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McDowall S, Aung-Htut M, Wilton S, Li D. Antisense oligonucleotides and their applications in rare neurological diseases. Front Neurosci 2024; 18:1414658. [PMID: 39376536 PMCID: PMC11456401 DOI: 10.3389/fnins.2024.1414658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 08/20/2024] [Indexed: 10/09/2024] Open
Abstract
Rare diseases affect almost 500 million people globally, predominantly impacting children and often leading to significantly impaired quality of life and high treatment costs. While significant contributions have been made to develop effective treatments for those with rare diseases, more rapid drug discovery strategies are needed. Therapeutic antisense oligonucleotides can modulate target gene expression with high specificity through various mechanisms determined by base sequences and chemical modifications; and have shown efficacy in clinical trials for a few rare neurological conditions. Therefore, this review will focus on the applications of antisense oligonucleotides, in particular splice-switching antisense oligomers as promising therapeutics for rare neurological diseases, with key examples of Duchenne muscular dystrophy and spinal muscular atrophy. Challenges and future perspectives in developing antisense therapeutics for rare conditions including target discovery, antisense chemical modifications, animal models for therapeutic validations, and clinical trial designs will also be briefly discussed.
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Affiliation(s)
- Simon McDowall
- School of Human Sciences, The University of Western Australia, Crawley, WA, Australia
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA, Australia
| | - May Aung-Htut
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Steve Wilton
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Dunhui Li
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
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2
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Hatanaka F, Suzuki K, Shojima K, Yu J, Takahashi Y, Sakamoto A, Prieto J, Shokhirev M, Nuñez Delicado E, Rodriguez Esteban C, Izpisua Belmonte JC. Therapeutic strategy for spinal muscular atrophy by combining gene supplementation and genome editing. Nat Commun 2024; 15:6191. [PMID: 39048567 PMCID: PMC11269569 DOI: 10.1038/s41467-024-50095-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
Defect in the SMN1 gene causes spinal muscular atrophy (SMA), which shows loss of motor neurons, muscle weakness and atrophy. While current treatment strategies, including small molecules or viral vectors, have shown promise in improving motor function and survival, achieving a definitive and long-term correction of SMA's endogenous mutations and phenotypes remains highly challenging. We have previously developed a CRISPR-Cas9 based homology-independent targeted integration (HITI) strategy, enabling unidirectional DNA knock-in in both dividing and non-dividing cells in vivo. In this study, we demonstrated its utility by correcting an SMA mutation in mice. When combined with Smn1 cDNA supplementation, it exhibited long-term therapeutic benefits in SMA mice. Our observations may provide new avenues for the long-term and efficient treatment of inherited diseases.
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Affiliation(s)
- Fumiyuki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Altos Labs, Inc., 5510 Morehouse Dr., Ste. 300, San Diego, CA, 92121, USA
| | - Keiichiro Suzuki
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, 560-8531, Japan
- Graduate School of Engineering Science, Osaka University, Osaka, 560-8531, Japan
- Graduate School of Frontier Bioscience, Osaka University, Osaka, 565-0871, Japan
| | - Kensaku Shojima
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of General Internal Medicine, Hyogo Medical University School of Medicine, Hyogo, 663-8131, Japan
| | - Jingting Yu
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Yuta Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Altos Labs, Inc., 5510 Morehouse Dr., Ste. 300, San Diego, CA, 92121, USA
| | - Akihisa Sakamoto
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Javier Prieto
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Maxim Shokhirev
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Estrella Nuñez Delicado
- Universidad Catolica, San Antonio de Murcia, Campus de los Jeronimos, 135, 30107, Guadalupe, Spain
| | - Concepcion Rodriguez Esteban
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Altos Labs, Inc., 5510 Morehouse Dr., Ste. 300, San Diego, CA, 92121, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Altos Labs, Inc., 5510 Morehouse Dr., Ste. 300, San Diego, CA, 92121, USA.
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3
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Binda CS, Lelos MJ, Rosser AE, Massey TH. Using gene or cell therapies to treat Huntington's disease. HANDBOOK OF CLINICAL NEUROLOGY 2024; 205:193-215. [PMID: 39341655 DOI: 10.1016/b978-0-323-90120-8.00014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Huntington's disease is caused by a CAG repeat expansion in the first exon of the HTT gene, leading to the production of gain-of-toxic-function mutant huntingtin protein species and consequent transcriptional dysregulation and disrupted cell metabolism. The brunt of the disease process is borne by the striatum from the earliest disease stages, with striatal atrophy beginning approximately a decade prior to the onset of neurologic signs. Although the expanded CAG repeat in the HTT gene is necessary and sufficient to cause HD, other genes can influence the age at onset of symptoms and how they progress. Many of these modifier genes have roles in DNA repair and are likely to modulate the stability of the CAG repeat in somatic cells. Currently, there are no disease-modifying treatments for HD that can be prescribed to patients and few symptomatic treatments, but there is a lot of interest in therapeutics that can target the pathogenic pathways at the DNA and RNA levels, some of which have reached the stage of human studies. In contrast, cell therapies aim to replace key neural cells lost to the disease process and/or to support the host vulnerable striatum by direct delivery of cells to the brain. Ultimately it may be possible to combine gene and cell therapies to both slow disease processes and provide some level of neural repair. In this chapter we consider the current status of these therapeutic strategies along with their prospects and challenges.
