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Nie D, Tang X, Deng H, Yang X, Tao J, Xu F, Liu Y, Wu K, Wang K, Mei Z, Huang A, Tang N. Metabolic Enzyme SLC27A5 Regulates PIP4K2A pre-mRNA Splicing as a Noncanonical Mechanism to Suppress Hepatocellular Carcinoma Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305374. [PMID: 38059827 PMCID: PMC10837360 DOI: 10.1002/advs.202305374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/24/2023] [Indexed: 12/08/2023]
Abstract
Solute carrier family 27 member 5, a key enzyme in fatty acid transport and bile acid metabolism in the liver, is frequently expressed in low quantities in patients with hepatocellular carcinoma, resulting in poor prognosis. However, it is unclear whether SLC27A5 plays non-canonical functions and regulates HCC progression. Here, an unexpected non-canonical role of SLC27A5 is reported: regulating the alternative splicing of mRNA to inhibit the metastasis of HCC independently of its metabolic enzyme activity. Mechanistically, SLC27A5 interacts with IGF2BP3 to prevent its translocation into the nucleus, thereby inhibiting its binding to target mRNA and modulating PIP4K2A pre-mRNA splicing. Loss of SLC27A5 results in elevated levels of the PIP4K2A-S isoform, thus positively regulating phosphoinositide 3-kinase signaling via enhanced p85 stability in HCC. SLC27A5 restoration by AAV-Slc27a5 or IGF2BP3 RNA decoy oligonucleotides exerts an inhibitory effect on HCC metastasis with reduced expression of the PIP4K2A-S isoform. Therefore, PIP4K2A-S may be a novel target for treating HCC with SLC27A5 deficiency.
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Affiliation(s)
- Dan Nie
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- Department of GastroenterologyThe Chongqing Hospital of Traditional Chinese MedicineChongqing Academy of Traditional Chinese MedicineChongqing400016China
| | - Xin Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Haijun Deng
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Xiaojun Yang
- Department of GastroenterologyThe Chongqing Hospital of Traditional Chinese MedicineChongqing Academy of Traditional Chinese MedicineChongqing400016China
| | - Junji Tao
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Fengli Xu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Yi Liu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Kang Wu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Kai Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Zhechuan Mei
- Department of GastroenterologyThe Second Affiliated HospitalChongqing Medical UniversityChongqing400016China
| | - Ailong Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Ni Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
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2
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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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3
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Li Y, Chen B, Jiang X, Li Y, Wang X, Huang S, Wu X, Xiao Y, Shi D, Huang X, He L, Chen X, Ouyang Y, Li J, Song L, Lin C. A Wnt-induced lncRNA-DGCR5 splicing switch drives tumor-promoting inflammation in esophageal squamous cell carcinoma. Cell Rep 2023; 42:112542. [PMID: 37210725 DOI: 10.1016/j.celrep.2023.112542] [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: 11/19/2022] [Revised: 04/04/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023] Open
Abstract
Alternative splicing (AS) is a critical mechanism for the aberrant biogenesis of long non-coding RNA (lncRNA). Although the role of Wnt signaling in AS has been implicated, it remains unclear how it mediates lncRNA splicing during cancer progression. Herein, we identify that Wnt3a induces a splicing switch of lncRNA-DGCR5 to generate a short variant (DGCR5-S) that correlates with poor prognosis in esophageal squamous cell carcinoma (ESCC). Upon Wnt3a stimulation, active nuclear β-catenin acts as a co-factor of FUS to facilitate the spliceosome assembly and the generation of DGCR5-S. DGCR5-S inhibits TTP's anti-inflammatory activity by protecting it from PP2A-mediated dephosphorylation, thus fostering tumor-promoting inflammation. Importantly, synthetic splice-switching oligonucleotides (SSOs) disrupt the splicing switch of DGCR5 and potently suppress ESCC tumor growth. These findings uncover the mechanism for Wnt signaling in lncRNA splicing and suggest that the DGCR5 splicing switch may be a targetable vulnerability in ESCC.
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Affiliation(s)
- Yue Li
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Boyu Chen
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xingyu Jiang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yudong Li
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xin Wang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shumei Huang
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xuxia Wu
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yunyun Xiao
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Dongni Shi
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xinjian Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Lixin He
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiangfu Chen
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ying Ouyang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jun Li
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
| | - Libing Song
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Institute of Oncology, Tumor Hospital, Guangzhou Medical University, Guangzhou 511436, China.
| | - Chuyong Lin
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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4
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Johnson KC, Corey DR. RNAi in cell nuclei: potential for a new layer of biological regulation and a new strategy for therapeutic discovery. RNA (NEW YORK, N.Y.) 2023; 29:415-422. [PMID: 36657971 PMCID: PMC10019369 DOI: 10.1261/rna.079500.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
RNA interference is almost always associated with post-transcriptional silencing in the cytoplasm. MicroRNAs (miRNAs) and critical RNAi protein factors like argonaute (AGO) and trinucleotide repeat binding containing 6 protein (TNRC6), however, are also found in cell nuclei, suggesting that nuclear miRNAs may be targets for gene regulation. Designed small duplex RNAs (dsRNAs) can modulate nuclear processes such as transcription and splicing, suggesting that they can also provide leads for therapeutic discovery. The goal of this Perspective is to provide the background on nuclear RNAi necessary to guide discussions on whether nuclear RNAi can play a role in therapeutic development programs.
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Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
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5
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Disturbances of Ocular Circulation in Color Doppler Imaging, Retinal Changes and Electrophysiological Tests with Neuro-Ophthalmological Clinical Symptoms in the Course of CADASIL Syndrome-A Case Report. J Clin Med 2023; 12:jcm12051964. [PMID: 36902751 PMCID: PMC10004637 DOI: 10.3390/jcm12051964] [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: 01/25/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The authors present a new paper examining the disturbances in ocular circulation and electrophysiological changes in the presence of neuro-ophthalmic manifestations in a patient with cerebral autosomal dominant arteriopathy with subcortical infracts and leucoencephalopathy (CADASIL). Symptoms reported by the patient included: transient vision loss (TVL), migraines, diplopia, bilateral peripheral visual field loss and convergence insufficiency. CADASIL was confirmed by the presence of NOTCH3 gene mutation (p.Cys212Gly), the presence of granular osmiophilic material (GOM) in cutaneous vessels in an immunohistochemistry test (IHC) and bilateral focal vasogenic lesions in the white matter of the cerebral hemisphere, with micro-focal infarct in the left external capsule on a magnetic resonance imaging test (MRI). Color Doppler imaging (CDI) confirmed decreased blood flow and increased vascular resistance in the retinal and posterior ciliary arteries, with reduced P50 wave amplitude on a pattern electroretinogram (PERG). An eye fundus examination and fluorescein angiography (FA) revealed the constriction of retinal vessels and a peripheral retinal pigment epithelium (RPE) atrophy with focal drusen. The authors suggest that the cause of TVL may be changes in the hemodynamics of the retinochoroid vessels associated with the narrowing of small vessels and the presence of druses in the retina-which is supported by a decrease in the amplitude of the P50 wave in PERG, changes in OCT correlating simultaneously with changes in MRI imaging and other neurological symptoms.
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6
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Therapeutic strategies for autism: targeting three levels of the central dogma of molecular biology. Transl Psychiatry 2023; 13:58. [PMID: 36792602 PMCID: PMC9931756 DOI: 10.1038/s41398-023-02356-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
The past decade has yielded much success in the identification of risk genes for Autism Spectrum Disorder (ASD), with many studies implicating loss-of-function (LoF) mutations within these genes. Despite this, no significant clinical advances have been made so far in the development of therapeutics for ASD. Given the role of LoF mutations in ASD etiology, many of the therapeutics in development are designed to rescue the haploinsufficient effect of genes at the transcriptional, translational, and protein levels. This review will discuss the various therapeutic techniques being developed from each level of the central dogma with examples including: CRISPR activation (CRISPRa) and gene replacement at the DNA level, antisense oligonucleotides (ASOs) at the mRNA level, and small-molecule drugs at the protein level, followed by a review of current delivery methods for these therapeutics. Since central nervous system (CNS) penetrance is of utmost importance for ASD therapeutics, it is especially necessary to evaluate delivery methods that have higher efficiency in crossing the blood-brain barrier (BBB).
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7
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Goyenvalle A, Jimenez-Mallebrera C, van Roon W, Sewing S, Krieg AM, Arechavala-Gomeza V, Andersson P. Considerations in the Preclinical Assessment of the Safety of Antisense Oligonucleotides. Nucleic Acid Ther 2023; 33:1-16. [PMID: 36579950 PMCID: PMC9940817 DOI: 10.1089/nat.2022.0061] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nucleic acid therapeutics field has made tremendous progress in the past decades. Continuous advances in chemistry and design have led to many successful clinical applications, eliciting even more interest from researchers including both academic groups and drug development companies. Many preclinical studies in the field focus on improving the delivery of antisense oligonucleotide drugs (ONDs) and/or assessing their efficacy in target tissues, often neglecting the evaluation of toxicity, at least in early phases of development. A series of consensus recommendations regarding regulatory considerations and expectations have been generated by the Oligonucleotide Safety Working Group and the Japanese Research Working Group for the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use S6 and Related Issues (WGS6) in several white papers. However, safety aspects should also be kept in sight in earlier phases while screening and designing OND to avoid subsequent failure in the development phase. Experts and members of the network "DARTER," a COST Action funded by the Cooperation in Science and Technology of the EU, have utilized their collective experience working with OND, as well as their insights into OND-mediated toxicities, to generate a series of consensus recommendations to assess OND toxicity in early stages of preclinical research. In the past few years, several publications have described predictive assays, which can be used to assess OND-mediated toxicity in vitro or ex vivo to filter out potential toxic candidates before moving to in vivo phases of preclinical development, that is, animal toxicity studies. These assays also have the potential to provide translational insight since they allow a safety evaluation in human in vitro systems. Yet, small preliminary in vivo studies should also be considered to complement this early assessment. In this study, we summarize the state of the art and provide guidelines and recommendations on the different tests available for these early stage preclinical assessments.
