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Liu Y, Tang Y, Zhang H, Chen H, Luo Q, Liu J. Duchenne muscular dystrophy caused by a deletion (c.5021del) in exon 35 of the DMD gene: A case report and review of the literature. Heliyon 2024; 10:e28677. [PMID: 38586344 PMCID: PMC10998125 DOI: 10.1016/j.heliyon.2024.e28677] [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: 09/03/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
Duchenne muscular dystrophy (DMD MIM#310200) is a degenerative muscle disease caused by mutations in the dystrophin gene located on Xp21.2. The clinical features encompass muscle weakness and markedly elevated serum creatine kinase levels. An 8-year-old Chinese boy was diagnosed with Duchenne muscular dystrophy (DMD). Whole exome gene sequencing was conducted and the Sanger method was used to validate sequencing. A deletion (c.5021del) in exon 35 of the dystrophin gene was identified, which was predicted to generate a frameshift mutation and create an early termination codon (p.Leu1674CysfsTer47). It has a pathogenic effect against dystrophin in the muscle cell membrane of the patient. As such, prednisone treatment at a dose of 0.75 mg/kg.d was administered. After one month, a notable reduction in fall frequency was observed. Our new finding will expand the pathogenic mutation spectrum causing DMD.
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Affiliation(s)
- Yue Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Yanhui Tang
- Department of Pediatric, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Hui Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Hongying Chen
- Department of Pediatric, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qing Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, China
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2
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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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3
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Rozza R, Janoš P, Spinello A, Magistrato A. Role of computational and structural biology in the development of small-molecule modulators of the spliceosome. Expert Opin Drug Discov 2022; 17:1095-1109. [PMID: 35983696 DOI: 10.1080/17460441.2022.2114452] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION RNA splicing is a pivotal step of eukaryotic gene expression during which the introns are excised from the precursor (pre-)RNA and the exons are joined together to form mature RNA products (i.e a protein-coding mRNA or long non-coding (lnc)RNAs). The spliceosome, a complex ribonucleoprotein machine, performs pre-RNA splicing with extreme precision. Deregulated splicing is linked to cancer, genetic, and neurodegenerative diseases. Hence, the discovery of small-molecules targeting core spliceosome components represents an appealing therapeutic opportunity. AREA COVERED Several atomic-level structures of the spliceosome and distinct splicing-modulators bound to its protein/RNA components have been solved. Here, we review recent advances in the discovery of small-molecule splicing-modulators, discuss opportunities and challenges for their therapeutic applicability, and showcase how structural data and/or all-atom simulations can illuminate key facets of their mechanism, thus contributing to future drug-discovery campaigns. EXPERT OPINION This review highlights the potential of modulating pre-RNA splicing with small-molecules, and anticipates how the synergy of computer and wet-lab experiments will enrich our understanding of splicing regulation/deregulation mechanisms. This information will aid future structure-based drug-discovery efforts aimed to expand the currently limited portfolio of selective splicing-modulators.
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Affiliation(s)
- Riccardo Rozza
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| | - Pavel Janoš
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| | - Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, Palermo, Italy
| | - Alessandra Magistrato
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
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4
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Matsuo M. Antisense Oligonucleotide-Mediated Exon-skipping Therapies: Precision Medicine Spreading from Duchenne Muscular Dystrophy. JMA J 2021; 4:232-240. [PMID: 34414317 PMCID: PMC8355726 DOI: 10.31662/jmaj.2021-0019] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/13/2021] [Indexed: 11/12/2022] Open
Abstract
In 1995, we were the first to propose antisense oligonucleotide (ASO)-mediated exon-skipping therapy for the treatment of Duchenne muscular dystrophy (DMD), a noncurable, progressive muscle-wasting disease. DMD is caused by deletion mutations in one or more exons of the DMD gene that shift the translational reading frame and create a premature stop codon, thus prohibiting dystrophin production. The therapy aims to correct out-of-frame mRNAs to produce in-frame transcripts by removing an exon during splicing, with the resumption of dystrophin production. As this treatment is recognized as the most promising, many extensive studies have been performed to develop ASOs that induce the skipping of DMD exons. In 2016, an ASO designed to skip exon 51 was first approved by the Food and Drug Administration, which accelerated studies on the use of ASOs to treat other monogenic diseases. The ease of mRNA editing by ASO-mediated exon skipping has resulted in the further application of exon-skipping therapy to nonmonogenic diseases, such as diabetes mellites. Recently, this precision medicine strategy was drastically transformed for the emergent treatment of only one patient with one ASO, which represents a future aspect of ASO-mediated exon-skipping therapy for extremely rare diseases. Herein, the invention of ASO-mediated exon-skipping therapy for DMD and the current applications of ASO-mediated exon-skipping therapies are reviewed, and future perspectives on this therapeutic strategy are discussed. This overview will encourage studies on ASO-mediated exon-skipping therapy and will especially contribute to the development of treatments for noncurable diseases.
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Affiliation(s)
- Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Department of Physical Rehabilitation and Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Japan
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5
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Bizot F, Vulin A, Goyenvalle A. Current Status of Antisense Oligonucleotide-Based Therapy in Neuromuscular Disorders. Drugs 2021; 80:1397-1415. [PMID: 32696107 DOI: 10.1007/s40265-020-01363-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Neuromuscular disorders include a wide range of diseases affecting the peripheral nervous system, which are primarily characterized by progressive muscle weakness and wasting. While there were no effective therapies until recently, several therapeutic approaches have advanced to clinical trials in the past few years. Among these, the antisense technology aiming at modifying RNA processing and function has remarkably progressed and a few antisense oligonucleotides (ASOs) have now been approved. Despite these recent clinical successes, several ASOs have also failed and clinical programs have been suspended, in most cases when the route of administration was systemic, highlighting the existing challenges notably with respect to effective ASO delivery. In this review we summarize the recent advances and current status of antisense based-therapies for neuromuscular disorders, using successful as well as unsuccessful examples to highlight the variability of outcomes depending on the target tissue and route of administration. We describe the different ASO-mediated therapeutic approaches, including splice-switching applications, steric-blocking strategies and targeted gene knock-down mediated by ribonuclease H recruitment. In this overview, we discuss the merits and challenges of the current ASO technology, and discuss the future of ASO development.