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Affiliation(s)
- Caroline S Binda
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom; UK Dementia Research Institute at Cardiff, Cardiff University, Cardiff, United Kingdom
| | - Mariah J Lelos
- Brain Repair Group, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Anne E Rosser
- Brain Repair Group, School of Biosciences, Cardiff University, Cardiff, United Kingdom; BRAIN Unit, Neuroscience and Mental Health Research Institute, Cardiff, United Kingdom.
| | - Thomas H Massey
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom; UK Dementia Research Institute at Cardiff, Cardiff University, Cardiff, United Kingdom
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4
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Le BT, Chen S, Veedu RN. Evaluation of Chemically Modified Nucleic Acid Analogues for Splice Switching Application. ACS OMEGA 2023; 8:48650-48661. [PMID: 38162739 PMCID: PMC10753547 DOI: 10.1021/acsomega.3c07618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
In recent years, several splice switching antisense oligonucleotide (ASO)-based therapeutics have gained significant interest, and several candidates received approval for clinical use for treating rare diseases, in particular, Duchenne muscular dystrophy and spinal muscular atrophy. These ASOs are fully modified; in other words, they are composed of chemically modified nucleic acid analogues instead of natural RNA oligomers. This has significantly improved drug-like properties of these ASOs in terms of efficacy, stability, pharmacokinetics, and safety. Although chemical modifications of oligonucleotides have been discussed previously for numerous applications including nucleic acid aptamers, small interfering RNA, DNAzyme, and ASO, to the best of our knowledge, none of them have solely focused on the analogues that have been utilized for splice switching applications. To this end, we present here a comprehensive review of different modified nucleic acid analogues that have been explored for developing splice switching ASOs. In addition to the antisense chemistry, we also endeavor to provide a brief historical overview of the approved spice switching ASO drugs, including a list of drugs that have entered human clinical trials. We hope this work will inspire further investigations into expanding the potential of novel nucleic acid analogues for constructing splice switching ASOs.
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Affiliation(s)
- Bao T. Le
- Centre
for Molecular Medicine and Innovative Therapeutics, Health Futures
Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
- Precision
Nucleic Acid Therapeutics, Perron Institute
for Neurological and Translational Science, Nedlands, Western Australia 6009, Australia
- ProGenis
Pharmaceuticals Pty Ltd., Bentley, Western Australia 6102, Australia
| | - Suxiang Chen
- Centre
for Molecular Medicine and Innovative Therapeutics, Health Futures
Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
- Precision
Nucleic Acid Therapeutics, Perron Institute
for Neurological and Translational Science, Nedlands, Western Australia 6009, Australia
| | - Rakesh N. Veedu
- Centre
for Molecular Medicine and Innovative Therapeutics, Health Futures
Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
- Precision
Nucleic Acid Therapeutics, Perron Institute
for Neurological and Translational Science, Nedlands, Western Australia 6009, Australia
- ProGenis
Pharmaceuticals Pty Ltd., Bentley, Western Australia 6102, Australia
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5
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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6
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Saoudi A, Barberat S, le Coz O, Vacca O, Doisy Caquant M, Tensorer T, Sliwinski E, Garcia L, Muntoni F, Vaillend C, Goyenvalle A. Partial restoration of brain dystrophin by tricyclo-DNA antisense oligonucleotides alleviates emotional deficits in mdx52 mice. MOLECULAR THERAPY - NUCLEIC ACIDS 2023; 32:173-188. [PMID: 37078061 PMCID: PMC10106732 DOI: 10.1016/j.omtn.2023.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/16/2023] [Indexed: 04/05/2023]
Abstract
The mdx52 mouse model recapitulates a frequent mutation profile associated with brain involvement in Duchenne muscular dystrophy. Deletion of exon 52 impedes expression of two dystrophins (Dp427, Dp140) expressed in brain, and is eligible for therapeutic exon-skipping strategies. We previously showed that mdx52 mice display enhanced anxiety and fearfulness, and impaired associative fear learning. In this study, we examined the reversibility of these phenotypes using exon 51 skipping to restore exclusively Dp427 expression in the brain of mdx52 mice. We first show that a single intracerebroventricular administration of tricyclo-DNA antisense oligonucleotides targeting exon 51 restores 5%-15% of dystrophin protein expression in the hippocampus, cerebellum, and cortex, at stable levels between 7 and 11 week after injection. Anxiety and unconditioned fear were significantly reduced in treated mdx52 mice and acquisition of fear conditioning appeared fully rescued, while fear memory tested 24 h later was only partially improved. Additional restoration of Dp427 in skeletal and cardiac muscles by systemic treatment did not further improve the unconditioned fear response, confirming the central origin of this phenotype. These findings indicate that some emotional and cognitive deficits associated with dystrophin deficiency may be reversible or at least improved by partial postnatal dystrophin rescue.
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Affiliation(s)
- Amel Saoudi
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400 Saclay, France
| | - Sacha Barberat
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | - Olivier le Coz
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | - Ophélie Vacca
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | | | - Thomas Tensorer
- SQY Therapeutics – Synthena, UVSQ, 78180 Montigny le Bretonneux, France
| | - Eric Sliwinski
- SQY Therapeutics – Synthena, UVSQ, 78180 Montigny le Bretonneux, France
| | - Luis Garcia
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, Developmental Neurosciences Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Cyrille Vaillend
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400 Saclay, France
- Corresponding author Cyrille Vaillend, Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400 Saclay, France.
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
- Corresponding author Aurélie Goyenvalle, Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.
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7
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Aslesh T, Erkut E, Ren J, Lim KRQ, Woo S, Hatlevig S, Moulton HM, Gosgnach S, Greer J, Maruyama R, Yokota T. DG9-conjugated morpholino rescues phenotype in SMA mice by reaching the CNS via a subcutaneous administration. JCI Insight 2023; 8:160516. [PMID: 36719755 PMCID: PMC10077475 DOI: 10.1172/jci.insight.160516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
Antisense oligonucleotide-mediated (AO-mediated) therapy is a promising strategy to treat several neurological diseases, including spinal muscular atrophy (SMA). However, limited delivery to the CNS with AOs administered intravenously or subcutaneously is a major challenge. Here, we demonstrate a single subcutaneous administration of cell-penetrating peptide DG9 conjugated to an AO called phosphorodiamidate morpholino oligomer (PMO) reached the CNS and significantly prolonged the median survival compared with unconjugated PMO and R6G-PMO in a severe SMA mouse model. Treated mice exhibited substantially higher expression of full-length survival of motor neuron 2 in both the CNS and systemic tissues compared with nontreated and unmodified AO-treated mice. The treatment ameliorated the atrophic musculature and improved breathing function accompanied by improved muscle strength and innervation at the neuromuscular junction with no signs of apparent toxicity. We also demonstrated DG9-conjugated PMO localized in nuclei in the spinal cord and brain after subcutaneous injections. Our data identify DG9 peptide conjugation as a powerful way to improve the efficacy of AO-mediated splice modulation. Finally, DG9-PMO is a promising therapeutic option to treat SMA and other neurological diseases, overcoming the necessity for intrathecal injections and treating body-wide tissues without apparent toxicity.