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Affiliation(s)
- Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Versailles, France.,Address correspondence to: Aurélie Goyenvalle, PhD, Université Paris-Saclay, UVSQ, Inserm, END-ICAP, Versailles 78000, France
| | - Cecilia Jimenez-Mallebrera
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Genética, Microbiología y Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Willeke van Roon
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sabine Sewing
- Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Arthur M. Krieg
- RNA Therapeutics Institute, University of Massachusetts, Worcester, Massachusetts, USA
| | - Virginia Arechavala-Gomeza
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Patrik Andersson
- Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden.,Address correspondence to: Patrik Andersson, PhD, Safety Innovation, Safety Sciences, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Pepparedsleden 1, Mölndal, Gothenburg 431 83, Sweden
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8
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Filonova G, Aartsma-Rus A. Next steps for the optimization of exon therapy for Duchenne muscular dystrophy. Expert Opin Biol Ther 2023; 23:133-143. [PMID: 36655939 DOI: 10.1080/14712598.2023.2169070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION It is established that the exon-skipping approach can restore dystrophin in Duchenne muscular dystrophy (DMD) patients. However, dystrophin restoration levels are low, and the field is evolving to provide solutions for improved exon skipping. DMD is a neuromuscular disorder associated with chronic muscle tissue loss attributed to the lack of dystrophin, which causes muscle inflammation, fibrosis formation, and impaired regeneration. Currently, four antisense oligonucleotides (AONs) based on phosphorodiamidate morpholino oligomer (PMO) chemistry are approved by US Food and Drug Administration for exon skipping therapy of eligible DMD patients. AREAS COVERED This review describes a preclinical and clinical experience with approved and newly developed AONs for DMD, outlines efforts that have been done to enhance AON efficiency, reviews challenges of clinical trials, and summarizes the current state of the exon skipping approach in the DMD field. EXPERT OPINION The exon skipping approach for DMD is under development, and several chemical modifications with improved properties are under (pre)-clinical investigation. Despite existing advantages of these modifications, their safety and effectiveness have to be examined in clinical trials, which are planned or ongoing. Furthermore, we propose clinical settings using natural history controls to facilitate studying the functional effect of the therapy.
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Affiliation(s)
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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9
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Hedgespeth BA, Snider DB, Bitting KJ, Cruse G. The exon-skipping oligonucleotide, KitStop, depletes tissue-resident mast cells in vivo to ameliorate anaphylaxis. Front Immunol 2023; 14:1006741. [PMID: 36798116 PMCID: PMC9927222 DOI: 10.3389/fimmu.2023.1006741] [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: 07/29/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Anaphylaxis represents the most extreme and life-threatening form of allergic disease and is considered a medical emergency requiring immediate intervention. Additionally, some people with mastocytosis experience recurrent episodes of anaphylaxis during normal daily activities without exposure to known triggers. While acute therapy consists primarily of epinephrine and supportive care, chronic therapy relies mostly on desensitization and immunotherapy against the offending allergen, which is a time-consuming and sometimes unsuccessful process. These treatments also necessitate identification of the triggering allergen which is not always possible, and thus highlighting a need for alternative treatments for mast cell-mediated diseases. Methods The exon-skipping oligonucleotide KitStop was administered to mice intradermally, intraperitoneally, or systemically at a dose of 12.5 mg/kg. Local mast cell numbers were enumerated via peritoneal lavage or skin histology, and passive systemic anaphylaxis was induced to evaluate KitStop's global systemic effect. A complete blood count and biochemistry panel were performed to assess the risk of acute toxicity following KitStop administration. Results Here, we report the use of an exon-skipping oligonucleotide, which we have previously termed KitStop, to safely reduce the severity and duration of the anaphylactic response via mast cell depopulation in tissues. KitStop administration results in the integration of a premature stop codon within the mRNA transcript of the KIT receptor-a receptor tyrosine kinase found primarily on mast cells and whose gain-of-function mutation can lead to systemic mastocytosis. Following either local or systemic KitStop treatment, mice had significantly reduced mast cell numbers in the skin and peritoneum. In addition, KitStop-treated mice experienced a significantly diminished anaphylactic response using a model of passive systemic anaphylaxis when compared with control mice. Discussion KitStop treatment results in a significant reduction in systemic mast cell responses, thus offering the potential to serve as a powerful additional treatment modality for patients that suffer from anaphylaxis.
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Affiliation(s)
- Barry A Hedgespeth
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Department of Clinical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States.,Comparative Medicine and Translational Research Training Program, North Carolina State University, Raleigh, NC, United States
| | - Douglas B Snider
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Department of Clinical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States.,Comparative Medicine and Translational Research Training Program, North Carolina State University, Raleigh, NC, United States
| | - Katie J Bitting
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States
| | - Glenn Cruse
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
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10
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Flynn LL, Li R, Pitout IL, Aung-Htut MT, Larcher LM, Cooper JAL, Greer KL, Hubbard A, Griffiths L, Bond CS, Wilton SD, Fox AH, Fletcher S. Single Stranded Fully Modified-Phosphorothioate Oligonucleotides can Induce Structured Nuclear Inclusions, Alter Nuclear Protein Localization and Disturb the Transcriptome In Vitro. Front Genet 2022; 13:791416. [PMID: 35464859 PMCID: PMC9019733 DOI: 10.3389/fgene.2022.791416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/02/2022] [Indexed: 01/12/2023] Open
Abstract
Oligonucleotides and nucleic acid analogues that alter gene expression are now showing therapeutic promise in human disease. Whilst the modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, such modifications may also confer unexpected physicochemical and biological properties. Gapmer mixed-modified and DNA oligonucleotides on a phosphorothioate backbone can bind non-specifically to intracellular proteins to form a variety of toxic inclusions, driven by the phosphorothioate linkages, but also influenced by the oligonucleotide sequence. Recently, the non-antisense or other off-target effects of 2′ O- fully modified phosphorothioate linkage oligonucleotides are becoming better understood. Here, we report chemistry-specific effects of oligonucleotides composed of modified or unmodified bases, with phosphorothioate linkages, on subnuclear organelles and show altered distribution of nuclear proteins, the appearance of highly stable and strikingly structured nuclear inclusions, and disturbed RNA processing in primary human fibroblasts and other cultured cells. Phosphodiester, phosphorodiamidate morpholino oligomers, and annealed complimentary phosphorothioate oligomer duplexes elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of transfected fibroblasts exhibiting such disruption. Our data add to the growing body of evidence of off-target effects of some phosphorothioate nucleic acid drugs in primary cells and suggest alternative approaches to mitigate these effects.
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Affiliation(s)
- Loren L Flynn
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,Black Swan Pharmaceuticals, Wake Forest, NC, United States
| | - Ruohan Li
- Cell and Tissue Therapies WA, Royal Perth Hospital, Perth, WA, Australia.,School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Ianthe L Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,PYC Therapeutics, Nedlands, WA, Australia
| | - May T Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Leon M Larcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Jack A L Cooper
- School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Kane L Greer
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Alysia Hubbard
- Centre for Microscopy, Characterization and Analysis, The University of Western Australia, Nedlands, WA, Australia
| | - Lisa Griffiths
- Anatomical Pathology, Department of Health, Nedlands, WA, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Perron Institute, Nedlands, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA, Australia.,PYC Therapeutics, Nedlands, WA, Australia
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11
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Kauffmann AD, Kennedy SD, Moss WN, Kierzek E, Kierzek R, Turner DH. Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides. RNA (NEW YORK, N.Y.) 2022; 28:508-522. [PMID: 34983822 PMCID: PMC8925974 DOI: 10.1261/rna.078951.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Influenza A kills hundreds of thousands of people globally every year and has the potential to generate more severe pandemics. Influenza A's RNA genome and transcriptome provide many potential therapeutic targets. Here, nuclear magnetic resonance (NMR) experiments suggest that one such target could be a hairpin loop of 8 nucleotides in a pseudoknot that sequesters a 3' splice site in canonical pairs until a conformational change releases it into a dynamic 2 × 2-nt internal loop. NMR experiments reveal that the hairpin loop is dynamic and able to bind oligonucleotides as short as pentamers. A 3D NMR structure of the complex contains 4 and likely 5 bp between pentamer and loop. Moreover, a hairpin sequence was discovered that mimics the equilibrium of the influenza hairpin between its structure in the pseudoknot and upon release of the splice site. Oligonucleotide binding shifts the equilibrium completely to the hairpin secondary structure required for pseudoknot folding. The results suggest this hairpin can be used to screen for compounds that stabilize the pseudoknot and potentially reduce splicing.
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Affiliation(s)
- Andrew D Kauffmann
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Walter N Moss
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
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12
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Ferizovic N, Summers J, de Zárate IBO, Werner C, Jiang J, Landfeldt E, Buesch K. Prognostic indicators of disease progression in Duchenne muscular dystrophy: A literature review and evidence synthesis. PLoS One 2022; 17:e0265879. [PMID: 35333888 PMCID: PMC8956179 DOI: 10.1371/journal.pone.0265879] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/09/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is a rare, severely debilitating, and fatal neuromuscular disease characterized by progressive muscle degeneration. Like in many orphan diseases, randomized controlled trials are uncommon in DMD, resulting in the need to indirectly compare treatment effects, for example by pooling individual patient-level data from multiple sources. However, to derive reliable estimates, it is necessary to ensure that the samples considered are comparable with respect to factors significantly affecting the clinical progression of the disease. To help inform such analyses, the objective of this study was to review and synthesise published evidence of prognostic indicators of disease progression in DMD. We searched MEDLINE (via Ovid), Embase (via Ovid) and the Cochrane Library (via Wiley) for records published from inception up until April 23 2021, reporting evidence of prognostic indicators of disease progression in DMD. Risk of bias was established with the grading system of the Centre for Evidence-Based Medicine (CEBM). RESULTS Our search included 135 studies involving 25,610 patients from 18 countries across six continents (Africa, Asia, Australia, Europe, North America and South America). We identified a total of 23 prognostic indicators of disease progression in DMD, namely age at diagnosis, age at onset of symptoms, ataluren treatment, ATL1102, BMI, cardiac medication, DMD genetic modifiers, DMD mutation type, drisapersen, edasalonexent, eteplirsen, glucocorticoid exposure, height, idebenone, lower limb surgery, orthoses, oxandrolone, spinal surgery, TAS-205, vamorolone, vitlolarsen, ventilation support, and weight. Of these, cardiac medication, DMD genetic modifiers, DMD mutation type, and glucocorticoid exposure were designated core prognostic indicators, each supported by a high level of evidence and significantly affecting a wide range of clinical outcomes. CONCLUSION This study provides a current summary of prognostic indicators of disease progression in DMD, which will help inform the design of comparative analyses and future data collection initiatives in this patient population.
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Affiliation(s)
- Nermina Ferizovic
- MAP BioPharma Ltd, Cambridge, England, United Kingdom
- BresMed Health Solutions, Sheffield, England, United Kingdom
| | | | | | | | - Joel Jiang
- PTC Therapeutics, South Plainfield, New Jersey, United States of America
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13
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Attias Cohen S, Simaan-Yameen H, Fuoco C, Gargioli C, Seliktar D. Injectable hydrogel microspheres for sustained gene delivery of antisense oligonucleotides to restore the expression of dystrophin protein in duchenne muscular dystrophy. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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14
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Narayanaswami P, Živković S. Molecular and Genetic Therapies. Neuromuscul Disord 2022. [DOI: 10.1016/b978-0-323-71317-7.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Szabo SM, Gooch KL, Mickle AT, Salhany RM, Connolly AM. The impact of genotype on outcomes in individuals with Duchenne muscular dystrophy: A systematic review. Muscle Nerve 2021; 65:266-277. [PMID: 34878187 DOI: 10.1002/mus.27463] [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: 11/12/2020] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/07/2022]
Abstract
Duchenne muscular dystrophy (DMD) is associated with progressive muscle weakness, loss of ambulation (LOA), and early mortality. In this review we have synthesized published data on the clinical course of DMD by genotype. Using a systematic search implemented in Medline and Embase, 53 articles were identified that describe the clinical course of DMD, with pathogenic variants categorizable by exon skip or stop-codon readthrough amenability and outcomes presented by age. Outcomes described included those related to ambulatory, cardiac, pulmonary, or cognitive function. Estimates of the mean (95% confidence interval) age at LOA ranged from 9.1 (8.7-9.6) years among 90 patients amenable to skipping exon 53 to 11.5 (9.5-13.5) years among three patients amenable to skipping exon 8. Although function worsened with age, the impact of genotype was less clear for other outcomes (eg, forced vital capacity and left ventricular ejection fraction). Understanding the distribution of pathogenic variants is important for studies in DMD, as this research suggests major differences in the natural history of disease. In addition, specific details of the use of key medications, including corticosteroids, antisense oligonucleotides, and cardiac medications, should be reported.
