: 10.1016/j.nmd.2010.07.276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 07/12/2010] [Accepted: 07/27/2010] [Indexed: 11/30/2022]
Abstract
Antisense oligomer induced exon skipping is showing promise as a therapy to reduce the severity of Duchenne muscular dystrophy. To date, the focus has been on excluding single exons flanking frame-shifting deletions in the dystrophin gene. However, a third of all Duchenne muscular dystrophy causing mutations are more subtle DNA changes. Thirty nine dystrophin exons are potentially frame-shifting and mutations in these will require the targeted removal of exon blocks to generate in-frame transcripts. We report that clustered non-deletion mutations in the dystrophin gene respond differently to different antisense oligomer preparations targeting the same dual exon block, the removal of which bypasses the mutation and restores the open reading-frame. The personalized nature of the responses to antisense oligomer application presents additional challenges to the induction of multi-exon skipping with a single oligomer preparation.
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Affiliation(s)
- Sarah Forrest
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Perth, WA 6009, Australia
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Takeshima Y, Yagi M, Okizuka Y, Awano H, Zhang Z, Yamauchi Y, Nishio H, Matsuo M. Mutation spectrum of the dystrophin gene in 442 Duchenne/Becker muscular dystrophy cases from one Japanese referral center. J Hum Genet 2010; 55:379-88. [PMID: 20485447 DOI: 10.1038/jhg.2010.49] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Recent developments in molecular therapies for Duchenne muscular dystrophy (DMD) demand accurate genetic diagnosis, because therapies are mutation specific. The KUCG (Kobe University Clinical Genetics) database for DMD and Becker muscular dystrophy is a hospital-based database comprising 442 cases. Using a combination of complementary DNA (cDNA) and chromosome analysis in addition to conventional genomic DNA-based method, mutation detection was successfully accomplished in all cases, and the largest mutation database of Japanese dystrophinopathy was established. Among 442 cases, deletions and duplications encompassing one or more exons were identified in 270 (61%) and 38 (9%) cases, respectively. Nucleotide changes leading to nonsense mutations or disrupting a splice site were identified in 69 (16%) or 24 (5%) cases, respectively. Small deletion/insertion mutations were identified in 34 (8%) cases. Remarkably, two retrotransposon insertion events were also identified. Dystrophin cDNA analysis successfully revealed novel transcripts with a pseudoexon created by a single-nucleotide change deep within an intron in four cases. X-chromosome abnormalities were identified in two cases. The reading frame rule was upheld for 93% of deletion and 66% of duplication mutation cases. For the application of molecular therapies, induction of exon skipping was deemed the first priority for dystrophinopathy treatment. At one Japanese referral center, the hospital-based mutation database of the dystrophin gene was for the first time established with the highest levels of quality and patient's number.
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Affiliation(s)
- Yasuhiro Takeshima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
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O'Leary DA, Sharif O, Anderson P, Tu B, Welch G, Zhou Y, Caldwell JS, Engels IH, Brinker A. Identification of small molecule and genetic modulators of AON-induced dystrophin exon skipping by high-throughput screening. PLoS One 2009; 4:e8348. [PMID: 20020055 PMCID: PMC2791862 DOI: 10.1371/journal.pone.0008348] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 11/23/2009] [Indexed: 11/28/2022] Open
Abstract
One therapeutic approach to Duchenne Muscular Dystrophy (DMD) recently entering clinical trials aims to convert DMD phenotypes to that of a milder disease variant, Becker Muscular Dystrophy (BMD), by employing antisense oligonucleotides (AONs) targeting splice sites, to induce exon skipping and restore partial dystrophin function. In order to search for small molecule and genetic modulators of AON-dependent and independent exon skipping, we screened ∼10,000 known small molecule drugs, >17,000 cDNA clones, and >2,000 kinase- targeted siRNAs against a 5.6 kb luciferase minigene construct, encompassing exon 71 to exon 73 of human dystrophin. As a result, we identified several enhancers of exon skipping, acting on both the reporter construct as well as endogenous dystrophin in mdx cells. Multiple mechanisms of action were identified, including histone deacetylase inhibition, tubulin modulation and pre-mRNA processing. Among others, the nucleolar protein NOL8 and staufen RNA binding protein homolog 2 (Stau2) were found to induce endogenous exon skipping in mdx cells in an AON-dependent fashion. An unexpected but recurrent theme observed in our screening efforts was the apparent link between the inhibition of cell cycle progression and the induction of exon skipping.
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Affiliation(s)
- Debra A. O'Leary
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * E-mail: (DAO); (IHE)
| | - Orzala Sharif
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Paul Anderson
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Buu Tu
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Genevieve Welch
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Jeremy S. Caldwell
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Ingo H. Engels
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * E-mail: (DAO); (IHE)
| | - Achim Brinker
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
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