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Affiliation(s)
| | | | - Jun Ren
- Neuroscience and Mental Health Institute.,Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Susan Hatlevig
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
| | - Hong M Moulton
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
| | - Simon Gosgnach
- Neuroscience and Mental Health Institute.,Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - John Greer
- Neuroscience and Mental Health Institute.,Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Toshifumi Yokota
- Neuroscience and Mental Health Institute.,Department of Medical Genetics, and
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8
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Goto A, Yamamoto S, Iwasaki S. Biodistribution and delivery of oligonucleotide therapeutics to the central nervous system: Advances, challenges, and future perspectives. Biopharm Drug Dispos 2023; 44:26-47. [PMID: 36336817 DOI: 10.1002/bdd.2338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
Considerable advances have been made in the research and development of oligonucleotide therapeutics (OTs) for treating central nervous system (CNS) diseases, such as psychiatric and neurodegenerative disorders, because of their promising mode of action. However, due to the tight barrier function and complex physiological structure of the CNS, the efficient delivery of OTs to target the brain has been a major challenge, and intensive efforts have been made to overcome this limitation. In this review, we summarize the representative methodologies and current knowledge of biodistribution, along with the pharmacokinetic/pharmacodynamic (PK/PD) relationship of OTs in the CNS, which are critical elements for the successful development of OTs for CNS diseases. First, quantitative bioanalysis methods and imaging-based approaches for the evaluation of OT biodistribution are summarized. Next, information available on the biodistribution profile, distribution pathways, quantitative PK/PD modeling, and simulation of OTs following intrathecal or intracerebroventricular administration are reviewed. Finally, the latest knowledge on the drug delivery systems to the brain via intranasal or systemic administration as noninvasive routes for improved patient quality of life is reviewed. The aim of this review is to enrich research on the successful development of OTs by clarifying OT distribution profiles and pathways to the target brain regions or cells, and by identifying points that need further investigation for a mechanistic approach to generate efficient OTs.
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Affiliation(s)
- Akihiko Goto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Syunsuke Yamamoto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Shinji Iwasaki
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
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9
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Zarrouki F, Relizani K, Bizot F, Tensorer T, Garcia L, Vaillend C, Goyenvalle A. Partial restoration of brain dystrophin and behavioral deficits by exon skipping in the muscular dystrophy X-linked (mdx) mouse. Ann Neurol 2022; 92:213-229. [PMID: 35587226 PMCID: PMC9544349 DOI: 10.1002/ana.26409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/08/2022]
Abstract
Objectives Duchenne muscular dystrophy is associated with various degrees of cognitive impairment and behavioral disturbances. Emotional and memory deficits also constitute reliable outcome measures to assess efficacy of treatments in the mdx mouse lacking the muscle and neuronal full‐length dystrophins. The present study aimed to evaluate whether these deficits could be alleviated by the restoration of brain dystrophin. Methods We performed intracerebroventricular administration of a new potent tricyclo‐DNA antisense oligonucleotide (tcDNA‐ASO) containing a full phosphodiester backbone conjugated to a palmitic acid moiety (tcDNA‐ASO), designed to skip the mutated exon 23 of mdx mice. Results We first show that the tcDNA‐ASO rescues expression of brain dystrophin to 10–30% of wild‐type levels and significantly reduces the abnormal unconditioned fear responses in mdx mice in a dose‐dependent manner, 5 weeks post‐injection. Exon skipping efficiency, ASO biodistribution, protein restoration and effect on the fear response were optimal with a dose of 400 μg at 6–7 weeks post‐injection, with synaptic‐like expression in brain tissues such as the hippocampus and amygdala. Furthermore, this dose of tcDNA‐ASO restored long‐term memory retention of mdx mice in an object recognition task, but only had minor effects on fear conditioning. Interpretation These results suggest for the first time that postnatal re‐expression of brain dystrophin could reverse or at least alleviate some cognitive deficits associated with Duchenne muscular dystrophy. ANN NEUROL 2022;92:213–229
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Affiliation(s)
- Faouzi Zarrouki
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000, Versailles, France.,Université Paris-Saclay, CNRS, Institut des Neurosciences Paris Saclay, 91400, Saclay, France
| | - Karima Relizani
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000, Versailles, France.,SQY Therapeutics, UVSQ, 78180, Montigny le Bretonneux, France
| | - Flavien Bizot
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000, Versailles, France
| | - Thomas Tensorer
- SQY Therapeutics, UVSQ, 78180, Montigny le Bretonneux, France
| | - Luis Garcia
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000, Versailles, France.,LIA BAHN, centre scientifique de Monaco, 98000, Monaco
| | - Cyrille Vaillend
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris Saclay, 91400, Saclay, France
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000, Versailles, France.,LIA BAHN, centre scientifique de Monaco, 98000, Monaco
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10
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Soukarieh O, Meguerditchian C, Proust C, Aïssi D, Eyries M, Goyenvalle A, Trégouët DA. Common and Rare 5′UTR Variants Altering Upstream Open Reading Frames in Cardiovascular Genomics. Front Cardiovasc Med 2022; 9:841032. [PMID: 35387445 PMCID: PMC8977850 DOI: 10.3389/fcvm.2022.841032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/21/2022] [Indexed: 01/16/2023] Open
Abstract
High-throughput sequencing (HTS) technologies are revolutionizing the research and molecular diagnosis landscape by allowing the exploration of millions of nucleotide sequences at an unprecedented scale. These technologies are of particular interest in the identification of genetic variations contributing to the risk of rare (Mendelian) and common (multifactorial) human diseases. So far, they have led to numerous successes in identifying rare disease-causing mutations in coding regions, but few in non-coding regions that include introns, untranslated (UTR), and intergenic regions. One class of neglected non-coding variations is that of 5′UTR variants that alter upstream open reading frames (upORFs) of the coding sequence (CDS) of a natural protein coding transcript. Following a brief summary of the molecular bases of the origin and functions of upORFs, we will first review known 5′UTR variations altering upORFs and causing rare cardiovascular disorders (CVDs). We will then investigate whether upORF-affecting single nucleotide polymorphisms could be good candidates for explaining association signals detected in the context of genome-wide association studies for common complex CVDs.