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Affiliation(s)
- Shelagh M Szabo
- Broadstreet Heath Economics & Outcomes Research, Vancouver, British Columbia, Canada
| | | | - Alexis T Mickle
- Broadstreet Heath Economics & Outcomes Research, Vancouver, British Columbia, Canada
| | | | - Anne M Connolly
- Division of Neurology, Nationwide Children's Hospital, Ohio State University, Columbus, Ohio, USA
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16
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Passi GR, Paharia M, Jaiswal SP. What Percentage of Patients with Duchene Muscular Dystrophy are Potentially Treatable with Gene Therapies? Ann Indian Acad Neurol 2021; 24:993-994. [PMID: 35359553 PMCID: PMC8965968 DOI: 10.4103/aian.aian_727_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 11/04/2022] Open
Affiliation(s)
- Gouri Rao Passi
- Department of Pediatrics, Choithram Hospital & Research Centre, Indore, Madhya Pradesh, India
| | - Manjari Paharia
- Department of Pediatrics, Choithram Hospital & Research Centre, Indore, Madhya Pradesh, India
| | - Shree Prakash Jaiswal
- Department of Pathology & Microbiology, Choithram Hospital & Research Centre, Indore, Madhya Pradesh, India
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17
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Passi GR, Paharia M, Jaiswal SP. What Percentage of Patients with Duchene Muscular Dystrophy are Potentially Treatable with Gene Therapies? Ann Indian Acad Neurol 2021. [PMID: 34728964 PMCID: PMC8513967 DOI: 10.4103/aian.aian_806_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Gouri Rao Passi
- Department of Pediatrics, Choithram Hospital & Research Centre, Indore, Madhya Pradesh, India
| | - Manjari Paharia
- Department of Pediatrics, Choithram Hospital & Research Centre, Indore, Madhya Pradesh, India
| | - Shree Prakash Jaiswal
- Department of Pathology & Microbiology, Choithram Hospital & Research Centre, Indore, Madhya Pradesh, India
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18
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Markati T, De Waele L, Schara-Schmidt U, Servais L. Lessons Learned from Discontinued Clinical Developments in Duchenne Muscular Dystrophy. Front Pharmacol 2021; 12:735912. [PMID: 34790118 PMCID: PMC8591262 DOI: 10.3389/fphar.2021.735912] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/12/2021] [Indexed: 02/04/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked condition caused by a deficiency of functional dystrophin protein. Patients experience progressive muscle weakness, cardiomyopathy and have a decreased life expectancy. Standards of care, including treatment with steroids, and multidisciplinary approaches have extended the life expectancy and improved the quality of life of patients. In the last 30 years, several compounds have been assessed in preclinical and clinical studies for their ability to restore functional dystrophin levels or to modify pathways involved in DMD pathophysiology. However, there is still an unmet need with regards to a disease-modifying treatment for DMD and the attrition rate between early-phase and late-phase clinical development remains high. Currently, there are 40 compounds in clinical development for DMD, including gene therapy and antisense oligonucleotides for exon skipping. Only five of them have received conditional approval in one jurisdiction subject to further proof of efficacy. In this review, we present data of another 16 compounds that failed to complete clinical development, despite positive results in early phases of development in some cases. We examine the reasons for the high attrition rate and we suggest solutions to avoid similar mistakes in the future.
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Affiliation(s)
- Theodora Markati
- MDUK Oxford Neuromuscular Center, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Liesbeth De Waele
- KU Leuven Department of Development and Regeneration, Leuven, Belgium
- Department of Paediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Urlike Schara-Schmidt
- Department of Pediatric Neurology, Center for Neuromuscular Diseases, Center for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Laurent Servais
- MDUK Oxford Neuromuscular Center, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- Division of Child Neurology, Reference Center for Neuromuscular Disease, Centre Hospitalier Régional de Références des Maladies Neuromusculaires, Department of Pediatrics, University Hospital Liège, Liège, Belgium
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19
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Intramuscular Evaluation of Chimeric Locked Nucleic Acid/2' OMethyl-Modified Antisense Oligonucleotides for Targeted Exon 23 Skipping in Mdx Mice. Pharmaceuticals (Basel) 2021; 14:ph14111113. [PMID: 34832896 PMCID: PMC8622172 DOI: 10.3390/ph14111113] [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: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/02/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal disorder characterised by progressive muscle wasting. It is caused by mutations in the dystrophin gene, which disrupt the open reading frame leading to the loss of functional dystrophin protein in muscle fibres. Antisense oligonucleotide (AON)-mediated skipping of the mutated exon, which allows production of a truncated but partially functional dystrophin protein, has been at the forefront of DMD therapeutic research for over two decades. Nonetheless, novel nucleic acid modifications and AON designs are continuously being developed to improve the clinical benefit profile of current drugs in the DMD pipeline. We herein designed a series of 15mer and 20mer AONs, consisting of 2′O-Methyl (2′OMe)- and locked nucleic acid (LNA)-modified nucleotides in different percentage compositions, and assessed their efficiency in inducing exon 23 skipping and dystrophin restoration in locally injected muscles of mdx mice. We demonstrate that LNA/2′OMe AONs with a 30% LNA composition were significantly more potent in inducing exon skipping and dystrophin restoration in treated mdx muscles, compared to a previously tested 2′OMe AON and LNA/2′OMe chimeras with lower or higher LNA compositions. These results underscore the therapeutic potential of LNA/2′OMe AONs, paving the way for further experimentation to evaluate their benefit-toxicity profile following systemic delivery.
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20
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Benny Klimek ME, Vila MC, Edwards K, Boehler J, Novak J, Zhang A, Van der Meulen J, Tatum K, Quinn J, Fiorillo A, Burki U, Straub V, Lu QL, Hathout Y, van Den Anker J, Partridge TA, Morales M, Hoffman E, Nagaraju K. Effects of Chronic, Maximal Phosphorodiamidate Morpholino Oligomer (PMO) Dosing on Muscle Function and Dystrophin Restoration in a Mouse Model of Duchenne Muscular Dystrophy. J Neuromuscul Dis 2021; 8:S369-S381. [PMID: 34569970 DOI: 10.3233/jnd-210701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Phosphorodiamidate morpholino oligomer (PMO)-mediated exon skipping is currently used in clinical development to treat Duchenne muscular dystrophy (DMD), with four exon-skipping drugs achieving regulatory approval. Exon skipping elicits a truncated, but semi-functional dystrophin protein, similar to the truncated dystrophin expressed in patients with Becker Muscular dystrophy (BMD) where the disease phenotype is less severe than DMD. Despite promising results in both dystrophic animal models and DMD boys, restoration of dystrophin by exon skipping is highly variable, leading to contradictory functional outcomes in clinical trials. OBJECTIVE To develop optimal PMO dosing protocols that result in increased dystrophin and improved outcome measures in preclinical models of DMD. METHODS Tested effectiveness of multiple chronic, high dose PMO regimens using biochemical, histological, molecular, and imaging techniques in mdx mice. RESULTS A chronic, monthly regimen of high dose PMO increased dystrophin rescue in mdx mice and improved specific force in the extensor digitorum longus (EDL) muscle. However, monthly high dose PMO administration still results in variable dystrophin expression localized throughout various muscles. CONCLUSIONS High dose monthly PMO administration restores dystrophin expression and increases muscle force; however, the variability of dystrophin expression at both the inter-and intramuscular level remains. Additional strategies to optimize PMO uptake including increased dosing frequencies or combination treatments with other yet-to-be-defined therapies may be necessary to achieve uniform dystrophin restoration and increases in muscle function.
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Affiliation(s)
| | - Maria Candida Vila
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA.,The George Washington University, Institute of Biomedical Sciences, Washington, DC, USA
| | - Katie Edwards
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - Jessica Boehler
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA.,The George Washington University, Institute of Biomedical Sciences, Washington, DC, USA
| | - James Novak
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Aiping Zhang
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Jack Van der Meulen
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Kathleen Tatum
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - James Quinn
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Alyson Fiorillo
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Umar Burki
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases at Newcastle, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Qi Long Lu
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Neuromuscular/ALS Center, Department of Neurology, Carolinas Medical Center, Charlotte, NC, USA
| | - Yetrib Hathout
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA.,The George Washington University, Institute of Biomedical Sciences, Washington, DC, USA.,School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - John van Den Anker
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA.,Center for Translational Science, Children's National Health System, Washington, DC, USA
| | - Terence A Partridge
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA.,The George Washington University, Institute of Biomedical Sciences, Washington, DC, USA
| | - Melissa Morales
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - Eric Hoffman
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA.,The George Washington University, Institute of Biomedical Sciences, Washington, DC, USA.,School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
| | - Kanneboyina Nagaraju
- Center for Genetic Medicine, Children's National Health System, Washington, DC, USA.,The George Washington University, Institute of Biomedical Sciences, Washington, DC, USA.,School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
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21
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Ito K, Takakusa H, Kakuta M, Kanda A, Takagi N, Nagase H, Watanabe N, Asano D, Goda R, Masuda T, Nakamura A, Onishi Y, Onoda T, Koizumi M, Takeshima Y, Matsuo M, Takaishi K. Renadirsen, a Novel 2'OMeRNA/ENA ® Chimera Antisense Oligonucleotide, Induces Robust Exon 45 Skipping for Dystrophin In Vivo. Curr Issues Mol Biol 2021; 43:1267-1281. [PMID: 34698059 PMCID: PMC8928966 DOI: 10.3390/cimb43030090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 01/16/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a progressive muscle-wasting disease caused by out-of-frame or nonsense mutation in the dystrophin gene. It begins with a loss of ambulation between 9 and 14 years of age, followed by various other symptoms including cardiac dysfunction. Exon skipping of patients’ DMD pre-mRNA induced by antisense oligonucleotides (AOs) is expected to produce shorter but partly functional dystrophin proteins, such as those possessed by patients with the less severe Becker muscular dystrophy. We are working on developing modified nucleotides, such as 2′-O,4′-C-ethylene-bridged nucleic acids (ENAs), possessing high nuclease resistance and high affinity for complementary RNA strands. Here, we demonstrate the preclinical characteristics (exon-skipping activity in vivo, stability in blood, pharmacokinetics, and tissue distribution) of renadirsen, a novel AO modified with 2′-O-methyl RNA/ENA chimera phosphorothioate designed for dystrophin exon 45 skipping and currently under clinical trials. Notably, systemic delivery of renadirsen sodium promoted dystrophin exon skipping in cardiac muscle, skeletal muscle, and diaphragm, compared with AOs with the same sequence as renadirsen but conventionally modified by PMO and 2′OMePS. These findings suggest the promise of renadirsen sodium as a therapeutic agent that improves not only skeletal muscle symptoms but also other symptoms in DMD patients, such as cardiac dysfunction.
