1
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Song Y, Zhang C, Omenn GS, O’Meara MJ, Welch JD. Predicting the Structural Impact of Human Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572928. [PMID: 38187531 PMCID: PMC10769328 DOI: 10.1101/2023.12.21.572928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice variants. To investigate the structural implications of alternative splicing, we used AlphaFold2 to predict the structures of more than 11,000 human isoforms. We employed multiple metrics to identify splicing-induced structural alterations, including template matching score, secondary structure composition, surface charge distribution, radius of gyration, accessibility of post-translational modification sites, and structure-based function prediction. We identified examples of how alternative splicing induced clear changes in each of these properties. Structural similarity between isoforms largely correlated with degree of sequence identity, but we identified a subset of isoforms with low structural similarity despite high sequence similarity. Exon skipping and alternative last exons tended to increase the surface charge and radius of gyration. Splicing also buried or exposed numerous post-translational modification sites, most notably among the isoforms of BAX. Functional prediction nominated numerous functional differences among isoforms of the same gene, with loss of function compared to the reference predominating. Finally, we used single-cell RNA-seq data from the Tabula Sapiens to determine the cell types in which each structure is expressed. Our work represents an important resource for studying the structure and function of splice isoforms across the cell types of the human body.
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Affiliation(s)
- Yuxuan Song
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D. Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA
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2
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Richard I. Basic notions about gene therapy from the nucleic acid perspective and applications in a pediatric disease: Duchenne muscular dystrophy. Arch Pediatr 2023; 30:8S2-8S11. [PMID: 38043979 DOI: 10.1016/s0929-693x(23)00221-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Gene therapy involves the introduction of genetic material into cells as a therapeutic molecule to cure a disease. Through the transfer of specific nucleic acid to the target tissue, gene expression can be downregulated, augmented, or corrected thanks to the nucleic acid sequence as a support of gene expression. This is achieved through molecular interactions according to the sequence arrangement or the secondary structure of the molecules or through their catalytic properties. Over the past two decades, the rapid advances of knowledge and technologies in gene therapy have led to the development of different strategies and to the extension of its use to numerous indications, including certain cancers. Major success has been achieved in clinical trials and the field of gene therapy is booming. Several gene therapy products are now on the market in Europe, the United States, and China. In this review, we cover the basic principles of gene therapy and the characteristics of the main vectors used to transfer genetic material into the cell. As an example of applications, we address the various strategies applied to a rare pediatric muscle disease: Duchenne muscular dystrophy. © 2023 Published by Elsevier Masson SAS on behalf of French Society of Pediatrics.
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Affiliation(s)
- Isabelle Richard
- Genethon, 91000, Evry, France; Université Paris-Saclay, Univ. Evry, Inserm, Integrare research unit UMR_S951, 91000, Evry-Courcouronnes, France; Atamyo Therapeutics, 1, bis rue de l'internationale, Evry, France.
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3
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Yu D. An overview of recent US-approved gene therapies for Duchenne muscular dystrophy and their respective clinical development programs. DRUGS & THERAPY PERSPECTIVES 2023. [DOI: 10.1007/s40267-023-00986-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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4
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Maruyama R, Yokota T. Antisense Oligonucleotide Treatment in a Humanized Mouse Model of Duchenne Muscular Dystrophy and Highly Sensitive Detection of Dystrophin Using Western Blotting. Methods Mol Biol 2021; 2224:203-214. [PMID: 33606217 DOI: 10.1007/978-1-0716-1008-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a devastating X-linked muscle disorder affecting many children. The disease is caused by the lack of dystrophin production and characterized by muscle wasting. The most common causes of death are respiratory failure and heart failure. Antisense oligonucleotide-mediated exon skipping using a phosphorodiamidate morpholino oligomer (PMO) is a promising therapeutic approach for the treatment of DMD. In preclinical studies, dystrophic mouse models are commonly used for the development of therapeutic oligos. We employ a humanized model carrying the full-length human DMD transgene along with the complete knockout of the mouse Dmd gene. In this model, the effects of human-targeting AOs can be tested without cross-reaction between mouse sequences and human sequences (note that mdx, a conventional dystrophic mouse model, carries a nonsense point mutation in exon 23 and express the full-length mouse Dmd mRNA, which is a significant complicating factor). To determine if dystrophin expression is restored, the Western blotting analysis is commonly performed; however, due to the extremely large protein size of dystrophin (427 kDa), detection and accurate quantification of full-length dystrophin can be a challenge. Here, we present methodologies to systemically inject PMOs into humanized DMD model mice and determine levels of dystrophin restoration via Western blotting. Using a tris-acetate gradient SDS gel and semi-dry transfer with three buffers, including the Concentrated Anode Buffer, Anode Buffer, and Cathode Buffer, less than 1% normal levels of dystrophin expression are easily detectable. This method is fast, easy, and sensitive enough for the detection of dystrophin from both cultured muscle cells and muscle biopsy samples.