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Affiliation(s)
- Flavien Bizot
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000, Versailles, France
| | - Adeline Vulin
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000, Versailles, France.,SQY Therapeutics, Université de Versailles St-Quentin, Montigny le Bretonneux, France
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000, Versailles, France. .,LIA BAHN, Centre scientifique de Monaco, Monaco, Monaco.
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6
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Early career investigator highlight biocommentary. Pediatr Res 2021; 89:1331-1332. [PMID: 33603206 DOI: 10.1038/s41390-021-01404-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 11/09/2022]
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7
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Salmaninejad A, Jafari Abarghan Y, Bozorg Qomi S, Bayat H, Yousefi M, Azhdari S, Talebi S, Mojarrad M. Common therapeutic advances for Duchenne muscular dystrophy (DMD). Int J Neurosci 2020; 131:370-389. [DOI: 10.1080/00207454.2020.1740218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Arash Salmaninejad
- Halal Research Center of IRI, FDA, Tehran, Iran
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yousef Jafari Abarghan
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Bozorg Qomi
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadi Bayat
- Medical Nano-Technology & Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Meysam Yousefi
- Department of Medical Genetics Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sara Azhdari
- Department of Anatomy and Embryology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Samaneh Talebi
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Mojarrad
- Medical Genetics Research Center, Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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8
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Kar D, Sellamuthu K, Kumar SD, Eswarappa SM. Induction of Translational Readthrough across the Thalassemia-Causing Premature Stop Codon in β-Globin-Encoding mRNA. Biochemistry 2019; 59:80-84. [PMID: 31577420 DOI: 10.1021/acs.biochem.9b00761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonsense mutations that result in premature stop codons in the HBB gene cause β-thalassemia. This disease is characterized by a reduced hemoglobin level due to the lack of β-globin. Compounds that induce translational readthrough across the thalassemia-causing premature stop codon will have therapeutic benefits. Currently available molecules that induce translational readthrough lack specificity, and some of them show toxicity after prolonged use. In this study, we have developed an oligonucleotide-based approach to induce translational readthrough across the thalassemia-causing premature stop codon. Oligonucleotides that target HBB mRNA downstream of the premature stop codon could induce translational readthrough, generating a full-length β-globin protein. We show this effect using fluorescence- and luminescence-based readthrough assays and by Western blot. Remarkably, the amount of oligonucleotide-induced translational readthrough product is comparable to that of the protein generated by normal translation when there was no premature stop codon. Thus, these oligonucleotides, with certain modifications, have the potential to be used as drugs for the treatment of β-thalassemia. Also, this strategy can be extended to treat other genetic diseases caused by premature stop codons.
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Affiliation(s)
- Debaleena Kar
- Department of Biochemistry , Indian Institute of Science , Bengaluru , Karnataka 560012 , India
| | - Karthi Sellamuthu
- Department of Biochemistry , Indian Institute of Science , Bengaluru , Karnataka 560012 , India
| | - Sangeetha Devi Kumar
- Department of Biochemistry , Indian Institute of Science , Bengaluru , Karnataka 560012 , India
| | - Sandeep M Eswarappa
- Department of Biochemistry , Indian Institute of Science , Bengaluru , Karnataka 560012 , India
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9
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Tomar S, Moorthy V, Sethi R, Chai J, Low PS, Hong STK, Lai PS. Mutational spectrum of dystrophinopathies in Singapore: Insights for genetic diagnosis and precision therapy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:230-244. [DOI: 10.1002/ajmg.c.31704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Vikaesh Moorthy
- Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Josiah Chai
- Department of Neurology, National Neuroscience Institute Singapore
| | - Poh Sim Low
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Stacey Tay Kiat Hong
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
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10
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Abstract
Since its discovery in 1977, much has been known about RNA splicing and how it plays a central role in human development, function, and, notably, disease. Defects in RNA splicing account for at least 10% of all genetic disorders, with the number expected to increase as more information is uncovered on the contribution of noncoding genomic regions to disease. Splice modulation through the use of antisense oligonucleotides (AOs) has emerged as a promising avenue for the treatment of these disorders. In fact, two splice-switching AOs have recently obtained approval from the US Food and Drug Administration: eteplirsen (Exondys 51) for Duchenne muscular dystrophy, and nusinersen (Spinraza) for spinal muscular atrophy. These work by exon skipping and exon inclusion, respectively. In this chapter, we discuss the early development of AO-based splice modulation therapy-its invention, first applications, and its evolution into the approach we are now familiar with. We give a more extensive history of exon skipping in particular, as it is the splice modulation approach given the most focus in this book.
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Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
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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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Sardone V, Zhou H, Muntoni F, Ferlini A, Falzarano MS. Antisense Oligonucleotide-Based Therapy for Neuromuscular Disease. Molecules 2017; 22:molecules22040563. [PMID: 28379182 PMCID: PMC6154734 DOI: 10.3390/molecules22040563] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/28/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
Neuromuscular disorders such as Duchenne Muscular Dystrophy and Spinal Muscular Atrophy are neurodegenerative genetic diseases characterized primarily by muscle weakness and wasting. Until recently there were no effective therapies for these conditions, but antisense oligonucleotides, a new class of synthetic single stranded molecules of nucleic acids, have demonstrated promising experimental results and are at different stages of regulatory approval. The antisense oligonucleotides can modulate the protein expression via targeting hnRNAs or mRNAs and inducing interference with splicing, mRNA degradation, or arrest of translation, finally, resulting in rescue or reduction of the target protein expression. Different classes of antisense oligonucleotides are being tested in several clinical trials, and limitations of their clinical efficacy and toxicity have been reported for some of these compounds, while more encouraging results have supported the development of others. New generation antisense oligonucleotides are also being tested in preclinical models together with specific delivery systems that could allow some of the limitations of current antisense oligonucleotides to be overcome, to improve the cell penetration, to achieve more robust target engagement, and hopefully also be associated with acceptable toxicity. This review article describes the chemical properties and molecular mechanisms of action of the antisense oligonucleotides and the therapeutic implications these compounds have in neuromuscular diseases. Current strategies and carrier systems available for the oligonucleotides delivery will be also described to provide an overview on the past, present and future of these appealing molecules.
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Affiliation(s)
- Valentina Sardone
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Programme, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK.
| | - Haiyan Zhou
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Programme, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK.