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Affiliation(s)
- Kentaro Ito
- Specialty Medicine Research Laboratories I, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1408710, Japan; (K.I.); (A.K.); (H.N.)
| | - Hideo Takakusa
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1408710, Japan; (H.T.); (N.W.); (D.A.); (R.G.)
| | - Masayo Kakuta
- Medical Information Department, Daiichi Sankyo Co., Ltd., Chuo, Tokyo 1038426, Japan;
| | - Akira Kanda
- Specialty Medicine Research Laboratories I, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1408710, Japan; (K.I.); (A.K.); (H.N.)
| | - Nana Takagi
- Safety and Risk Management Department, Daiichi Sankyo Co., Ltd., Chuo, Tokyo 1038426, Japan;
| | - Hiroyuki Nagase
- Specialty Medicine Research Laboratories I, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1408710, Japan; (K.I.); (A.K.); (H.N.)
| | - Nobuaki Watanabe
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1408710, Japan; (H.T.); (N.W.); (D.A.); (R.G.)
| | - Daigo Asano
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1408710, Japan; (H.T.); (N.W.); (D.A.); (R.G.)
| | - Ryoya Goda
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1408710, Japan; (H.T.); (N.W.); (D.A.); (R.G.)
| | - Takeshi Masuda
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1409710, Japan; (T.M.); (A.N.); (Y.O.); (M.K.)
| | - Akifumi Nakamura
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1409710, Japan; (T.M.); (A.N.); (Y.O.); (M.K.)
| | - Yoshiyuki Onishi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1409710, Japan; (T.M.); (A.N.); (Y.O.); (M.K.)
| | - Toshio Onoda
- Intellectual Property Department, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1409710, Japan;
| | - Makoto Koizumi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1409710, Japan; (T.M.); (A.N.); (Y.O.); (M.K.)
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638501, Japan;
| | - Masafumi Matsuo
- Research Center for Locomotion Biology, Kobe Gakuin University, Nishi, Kobe 6512180, Japan;
| | - Kiyosumi Takaishi
- Specialty Medicine Research Laboratories I, Daiichi Sankyo Co., Ltd., Shinagawa, Tokyo 1408710, Japan; (K.I.); (A.K.); (H.N.)
- Correspondence:
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22
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Buonaiuto G, Desideri F, Taliani V, Ballarino M. Muscle Regeneration and RNA: New Perspectives for Ancient Molecules. Cells 2021; 10:cells10102512. [PMID: 34685492 PMCID: PMC8533951 DOI: 10.3390/cells10102512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/21/2022] Open
Abstract
The ability of the ribonucleic acid (RNA) to self-replicate, combined with a unique cocktail of chemical properties, suggested the existence of an RNA world at the origin of life. Nowadays, this hypothesis is supported by innovative high-throughput and biochemical approaches, which definitively revealed the essential contribution of RNA-mediated mechanisms to the regulation of fundamental processes of life. With the recent development of SARS-CoV-2 mRNA-based vaccines, the potential of RNA as a therapeutic tool has received public attention. Due to its intrinsic single-stranded nature and the ease with which it is synthesized in vitro, RNA indeed represents the most suitable tool for the development of drugs encompassing every type of human pathology. The maximum effectiveness and biochemical versatility is achieved in the guise of non-coding RNAs (ncRNAs), which are emerging as multifaceted regulators of tissue specification and homeostasis. Here, we report examples of coding and ncRNAs involved in muscle regeneration and discuss their potential as therapeutic tools. Small ncRNAs, such as miRNA and siRNA, have been successfully applied in the treatment of several diseases. The use of longer molecules, such as lncRNA and circRNA, is less advanced. However, based on the peculiar properties discussed below, they represent an innovative pool of RNA biomarkers and possible targets of clinical value.
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MESH Headings
- Animals
- Biomarkers/metabolism
- COVID-19
- Homeostasis
- Humans
- Mice
- MicroRNAs/metabolism
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscle, Skeletal/virology
- Myocardium/metabolism
- Origin of Life
- RNA, Circular
- RNA, Long Noncoding/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- RNA, Small Untranslated/genetics
- RNA, Untranslated/genetics
- RNA, Viral/metabolism
- Regeneration
- SARS-CoV-2/genetics
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Affiliation(s)
- Giulia Buonaiuto
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.B.); (F.D.); (V.T.)
| | - Fabio Desideri
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.B.); (F.D.); (V.T.)
- Center for Life Nano & Neuro-Science of Instituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Valeria Taliani
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.B.); (F.D.); (V.T.)
| | - Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (G.B.); (F.D.); (V.T.)
- Correspondence:
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23
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Mitelman O, Abdel-Hamid HZ, Byrne BJ, Connolly AM, Heydemann P, Proud C, Shieh PB, Wagner KR, Dugar A, Santra S, Signorovitch J, Goemans N, McDonald CM, Mercuri E, Mendell JR. A Combined Prospective and Retrospective Comparison of Long-Term Functional Outcomes Suggests Delayed Loss of Ambulation and Pulmonary Decline with Long-Term Eteplirsen Treatment. J Neuromuscul Dis 2021; 9:39-52. [PMID: 34420980 PMCID: PMC8842766 DOI: 10.3233/jnd-210665] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Studies 4658-201/202 (201/202) evaluated treatment effects of eteplirsen over 4 years in patients with Duchenne muscular dystrophy and confirmed exon-51 amenable genetic mutations. Chart review Study 4658-405 (405) further followed these patients while receiving eteplirsen during usual clinical care. Objective: To compare long-term clinical outcomes of eteplirsen-treated patients from Studies 201/202/405 with those of external controls. Methods: Median total follow-up time was approximately 6 years of eteplirsen treatment. Outcomes included loss of ambulation (LOA) and percent-predicted forced vital capacity (FVC%p). Time to LOA was compared between eteplirsen-treated patients and standard of care (SOC) external controls and was measured from eteplirsen initiation in 201/202 or, in the SOC group, from the first study visit. Comparisons were conducted using univariate Kaplan-Meier analyses and log-rank tests, and multivariate Cox proportional hazards models with regression adjustment for baseline characteristics. Annual change in FVC%p was compared between eteplirsen-treated patients and natural history study patients using linear mixed models with repeated measures. Results: Data were included from all 12 patients in Studies 201/202 and the 10 patients with available data from 405. Median age at LOA was 15.16 years. Eteplirsen-treated patients experienced a statistically significant longer median time to LOA by 2.09 years (5.09 vs. 3.00 years, p < 0.01) and significantly attenuated rates of pulmonary decline vs. natural history patients (FVC%p change: –3.3 vs. –6.0 percentage points annually, p < 0.0001). Conclusions: Study 405 highlights the functional benefits of eteplirsen on ambulatory and pulmonary function outcomes up to 7 years of follow-up in comparison to external controls.
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Affiliation(s)
| | | | | | - Anne M Connolly
- Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Crystal Proud
- Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Perry B Shieh
- University of California Los Angeles, Los Angeles, CA, USA
| | - Kathryn R Wagner
- Kennedy Krieger Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | | | | | | | - Craig M McDonald
- University of California Davis Health System, Sacramento, CA, USA
| | | | | | | | - Jerry R Mendell
- Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
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24
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Poleur M, Ulinici A, Daron A, Schneider O, Farra FD, Demonceau M, Annoussamy M, Vissière D, Eggenspieler D, Servais L. Normative data on spontaneous stride velocity, stride length, and walking activity in a non-controlled environment. Orphanet J Rare Dis 2021; 16:318. [PMID: 34281599 PMCID: PMC8287788 DOI: 10.1186/s13023-021-01956-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/11/2021] [Indexed: 01/14/2023] Open
Abstract
Background Normative data are necessary for validation of new outcome measures. Recently, the 95th centile of stride speed was qualified by the European Medicines Agency as a valid secondary outcome for clinical trials in subjects with Duchenne muscular dystrophy. This study aims to obtain normative data on spontaneous stride velocity and length in a non-controlled environment and their evolution after 12 months. Method Ninety-one healthy volunteers (50 females, 41 males), with a mean age of 16 years and 2 months, were recruited and assessed at baseline and 12 months later. The 4-stair climb, 6-min walk test, 10-m walk test and rise from floor assessments were performed. Stride length, stride velocity, and the distance walked per hour were studied in an everyday setting for one month after each evaluation. Results Of the 91 subjects assessed, 82 provided more than 50 h of recordings at baseline; and 73 subjects provided the same at the end of the year. We observed significant positive correlations of the stride length with age and height of participants, and a significant increase of the median stride length in children after the period. In this group, the 95th centile stride velocity was not correlated with age and was stable after one year. All measures but the 10MWT were stable in adults after a one-year period. Conclusion This study provides with data on the influence of age, height, and gender on stride velocity and length as well as accounting for natural changes after one year in controls.
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Affiliation(s)
- Margaux Poleur
- Centre de Référence des Maladies Neuromusculaires, Centre Hospitalier Régional de la Citadelle, Boulevard du 12eme de Ligne 1, 4000, Liège, Belgium
| | - Ana Ulinici
- Centre de Référence des Maladies Neuromusculaires, Centre Hospitalier Régional de la Citadelle, Boulevard du 12eme de Ligne 1, 4000, Liège, Belgium
| | - Aurore Daron
- Centre de Référence des Maladies Neuromusculaires, Centre Hospitalier Régional de la Citadelle, Boulevard du 12eme de Ligne 1, 4000, Liège, Belgium
| | - Olivier Schneider
- Centre de Référence des Maladies Neuromusculaires, Centre Hospitalier Régional de la Citadelle, Boulevard du 12eme de Ligne 1, 4000, Liège, Belgium
| | - Fabian Dal Farra
- Centre de Référence des Maladies Neuromusculaires, Centre Hospitalier Régional de la Citadelle, Boulevard du 12eme de Ligne 1, 4000, Liège, Belgium
| | - Marie Demonceau
- Centre de Référence des Maladies Neuromusculaires, Centre Hospitalier Régional de la Citadelle, Boulevard du 12eme de Ligne 1, 4000, Liège, Belgium
| | | | | | | | - Laurent Servais
- Centre de Référence des Maladies Neuromusculaires, Centre Hospitalier Régional de la Citadelle, Boulevard du 12eme de Ligne 1, 4000, Liège, Belgium. .,Department of Paediatrics, MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK.