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Affiliation(s)
- Rika Maruyama
- Faculty of Medicine and Dentistry, Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Faculty of Medicine and Dentistry, Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada. .,The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
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5
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Denzer L, Schroten H, Schwerk C. From Gene to Protein-How Bacterial Virulence Factors Manipulate Host Gene Expression During Infection. Int J Mol Sci 2020; 21:ijms21103730. [PMID: 32466312 PMCID: PMC7279228 DOI: 10.3390/ijms21103730] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacteria evolved many strategies to survive and persist within host cells. Secretion of bacterial effectors enables bacteria not only to enter the host cell but also to manipulate host gene expression to circumvent clearance by the host immune response. Some effectors were also shown to evade the nucleus to manipulate epigenetic processes as well as transcription and mRNA procession and are therefore classified as nucleomodulins. Others were shown to interfere downstream with gene expression at the level of mRNA stability, favoring either mRNA stabilization or mRNA degradation, translation or protein stability, including mechanisms of protein activation and degradation. Finally, manipulation of innate immune signaling and nutrient supply creates a replicative niche that enables bacterial intracellular persistence and survival. In this review, we want to highlight the divergent strategies applied by intracellular bacteria to evade host immune responses through subversion of host gene expression via bacterial effectors. Since these virulence proteins mimic host cell enzymes or own novel enzymatic functions, characterizing their properties could help to understand the complex interactions between host and pathogen during infections. Additionally, these insights could propose potential targets for medical therapy.
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6
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Nguyen AL, Morren MA, van Doorn R. Severe Lipodystrophy Following Prolonged Subcutaneous Administration of Antisense Oligonucleotides. JAMA Dermatol 2019; 155:1084-1086. [PMID: 31241724 DOI: 10.1001/jamadermatol.2019.1404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Anh Ly Nguyen
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marie-Anne Morren
- Department of Pediatrics and Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
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7
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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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8
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Chauhan K, Kalam H, Dutt R, Kumar D. RNA Splicing: A New Paradigm in Host-Pathogen Interactions. J Mol Biol 2019; 431:1565-1575. [PMID: 30857970 DOI: 10.1016/j.jmb.2019.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/21/2022]
Abstract
RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pathologies including cancer. Emerging evidence suggests precise regulation of splicing as fundamental to normal well-being. In this context, infection-induced alternative splicing has emerged as a new pivot of host function, which pathogenic microbes can alter-directly or indirectly-to tweak the host immune responses against the pathogen. The implications of these findings are vast, and although not explored much in the case of pathogenic infections, we present here examples from splicing mediated regulation of immune responses across a variety of conditions and explore how this fascinating finding brings a new paradigm to host-pathogen interactions.
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Affiliation(s)
- Komal Chauhan
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Haroon Kalam
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ravi Dutt
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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9
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Iyer PS, Mavoungou LO, Ronzoni F, Zemla J, Schmid-Siegert E, Antonini S, Neff LA, Dorchies OM, Jaconi M, Lekka M, Messina G, Mermod N. Autologous Cell Therapy Approach for Duchenne Muscular Dystrophy using PiggyBac Transposons and Mesoangioblasts. Mol Ther 2018; 26:1093-1108. [PMID: 29503200 PMCID: PMC6079556 DOI: 10.1016/j.ymthe.2018.01.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/24/2018] [Accepted: 01/29/2018] [Indexed: 01/07/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a lethal muscle-wasting disease currently without cure. We investigated the use of the PiggyBac transposon for full-length dystrophin expression in murine mesoangioblast (MABs) progenitor cells. DMD murine MABs were transfected with transposable expression vectors for full-length dystrophin and transplanted intramuscularly or intra-arterially into mdx/SCID mice. Intra-arterial delivery indicated that the MABs could migrate to regenerating muscles to mediate dystrophin expression. Intramuscular transplantation yielded dystrophin expression in 11%-44% of myofibers in murine muscles, which remained stable for the assessed period of 5 months. The satellite cells isolated from transplanted muscles comprised a fraction of MAB-derived cells, indicating that the transfected MABs may colonize the satellite stem cell niche. Transposon integration site mapping by whole-genome sequencing indicated that 70% of the integrations were intergenic, while none was observed in an exon. Muscle resistance assessment by atomic force microscopy indicated that 80% of fibers showed elasticity properties restored to those of wild-type muscles. As measured in vivo, transplanted muscles became more resistant to fatigue. This study thus provides a proof-of-principle that PiggyBac transposon vectors may mediate full-length dystrophin expression as well as functional amelioration of the dystrophic muscles within a potential autologous cell-based therapeutic approach of DMD.