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Programme, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK.
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK.
| | - Alessandra Ferlini
- Dubowitz Neuromuscular Centre, Molecular Neurosciences Section, Developmental Neuroscience Programme, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK.
- UOL Medical Genetics, University of Ferrara, Ferrara 44121, Italy.
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13
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Lee T, Awano H, Yagi M, Matsumoto M, Watanabe N, Goda R, Koizumi M, Takeshima Y, Matsuo M. 2'-O-Methyl RNA/Ethylene-Bridged Nucleic Acid Chimera Antisense Oligonucleotides to Induce Dystrophin Exon 45 Skipping. Genes (Basel) 2017; 8:genes8020067. [PMID: 28208626 PMCID: PMC5333056 DOI: 10.3390/genes8020067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/02/2017] [Accepted: 02/07/2017] [Indexed: 12/17/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle-wasting disease characterized by dystrophin deficiency from mutations in the dystrophin gene. Antisense oligonucleotide (AO)-mediated exon skipping targets restoration of the dystrophin reading frame to allow production of an internally deleted dystrophin protein with functional benefit for DMD patients who have out-of-frame deletions. After accelerated US approval of eteplirsen (Exondys 51), which targets dystrophin exon 51 for skipping, efforts are now focused on targeting other exons. For improved clinical benefits, this strategy requires more studies of the delivery method and modification of nucleic acids. We studied a nucleotide with a 2′-O,4′-C-ethylene-bridged nucleic acid (ENA), which shows high nuclease resistance and high affinity for complementary RNA strands. Here, we describe the process of developing a 2′-O-methyl RNA(2′-OMeRNA)/ENA chimera AO to induce dystrophin exon 45 skipping. One 18-mer 2′-OMeRNA/ENA chimera (AO85) had the most potent activity for inducing exon 45 skipping in cultured myotubes. AO85 was administered to mdx mice without significant side effects. AO85 transfection into cultured myotubes from 13 DMD patients induced exon 45 skipping in all samples at different levels and dystrophin expression in 11 patients. These results suggest the possible efficacy of AO-mediated exon skipping changes in individual patients and highlight the 2′-OMeRNA/ENA chimera AO as a potential fundamental treatment for DMD.
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Affiliation(s)
- Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638501, Japan.
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 6500017, Japan.
| | - Mariko Yagi
- Nikoniko House Medical and Welfare Center, Kobe 6511102, Japan.
| | - Masaaki Matsumoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 6500017, Japan.
| | - Nobuaki Watanabe
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo 1408710, Japan.
| | - Ryoya Goda
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo 1408710, Japan.
| | - Makoto Koizumi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo 1408710, Japan.
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638501, Japan.
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Kobe 6512180, Japan.
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14
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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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Fletcher S, Bellgard MI, Price L, Akkari AP, Wilton SD. Translational development of splice-modifying antisense oligomers. Expert Opin Biol Ther 2016; 17:15-30. [PMID: 27805416 DOI: 10.1080/14712598.2017.1250880] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Antisense nucleic acid analogues can interact with pre-mRNA motifs and influence exon or splice site selection and thereby alter gene expression. Design of antisense molecules to target specific motifs can result in either exon exclusion or exon inclusion during splicing. Novel drugs exploiting the antisense concept are targeting rare, life-limiting diseases; however, the potential exists to treat a wide range of conditions by antisense-mediated splice intervention. Areas covered: In this review, the authors discuss the clinical translation of novel molecular therapeutics to address the fatal neuromuscular disorders Duchenne muscular dystrophy and spinal muscular atrophy. The review also highlights difficulties posed by issues pertaining to restricted participant numbers, variable phenotype and disease progression, and the identification and validation of study endpoints. Expert opinion: Translation of novel therapeutics for Duchenne muscular dystrophy and spinal muscular atrophy has been greatly advanced by multidisciplinary research, academic-industry partnerships and in particular, the engagement and support of the patient community. Sponsors, supporters and regulators are cooperating to deliver new drugs and identify and define meaningful outcome measures. Non-conventional and adaptive trial design could be particularly suited to clinical evaluation of novel therapeutics and strategies to treat serious, rare diseases that may be problematic to study using more conventional clinical trial structures.
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Affiliation(s)
- S Fletcher
- a Centre for Neuromuscular and Neurological Disorders , University of Western Australia , Nedlands , Western Australia , Australia.,b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia
| | - M I Bellgard
- b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia
| | - L Price
- a Centre for Neuromuscular and Neurological Disorders , University of Western Australia , Nedlands , Western Australia , Australia.,b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia
| | - A P Akkari
- b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia.,d Shiraz Pharmaceuticals, Inc , Chapel Hill , NC , USA
| | - S D Wilton
- a Centre for Neuromuscular and Neurological Disorders , University of Western Australia , Nedlands , Western Australia , Australia.,b Western Australian Neuroscience Research Institute , Nedlands , Western Australia , Australia.,c Centre for Comparative Genomics , Murdoch University , Western Australia , Australia
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Havens MA, Hastings ML. Splice-switching antisense oligonucleotides as therapeutic drugs. Nucleic Acids Res 2016; 44:6549-63. [PMID: 27288447 PMCID: PMC5001604 DOI: 10.1093/nar/gkw533] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/02/2016] [Indexed: 01/09/2023] Open
Abstract
Splice-switching oligonucleotides (SSOs) are short, synthetic, antisense, modified nucleic acids that base-pair with a pre-mRNA and disrupt the normal splicing repertoire of the transcript by blocking the RNA–RNA base-pairing or protein–RNA binding interactions that occur between components of the splicing machinery and the pre-mRNA. Splicing of pre-mRNA is required for the proper expression of the vast majority of protein-coding genes, and thus, targeting the process offers a means to manipulate protein production from a gene. Splicing modulation is particularly valuable in cases of disease caused by mutations that lead to disruption of normal splicing or when interfering with the normal splicing process of a gene transcript may be therapeutic. SSOs offer an effective and specific way to target and alter splicing in a therapeutic manner. Here, we discuss the different approaches used to target and alter pre-mRNA splicing with SSOs. We detail the modifications to the nucleic acids that make them promising therapeutics and discuss the challenges to creating effective SSO drugs. We highlight the development of SSOs designed to treat Duchenne muscular dystrophy and spinal muscular atrophy, which are currently being tested in clinical trials.