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25
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Abstract
Duchenne muscular dystrophy (DMD) is a devastating, rare disease. While clinically described in the 19th century, the genetic foundation of DMD was not discovered until more than 100 years later. This genetic understanding opened the door to the development of genetic treatments for DMD. Over the course of the last 30 years, the research that supports this development has moved into the realm of clinical trials and regulatory drug approvals. Exon skipping to therapeutically restore the frame of an out-of-frame dystrophin mutation has taken center stage in drug development for DMD. The research reviewed here focuses on the clinical development of exon skipping for the treatment of DMD. In addition to the generation of clinical treatments that are being used for patient care, this research sets the stage for future therapeutic development with a focus on increasing efficacy while providing safety and addressing the multi-systemic aspects of DMD.
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Affiliation(s)
- Shin'ichi Takeda
- Honorary Director General, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Japan
| | - Paula R Clemens
- Professor and Vice Chair of VA Affairs, Department of Neurology, University of Pittsburgh School of Medicine, Division Chief, Neurology, Medical Service Line, VA Pittsburgh Healthcare System, Pittsburgh, PA USA
| | - Eric P Hoffman
- Professor, Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University - State University of New York, Binghamton, NY USA
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26
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Murphy AP, Greally E, O'Hogain D, Blamire A, Caravan P, Straub V. Use of EP3533-Enhanced Magnetic Resonance Imaging as a Measure of Disease Progression in Skeletal Muscle of mdx Mice. Front Neurol 2021; 12:636719. [PMID: 34220666 PMCID: PMC8248789 DOI: 10.3389/fneur.2021.636719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
As putative treatments are developed for Duchenne muscular dystrophy (DMD), sensitive, non-invasive measures are increasingly important to quantify disease progression. Fibrosis is one of the histological hallmarks of muscular dystrophy and has been directly linked to prognosis. EP3533 is a novel contrast agent with an affinity to collagen 1 that has demonstrated a significant and high correlation to ex vivo fibrosis quantification. Halofuginone is an established anti-fibrotic compound shown to reduce collagen skeletal muscle fibrosis in murine models of DMD. This experiment explored whether EP3533 could be used to detect signal change in skeletal muscle of mdx mice before and after a 12 week course of halofuginone compared to controls. Four age-matched groups of treated and untreated mice were evaluated: 2 groups of mdx (n = 8 and n = 13, respectively), and 2 groups of BL10 mice (n = 5 and n = 3, respectively). Treated mice received an intraperitoneal injection with halofuginone three times per week for 12 weeks, with the remaining mice being given vehicle. Both mdx groups and the untreated BL10 were scanned at baseline, then all groups were scanned on week 13. All subjects were scanned using a 7T Varian scanner before and after administration of EP3533 using a T1 mapping technique. Mice underwent grip testing in week 13 prior to dissection. Skeletal muscle was used for Masson's trichrome quantification, hydroxyproline assay, and immunofluorescent antibody staining. Untreated mdx mice demonstrated a significant increase in R1 signal from pre- to post-treatment scan in three out of four muscles (gastrocnemius p = 0.04, hamstrings p = 0.009, and tibialis anterior p = 0.01), which was not seen in either the treated mdx or the BL10 groups. Histological quantification of fibrosis also demonstrated significantly higher levels in the untreated mdx mice with significant correlation seen between histology and EP3533 signal change. Forelimb weight adjusted-grip strength was significantly lower in the untreated mdx group, compared to the treated group. EP3533 can be used over time as an outcome measure to quantify treatment effect of an established anti-fibrotic drug. Further studies are needed to evaluate the use of this contrast agent in humans.
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Affiliation(s)
- Alexander Peter Murphy
- The Institute of Cancer and Genomics, Birmingham University, Birmingham, United Kingdom.,The John Walton Muscular Dystrophy Research Centre, Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Elizabeth Greally
- The John Walton Muscular Dystrophy Research Centre, Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Dara O'Hogain
- Newcastle Magnetic Resonance Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew Blamire
- Newcastle Magnetic Resonance Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Peter Caravan
- Department of Radiology, Martinos Center for Biomedical Imaging, Harvard Medical School, Massachusetts General Hospital, Charlestown, MA, United States
| | - Volker Straub
- The Institute of Cancer and Genomics, Birmingham University, Birmingham, United Kingdom.,Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle University, Newcastle upon Tyne, United Kingdom
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27
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Advances of Antisense Oligonucleotide Technology in the Treatment of Hereditary Neurodegenerative Diseases. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6678422. [PMID: 34211575 PMCID: PMC8211492 DOI: 10.1155/2021/6678422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/13/2021] [Accepted: 05/29/2021] [Indexed: 12/11/2022]
Abstract
Antisense nucleic acids are single-stranded oligonucleotides that have been specially chemically modified, which can bind to RNA expressed by target genes through base complementary pairing and affect protein synthesis at the level of posttranscriptional processing or protein translation. In recent years, the application of antisense nucleic acid technology in the treatment of neuromuscular diseases has made remarkable progress. In 2016, the US FDA approved two antisense nucleic acid drugs for the treatment of Duchenne muscular dystrophy (DMD) and spinal muscular atrophy (SMA), and the development to treat other neurodegenerative diseases has also entered the clinical stage. Therefore, ASO represents a treatment with great potential. The article will summarize ASO therapies in terms of mechanism of action, chemical modification, and administration methods and analyze their role in several common neurodegenerative diseases, such as SMA, DMD, and amyotrophic lateral sclerosis (ALS). This article systematically summarizes the great potential of antisense nucleic acid technology in the treatment of hereditary neurodegenerative diseases.
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28
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Kitamura K, Nimura K. Regulation of RNA Splicing: Aberrant Splicing Regulation and Therapeutic Targets in Cancer. Cells 2021; 10:923. [PMID: 33923658 PMCID: PMC8073995 DOI: 10.3390/cells10040923] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/16/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023] Open
Abstract
RNA splicing is a critical step in the maturation of precursor mRNA (pre-mRNA) by removing introns and exons. The combination of inclusion and exclusion of introns and exons in pre-mRNA can generate vast diversity in mature mRNA from a limited number of genes. Cancer cells acquire cancer-specific mechanisms through aberrant splicing regulation to acquire resistance to treatment and to promote malignancy. Splicing regulation involves many factors, such as proteins, non-coding RNAs, and DNA sequences at many steps. Thus, the dysregulation of splicing is caused by many factors, including mutations in RNA splicing factors, aberrant expression levels of RNA splicing factors, small nuclear ribonucleoproteins biogenesis, mutations in snRNA, or genomic sequences that are involved in the regulation of splicing, such as 5' and 3' splice sites, branch point site, splicing enhancer/silencer, and changes in the chromatin status that affect the splicing profile. This review focuses on the dysregulation of RNA splicing related to cancer and the associated therapeutic methods.
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Affiliation(s)
- Koji Kitamura
- Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan;
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Keisuke Nimura
- Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan;
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29
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Hammond SM, Aartsma‐Rus A, Alves S, Borgos SE, Buijsen RAM, Collin RWJ, Covello G, Denti MA, Desviat LR, Echevarría L, Foged C, Gaina G, Garanto A, Goyenvalle AT, Guzowska M, Holodnuka I, Jones DR, Krause S, Lehto T, Montolio M, Van Roon‐Mom W, Arechavala‐Gomeza V. Delivery of oligonucleotide-based therapeutics: challenges and opportunities. EMBO Mol Med 2021; 13:e13243. [PMID: 33821570 PMCID: PMC8033518 DOI: 10.15252/emmm.202013243] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleic acid-based therapeutics that regulate gene expression have been developed towards clinical use at a steady pace for several decades, but in recent years the field has been accelerating. To date, there are 11 marketed products based on antisense oligonucleotides, aptamers and small interfering RNAs, and many others are in the pipeline for both academia and industry. A major technology trigger for this development has been progress in oligonucleotide chemistry to improve the drug properties and reduce cost of goods, but the main hurdle for the application to a wider range of disorders is delivery to target tissues. The adoption of delivery technologies, such as conjugates or nanoparticles, has been a game changer for many therapeutic indications, but many others are still awaiting their eureka moment. Here, we cover the variety of methods developed to deliver nucleic acid-based therapeutics across biological barriers and the model systems used to test them. We discuss important safety considerations and regulatory requirements for synthetic oligonucleotide chemistries and the hurdles for translating laboratory breakthroughs to the clinic. Recent advances in the delivery of nucleic acid-based therapeutics and in the development of model systems, as well as safety considerations and regulatory requirements for synthetic oligonucleotide chemistries are discussed in this review on oligonucleotide-based therapeutics.
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Affiliation(s)
| | | | - Sandra Alves
- Department of Human Genetics, Research and Development UnitNational Health Institute Doutor Ricardo JorgePortoPortugal
| | - Sven E Borgos
- Department of Biotechnology and NanomedicineSINTEF ASTrondheimNorway
| | - Ronald A M Buijsen
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
| | - Giuseppina Covello
- Department of BiologyUniversity of PadovaPadovaItaly
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
| | - Michela A Denti
- Department of Cellular, Computational and Integrative Biology ‐ CIBIOUniversity of TrentoTrentoItaly
| | - Lourdes R Desviat
- Centro de Biología Molecular Severo Ochoa UAM‐CSICCIBERER, IdiPazUniversidad Autónoma de MadridMadridSpain
| | | | - Camilla Foged
- Department of PharmacyFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagen ØDenmark
| | - Gisela Gaina
- Victor Babes National Institute of PathologyBucharestRomania
- Department of Biochemistry and Molecular BiologyUniversity of BucharestBucharestRomania
| | - Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
- Department of PediatricsRadboud University Medical CenterNijmegenThe Netherlands
| | | | - Magdalena Guzowska
- Department of Physiological SciencesFaculty of Veterinary MedicineWarsaw University of Life Sciences – SGGWWarsawPoland
| | - Irina Holodnuka
- Institute of Microbiology and VirologyRiga Stradins UniversityRigaLatvia
| | | | - Sabine Krause
- Department of NeurologyFriedrich‐Baur‐InstituteLudwig‐Maximilians‐University of MunichMunichGermany
| | - Taavi Lehto
- Institute of TechnologyUniversity of TartuTartuEstonia
- Division of Biomolecular and Cellular MedicineDepartment of Laboratory MedicineKarolinska InstitutetHuddingeSweden
| | - Marisol Montolio
- Duchenne Parent Project EspañaMadridSpain
- Department of Cell Biology, Fisiology and ImmunologyFaculty of BiologyUniversity of BarcelonaBarcelonaSpain
| | - Willeke Van Roon‐Mom
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Virginia Arechavala‐Gomeza
- Neuromuscular Disorders GroupBiocruces Bizkaia Health Research InstituteBarakaldoSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
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30
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Antisense technology: an overview and prospectus. Nat Rev Drug Discov 2021; 20:427-453. [PMID: 33762737 DOI: 10.1038/s41573-021-00162-z] [Citation(s) in RCA: 274] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/13/2022]
Abstract
Antisense technology is now beginning to deliver on its promise to treat diseases by targeting RNA. Nine single-stranded antisense oligonucleotide (ASO) drugs representing four chemical classes, two mechanisms of action and four routes of administration have been approved for commercial use, including the first RNA-targeted drug to be a major commercial success, nusinersen. Although all the approved drugs are for use in patients with rare diseases, many of the ASOs in late- and middle-stage clinical development are intended to treat patients with very common diseases. ASOs in development are showing substantial improvements in potency and performance based on advances in medicinal chemistry, understanding of molecular mechanisms and targeted delivery. Moreover, the ASOs in development include additional mechanisms of action and routes of administration such as aerosol and oral formulations. Here, we describe the key technological advances that have enabled this progress and discuss recent clinical trials that illustrate the impact of these advances on the performance of ASOs in a wide range of therapeutic applications. We also consider strategic issues such as target selection and provide perspectives on the future of the field.