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Affiliation(s)
- Omar Soukarieh
- INSERM, Bordeaux Population Health, U1219, Molecular Epidemiology of Vascular and Brain Disorders, University of Bordeaux, Bordeaux, France
- *Correspondence: Omar Soukarieh,
| | - Caroline Meguerditchian
- INSERM, Bordeaux Population Health, U1219, Molecular Epidemiology of Vascular and Brain Disorders, University of Bordeaux, Bordeaux, France
| | - Carole Proust
- INSERM, Bordeaux Population Health, U1219, Molecular Epidemiology of Vascular and Brain Disorders, University of Bordeaux, Bordeaux, France
| | - Dylan Aïssi
- INSERM, Bordeaux Population Health, U1219, Molecular Epidemiology of Vascular and Brain Disorders, University of Bordeaux, Bordeaux, France
| | - Mélanie Eyries
- Department of Genetics, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Paris, France
| | | | - David-Alexandre Trégouët
- INSERM, Bordeaux Population Health, U1219, Molecular Epidemiology of Vascular and Brain Disorders, University of Bordeaux, Bordeaux, France
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11
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Relizani K, Echevarría L, Zarrouki F, Gastaldi C, Dambrune C, Aupy P, Haeberli A, Komisarski M, Tensorer T, Larcher T, Svinartchouk F, Vaillend C, Garcia L, Goyenvalle A. Palmitic acid conjugation enhances potency of tricyclo-DNA splice switching oligonucleotides. Nucleic Acids Res 2021; 50:17-34. [PMID: 34893881 PMCID: PMC8754652 DOI: 10.1093/nar/gkab1199] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 01/16/2023] Open
Abstract
Tricyclo-DNA (tcDNA) is a conformationally constrained oligonucleotide analog that has demonstrated great therapeutic potential as antisense oligonucleotide (ASO) for several diseases. Like most ASOs in clinical development, tcDNA were modified with phosphorothioate (PS) backbone for therapeutic purposes in order to improve their biodistribution by enhancing association with plasma and cell protein. Despite the advantageous protein binding properties, systemic delivery of PS-ASO remains limited and PS modifications can result in dose limiting toxicities in the clinic. Improving extra-hepatic delivery of ASO is highly desirable for the treatment of a variety of diseases including neuromuscular disorders such as Duchenne muscular dystrophy. We hypothesized that conjugation of palmitic acid to tcDNA could facilitate the delivery of the ASO from the bloodstream to the interstitium of the muscle tissues. We demonstrate here that palmitic acid conjugation enhances the potency of tcDNA-ASO in skeletal and cardiac muscles, leading to functional improvement in dystrophic mice with significantly reduced dose of administered ASO. Interestingly, palmitic acid-conjugated tcDNA with a full phosphodiester backbone proved effective with a particularly encouraging safety profile, offering new perspectives for the clinical development of PS-free tcDNA-ASO for neuromuscular diseases.
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Affiliation(s)
- Karima Relizani
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,SQY Therapeutics, UVSQ, 78180 Montigny le Bretonneux, France
| | - Lucía Echevarría
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,SQY Therapeutics, UVSQ, 78180 Montigny le Bretonneux, France
| | - Faouzi Zarrouki
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,Université Paris-Saclay, CNRS, Institut des Neurosciences Paris Saclay, 91190, Gif-sur-Yvette, France
| | | | - Chloe Dambrune
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | - Philippine Aupy
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | | | | | - Thomas Tensorer
- SQY Therapeutics, UVSQ, 78180 Montigny le Bretonneux, France.,SYNTHENA AG, Bern, Switzerland
| | | | | | - Cyrille Vaillend
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris Saclay, 91190, Gif-sur-Yvette, France
| | - Luis Garcia
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,LIA BAHN, centre scientifique de Monaco, 98000, Monaco
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France.,LIA BAHN, centre scientifique de Monaco, 98000, Monaco
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12
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Raguraman P, Balachandran AA, Chen S, Diermeier SD, Veedu RN. Antisense Oligonucleotide-Mediated Splice Switching: Potential Therapeutic Approach for Cancer Mitigation. Cancers (Basel) 2021; 13:5555. [PMID: 34771719 PMCID: PMC8583451 DOI: 10.3390/cancers13215555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
Splicing is an essential process wherein precursor messenger RNA (pre-mRNA) is reshaped into mature mRNA. In alternative splicing, exons of any pre-mRNA get rearranged to form mRNA variants and subsequently protein isoforms, which are distinct both by structure and function. On the other hand, aberrant splicing is the cause of many disorders, including cancer. In the past few decades, developments in the understanding of the underlying biological basis for cancer progression and therapeutic resistance have identified many oncogenes as well as carcinogenic splice variants of essential genes. These transcripts are involved in various cellular processes, such as apoptosis, cell signaling and proliferation. Strategies to inhibit these carcinogenic isoforms at the mRNA level are promising. Antisense oligonucleotides (AOs) have been developed to inhibit the production of alternatively spliced carcinogenic isoforms through splice modulation or mRNA degradation. AOs can also be used to induce splice switching, where the expression of an oncogenic protein can be inhibited by the induction of a premature stop codon. In general, AOs are modified chemically to increase their stability and binding affinity. One of the major concerns with AOs is efficient delivery. Strategies for the delivery of AOs are constantly being evolved to facilitate the entry of AOs into cells. In this review, the different chemical modifications employed and delivery strategies applied are discussed. In addition to that various AOs in clinical trials and their efficacy are discussed herein with a focus on six distinct studies that use AO-mediated exon skipping as a therapeutic strategy to combat cancer.