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Affiliation(s)
- Mallory A Havens
- Department of Biology, Lewis University, Romeoville, IL 60446, USA
| | - Michelle L Hastings
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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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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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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Le Rumeur E. Dystrophin and the two related genetic diseases, Duchenne and Becker muscular dystrophies. Bosn J Basic Med Sci 2015; 15:14-20. [PMID: 26295289 DOI: 10.17305/bjbms.2015.636] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/20/2015] [Indexed: 01/01/2023] Open
Abstract
Mutations of the dystrophin DMD gene, essentially deletions of one or several exons, are the cause of two devastating and to date incurable diseases, Duchenne (DMD) and Becker (BMD) muscular dystrophies. Depending upon the preservation or not of the reading frame, dystrophin is completely absent in DMD, or present in either a mutated or a truncated form in BMD. DMD is a severe disease which leads to a premature death of the patients. Therapy approaches are evolving with the aim to transform the severe DMD in the BMD form of the disease by restoring the expression of a mutated or truncated dystrophin. These therapies are based on the assumption that BMD is a mild disease. However, this is not completely true as BMD patients are more or less severely affected and no molecular basis of this heterogeneity of the BMD form of the disease is yet understood. The aim of this review is to report for the correlation between dystrophin structures in BMD deletions in view of this heterogeneity and to emphasize that examining BMD patients in details is highly relevant to anticipate for DMD therapy effects.
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Affiliation(s)
- Elisabeth Le Rumeur
- Institut de Génétique et Développement de Rennes (IGDR), Faculté de Médecine, Rennes Cedex.
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20
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Wilton SD, Veedu RN, Fletcher S. The emperor's new dystrophin: finding sense in the noise. Trends Mol Med 2015; 21:417-26. [PMID: 26051381 DOI: 10.1016/j.molmed.2015.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 01/16/2023]
Abstract
Targeted dystrophin exon removal is a promising therapy for Duchenne muscular dystrophy (DMD); however, dystrophin expression in some reports is not supported by the associated data. As in the account of 'The Emperor's New Clothes', the validity of such claims must be questioned, with critical re-evaluation of available data. Is it appropriate to report clinical benefit and induction of dystrophin as dose dependent when the baseline is unclear? The inability to induce meaningful levels of dystrophin does not mean that dystrophin expression as an end point is irrelevant, nor that induced exon skipping as a strategy is flawed, but demands that drug safety and efficacy, and study parameters be addressed, rather than questioning the strategy or the validity of dystrophin as a biomarker.
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Affiliation(s)
- S D Wilton
- Centre for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia; West Australian Neuroscience Research Institute, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia.
| | - R N Veedu
- Centre for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia; West Australian Neuroscience Research Institute, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia
| | - S Fletcher
- Centre for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia; West Australian Neuroscience Research Institute, Murdoch University, 90 South Street, Murdoch, WA 6009, Australia
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21
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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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22
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Brolin C, Shiraishi T. Antisense mediated exon skipping therapy for duchenne muscular dystrophy (DMD). ARTIFICIAL DNA, PNA & XNA 2014; 2:6-15. [PMID: 21686247 DOI: 10.4161/adna.2.1.15425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/07/2011] [Accepted: 03/10/2011] [Indexed: 11/19/2022]
Abstract
Duchenne Muscular Dystrophy (DMD) is a lethal disease caused by mutations in the dystrophin gene (DMD) that result in the absence of essential muscle protein dystrophin. Among many different approaches for DMD treatment, exon skipping, mediated by antisense oligonucleotides, is one of the most promising methods for restoration of dystrophin expression. This approach has been tested extensively targeting different exons in numerous models both in vitro and in vivo. During the past 10 years, there has been a considerable progress by using DMD animal models involving three types of antisense oligonucleotides (2'-O-methyl phosphorothioate (2OME-PS), phosphorodiamidate morpholino oligomer (PMO)) and peptide nucleic acid (PNA).
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Affiliation(s)
- Camilla Brolin
- Center for Experimental Drug and Gene Electrotransfer (CEDGE); Department of Oncology 54B1; Copenhagen University Hospital Herlev, Copenhagen, Denmark
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23
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Chen C, Ma H, Zhang F, Chen L, Xing X, Wang S, Zhang X, Luo Y. Screening of Duchenne muscular dystrophy (DMD) mutations and investigating its mutational mechanism in Chinese patients. PLoS One 2014; 9:e108038. [PMID: 25244321 PMCID: PMC4171529 DOI: 10.1371/journal.pone.0108038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a common X-linked recessive disease of muscle degeneration and death. In order to provide accurate and reliable genetic counseling and prenatal diagnosis, we screened DMD mutations in a cohort of 119 Chinese patients using multiplex ligation-dependent probe amplification (MLPA) and denaturing high performance liquid chromatography (DHPLC) followed by Sanger sequencing. In these unrelated DMD patients, we identified 11 patients with DMD small mutations (9.2%) and 81 patients with DMD deletions/duplications (del/dup) (68.1%), of which 64 (79.0%) were deletions, 16 (19.8%) were duplications, and one (1.2%) was both deletion and duplication. Furthermore, we analyzed the frequency of DMD breakpoint in the 64 deletion cases by calculating exon-deletion events of certain exon interval that revealed a novel mutation hotspot boundary. To explore why DMD rearrangement breakpoints were predisposed to specific regions (hotspot), we precisely characterized junction sequences of breakpoints at the nucleotide level in 21 patients with exon deleted/duplicated in DMD with a high-resolution SNP microarray assay. There were no exactly recurrent breakpoints and there was also no significant difference between single-exon del/dup and multiple-exon del/dup cases. The data from the current study provided a comprehensive strategy to detect DMD mutations for clinical practice, and identified two deletion hotspots at exon 43–55 and exon 10–23 by calculating exon-deletion events of certain exon interval. Furthermore, this is the first study to characterize DMD breakpoint at the nucleotide level in a Chinese population. Our observations provide better understanding of the mechanism for DMD gene rearrangements.