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Affiliation(s)
- Pavithra S Iyer
- Institute of Biotechnology, University of Lausanne, Lausanne, Switzerland
| | - Lionel O Mavoungou
- Institute of Biotechnology, University of Lausanne, Lausanne, Switzerland
| | - Flavio Ronzoni
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Joanna Zemla
- Institute of Nuclear Physics, Polish Academy of Sciences, 31342 Krakow, Poland
| | | | | | - Laurence A Neff
- School of Pharmaceutical Sciences, University of Geneva and University of Lausanne, 1211 Geneva, Switzerland
| | - Olivier M Dorchies
- School of Pharmaceutical Sciences, University of Geneva and University of Lausanne, 1211 Geneva, Switzerland
| | - Marisa Jaconi
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Malgorzata Lekka
- Institute of Nuclear Physics, Polish Academy of Sciences, 31342 Krakow, Poland
| | | | - Nicolas Mermod
- Institute of Biotechnology, University of Lausanne, Lausanne, Switzerland.
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10
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Bates DO, Morris JC, Oltean S, Donaldson LF. Pharmacology of Modulators of Alternative Splicing. Pharmacol Rev 2017; 69:63-79. [PMID: 28034912 PMCID: PMC5226212 DOI: 10.1124/pr.115.011239] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
More than 95% of genes in the human genome are alternatively spliced to form multiple transcripts, often encoding proteins with differing or opposing function. The control of alternative splicing is now being elucidated, and with this comes the opportunity to develop modulators of alternative splicing that can control cellular function. A number of approaches have been taken to develop compounds that can experimentally, and sometimes clinically, affect splicing control, resulting in potential novel therapeutics. Here we develop the concepts that targeting alternative splicing can result in relatively specific pathway inhibitors/activators that result in dampening down of physiologic or pathologic processes, from changes in muscle physiology to altering angiogenesis or pain. The targets and pharmacology of some of the current inhibitors/activators of alternative splicing are demonstrated and future directions discussed.
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Affiliation(s)
- David O Bates
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Jonathan C Morris
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Sebastian Oltean
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Lucy F Donaldson
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
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11
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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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12
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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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13
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Iyombe-Engembe JP, Ouellet DL, Barbeau X, Rousseau J, Chapdelaine P, Lagüe P, Tremblay JP. Efficient Restoration of the Dystrophin Gene Reading Frame and Protein Structure in DMD Myoblasts Using the CinDel Method. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e283. [PMID: 26812655 PMCID: PMC5012554 DOI: 10.1038/mtna.2015.58] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 12/10/2015] [Indexed: 12/18/2022]
Abstract
The CRISPR/Cas9 system is a great revolution in biology. This technology allows the modification of genes in vitro and in vivo in a wide variety of living organisms. In most Duchenne muscular dystrophy (DMD) patients, expression of dystrophin (DYS) protein is disrupted because exon deletions result in a frame shift. We present here the CRISPR-induced deletion (CinDel), a new promising genome-editing technology to correct the DMD gene. This strategy is based on the use of two gRNAs targeting specifically exons that precede and follow the patient deletion in the DMD gene. This pair of gRNAs induced a precise large additional deletion leading to fusion of the targeted exons. Using an adequate pair of gRNAs, the deletion of parts of these exons and the intron separating them restored the DMD reading frame in 62% of the hybrid exons in vitro in DMD myoblasts and in vivo in electroporated hDMD/mdx mice. Moreover, adequate pairs of gRNAs also restored the normal spectrin-like repeat of the dystrophin rod domain; such restoration is not obtained by exon skipping or deletion of complete exons. The expression of an internally deleted DYS protein was detected following the formation of myotubes by the unselected, treated DMD myoblasts. Given that CinDel induces permanent reparation of the DMD gene, this treatment would not have to be repeated as it is the case for exon skipping induced by oligonucleotides.