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Affiliation(s)
- Prithi Raguraman
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (P.R.); (A.A.B.); (S.C.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Akilandeswari Ashwini Balachandran
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (P.R.); (A.A.B.); (S.C.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (P.R.); (A.A.B.); (S.C.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Sarah D. Diermeier
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand;
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia; (P.R.); (A.A.B.); (S.C.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
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13
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Ottesen EW, Luo D, Singh NN, Singh RN. High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome. Int J Mol Sci 2021; 22:ijms22168378. [PMID: 34445083 PMCID: PMC8395096 DOI: 10.3390/ijms22168378] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/14/2021] [Accepted: 07/31/2021] [Indexed: 12/17/2022] Open
Abstract
Intronic splicing silencer N1 (ISS-N1) located within Survival Motor Neuron 2 (SMN2) intron 7 is the target of a therapeutic antisense oligonucleotide (ASO), nusinersen (Spinraza), which is currently being used for the treatment of spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. The discovery of ISS-N1 as a promising therapeutic target was enabled in part by Anti-N1, a 20-mer ASO that restored SMN2 exon 7 inclusion by annealing to ISS-N1. Here, we analyzed the transcriptome of SMA patient cells treated with 100 nM of Anti-N1 for 30 h. Such concentrations are routinely used to demonstrate the efficacy of an ASO. While 100 nM of Anti-N1 substantially stimulated SMN2 exon 7 inclusion, it also caused massive perturbations in the transcriptome and triggered widespread aberrant splicing, affecting expression of essential genes associated with multiple cellular processes such as transcription, splicing, translation, cell signaling, cell cycle, macromolecular trafficking, cytoskeletal dynamics, and innate immunity. We validated our findings with quantitative and semiquantitative PCR of 39 candidate genes associated with diverse pathways. We also showed a substantial reduction in off-target effects with shorter ISS-N1-targeting ASOs. Our findings are significant for implementing better ASO design and dosing regimens of ASO-based drugs.
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14
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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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15
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Saoudi A, Goyenvalle A. [RNA splicing modulation: Therapeutic progress and perspectives]. Med Sci (Paris) 2021; 37:625-631. [PMID: 34180822 DOI: 10.1051/medsci/2021091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Advances in genetic and genomic research continue to increase our knowledge of hereditary diseases, and an increasing number of them are being attributed to aberrant splicing, thus representing ideal targets for RNA modulation therapies. New strategies to skip or re-include exons during the splicing process have emerged and are now widely evaluated in the clinic. Several drugs have recently been approved in particular for the treatment of Duchenne muscular dystrophy and spinal muscular atrophy. Among these molecules, antisense oligonucleotides, or ASOs, have gained increasing interest and have constantly been improved over the years through chemical modifications and design. However, their limited biodistribution following systemic administration still represents a major hurdle and the development of more potent alternative chemistries or new delivery systems has become a very active line of research in the past few years. In parallel, the use of small molecules with excellent biodistribution properties or of viral vectors to convey antisense sequences is also being investigated. In this review, we summarize the recent advances in splicing therapies through two examples of neuromuscular diseases and we discuss their main benefits and current limitations.
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Affiliation(s)
- Amel Saoudi
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Handicap neuromusculaire - physiopathologie, biothérapie et pharmacologie appliquées, 78000 Versailles, France - Université Paris-Saclay, CNRS, Institut des neurosciences Paris Saclay, 91190 Gif-sur-Yvette, France
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Handicap neuromusculaire - physiopathologie, biothérapie et pharmacologie appliquées, 78000 Versailles, France - Laboratoire international associé Biothérapies appliquées aux handicaps neuromusculaires (LIA BAHN), Centre scientifique de Monaco, Monaco
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16
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Singh RN, Seo J, Singh NN. RNA in spinal muscular atrophy: therapeutic implications of targeting. Expert Opin Ther Targets 2020; 24:731-743. [PMID: 32538213 DOI: 10.1080/14728222.2020.1783241] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Spinal muscular atrophy (SMA) is caused by low levels of the Survival Motor Neuron (SMN) protein due to deletions of or mutations in the SMN1 gene. Humans carry another nearly identical gene, SMN2, which mostly produces a truncated and less stable protein SMNΔ7 due to predominant skipping of exon 7. Elevation of SMN upon correction of SMN2 exon 7 splicing and gene therapy have been proven to be the effective treatment strategies for SMA. AREAS COVERED This review summarizes existing and potential SMA therapies that are based on RNA targeting.We also discuss the mechanistic basis of RNA-targeting molecules. EXPERT OPINION The discovery of intronic splicing silencer N1 (ISS-N1) was the first major step towards developing the currently approved antisense-oligonucleotide (ASO)-directed therapy (SpinrazaTM) based on the correction of exon 7 splicing of the endogenous SMN2pre-mRNA. Recently, gene therapy (Zolgensma) has become the second approved treatment for SMA. Small compounds (currently in clinical trials) capable of restoring SMN2 exon 7 inclusion further expand the class of the RNA targeting molecules for SMA therapy. Endogenous RNA targets, such as long non-coding RNAs, circular RNAs, microRNAs and ribonucleoproteins, could be potentially exploited for developing additional SMA therapies.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University , Ames, IA, USA
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University , Ames, IA, USA
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University , Ames, IA, USA
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17
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Sheng L, Rigo F, Bennett CF, Krainer AR, Hua Y. Comparison of the efficacy of MOE and PMO modifications of systemic antisense oligonucleotides in a severe SMA mouse model. Nucleic Acids Res 2020; 48:2853-2865. [PMID: 32103257 PMCID: PMC7102994 DOI: 10.1093/nar/gkaa126] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a motor neuron disease. Nusinersen, a splice-switching antisense oligonucleotide (ASO), was the first approved drug to treat SMA. Based on prior preclinical studies, both 2′-O-methoxyethyl (MOE) with a phosphorothioate backbone and morpholino with a phosphorodiamidate backbone—with the same or extended target sequence as nusinersen—displayed efficient rescue of SMA mouse models. Here, we compared the therapeutic efficacy of these two modification chemistries in rescue of a severe mouse model using ASO10-29—a 2-nt longer version of nusinersen—via subcutaneous injection. Although both chemistries efficiently corrected SMN2 splicing in various tissues, restored motor function and improved the integrity of neuromuscular junctions, MOE-modified ASO10-29 (MOE10-29) was more efficacious than morpholino-modified ASO10-29 (PMO10-29) at the same molar dose, as seen by longer survival, greater body-weight gain and better preservation of motor neurons. Time-course analysis revealed that MOE10-29 had more persistent effects than PMO10-29. On the other hand, PMO10-29 appears to more readily cross an immature blood-brain barrier following systemic administration, showing more robust initial effects on SMN2 exon 7 inclusion, but less persistence in the central nervous system. We conclude that both modifications can be effective as splice-switching ASOs in the context of SMA and potentially other diseases, and discuss the advantages and disadvantages of each.