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31
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Cohen J, DeSimone A, Lek M, Lek A. Therapeutic Approaches in Facioscapulohumeral Muscular Dystrophy. Trends Mol Med 2021; 27:123-137. [PMID: 33092966 PMCID: PMC8048701 DOI: 10.1016/j.molmed.2020.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/13/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common types of muscular dystrophy, affecting roughly one in 8000 individuals. The complex underlying genetics and poor mechanistic understanding has caused a bottleneck in therapeutic development. Until the discovery of DUX4 and its causal role in FSHD, most trials were untargeted with limited results. Emerging approaches can learn from these early trials to increase their chance of success. Here, we explore the evolution of FSHD clinical trials from nonspecific anabolic or anti-inflammatory/oxidant strategies to cutting-edge molecular therapies targeting DUX4, and we discuss the importance of clinical outcome measures. With combined advances across multiple facets of FSHD research, the field is now poised to accelerate the process of therapeutic discovery and testing.
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Affiliation(s)
- Justin Cohen
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Alec DeSimone
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Angela Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
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32
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Manini A, Pantoni L. CADASIL from Bench to Bedside: Disease Models and Novel Therapeutic Approaches. Mol Neurobiol 2021; 58:2558-2573. [PMID: 33464533 PMCID: PMC8128844 DOI: 10.1007/s12035-021-02282-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022]
Abstract
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a monogenic disease caused by NOTCH3 mutations and characterized by typical clinical, neuroradiological, and pathological features. NOTCH3 belongs to a family of highly conserved transmembrane receptors rich of epidermal growth factor repeats, mostly expressed in vascular smooth muscle cells and pericytes, which perform essential developmental functions and are involved in tissues maintenance and renewal. To date, no therapeutic option for CADASIL is available except for few symptomatic treatments. Novel in vitro and in vivo models are continuously explored with the aim to investigate underlying pathogenic mechanisms and to test novel therapeutic approaches. In this scenario, knock-out, knock-in, and transgenic mice studies have generated a large amount of information on molecular and biological aspects of CADASIL, despite that they incompletely reproduce the human phenotype. Moreover, the field of in vitro models has been revolutionized in the last two decades by the introduction of induced pluripotent stem cells (iPSCs) technology. As a consequence, novel therapeutic approaches, including immunotherapy, growth factors administration, and antisense oligonucleotides, are currently under investigation. While waiting that further studies confirm the promising results obtained, the data reviewed suggest that our therapeutic approach to the disease could be transformed, generating new hope for the future.
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Affiliation(s)
- Arianna Manini
- Stroke and Dementia Lab, "Luigi Sacco" Department of Biomedical and Clinical Sciences, University of Milan, Via Giovanni Battista Grassi 74, 20157, Milano, Italy
| | - Leonardo Pantoni
- Stroke and Dementia Lab, "Luigi Sacco" Department of Biomedical and Clinical Sciences, University of Milan, Via Giovanni Battista Grassi 74, 20157, Milano, Italy.
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33
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Crooke ST, Liang XH, Baker BF, Crooke RM. Antisense technology: A review. J Biol Chem 2021; 296:100416. [PMID: 33600796 PMCID: PMC8005817 DOI: 10.1016/j.jbc.2021.100416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Antisense technology is beginning to deliver on the broad promise of the technology. Ten RNA-targeted drugs including eight single-strand antisense drugs (ASOs) and two double-strand ASOs (siRNAs) have now been approved for commercial use, and the ASOs in phase 2/3 trials are innovative, delivered by multiple routes of administration and focused on both rare and common diseases. In fact, two ASOs are used in cardiovascular outcome studies and several others in very large trials. Interest in the technology continues to grow, and the field has been subject to a significant number of reviews. In this review, we focus on the molecular events that result in the effects observed and use recent clinical results involving several different ASOs to exemplify specific molecular mechanisms and specific issues. We conclude with the prospective on the technology.
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Affiliation(s)
- Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA.
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Brenda F Baker
- Development Communication, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Rosanne M Crooke
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
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34
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Rashnonejad A, Amini-Chermahini G, Taylor NK, Wein N, Harper SQ. Designed U7 snRNAs inhibit DUX4 expression and improve FSHD-associated outcomes in DUX4 overexpressing cells and FSHD patient myotubes. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 23:476-486. [PMID: 33510937 PMCID: PMC7807095 DOI: 10.1016/j.omtn.2020.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/06/2020] [Indexed: 12/21/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) arises from epigenetic changes that de-repress the DUX4 gene in muscle. The full-length DUX4 protein causes cell death and muscle toxicity, and therefore we hypothesize that FSHD therapies should center on inhibiting full-length DUX4 expression. In this study, we developed a strategy to accomplish DUX4 inhibition using U7-small nuclear RNA (snRNA) antisense expression cassettes (called U7-asDUX4). These non-coding RNAs were designed to inhibit production or maturation of the full-length DUX4 pre-mRNA by masking the DUX4 start codon, splice sites, or polyadenylation signal. In so doing, U7-asDUX4 snRNAs operate similarly to antisense oligonucleotides. However, in contrast to oligonucleotides, which are limited by poor uptake in muscle and a requirement for lifelong repeated dosing, U7-asDUX4 snRNAs can be packaged within myotropic gene therapy vectors and may require only a single administration when delivered to post-mitotic cells in vivo. We tested several U7-asDUX4s that reduced DUX4 expression in vitro and improved DUX4-associated outcomes. Inhibition of DUX4 expression via U7-snRNAs could be a new prospective gene therapy approach for FSHD or be used in combination with other strategies, like RNAi therapy, to maximize DUX4 silencing in individuals with FSHD.
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Affiliation(s)
- Afrooz Rashnonejad
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Gholamhossein Amini-Chermahini
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Noah K Taylor
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Nicolas Wein
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Scott Q Harper
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
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Apaydin EA, Richardson AS, Baxi S, Vockley J, Akinniranye O, Ross R, Larkin J, Motala A, Azhar G, Hempel S. An evidence map of randomised controlled trials evaluating genetic therapies. BMJ Evid Based Med 2020; 26:bmjebm-2020-111448. [PMID: 33172937 DOI: 10.1136/bmjebm-2020-111448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/18/2020] [Indexed: 01/11/2023]
Abstract
OBJECTIVES Genetic therapies replace or inactivate disease-causing genes or introduce new or modified genes. These therapies have the potential to cure in a single application rather than treating symptoms through repeated administrations. This evidence map provides a broad overview of the genetic therapies that have been evaluated in randomised controlled trials (RCTs) for efficacy and safety. ELIGIBILITY CRITERIA Two independent reviewers screened publications using predetermined eligibility criteria. Study details and data on safety and efficacy were abstracted from included trials. Results were visualised in an evidence map. INFORMATION SOURCES We searched PubMed, EMBASE, Web of Science, ClinicalTrials.gov and grey literature to November 2018. RISK OF BIAS Only RCTs were included in this review to reduce the risk of selection bias in the evaluation of genetic therapy safety and efficacy. INCLUDED STUDIES We identified 119 RCTs evaluating genetic therapies for a variety of clinical conditions. SYNTHESIS OF RESULTS On average, samples included 107 participants (range: 1-1022), and were followed for 15 months (range: 0-124). Interventions using adenoviruses (40%) to treat cardiovascular diseases (29%) were the most common. DESCRIPTION OF THE EFFECT In RCTs reporting safety and efficacy outcomes, in the majority (60%) genetic therapies were associated with improved symptoms but in nearly half (45%) serious adverse event (SAEs) were also reported. Improvement was reported in trials treating cancer, cardiovascular, ocular and muscular diseases. However, only 19 trials reported symptom improvement for at least 1 year. STRENGTHS AND LIMITATIONS OF EVIDENCE This is the first comprehensive evidence map of RCTs evaluating the safety and efficacy of genetic therapies. Evidence for long-term effectiveness and safety is still sparse. This lack of evidence has implications for the use, ethics, pricing and logistics of genetic therapies. INTERPRETATION This evidence map provides a broad overview of research studies that allow strong evidence statements regarding the safety and efficacy of genetic therapies. Most interventions improve symptoms, but SAE are also common. More research is needed to evaluate genetic therapies with regard to the potential to cure diseases.
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Affiliation(s)
- Eric A Apaydin
- Southern California Evidence-based Practice Center, Health Care, RAND Corporation, Santa Monica, California, USA
- Center for the Study of Healthcare Innovation, Implementation and Policy, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Andrea S Richardson
- Southern California Evidence-based Practice Center, Health Care, RAND Corporation, Pittsburgh, Pennsylvania, USA
| | - Sangita Baxi
- Southern California Evidence-based Practice Center, Health Care, RAND Corporation, Santa Monica, California, USA
| | - Jerry Vockley
- Division of Medical Genetics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Olamigoke Akinniranye
- Southern California Evidence-based Practice Center, Health Care, RAND Corporation, Santa Monica, California, USA
| | - Rachel Ross
- West Los Angeles Medical Center, Kaiser Foundation Hospitals, Los Angeles, California, USA
| | - Jody Larkin
- Southern California Evidence-based Practice Center, Health Care, RAND Corporation, Santa Monica, California, USA
| | - Aneesa Motala
- Southern California Evidence-based Practice Center, Health Care, RAND Corporation, Santa Monica, California, USA
| | - Gulrez Azhar
- Southern California Evidence-based Practice Center, Health Care, RAND Corporation, Santa Monica, California, USA
| | - Susanne Hempel
- Southern California Evidence-based Practice Center, Health Care, RAND Corporation, Santa Monica, California, USA
- Southern California Evidence Review Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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Schneider AFE, Aartsma-Rus A. Developments in reading frame restoring therapy approaches for Duchenne muscular dystrophy. Expert Opin Biol Ther 2020; 21:343-359. [PMID: 33074029 DOI: 10.1080/14712598.2021.1832462] [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: 12/11/2022]
Abstract
INTRODUCTION Exon skipping compounds restoring the dystrophin transcript reading frame have received regulatory approval for Duchenne muscular dystrophy (DMD). Recently, focus shifted to developing compounds to skip additional exons, improving delivery to skeletal muscle, and to genome editing, to restore the reading frame on DNA level. AREAS COVERED We outline developments for reading frame restoring approaches, challenges of mutation specificity, and optimizing delivery. Also, we highlight ongoing efforts to better detect exon skipping therapeutic effects in clinical trials. Searches on relevant terms were performed, focusing on recent publications (<3 years). EXPERT OPINION Currently, 3 AONS are approved. Whether dystrophin levels are sufficient to slowdown disease progression needs to be confirmed. Enhancing AON uptake by muscles is currently under investigation. Gene editing is an alternative, but one that involves practical and ethical concerns. Given the field's momentum, we believe the efficiency of frame-restoring approaches will improve.