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Affiliation(s)
- Chen Chen
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Hongwei Ma
- Department of Developing Pediatrics, Shengjing Hospital, China Medical University, Shenyang, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Lu Chen
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuesha Xing
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Shusen Wang
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Luo
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
- * E-mail:
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Braun S. Gene-based therapies of neuromuscular disorders: an update and the pivotal role of patient organizations in their discovery and implementation. J Gene Med 2014; 15:397-413. [PMID: 24123726 DOI: 10.1002/jgm.2747] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 10/03/2013] [Indexed: 12/13/2022] Open
Abstract
This review updates the state-of-the art accomplishments of the multifaceted gene-based therapies, which include DNA or RNA as either therapeutic tools or targets for the treatment of neuromuscular diseases. It also provides insights into the key role that patient organizations have played in research and development; in particular, by addressing bottlenecks and generating boundary conditions that have contributed to scientific breakthroughs, and the effectiveness of innovation processes. Several gene therapy methods have reached the clinical stage and are now addressing both specific and classical issues related to this novel technology. Not ready yet for clinical application, genome editing is at its infancy. More rapidly progressing, RNA-based therapeutics, and especially exon skipping, exon inclusion and stop codon readthrough strategies, are about to move to the market. Most importantly, patients were at the forefront of this discovery process, from basic knowledge to innovation and translational research in a rapidly growing field of unmet medical needs. In recent years, Duchenne muscular dystrophy was the fertile ground for new therapeutic concepts that have been extended to other neuromuscular disorders, such as spinal muscular atrophy, myotonic dystrophies or fascioscapulohumeral dystrophy. In line with their longstanding policy, patient organizations will keep working in a proactive manner to bring together all stakeholders with a view to working out truly therapeutic solutions over a long-term perspective.
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Abstract
Duchenne muscular dystrophy (DMD) is the most common form of inherited muscle disease and is characterized by progressive muscle wasting ultimately resulting in death of the patients in their twenties. DMD is characterized by a deficiency of the muscle dystrophin as a result of mutations in the dystrophin gene. Currently, no effective treatment for DMD is available. Promising molecular therapies which are mutation specific have been developed. Induction of the readthrough of nonsense mutations is expected to produce dystrophin in DMD patients with nonsense mutations, which are detected in 19% of DMD cases. Clinical effectiveness of gentamicin and PTC124 have been suggested. We have demonstrated that arbekacin-mediated readthrough can substantially ameliorate muscular dystrophy. We already have begun the clinical trial of the nonsense mutation readthrough therapy using arbekacin. We hope that this molecular therapy will contribute towards the treatment for DMD.
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Biodistribution and molecular studies on orally administered nanoparticle-AON complexes encapsulated with alginate aiming at inducing dystrophin rescue in mdx mice. BIOMED RESEARCH INTERNATIONAL 2013; 2013:527418. [PMID: 24392452 PMCID: PMC3874323 DOI: 10.1155/2013/527418] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
We have previously demonstrated that intraperitoneal injections of 2'-O-methyl-phosphorothioate (2'OMePS) antisense oligoribonucleotides adsorbed onto a cationic core-shell nanoparticles (NPs), termed ZM2, provoke dystrophin restoration in the muscles of mdx mice. The aim of the present work was to evaluate the oral route as an alternative way of administration for ZM2-antisense oligoribonucleotides complexes. The biodistribution and elimination of nanoparticles were evaluated after single and multiple oral doses of IR-dye conjugated nanoparticles. Labeled nanoparticles were tracked in vivo as well as in tissue cryosections, urines and feces by Odyssey infrared imaging system, and revealed a permanence in the intestine and abdominal lymph nodes for 72 hours to 7 days before being eliminated. We subsequently tested alginate-free and alginate-encapsulated ZM2-antisense oligoribonucleotides (AON) complexes orally administered 2 and 3 times per week, respectively, in mdx mice for a total of 12 weeks. Treatment with alginate ZM2-AON induced a slight dystrophin rescue in diaphragm and intestine smooth muscles, while no dystrophin was detected in alginate-free ZM2-AON treated mice. These data encourage further experiments on oral administration testing of NP and AON complexes, possibly translatable in oligoribonucleotides-mediated molecular therapies.
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Järver P, O'Donovan L, Gait MJ. A chemical view of oligonucleotides for exon skipping and related drug applications. Nucleic Acid Ther 2013; 24:37-47. [PMID: 24171481 DOI: 10.1089/nat.2013.0454] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Peter Järver
- Medical Research Council , Laboratory of Molecular Biology, Cambridge, United Kingdom
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Current Challenges and Future Directions in Recombinant AAV-Mediated Gene Therapy of Duchenne Muscular Dystrophy. Pharmaceuticals (Basel) 2013; 6:813-36. [PMID: 24276316 PMCID: PMC3816704 DOI: 10.3390/ph6070813] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/14/2013] [Accepted: 06/14/2013] [Indexed: 01/01/2023] Open
Abstract
Various characteristics of adeno-associated virus (AAV)-based vectors with long-term safe expression have made it an exciting transduction tool for clinical gene therapy of Duchenne muscular dystrophy (DMD). Although host immune reactions against the vector as well as transgene products were detected in some instances of the clinical studies, there have been promising observations. Methods of producing AAV vectors for considerable in vivo experimentation and clinical investigations have been developed and a number of studies with AAV vector-mediated muscle transduction were attempted. Notably, an intravenous limb perfusion transduction technique enables extensive transgene expression in the skeletal muscles without noticeable adverse events. Furthermore, cardiac transduction by the rAAV9-microdystrophin would be promising to prevent development of cardiac dysfunction. Recent achievements in transduction technology suggest that long-term transgene expression with therapeutic benefits in DMD treatment would be achieved by the rAAV-mediated transduction strategy with an adequate regimen to regulate host immune response.
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Koo T, Wood MJ. Clinical trials using antisense oligonucleotides in duchenne muscular dystrophy. Hum Gene Ther 2013; 24:479-88. [PMID: 23521559 DOI: 10.1089/hum.2012.234] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe muscle wasting disorder caused by mutations in the DMD gene, affecting 1 in 3500 newborn males. Complete loss of muscle dystrophin protein causes progressive muscle weakness and heart and respiratory failure, leading to premature death. Antisense oligonucleotides (AONs) that bind to complementary sequences of the dystrophin pre-mRNA to induce skipping of the targeted exon by modulating pre-mRNA splicing are promising therapeutic agents for DMD. Such AONs can restore the open reading frame of the DMD gene and produce internally deleted, yet partially functional dystrophin protein isoforms in skeletal muscle. Within the last few years, clinical trials using AONs have made considerable progress demonstrating the restoration of functional dystrophin protein and acceptable safety profiles following both local and systemic delivery in DMD patients. However, improvement of AON delivery and efficacy, along with the development of multiple AONs to treat as many DMD patients as possible needs to be addressed for this approach to fulfill its potential. Here, we review the recent progress made in clinical trials using AONs to treat DMD and discuss the current challenges to the development of AON-based therapy for DMD.