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Affiliation(s)
- Lei Sheng
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.,Department of Orthopedics, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.,Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, New York, NY 11724, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | | | - Adrian R Krainer
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, New York, NY 11724, USA
| | - Yimin Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.,Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, New York, NY 11724, USA.,Institute of Neuroscience, Soochow University, 199 Ren-Ai Road, Suzhou, Jiangsu 215123, China
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18
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Lundin KE, Gissberg O, Smith CIE, Zain R. Chemical Development of Therapeutic Oligonucleotides. Methods Mol Biol 2020; 2036:3-16. [PMID: 31410788 DOI: 10.1007/978-1-4939-9670-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of several different chemical modifications of nucleic acids, with improved base-pairing affinity and specificity as well as increased resistance against nucleases, has been described. These new chemistries have allowed the synthesis of different types of therapeutic oligonucleotides. Here we discuss selected chemistries used in antisense oligonucleotide (ASO) applications (e.g., small interfering RNA (siRNA), RNase H activation, translational block, splice-switching, and also as aptamers). Recently approved oligonucleotide-based drugs are also presented briefly.
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Affiliation(s)
- Karin E Lundin
- Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska Institutet, Stockholm, Sweden.
| | - Olof Gissberg
- Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska Institutet, Stockholm, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Center for Advanced Therapies, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Center for Rare Diseases, Karolinska University Hospital, Stockholm, Sweden
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19
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Aupy P, Echevarría L, Relizani K, Zarrouki F, Haeberli A, Komisarski M, Tensorer T, Jouvion G, Svinartchouk F, Garcia L, Goyenvalle A. Identifying and Avoiding tcDNA-ASO Sequence-Specific Toxicity for the Development of DMD Exon 51 Skipping Therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 19:371-383. [PMID: 31881528 PMCID: PMC7063478 DOI: 10.1016/j.omtn.2019.11.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/27/2022]
Abstract
Tricyclo-DNA (tcDNA) antisense oligonucleotides (ASOs) hold promise for therapeutic splice-switching applications and the treatment of Duchenne muscular dystrophy (DMD) in particular. We have previously reported the therapeutic potential of tcDNA-ASO in mouse models of DMD, highlighting their unique pharmaceutical properties and unprecedented uptake in many tissues after systemic delivery, including the heart and central nervous system. Following these encouraging results, we developed phosphorothioate (PS)-modified tcDNA-ASOs targeting the human dystrophin exon 51 (H51). Preliminary evaluation of H51 PS-tcDNA in mice resulted in unexpected acute toxicity following intravenous administration of the selected candidate. In vivo and in vitro assays revealed complement activation, prolonged coagulation times, and platelet activation, correlating with the observed toxicity. In this study, we identify a novel PS-tcDNA sequence-specific toxicity induced by the formation of homodimer-like structures and investigate the therapeutic potential of a detoxified PS-tcDNA targeting exon 51. Modification of the H51-PS-tcDNA sequence, while maintaining target specificity through wobble pairing, abolished the observed toxicity by preventing homodimer formation. The resulting detoxified wobble-tcDNA candidate did not affect coagulation or complement pathways any longer nor activated platelets in vitro and was well tolerated in vivo in mice, confirming the possibility to detoxify specific tcDNA-ASO candidates successfully.
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Affiliation(s)
- Philippine Aupy
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | - Lucía Echevarría
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; SQY Therapeutics, 78180 Montigny le Bretonneux, France
| | - Karima Relizani
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; SQY Therapeutics, 78180 Montigny le Bretonneux, France
| | - Faouzi Zarrouki
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | | | | | | | - Grégory Jouvion
- Sorbonne Université, INSERM, Pathophysiology of Pediatric Genetic Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Armand-Trousseau, UF Génétique Moléculaire, 75012 Paris, France; Institut Pasteur, Experimental Neuropathology Unit, 75015 Paris, France
| | - Fedor Svinartchouk
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; SQY Therapeutics, 78180 Montigny le Bretonneux, France
| | - Luis Garcia
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; LIA BAHN, Centre Scientifique de Monaco, 98000 Monaco
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; LIA BAHN, Centre Scientifique de Monaco, 98000 Monaco.
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20
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Istrate A, Johannsen S, Istrate A, Sigel RKO, Leumann CJ. NMR solution structure of tricyclo-DNA containing duplexes: insight into enhanced thermal stability and nuclease resistance. Nucleic Acids Res 2019; 47:4872-4882. [PMID: 30916334 PMCID: PMC6511864 DOI: 10.1093/nar/gkz197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 01/14/2023] Open
Abstract
Tc-DNA is a conformationally constrained oligonucleotide analogue which shows significant increase in thermal stability when hybridized with RNA, DNA or tc-DNA. Remarkably, recent studies revealed that tc-DNA antisense oligonucleotides (AO) hold great promise for the treatment of Duchenne muscular dystrophy and spinal muscular atrophy. To date, no high-resolution structural data is available for fully modified tc-DNA duplexes and little is known about the origins of their enhanced thermal stability. Here, we report the structures of a fully modified tc-DNA oligonucleotide paired with either complementary RNA, DNA or tc-DNA. All three investigated duplexes maintain a right-handed helical structure with Watson-Crick base pairing and overall geometry intermediate between A- and B-type, but closer to A-type structures. All sugars of the tc-DNA and RNA residues adopt a North conformation whereas the DNA deoxyribose are found in a South-East-North conformation equilibrium. The conformation of the tc-DNA strand in the three determined structures is nearly identical and despite the different nature and local geometry of the complementary strand, the overall structures of the examined duplexes are very similar suggesting that the tc-DNA strand dominates the duplex structure.