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Affiliation(s)
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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"Betwixt Mine Eye and Heart a League Is Took": The Progress of Induced Pluripotent Stem-Cell-Based Models of Dystrophin-Associated Cardiomyopathy. Int J Mol Sci 2020; 21:ijms21196997. [PMID: 32977524 PMCID: PMC7582534 DOI: 10.3390/ijms21196997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
The ultimate goal of precision disease modeling is to artificially recreate the disease of affected people in a highly controllable and adaptable external environment. This field has rapidly advanced which is evident from the application of patient-specific pluripotent stem-cell-derived precision therapies in numerous clinical trials aimed at a diverse set of diseases such as macular degeneration, heart disease, spinal cord injury, graft-versus-host disease, and muscular dystrophy. Despite the existence of semi-adequate treatments for tempering skeletal muscle degeneration in dystrophic patients, nonischemic cardiomyopathy remains one of the primary causes of death. Therefore, cardiovascular cells derived from muscular dystrophy patients' induced pluripotent stem cells are well suited to mimic dystrophin-associated cardiomyopathy and hold great promise for the development of future fully effective therapies. The purpose of this article is to convey the realities of employing precision disease models of dystrophin-associated cardiomyopathy. This is achieved by discussing, as suggested in the title echoing William Shakespeare's words, the settlements (or "leagues") made by researchers to manage the constraints ("betwixt mine eye and heart") distancing them from achieving a perfect precision disease model.
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Antisense drug discovery and development technology considered in a pharmacological context. Biochem Pharmacol 2020; 189:114196. [PMID: 32800852 DOI: 10.1016/j.bcp.2020.114196] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
When coined, the term "antisense" included oligonucleotides of any structure, with any chemical modification and designed to work through any post-RNA hybridization mechanism. However, in practice the term "antisense" has been used to describe single stranded oligonucleotides (ss ASOs) designed to hybridize to RNAswhile the term "siRNA" has come to mean double stranded oligonucleotides designed to activate Ago2. However, the two approaches share many common features. The medicinal chemistry developed for ASOs greatly facilitated the development of siRNA technology and remains the chemical basis for both approaches. Many of challenges faced and solutions achieved share many common features. In fact, because ss ASOs can be designed to activate Ago2, the two approaches intersect at this remarkably important protein. There are also meaningful differences. The pharmacokinetic properties are quite different and thus potential routes of delivery differ. ASOs may be designedto use a variety of post-RNA binding mechanismswhile siRNAs depend solely on the robust activity of Ago2. However, siRNAs and ASOs are both used for therapeutic purposes and both must be and can be understood in a pharmacological context. Thus, the goals of this review are to put ASOs in pharmacological context and compare their behavior as pharmacological agents to the those of siRNAs.
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Pascual-Morena C, Cavero-Redondo I, Álvarez-Bueno C, Mesas AE, Pozuelo-Carrascosa D, Martínez-Vizcaíno V. Restorative treatments of dystrophin expression in Duchenne muscular dystrophy: A systematic review. Ann Clin Transl Neurol 2020; 7:1738-1752. [PMID: 33325654 PMCID: PMC7480922 DOI: 10.1002/acn3.51149] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/30/2020] [Accepted: 07/13/2020] [Indexed: 12/20/2022] Open
Abstract
To evaluate the effect of pharmacological treatments that increase the synthesis of dystrophin in Duchenne muscular dystrophy (DMD). Systematic searches were carried out in MEDLINE, EMBASE, and Web of Science, and in gray literature from inception to December 2019. Clinical trials addressing the effect of restorative treatments of dystrophin expression in children and adolescents with DMD on functional outcomes {(6-minute walking distance [6MWD], other timed functional tests [TFTs], The North Star Ambulatory Assessment)}, dystrophin expression, cardiorespiratory function, and biochemical tests were included. The DerSimonian-Laird method was used to calculate the pooled estimates for functional outcomes. Eleven studies were included in the systematic review and five in the meta-analysis. Eteplirsen showed a significant effect on 6MWD, Δ6MWD = 67.3 m (95% CI: 27.32, 107.28), and Δ6MWD = 151.0 m (95% CI: 36.15, 265.85) at 48 weeks and 3 years, respectively. In the systematic review, analyzing individually the clinical trials using Ataluren and Drisapersen showed a nonsignificant effect on 6MWD. However, the meta-analysis showed a significant effect on 6MWD for Ataluren and Drisapersen, Δ6MWD = 18.3 m (95% CI: 1.0, 35.5) and Δ6MWD = 21.5 m (95% CI: 4.7, 38.3), respectively. There were no significant differences according to baseline age for Drisapersen. Similarly, the meta-analysis showed effect in TFT with Ataluren. All drugs induced a partial synthesis of dystrophin, and exon skipping was obtained with Eteplirsen and Drisapersen. Eteplirsen also improved forced vital capacity (Δ%pFVC = 1.8%) and maximal inspiratory pressure (Δ%pMIP = 4.4%). Eteplirsen and Ataluren could modestly reduce disease progression. However, more trials are needed to confirm its efficacy, as well as quality of life and cost-utility studies.
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Affiliation(s)
- Carlos Pascual-Morena
- Health and Social Research Center, Universidad de Castilla - La Mancha, Cuenca, Spain
| | - Iván Cavero-Redondo
- Health and Social Research Center, Universidad de Castilla - La Mancha, Cuenca, Spain.,Universidad Politécnica y Artística del Paraguay, Asunción, Paraguay
| | - Celia Álvarez-Bueno
- Health and Social Research Center, Universidad de Castilla - La Mancha, Cuenca, Spain.,Universidad Politécnica y Artística del Paraguay, Asunción, Paraguay
| | - Arthur Eumann Mesas
- Health and Social Research Center, Universidad de Castilla - La Mancha, Cuenca, Spain
| | | | - Vicente Martínez-Vizcaíno
- Health and Social Research Center, Universidad de Castilla - La Mancha, Cuenca, Spain.,Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
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Houlihan G, Arangundy-Franklin S, Porebski BT, Subramanian N, Taylor AI, Holliger P. Discovery and evolution of RNA and XNA reverse transcriptase function and fidelity. Nat Chem 2020; 12:683-690. [PMID: 32690899 DOI: 10.1038/s41557-020-0502-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
The ability of reverse transcriptases (RTs) to synthesize a complementary DNA from natural RNA and a range of unnatural xeno nucleic acid (XNA) template chemistries, underpins key methods in molecular and synthetic genetics. However, RTs have proven challenging to discover and engineer, in particular for the more divergent XNA chemistries. Here we describe a general strategy for the directed evolution of RT function for any template chemistry called compartmentalized bead labelling and demonstrate it by the directed evolution of efficient RTs for 2'-O-methyl RNA and hexitol nucleic acids and the discovery of RTs for the orphan XNA chemistries D-altritol nucleic acid and 2'-methoxyethyl RNA, for which previously no RTs existed. Finally, we describe the engineering of XNA RTs with active exonucleolytic proofreading as well as the directed evolution of RNA RTs with very high complementary DNA synthesis fidelities, even in the absence of proofreading.
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Affiliation(s)
- Gillian Houlihan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Benjamin T Porebski
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Nithya Subramanian
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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Goemans N, Signorovitch J, Sajeev G, Yao Z, Gordish-Dressman H, McDonald CM, Vandenborne K, Miller D, Ward SJ, Mercuri E. Suitability of external controls for drug evaluation in Duchenne muscular dystrophy. Neurology 2020; 95:e1381-e1391. [PMID: 32611643 PMCID: PMC7538219 DOI: 10.1212/wnl.0000000000010170] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/06/2020] [Indexed: 12/19/2022] Open
Abstract
Objective To evaluate the suitability of real-world data (RWD) and natural history data (NHD) for use as external controls in drug evaluations for ambulatory Duchenne muscular dystrophy (DMD). Methods The consistency of changes in the 6-minute walk distance (Δ6MWD) was assessed across multiple clinical trial placebo arms and sources of NHD/RWD. Six placebo arms reporting 48-week Δ6MWD were identified via literature review and represented 4 sets of inclusion/exclusion criteria (n = 383 patients in total). Five sources of RWD/NHD were contributed by Universitaire Ziekenhuizen Leuven, DMD Italian Group, The Cooperative International Neuromuscular Research Group, ImagingDMD, and the PRO-DMD-01 study (n = 430 patients, in total). Mean Δ6MWD was compared between each placebo arm and RWD/NHD source after subjecting the latter to the inclusion/exclusion criteria of the trial for baseline age, ambulatory function, and steroid use. Baseline covariate adjustment was investigated in a subset of patients with available data. Results Analyses included ∼1,200 patient-years of follow-up. Differences in mean Δ6MWD between trial placebo arms and RWD/NHD cohorts ranged from −19.4 m (i.e., better outcomes in RWD/NHD) to 19.5 m (i.e., worse outcomes in RWD/NHD) and were not statistically significant before or after covariate adjustment. Conclusions We found that Δ6MWD was consistent between placebo arms and RWD/NHD subjected to equivalent inclusion/exclusion criteria. No evidence for systematic bias was detected. These findings are encouraging for the use of RWD/NHD to augment, or possibly replace, placebo controls in DMD trials. Multi-institution collaboration through the Collaborative Trajectory Analysis Project rendered this study feasible.
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Affiliation(s)
- Nathalie Goemans
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - James Signorovitch
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - Gautam Sajeev
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - Zhiwen Yao
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - Heather Gordish-Dressman
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - Craig M McDonald
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - Krista Vandenborne
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - Debra Miller
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - Susan J Ward
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy
| | - Eugenio Mercuri
- From the University Hospitals Leuven (N.G.), Child Neurology, Belgium; Analysis Group, Inc (J.S., G.S., Z.Y.), Boston; Collaborative Trajectory Analysis Project (J.S., S.J.W.), Cambridge, MA; Children's National Medical Center (H.G.-D.), Research Center for Genetic Medicine, Washington, DC; Department of Physical Medicine and Rehabilitation and Pediatrics (C.M.M.), University of California, Davis, Sacramento; Department of Physical Therapy (K.V.), University of Florida, Gainesville; CureDuchenne (D.M.), Newport Beach, CA; and Department of Pediatric Neurology (E.M.), Fondazione Policlinico Gemelli IRCCS, Catholic University, Rome, Italy.