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Affiliation(s)
- Taeyoung Koo
- Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom
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Konieczny P, Swiderski K, Chamberlain JS. Gene and cell-mediated therapies for muscular dystrophy. Muscle Nerve 2013; 47:649-63. [PMID: 23553671 DOI: 10.1002/mus.23738] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2012] [Indexed: 12/29/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a devastating muscle disorder that affects 1 in 3,500 boys. Despite years of research and considerable progress in understanding the molecular mechanism of the disease and advancement of therapeutic approaches, there is no cure for DMD. The current treatment options are limited to physiotherapy and corticosteroids, and although they provide a substantial improvement in affected children, they only slow the course of the disorder. On a more optimistic note, more recent approaches either significantly alleviate or eliminate muscular dystrophy in murine and canine models of DMD and importantly, many of them are being tested in early phase human clinical trials. This review summarizes advancements that have been made in viral and nonviral gene therapy as well as stem cell therapy for DMD with a focus on the replacement and repair of the affected dystrophin gene.
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Affiliation(s)
- Patryk Konieczny
- Department of Neurology, The University of Washington School of Medicine, Seattle, Washington 98105, USA
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Rani AQ, Sasongko TH, Sulong S, Bunyan D, Salmi AR, Zilfalil BA, Matsuo M, Zabidi-Hussin ZAMH. Mutation Spectrum ofDystrophinGene in Malaysian Patients with Duchenne/Becker Muscular Dystrophy. J Neurogenet 2013; 27:11-5. [DOI: 10.3109/01677063.2012.762580] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Yokota T, Duddy W, Echigoya Y, Kolski H. Exon skipping for nonsense mutations in Duchenne muscular dystrophy: too many mutations, too few patients? Expert Opin Biol Ther 2012; 12:1141-52. [PMID: 22650324 DOI: 10.1517/14712598.2012.693469] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Duchenne muscular dystrophy (DMD), one of the most common and lethal genetic disorders, is caused by mutations of the dystrophin gene. Removal of an exon or of multiple exons using antisense molecules has been demonstrated to allow synthesis of truncated 'Becker muscular dystrophy-like' dystrophin. AREAS COVERED Approximately 15% of DMD cases are caused by a nonsense mutation. Although patient databases have previously been surveyed for applicability to each deletion mutation pattern, this is not so for nonsense mutations. Here, we examine the world-wide database containing notations for more than 1200 patients with nonsense mutations. Approximately 47% of nonsense mutations can be potentially treated with single exon skipping, rising to 90% with double exon skipping, but to reach this proportion requires the development of exon skipping molecules targeting some 68 of dystrophin's 79 exons, with patient numbers spread thinly across those exons. In this review, we discuss progress and remaining hurdles in exon skipping and an alternative strategy, stop-codon readthrough. EXPERT OPINION Antisense-mediated exon skipping therapy is targeted highly at the individual patient and is a clear example of personalized medicine. An efficient regulatory path for drug approval will be a key to success.
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Affiliation(s)
- Toshifumi Yokota
- University of Alberta, Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, 829 Medical Sciences Building, Edmonton, AB T6G 2H7, Canada.
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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] [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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Abstract
Antisense-mediated exon skipping to restore the disrupted dystrophin reading frame is currently in clinical trials for Duchenne muscular dystrophy. This chapter describes the rationale of this approach and gives an overview of in vitro and in vivo experiments with antisense oligonucleotides and antisense genes. Finally, an overview of clinical trials is given and outstanding questions and hurdles are discussed.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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Abstract
The chemistry of the oligonucleotide backbone is crucial to obtaining high activity in vivo in exon skipping applications. Apart from the ability to bind strongly and sequence-specifically to pre-mRNA targets, the type of backbone also influences cell delivery, in vivo pharmacology, bio-distribution, toxicology, and ultimately the therapeutic use in humans. Reviewed here are classes of oligonucleotide commonly used for exon skipping applications, namely negatively charged backbones typified by RNA analogues having 2'-O-substitution and a phosphorothioate linkage and charge-neutral backbones such as PNA and PMO. Also discussed are peptide conjugates of PNA and PMO that enhance cellular and in vivo delivery and their potential for drug development. Finally, the prospects for development of other analogue types in exon skipping applications are outlined.
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Takeshima Y, Yagi M, Matsuo M. Optimizing RNA/ENA chimeric antisense oligonucleotides using in vitro splicing. Methods Mol Biol 2012; 867:131-41. [PMID: 22454059 DOI: 10.1007/978-1-61779-767-5_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A molecular therapy for Duchenne muscular dystrophy (DMD) that converts dystrophin mRNA from out-of-frame to in-frame transcripts by inducing exon skipping with antisense oligonucleotides (AOs) is now approaching clinical application. To exploit the broad therapeutic applicability of exon skipping therapy, it is necessary to identify AOs that are able to induce efficient and specific exon skipping. To optimize AOs, we have established an in vitro splicing system using cultured DMD myocytes. Here, we describe the process of identifying the best AO.Cultured DMD myocytes are established from a biopsy sample and the target exon is chosen. A series of AOs are designed to cover the whole target exon sequence. As AOs, we use 15-20-mer chimeric oligonucleotides consisting of 2'-O-methyl RNA and modified nucleic acid (2'-O, 4'-C-ethylene-bridged nucleic acid). Each AO is transfected individually into cultured DMD myocytes, and the resulting mRNA is analyzed by reverse transcription-PCR. The ability of each AO to induce exon skipping is examined by comparing the amount of cDNA with and without exon skipping. If necessary, having roughly localized the target region, another set of AOs are designed and the exon skipping abilities of the new AOs are examined. Finally, one AO is determined as the best for the molecular therapy.Our simple and reliable methods using an in vitro splicing system have enabled us to identify optimized AOs against many exons of the DMD gene.