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Affiliation(s)
- Andrei Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Silke Johannsen
- Department of Chemistry, Winterthurerstrasse 190, University of Zürich, Zürich CH-8057, Switzerland
| | - Alena Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, Winterthurerstrasse 190, University of Zürich, Zürich CH-8057, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
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21
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Hanly D, Esteller M, Berdasco M. Altered Long Non-coding RNA Expression in Cancer: Potential Biomarkers and Therapeutic Targets? ACTA ACUST UNITED AC 2019. [DOI: 10.1007/7355_2019_83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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Imbert M, Blandel F, Leumann C, Garcia L, Goyenvalle A. Lowering Mutant Huntingtin Using Tricyclo-DNA Antisense Oligonucleotides As a Therapeutic Approach for Huntington's Disease. Nucleic Acid Ther 2019; 29:256-265. [PMID: 31184975 DOI: 10.1089/nat.2018.0775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Huntington's disease is a neurodegenerative disorder caused by a CAG repeat expansion in the first exon of huntingtin gene (HTT) encoding for a toxic polyglutamine protein. This disease is characterized by motor, psychiatric, and cognitive impairments. Currently, there is no disease modifying treatment. However, reducing the expression of the huntingtin protein (HTT) using antisense oligonucleotides (ASOs) has been shown as a promising therapeutic strategy. In this study, we explore the therapeutic potential of ASO made of tricyclo-DNA (tcDNA), a conformationally constrained DNA analog, to silence HTT. We used a gapmer ASO, containing central DNA nucleotides flanked by tcDNA modifications on 5' and 3' ends, allowing the recruitment of RNAse H and subsequent degradation of the messenger RNA. After transfection of tcDNA-ASO in patient-derived fibroblast cell lines, we show a strong decrease of HTT mRNA and protein levels. As a control, 2'O-methyl-RNA targeting the same region of HTT was also tested and did not induce a significant effect. tcDNA-ASO were also evaluated in vivo in the YAC128 mice, containing the full-length human HTT gene with 128 CAG repeat expansion. Single intracerebroventricular (ICV) injections of tcDNA induce a significant decrease of HTT messenger and protein levels in the cortex, hippocampus, striatum, and cerebellum of treated mice. tcDNA-ASO were found well distributed in the central nervous system (CNS) and show long lasting effect with protein levels still low, 12 weeks after a single ICV injection. This proof of concept study suggests the therapeutic potential of gapmer tcDNA ASO to downregulate huntingtin in vitro and in vivo.
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Affiliation(s)
- Marine Imbert
- U1179 INSERM, UFR des Sciences de la Santé-LIA BAHN CSM, Université de Versailles St-Quentin, Montigny le Bretonneux, France
| | - Florence Blandel
- U1179 INSERM, UFR des Sciences de la Santé-LIA BAHN CSM, Université de Versailles St-Quentin, Montigny le Bretonneux, France
| | - Christian Leumann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Luis Garcia
- U1179 INSERM, UFR des Sciences de la Santé-LIA BAHN CSM, Université de Versailles St-Quentin, Montigny le Bretonneux, France
| | - Aurelie Goyenvalle
- U1179 INSERM, UFR des Sciences de la Santé-LIA BAHN CSM, Université de Versailles St-Quentin, Montigny le Bretonneux, France
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23
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Abstract
The application of antisense oligonucleotides (AONs) to modify pre-messenger RNA splicing has great potential for treating genetic diseases. The strategies used to redirect splicing for therapeutic purpose involve the use of AONs complementary to splice motifs, enhancer or silencer sequences. AONs to block intronic splicing silencer motifs can efficiently augment exon 7 inclusion in survival motor neuron 2 (SMN2) gene and have demonstrated robust therapeutic effects in both preclinical studies and clinical trials in spinal muscular atrophy (SMA), which has led to a recently approved drug. AONs with phosphorodiamidate morpholino oligomer (PMO) backbone have shown target engagement with restoration of the defective protein in Duchenne muscular dystrophy (DMD) and their safety profile lead to a recent conditional approval for one DMD PMO drug. PMO AONs are also effective in correcting SMN2 exon 7 splicing and rescuing SMA transgenic mice. Here we provide the details of methods that our lab has used to evaluate PMO-mediated SMN2 exon 7 inclusion in the in vivo studies conducted in SMA transgenic mice. The methods comprise mouse experiment procedures, assessment of PMOs on exon 7 inclusion at RNA levels by reverse transcription (RT-) PCR and quantitative real-time PCR. In addition, we present methodology for protein quantification using western blot in mouse tissues, on neuropathology assessment of skeletal muscle (muscle pathology and neuromuscular junction staining) as well as behaviour test in the SMA mice (righting reflex).
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Affiliation(s)
- Haiyan Zhou
- The Dubowitz Neuromuscular Centre, Molecular Neurosciences Session, Developmental Neurosciences Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, Molecular Neurosciences Session, Developmental Neurosciences Programme, Great Ormond Street Institute of Child Health, University College London, London, UK.
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24
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Singh NN, Luo D, Singh RN. Pre-mRNA Splicing Modulation by Antisense Oligonucleotides. Methods Mol Biol 2019; 1828:415-437. [PMID: 30171557 DOI: 10.1007/978-1-4939-8651-4_26] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pre-mRNA splicing, a dynamic process of intron removal and exon joining, is governed by a combinatorial control exerted by overlapping cis-elements that are unique to each exon and its flanking intronic sequences. Splicing cis-elements are usually 4-to-8-nucleotide-long linear motifs that provide binding sites for specific proteins. Pre-mRNA splicing is also influenced by secondary and higher order RNA structures that affect accessibility of splicing cis-elements. Antisense oligonucleotides (ASOs) that block splicing cis-elements and/or affect RNA structure have been shown to modulate splicing in vivo. Therefore, ASO-based strategies have emerged as a powerful tool for therapeutic manipulation of splicing in pathological conditions. Here we describe an ASO-based approach to increase the production of the full-length SMN2 mRNA in spinal muscular atrophy patient cells.
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Affiliation(s)
- Natalia N Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
| | - Diou Luo
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Ravindra N Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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25
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Abstract
Antisense oligonucleotides (AONs) have been actively developed for more than 30 years as a form of molecular medicine and represent promising therapeutic tools for many disorders. Significant progress has been made toward their clinical development in particular for splice switching AONs for the treatment of neuromuscular disorders such as Duchenne muscular dystrophy (DMD). Many different chemistries of AONs can be used for splice switching modulation, and some of them have now reached regulatory approval. However, despite advances in AON chemistry and design, systemic use of AONs is limited due to poor tissue uptake and sufficient therapeutic efficacy is difficult to achieve. Therefore, there is still a critical need to develop efficient AONs able to target all relevant tissues and international efforts are currently on going to advance new compounds or alternative chemistries with higher therapeutic potential. Here we describe the methods to evaluate the potency of tricyclo-DNA (tcDNA)-AONs, a novel class of AONs which displays unique pharmacological properties and unprecedented uptake in many tissues after systemic administration (Goyenvalle et al., Nat Med 21:270-275, 2015; Goyenvalle et al., J Neuromuscul Dis 3:157-167, 2016; Relizani et al., Mol Ther Nucleic Acids 8:144-157, 2017; Robin et al., Mol Ther Nucleic Acids 7:81-89, 2017). We will focus on the preclinical evaluation of these tcDNA for DMD, specifically targeting the exon 51 of the human dystrophin gene. We will first detail methods to analyze their efficacy both in vitro in human myoblasts and in vivo in the hDMD and mdx52 mouse models and then describe means to evaluate their potential renal toxicity.