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Affiliation(s)
- Jean-Paul Iyombe-Engembe
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
| | - Dominique L Ouellet
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
| | - Xavier Barbeau
- Department of Chemistry, Université Laval, Quebec City, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec City, Québec, Canada
| | - Joël Rousseau
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
| | - Pierre Chapdelaine
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
| | - Patrick Lagüe
- Department of Chemistry, Université Laval, Quebec City, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec City, Québec, Canada
| | - Jacques P Tremblay
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
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14
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Nancy MM, Nora RM, Rebeca MC. Peptidic tools applied to redirect alternative splicing events. Peptides 2015; 67:1-11. [PMID: 25748022 DOI: 10.1016/j.peptides.2015.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/05/2015] [Accepted: 02/26/2015] [Indexed: 01/25/2023]
Abstract
Peptides are versatile and attractive biomolecules that can be applied to modulate genetic mechanisms like alternative splicing. In this process, a single transcript yields different mature RNAs leading to the production of protein isoforms with diverse or even antagonistic functions. During splicing events, errors can be caused either by mutations present in the genome or by defects or imbalances in regulatory protein factors. In any case, defects in alternative splicing have been related to several genetic diseases including muscular dystrophy, Alzheimer's disease and cancer from almost every origin. One of the most effective approaches to redirect alternative splicing events has been to attach cell-penetrating peptides to oligonucleotides that can modulate a single splicing event and restore correct gene expression. Here, we summarize how natural existing and bioengineered peptides have been applied over the last few years to regulate alternative splicing and genetic expression. Under different genetic and cellular backgrounds, peptides have been shown to function as potent vehicles for splice correction, and their therapeutic benefits have reached clinical trials and patenting stages, emphasizing the use of regulatory peptides as an exciting therapeutic tool for the treatment of different genetic diseases.
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Affiliation(s)
- Martínez-Montiel Nancy
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Rosas-Murrieta Nora
- Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Martínez-Contreras Rebeca
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico.
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15
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Genomics of alternative splicing: evolution, development and pathophysiology. Hum Genet 2014; 133:679-87. [PMID: 24378600 DOI: 10.1007/s00439-013-1411-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/15/2013] [Indexed: 12/11/2022]
Abstract
Alternative splicing is a major cellular mechanism in metazoans for generating proteomic diversity. A large proportion of protein-coding genes in multicellular organisms undergo alternative splicing, and in humans, it has been estimated that nearly 90 % of protein-coding genes-much larger than expected-are subject to alternative splicing. Genomic analyses of alternative splicing have illuminated its universal role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. Disruption of the splicing machinery has been found to drive pathophysiology, and indeed reprogramming of aberrant splicing can provide novel approaches to the development of molecular therapy. This review focuses on the recent progress in our understanding of alternative splicing brought about by the unprecedented explosive growth of genomic data and highlights the relevance of human splicing variation on disease and therapy.
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16
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Behrens-Gawlik V, Mearini G, Gedicke-Hornung C, Richard P, Carrier L. MYBPC3 in hypertrophic cardiomyopathy: from mutation identification to RNA-based correction. Pflugers Arch 2013; 466:215-23. [PMID: 24337823 DOI: 10.1007/s00424-013-1409-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/18/2013] [Accepted: 11/22/2013] [Indexed: 01/16/2023]
Abstract
Mutations in MYBPC3 gene, encoding cardiac myosin-binding protein C (cMyBP-C), frequently cause hypertrophic cardiomyopathy (HCM), which affects 0.2 % of the general population. This myocardial autosomal-dominant disorder is the leading cause of sudden cardiac death particularly in young athletes. The current pharmacological and surgical treatments of HCM focus on symptoms relief, but do not address the cause of the disease. With the development of novel strategies targeting the endogenous mutation, causal HCM therapy is now possible. This review will discuss the current knowledge on HCM from the identification of MYBPC3 gene mutations to potential RNA-based correction.