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Affiliation(s)
- Yasuhiro Takeshima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
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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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Malueka RG, Yagi M, Awano H, Lee T, Dwianingsih EK, Nishida A, Takeshima Y, Matsuo M. Antisense oligonucleotide induced dystrophin exon 45 skipping at a low half-maximal effective concentration in a cell-free splicing system. Nucleic Acid Ther 2011; 21:347-53. [PMID: 21967521 DOI: 10.1089/nat.2011.0310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Antisense oligonucleotides (AOs) can facilitate the expression of internally deleted dystrophin in dystrophin-deficient Duchenne muscular dystrophy (DMD) by correcting the reading frame of the pre-mRNA with AO-mediated exon skipping. An antisense 18-mer 2'-O-methyl RNA/ethylene-bridged nucleic acid chimera AO targeting exon 45 of the dystrophin gene, AO85, can induce exon 45 skipping efficiently in cultured cells. AO85 is expected to facilitate dystrophin expression in 8%-9% of all DMD patients. Here, we examined the kinetics of AO85-mediated exon 45 skipping in a cell-free splicing system. In vitro transcribed pre-mRNAs containing dystrophin exon 45 and part of its flanking introns within a hybrid minigene were incubated with HeLa cell nuclear extract, and the resultant mRNAs were amplified by semiquantitative reverse transcriptase-polymerase chain reaction. Time-course analysis revealed that the splicing process fitted well to first order kinetics. Addition of AO85 produced an extra spliced product, deleting exon 45 (Δexon 45), indicating AO85-mediated exon 45 skipping. Production of Δexon 45 increased linearly with increasing concentrations of AO85, reaching a maximum of nearly 80% of the transcripts. The half-maximal effective concentration (EC(50)) of AO85 was 58.0 nM. The percentage of Δexon 45 among the transcripts decreased inversely with the pre-mRNA concentration; Lineweaver-Burk plotting revealed a competitive fashion of AO85 action. The low EC(50) indicates high potential of AO85 for clinical application.
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Abstract
Numerous chemically modified oligonucleotides have been developed so far and show their own unique chemical properties and pharmacodynamic/pharmacokinetic characteristics. Among all non-natural nucleotides, to the best of our knowledge, only five chemistries are currently being tested in clinical trials: phosphorothioate, 2´-O-methyl RNA, 2´-O-methoxyethyl RNA, 2´,4´-bridged nucleic acid/locked nucleic acid and the phosphorodiamidate morpholino oligomer. Since phosphorothioate modification can improve the pharmacokinetics of oligonucleotides, this modification is currently used in combination with all other modifications except phosphorodiamidate morpholino oligomer. For the treatment of metabolic, cardiovascular, cancer and other systemic diseases, the phosphorothioate class of drugs is obviously helpful, while superior efficacies can be observed in phosphorodiamidate morpholino oligomer compared to other classes of oligonucleotides for the treatment of Duchenne muscular dystrophy. Which properties of antisense molecules are actually essential for clinical applications? In this article, we provide an overview of the medicinal chemistry of existing non-natural antisense molecules, as well as their clinical applications, to discuss which properties of antisense oligonuculeotides affect therapeutic potency.
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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] [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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42
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Bioanalysis of siRNA and oligonucleotide therapeutics in biological fluids and tissues. Bioanalysis 2011; 1:595-609. [PMID: 21083155 DOI: 10.4155/bio.09.66] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This article summarizes bioanalytical avenues for the determination of siRNA and oligonucleotide therapeutics, with an emphasis on hybridization methods. Aspects of the chemistry and delivery of investigational oligonucleotide therapeutics are considered. The nature of the oligonucleotide under investigation will dictate the best analytical course of action; each method has its advantages and disadvantages, depending upon the oligonucleotide test article and the anticipated toxicokinetic and pharmacokinetic study parameters. Stringent method development and specific validation criteria are essential to attain the best quality results in support of a regulatory filing.
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43
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Wilton SD, Fletcher S. Novel compounds for the treatment of Duchenne muscular dystrophy: emerging therapeutic agents. APPLICATION OF CLINICAL GENETICS 2011; 4:29-44. [PMID: 23776365 PMCID: PMC3681176 DOI: 10.2147/tacg.s8762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The identification of dystrophin and the causative role of mutations in this gene in Duchenne and Becker muscular dystrophies (D/BMD) was expected to lead to timely development of effective therapies. Despite over 20 years of research, corticosteroids remain the only available pharmacological treatment for DMD, although significant benefits and extended life have resulted from advances in the clinical care and management of DMD individuals. Effective treatment of DMD will require dystrophin restitution in skeletal, cardiac, and smooth muscles and nonmuscle tissues; however, modulation of muscle loss and regeneration has the potential to play an important role in altering the natural history of DMD, particularly in combination with other treatments. Emerging biological, molecular, and small molecule therapeutics are showing promise in ameliorating this devastating disease, and it is anticipated that regulatory environments will need to display some flexibility in order to accommodate the new treatment paradigms.
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Affiliation(s)
- Steve D Wilton
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Crawley, Perth, WA, Australia
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44
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Abstract
Despite three decades of huge progress in molecular genetics, in cloning of disease causative gene as well as technology breakthroughs in viral biotechnology, out of thousands of gene therapy clinical trials that have been initiated, only very few are now reaching regulatory approval. We shall review some of the major hurdles, and based on the current either positive or negative examples, we try to initiate drawing a learning curve from experience and possibly identify the major drivers for future successful achievement of human gene therapy trials.
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Affiliation(s)
- Patrice P Denèfle
- Translational Sciences, IPSEN, and Biotherapies, ParisTech Institute, Paris-Descartes University, Paris, France.