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26
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Wang F, Cheng Y, Zhang C, Chang G, Geng X. A novel antisense oligonucleotide anchored on the intronic splicing enhancer of hTERT pre-mRNA inhibits telomerase activity and induces apoptosis in glioma cells. J Neurooncol 2019; 143:57-68. [PMID: 30887243 DOI: 10.1007/s11060-019-03150-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/11/2019] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Alternative splicing of hTERT pre-mRNA is an important step in the regulation of telomerase activity, but the regulation mechanisms and functions remain unclear. METHODS RT-PCR analysis was used to detect hTERT splicing in glioma cell lines and brain tissues. TRAP assay was used to detect the telomerase activity. Then, we designed and synthesized 2'-O-methyl-RNA phosphorothioate AONs and transfected them into glioma cells to detect the changes in telomerase activity. MTT assay, plate colony formation assay, western blotting and Annexin V/PI assay were used to detect cell proliferation and apoptosis. At last, bioinformatics analyses were used to predict the expression and function of splicing protein SRSF2 in gliomas. RESULTS hTERT splicing occurs both in glioma cell lines and glioma patients' tissues. The telomerase activity was related to the expression level of the full-length hTERT, rather than the total hTERT transcript level. AON-Ex726 was complementary to the sequence of the intronic splicing enhancer (ISE) in intron six, and significantly altered the splicing pattern of hTERT pre-mRNA, reducing the expression level of the full-length hTERT mRNA and increasing the expression level of the -β hTERT mRNA. After transfection with AON-Ex726, the level of apoptosis was increased, while telomerase activity and cell proliferation were significantly decreased. By bioinformatic predictions, we found the AON-Ex726 anchoring sequence in ISE overlaps the binding site of SRSF2 protein, which is up-regulated during the development of gliomas. CONCLUSIONS Our findings provided new targets and important clues for the gene therapy of gliomas by regulating the alternative splicing pattern of hTERT pre-mRNA.
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Affiliation(s)
- Fei Wang
- Department of Neurology, General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Yajing Cheng
- Department of Neurology, General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Chi Zhang
- Department of Neurology, General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Guangming Chang
- Department of Clinical Laboratory, General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Xin Geng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, 22nd Qixiangtai Road, Tianjin, 300070, China.
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Exon Skipping in a Dysf-Missense Mutant Mouse Model. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:198-207. [PMID: 30292141 PMCID: PMC6172476 DOI: 10.1016/j.omtn.2018.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/16/2018] [Accepted: 08/16/2018] [Indexed: 01/14/2023]
Abstract
Limb girdle muscular dystrophy 2B (LGMD2B) is without treatment and caused by mutations in the dysferlin gene (DYSF). One-third is missense mutations leading to dysferlin aggregation and amyloid formation, in addition to defects in sarcolemmal repair and progressive muscle wasting. Dysferlin-null mouse models do not allow study of the consequences of missense mutations. We generated a new mouse model (MMex38) carrying a missense mutation in exon 38 in analogy to a clinically relevant human DYSF variant (DYSF p.Leu1341Pro). The targeted mutation induces all characteristics of missense mutant dysferlinopathy, including a progressive dystrophic pattern, amyloid formation, and defects in membrane repair. We chose U7 small nuclear RNA (snRNA)-based splice switching to demonstrate a possible exon-skipping strategy in this new animal model. We show that Dysf exons 37 and 38 can successfully be skipped in vivo. Overall, the MMex38 mouse model provides an ideal tool for preclinical development of treatment strategies for dysferlinopathy.
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28
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Aupy P, Echevarría L, Relizani K, Goyenvalle A. The Use of Tricyclo-DNA Oligomers for the Treatment of Genetic Disorders. Biomedicines 2017; 6:E2. [PMID: 29271929 PMCID: PMC5874659 DOI: 10.3390/biomedicines6010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 01/16/2023] Open
Abstract
Antisense Oligonucleotides (ASOs) represent very attractive therapeutic compounds for the treatment of numerous diseases. The antisense field has remarkably progressed over the last few years with the approval of the first antisense drugs and with promising developments of more potent and nuclease resistant chemistries. Despite these recent clinical successes and advances in chemistry and design, effective delivery of ASOs to their target tissues remains a major issue. This review will describe the latest advances obtained with the tricyclo-DNA (tcDNA) chemistry which displays unique pharmacological properties and unprecedented uptake in many tissues after systemic administration. We will examine the variety of therapeutic approaches using both fully modified tcDNA-ASOs and gapmers, including splice switching applications, correction of aberrant splicing, steric blocking strategies and targeted gene knock-down mediated by RNase H recruitment. We will then discuss the merits and potential liabilities of the tcDNA chemistry in the context of ASO drug development.
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Affiliation(s)
- Philippine Aupy
- INSERM U1179, UFR des Sciences de la Santé, University of Versailles St-Quentin, 78180 Montigny le Bretonneux, France.
| | - Lucía Echevarría
- INSERM U1179, UFR des Sciences de la Santé, University of Versailles St-Quentin, 78180 Montigny le Bretonneux, France.
- SQY Therapeutics, University of Versailles St-Quentin, 78180 Montigny le Bretonneux, France.
| | - Karima Relizani
- INSERM U1179, UFR des Sciences de la Santé, University of Versailles St-Quentin, 78180 Montigny le Bretonneux, France.
- SQY Therapeutics, University of Versailles St-Quentin, 78180 Montigny le Bretonneux, France.
| | - Aurélie Goyenvalle
- INSERM U1179, UFR des Sciences de la Santé, University of Versailles St-Quentin, 78180 Montigny le Bretonneux, France.
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