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Affiliation(s)
- Verena Behrens-Gawlik
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
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17
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Aartsma-Rus A, Van Ommen GJ, Kaplan JC. Innovating therapies for muscle diseases. HANDBOOK OF CLINICAL NEUROLOGY 2013; 113:1497-501. [PMID: 23622373 DOI: 10.1016/b978-0-444-59565-2.00020-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The neuromuscular disorders (NMDs) involve many different genetic and acquired diseases. Corticosteroids (e.g., prednisone and deflazacort) are prescribed for some NMDs as a palliative treatment to slow down disease progression to some extent. For the vast majority of NMDs, no specific therapy is currently available that stops progression or reverses the clinical deficits of the diseases. However, recent progress with different therapeutic approaches is now resulting in numerous clinical trials. In this chapter, we give an overview of the current state of the art, opportunities and challenges for gene therapy, cell therapy, antisense-mediated modulation of splicing, and numerous drug therapies for NMDs in general, and Duchenne muscular dystrophy as a paradigm in particular. Although none of the proposed strategies has yet proven to be of therapeutic value in patients, it is reasonable to expect that clinical efficacy will soon be demonstrated for some of the more advanced approaches.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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18
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Perkins KJ, Davies KE. Recent advances in Duchenne muscular dystrophy. Degener Neurol Neuromuscul Dis 2012; 2:141-164. [PMID: 30890885 DOI: 10.2147/dnnd.s26637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Duchenne muscular dystrophy (DMD), an allelic X-linked progressive muscle-wasting disease, is one of the most common single-gene disorders in the developed world. Despite knowledge of the underlying genetic causation and resultant pathophysiology from lack of dystrophin protein at the muscle sarcolemma, clinical intervention is currently restricted to symptom management. In recent years, however, unprecedented advances in strategies devised to correct the primary defect through gene- and cell-based therapeutics hold particular promise for treating dystrophic muscle. Conventional gene replacement and endogenous modification strategies have greatly benefited from continued improvements in encapsidation capacity, transduction efficiency, and systemic delivery. In particular, RNA-based modifying approaches such as exon skipping enable expression of a shorter but functional dystrophin protein and rapid progress toward clinical application. Emerging combined gene- and cell-therapy strategies also illustrate particular promise in enabling ex vivo genetic correction and autologous transplantation to circumvent a number of immune challenges. These approaches are complemented by a vast array of pharmacological approaches, in particular the successful identification of molecules that enable functional replacement or ameliorate secondary DMD pathology. Animal models have been instrumental in providing proof of principle for many of these strategies, leading to several recent trials that have investigated their efficacy in DMD patients. Although none has reached the point of clinical use, rapid improvements in experimental technology and design draw this goal ever closer. Here, we review therapeutic approaches to DMD, with particular emphasis on recent progress in strategic development, preclinical evaluation and establishment of clinical efficacy. Further, we discuss the numerous challenges faced and synergistic approaches being devised to combat dystrophic pathology effectively.
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Affiliation(s)
- Kelly J Perkins
- Sir William Dunn School of Pathology.,MRC Functional Genomics Unit, University of Oxford, Oxford, UK,
| | - Kay E Davies
- MRC Functional Genomics Unit, University of Oxford, Oxford, UK,
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19
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Watts JK, Corey DR. Silencing disease genes in the laboratory and the clinic. J Pathol 2011; 226:365-79. [PMID: 22069063 DOI: 10.1002/path.2993] [Citation(s) in RCA: 315] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 08/23/2011] [Accepted: 08/30/2011] [Indexed: 12/17/2022]
Abstract
Synthetic nucleic acids are commonly used laboratory tools for modulating gene expression and have the potential to be widely used in the clinic. Progress towards nucleic acid drugs, however, has been slow and many challenges remain to be overcome before their full impact on patient care can be understood. Antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) are the two most widely used strategies for silencing gene expression. We first describe these two approaches and contrast their relative strengths and weaknesses for laboratory applications. We then review the choices faced during development of clinical candidates and the current state of clinical trials. Attitudes towards clinical development of nucleic acid silencing strategies have repeatedly swung from optimism to depression during the past 20 years. Our goal is to provide the information needed to design robust studies with oligonucleotides, making use of the strengths of each oligonucleotide technology.