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45
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Park KS, Oh D. Gene therapy for muscular dystrophies: progress and challenges. J Clin Neurol 2010; 6:111-6. [PMID: 20944811 PMCID: PMC2950915 DOI: 10.3988/jcn.2010.6.3.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Revised: 06/24/2010] [Accepted: 06/24/2010] [Indexed: 11/23/2022] Open
Abstract
Muscular dystrophies are groups of inherited progressive diseases of the muscle caused by mutations of diverse genes related to normal muscle function. Although there is no current effective treatment for these devastating diseases, various molecular strategies have been developed to restore the expressions of the associated defective proteins. In preclinical animal models, both viral and nonviral vectors have been shown to deliver recombinant versions of defective genes. Antisense oligonucleotides have been shown to modify the splicing mechanism of mesenger ribonucleic acid to produce an internally deleted but partially functional dystrophin in an experimental model of Duchenne muscular dystrophy. In addition, chemicals can induce readthrough of the premature stop codon in nonsense mutations of the dystrophin gene. On the basis of these preclinical data, several experimental clinical trials are underway that aim to demonstrate efficacy in treating these devastating diseases.
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Affiliation(s)
- Kyung Seok Park
- Department of Neurology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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Bauman J, Jearawiriyapaisarn N, Kole R. Therapeutic potential of splice-switching oligonucleotides. Oligonucleotides 2010; 19:1-13. [PMID: 19125639 DOI: 10.1089/oli.2008.0161] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alternative splicing enables a single pre-messenger RNA transcript to yield multiple protein isoforms, making it a major contributor to the diversity of the proteome. While this process is essential for normal development, aberrations in alternative splicing are the cause of a multitude of human diseases. Methods for manipulating alternative splicing would thus be of therapeutic value. Chemically modified antisense oligonucleotides that alter alternative splicing by directing splice site selection have been developed to achieve this end. These splice-switching oligonucleotides (SSOs) have been applied to correct aberrant splicing, induce expression of a therapeutic splice variant, or induce expression of a novel therapeutic splice variant in a number of disease-relevant genes. Recently, in vivo efficacy of SSOs has been reported using animal disease models, as well as in results from the first clinical trial.
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Affiliation(s)
- John Bauman
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
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David A, Srirangalingam U, Metherell LA, Khoo B, Clark AJL. Repair of aberrant splicing in growth hormone receptor by antisense oligonucleotides targeting the splice sites of a pseudoexon. J Clin Endocrinol Metab 2010; 95:3542-6. [PMID: 20427506 DOI: 10.1210/jc.2009-1968] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT The GH receptor (GHR) pseudoexon 6Psi defect is a frequent cause of GH insensitivity (GHI) resulting from a non-functioning GH receptor (GHR). It results in a broad range of phenotypes and may also be present in patients diagnosed as idiopathic short stature. OBJECTIVE Our objective was to correct aberrant GHR splicing and inclusion of 6Psi using exon-skipping antisense oligonucleotides (ASOs). DESIGN AND SETTING Three ASOs binding the 5' (ASO-5), 3' (ASO-3), and branch site (ASO-Br) of 6Psi were tested in an in vitro splicing assay and a cell transfection system. The wild-type (wt) and mutant (mt) DNA minigenes (wt- and mtL1-GHR6Psi-L2, respectively) were created by inserting the GHR 6Psi in a well-characterized splice reporter (Adml-par). For the in vitro splicing assay, the wt- and mtL1-GHR6Psi-L2 were transcribed into pre-mRNA in the presence of [alpha(32)P]GTP and incubated with ASOs in HeLa nuclear extracts. For the cell transfection studies, wt- and mtL1-GHR6Psi-L2 cloned into pcDNA 3.1 were transfected with ASOs into HEK293 cells. After 48 h, RNA was extracted and radiolabeled RT-PCR products quantified. RESULTS ASO-3 induced an almost complete pseudoexon skipping in vitro and in HEK293 cells. This effect was dose dependent and maximal at 125-250 nm. ASO-5 produced modest pseudoexon skipping, whereas ASO-Br had no effect. Targeting of two splice elements simultaneously was less effective than targeting one. ASO-Br was tested on the wtL1-GHR6Psi-L2 and did not act as an enhancer of 6Psi inclusion. CONCLUSIONS The exon-skipping ASO approach was effective in correcting aberrant GHR splicing and may be a promising therapeutic tool.
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Affiliation(s)
- Alessia David
- Centre for Endocrinology, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK.
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Kondo-Iida E. Commentary on 'Mutation spectrum of the dystrophin gene in 442 Duchenne/Becker muscular dystrophy cases from one Japanese referral center'. J Hum Genet 2010; 55:555-6. [PMID: 20555341 DOI: 10.1038/jhg.2010.69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eri Kondo-Iida
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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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] [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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Low incidence of limb-girdle muscular dystrophy type 2C revealed by a mutation study in Japanese patients clinically diagnosed with DMD. BMC MEDICAL GENETICS 2010; 11:49. [PMID: 20350330 PMCID: PMC2861025 DOI: 10.1186/1471-2350-11-49] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 03/30/2010] [Indexed: 11/21/2022]
Abstract
Background Limb-girdle muscular dystrophy type 2C (LGMD2C) is an autosomal recessive muscle dystrophy that resembles Duchenne muscular dystrophy (DMD). Although DMD is known to affect one in every 3500 males regardless of race, a widespread founder mutation causing LGMD2C has been described in North Africa. However, the incidence of LGMD2C in Japanese has been unknown because the genetic background remains uncharacterized in many patients clinically diagnosed with DMD. Methods We enrolled 324 patients referred to the Kobe University Hospital with suspected DMD. Mutations in the dystrophin or the SGCG genes were analyzed using not only genomic DNA but also cDNA. Results In 322 of the 324 patients, responsible mutations in the dystrophin were successfully revealed, confirming DMD diagnosis. The remaining two patients had normal dystrophin expression but absence of γ-sarcoglycan in skeletal muscle. Mutation analysis of the SGCG gene revealed homozygous deletion of exon 6 in one patient, while the other had a novel single nucleotide insertion in exon 7 in one allele and deletion of exon 6 in the other allele. These mutations created a stop codon that led to a γ-sarcoglycan deficiency, and we therefore diagnosed these two patients as having LGMD2C. Thus, the relative incidence of LGMD2C among Japanese DMD-like patients can be calculated as 1 in 161 patients suspected to have DMD (2 of 324 patients = 0.6%). Taking into consideration the DMD incidence for the overall population (1/3,500 males), the incidence of LGMD2C can be estimated as 1 per 560,000 or 1.8 per million. Conclusions To the best of our knowledge, this is the first study to demonstrate a low incidence of LGMD2C in the Japanese population.
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