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Affiliation(s)
- Jonathan K Watts
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
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20
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Chemical treatment enhances skipping of a mutated exon in the dystrophin gene. Nat Commun 2011; 2:308. [PMID: 21556062 PMCID: PMC3113229 DOI: 10.1038/ncomms1306] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [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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21
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van Putten M, Aartsma-Rus A. Opportunities and challenges for the development of antisense treatment in neuromuscular disorders. Expert Opin Biol Ther 2011; 11:1025-37. [PMID: 21510827 DOI: 10.1517/14712598.2011.579098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION Neuromuscular disorders are diseases of the musculature and/or the nervous system, generally leading to loss of muscle function. They are a frequent cause of disability and treatment options are often only symptomatic. Interestingly, for a number of neuromuscular disorders the application of antisense oligonucleotides has therapeutic potential. AREAS COVERED The authors describe how this approach is exploited for different neuromuscular diseases, focusing on literature published in the past 10 years. For each disease the opportunities of this approach, the state of the art, and current challenges are described. EXPERT OPINION A lot of progress has been made in the development of antisense-mediated approaches during recent years and they may become clinically applicable in the near future.
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Affiliation(s)
- Maaike van Putten
- Leiden University Medical Center, Department of Human Genetics, The Netherlands
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22
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Mechelli R, Annibali V, Ristori G, Vittori D, Coarelli G, Salvetti M. Multiple sclerosis etiology: beyond genes and environment. Expert Rev Clin Immunol 2010; 6:481-90. [PMID: 20441432 DOI: 10.1586/eci.10.11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiple sclerosis (MS) is a disorder of the CNS with inflammatory and neurodegenerative components. The etiology is unknown, but there is evidence for a role of both genetic and environmental factors. Among the heritable factors, MHC class II genes are strongly involved, as well as genes coding for others molecules of immunological relevance, genes controlling neurobiological pathways and genes of unknown function. Among nonheritable factors, many infectious agents (mainly viruses) and environmental factors (e.g., smoke, sun exposition and diet) seem to be of etiologic importance. Here, we report and discuss recent findings in MS on largely unexplored fields: the alternative splicing of mRNAs and regulatory noncoding RNAs, the major sources of transcriptome diversity; and epigenetic changes with special attention paid to DNA methylation and histone acetylation, the main regulators of gene expression.
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Affiliation(s)
- Rosella Mechelli
- Neurology and Center for Experimental Neurological Therapies, S. Andrea Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy
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23
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Heemskerk H, de Winter C, van Kuik P, Heuvelmans N, Sabatelli P, Rimessi P, Braghetta P, van Ommen GJB, de Kimpe S, Ferlini A, Aartsma-Rus A, van Deutekom JCT. Preclinical PK and PD studies on 2'-O-methyl-phosphorothioate RNA antisense oligonucleotides in the mdx mouse model. Mol Ther 2010; 18:1210-7. [PMID: 20407428 PMCID: PMC2889733 DOI: 10.1038/mt.2010.72] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Antisense oligonucleotides (AONs) are being developed as RNA therapeutic molecules for Duchenne muscular dystrophy. For oligonucleotides with the 2′-O-methyl-phosphorothioate (2OMePS) RNA chemistry, proof of concept has been obtained in patient-specific muscle cell cultures, the mouse and dog disease models, and recently by local administration in Duchenne patients. To further explore the pharmacokinetic (PK)/pharmacodynamic (PD) properties of this chemical class of oligonucleotides, we performed a series of preclinical studies in mice. The results demonstrate that the levels of oligonucleotides in dystrophin-deficient muscle fibers are much higher than in healthy fibers, leading to higher exon-skipping levels. Oligonucleotide levels and half-life differed for specific muscle groups, with heart muscle showing the lowest levels but longest half-life (~46 days). Intravenous (i.v.), subcutaneous (s.c.), and intraperitoneal (i.p.) delivery methods were directly compared. For each method, exon-skipping and novel dystrophin expression were observed in all muscles, including arrector pili smooth muscle in skin biopsies. After i.v. administration, the oligonucleotide peak levels in plasma, liver, and kidney were higher than after s.c. or i.p. injections. However, as the bioavailability was similar, and the levels of oligonucleotide, exon-skipping, and dystrophin steadily accumulated overtime after s.c. administration, we selected this patient-convenient delivery method for future clinical study protocols.
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Affiliation(s)
- Hans Heemskerk
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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