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Goemans N, Wong B, Van den Hauwe M, Signorovitch J, Sajeev G, Cox D, Landry J, Jenkins M, Dieye I, Yao Z, Hossain I, Ward SJ. Prognostic factors for changes in the timed 4-stair climb in patients with Duchenne muscular dystrophy, and implications for measuring drug efficacy: A multi-institutional collaboration. PLoS One 2020; 15:e0232870. [PMID: 32555695 PMCID: PMC7302444 DOI: 10.1371/journal.pone.0232870] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 04/22/2020] [Indexed: 12/25/2022] Open
Abstract
The timed 4-stair climb (4SC) assessment has been used to measure function in Duchenne muscular dystrophy (DMD) practice and research. We sought to identify prognostic factors for changes in 4SC, assess their consistency across data sources, and the extent to which prognostic scores could be useful in DMD clinical trial design and analysis. Data from patients with DMD in the placebo arm of a phase 3 trial (Tadalafil DMD trial) and two real-world sources (Universitaire Ziekenhuizen, Leuven, Belgium [Leuven] and Cincinnati Children's Hospital Medical Center [CCHMC]) were analyzed. One-year changes in 4SC completion time and velocity (stairs/second) were analyzed. Prognostic models included age, height, weight, steroid use, and multiple timed function tests and were developed using multivariable regression, separately in each data source. Simulations were used to quantify impacts on trial sample size requirements. Data on 1-year changes in 4SC were available from the Tadalafil DMD trial (n = 92) Leuven (n = 67), and CCHMC (n = 212). Models incorporating multiple timed function tests, height, and weight significantly improved prognostic accuracy for 1-year change in 4SC (R2: 29%-36% for 4SC velocity, and 29%-34% for 4SC time) compared to models including only age, baseline 4SC and steroid duration (R2:8%-17% for 4SC velocity and 2%-13% for 4SC time). Measures of walking and rising ability contributed important prognostic information for changes in 4SC. In a randomized trial with equal allocation to treatment and placebo, adjustment for such a prognostic score would enable detection (at 80% power) of a treatment effect of 0.25 stairs/second with 100–120 patients, compared to 170–190 patients without prognostic score adjustment. Combining measures of ambulatory function doubled prognostic accuracy for 1-year changes in 4SC completion time and velocity. Randomized clinical trials incorporating a validated prognostic score could reduce sample size requirements by approximately 40%. Knowledge of important prognostic factors can also inform adjusted comparisons to external controls.
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Affiliation(s)
- Nathalie Goemans
- Department of Child Neurology, University Hospitals Leuven, Leuven, Belgium
- * E-mail:
| | - Brenda Wong
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA, United States of America
| | | | - James Signorovitch
- Analysis Group Inc., Boston, Massachusetts, United States of America
- The Collaborative Trajectory Analysis Project, Cambridge, Massachusetts, United States of America
| | - Gautam Sajeev
- Analysis Group Inc., Boston, Massachusetts, United States of America
| | - David Cox
- Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - John Landry
- Eli Lilly and Company, Toronto, Ontario, Canada
| | | | - Ibrahima Dieye
- Analysis Group Inc., Boston, Massachusetts, United States of America
| | - Zhiwen Yao
- Analysis Group Inc., Boston, Massachusetts, United States of America
| | - Intekhab Hossain
- Analysis Group Inc., Boston, Massachusetts, United States of America
| | - Susan J. Ward
- The Collaborative Trajectory Analysis Project, Cambridge, Massachusetts, United States of America
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Scaglioni D, Ellis M, Catapano F, Torelli S, Chambers D, Feng L, Sewry C, Morgan J, Muntoni F, Phadke R. A high-throughput digital script for multiplexed immunofluorescent analysis and quantification of sarcolemmal and sarcomeric proteins in muscular dystrophies. Acta Neuropathol Commun 2020; 8:53. [PMID: 32303261 PMCID: PMC7165405 DOI: 10.1186/s40478-020-00918-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/16/2020] [Indexed: 12/21/2022] Open
Abstract
The primary molecular endpoint for many Duchenne muscular dystrophy (DMD) clinical trials is the induction, or increase in production, of dystrophin protein in striated muscle. For accurate endpoint analysis, it is essential to have reliable, robust and objective quantification methodologies capable of detecting subtle changes in dystrophin expression. In this work, we present further development and optimisation of an automated, digital, high-throughput script for quantitative analysis of multiplexed immunofluorescent (IF) whole slide images (WSI) of dystrophin, dystrophin associated proteins (DAPs) and regenerating myofibres (fetal/developmental myosin-positive) in transverse sections of DMD, Becker muscular dystrophy (BMD) and control skeletal muscle biopsies. The script enables extensive automated assessment of myofibre morphometrics, protein quantification by fluorescence intensity and sarcolemmal circumference coverage, colocalisation data for dystrophin and DAPs and regeneration at the single myofibre and whole section level. Analysis revealed significant variation in dystrophin intensity, percentage coverage and amounts of DAPs between differing DMD and BMD samples. Accurate identification of dystrophin via a novel background subtraction method allowed differential assessment of DAP fluorescence intensity within dystrophin positive compared to dystrophin negative sarcolemma regions. This enabled surrogate quantification of molecular functionality of dystrophin in the assembly of the DAP complex. Overall, the digital script is capable of multiparametric and unbiased analysis of markers of myofibre regeneration and dystrophin in relation to key DAPs and enabled better characterisation of the heterogeneity in dystrophin expression patterns seen in BMD and DMD alongside the surrogate assessment of molecular functionality of dystrophin. Both these aspects will be of significant relevance to ongoing and future DMD and other muscular dystrophies clinical trials to help benchmark therapeutic efficacy.
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Krooss S, Werwitzke S, Kopp J, Rovai A, Varnholt D, Wachs AS, Goyenvalle A, Aarstma-Rus A, Ott M, Tiede A, Langemeier J, Bohne J. Pathological mechanism and antisense oligonucleotide-mediated rescue of a non-coding variant suppressing factor 9 RNA biogenesis leading to hemophilia B. PLoS Genet 2020; 16:e1008690. [PMID: 32267853 PMCID: PMC7141619 DOI: 10.1371/journal.pgen.1008690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 02/22/2020] [Indexed: 01/25/2023] Open
Abstract
Loss-of-function mutations in the human coagulation factor 9 (F9) gene lead to hemophilia B. Here, we dissected the consequences and the pathomechanism of a non-coding mutation (c.2545A>G) in the F9 3’ untranslated region. Using wild type and mutant factor IX (FIX) minigenes we revealed that the mutation leads to reduced F9 mRNA and FIX protein levels and to lower coagulation activity of cell culture supernatants. The phenotype could not be compensated by increased transcription. The pathomechanism comprises the de novo creation of a binding site for the spliceosomal component U1snRNP, which is able to suppress the nearby F9 poly(A) site. This second, splicing-independent function of U1snRNP was discovered previously and blockade of U1snRNP restored mutant F9 mRNA expression. In addition, we explored the vice versa approach and masked the mutation by antisense oligonucleotides resulting in significantly increased F9 mRNA expression and coagulation activity. This treatment may transform the moderate/severe hemophilia B into a mild or subclinical form in the patients. This antisense based strategy is applicable to other mutations in untranslated regions creating deleterious binding sites for cellular proteins. The elucidation of the pathomechanisms of non-coding variants yields important insights into diseases as well as cellular processes causing the defect. Although these variants may account for the majority of phenotypic variation, only a minority of them can be explained mechanistically. The human coagulation factor 9 3’ UTR variant described here converts a non-essential sequence motif into a U1snRNP-binding site with deleterious effects on RNA 3’ end processing at the nearby poly(A) site. Poly(A) site suppression by U1snRNP was described before and it normally protects cellular mRNAs from premature termination. However, if misled by creation of a U1 site close the authentic poly(A) site as in the F9 3’ UTR, this nuclear surveillance mechanism results in the opposite. Since recognition by U1snRNP depends on sequence complementarity we were able to use antisense oligonucleotides to mask the mutant site and partially restored F9 mRNA levels. This antisense based strategy may be applicable to other variants in untranslated regions, which create deleterious binding sites for cellular proteins.
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Affiliation(s)
- Simon Krooss
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School and Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Sonja Werwitzke
- Clinic of Hematology, Oncology and Hemostaseology, Hannover Medical School, Hannover, Germany
| | - Johannes Kopp
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Alice Rovai
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School and Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Dirk Varnholt
- Clinic of Hematology, Oncology and Hemostaseology, Hannover Medical School, Hannover, Germany
| | - Amelie S. Wachs
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | | | | | - Michael Ott
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School and Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Andreas Tiede
- Clinic of Hematology, Oncology and Hemostaseology, Hannover Medical School, Hannover, Germany
| | - Jörg Langemeier
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Pediatric Intensive Care Unit, Children’s Hospital Bielefeld, Germany
- * E-mail: (JL); (JB)
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, Hannover, Germany
- * E-mail: (JL); (JB)
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45
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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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46
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Jin Y, Shen Y, Su X, Weintraub NL, Tang Y. Effective restoration of dystrophin expression in iPSC Mdx-derived muscle progenitor cells using the CRISPR/Cas9 system and homology-directed repair technology. Comput Struct Biotechnol J 2020; 18:765-773. [PMID: 32280431 PMCID: PMC7132053 DOI: 10.1016/j.csbj.2020.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/14/2020] [Accepted: 03/17/2020] [Indexed: 12/20/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a progressive myopathic disease caused by mutations in the gene encoding dystrophin protein that eventually leads to the exhaustion of myogenic progenitor cells (MPC). Autologous induced pluripotent stem cells (iPSCs) provide an endless source of MPC, which can potentially replenish the progenitor cell pool, repair muscle damage, and prevent DMD progression. Deletion of mutant exon 23 (ΔEx23) with clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) gene-editing technology can correct dystrophin gene expression in iPSCs. However, successful exon23 deletion and clonal isolation are very inefficient (~3%), and manual selection of each iPSC clone and genotyping to identify ΔEx23 is labor-intensive. To overcome these obstacles, we added a homology-directed repair (HDR) donor vector, which carries floxed fluorescent protein and antibiotic selection genes, thus allowing us to identify ΔEx23 iPSC with donor selective gene integration. Our results indicate that the HDR-mediated targeted integration enables ΔEx23 iPSC identification; the HDR donor vector increased the recognition efficiency of clonal isolation (>90% as confirmed by Sanger sequencing). After removal of the inserted genes by Cre-mediated recombination followed by doxycycline (Dox)-induced MyoD induction, ΔEx23 iPSC differentiated into MPC with restored dystrophin expression in vitro. Importantly, transplanted ΔEx23 iPSC-MPC express dystrophin in the muscles of a mouse model of DMD (Mdx mice). In conclusion, the use of HDR donor vector increased the efficiency of ΔEx23 gene correction by CRISPR/Cas9, and facilitate the identification of successfully edited iPSC clones for cell therapy of DMD.
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Affiliation(s)
| | | | | | | | - Yaoliang Tang
- Medical College of Georgia, Augusta University, Augusta, GA, USA
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47
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Grages SM, Bell M, Berlau DJ. New and emerging pharmacotherapy for duchenne muscular dystrophy: a focus on synthetic therapeutics. Expert Opin Pharmacother 2020; 21:841-851. [DOI: 10.1080/14656566.2020.1732350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sharon M. Grages
- Department of Pharmaceutical Sciences, Regis University School of Pharmacy, Denver, Colorado
| | - Michael Bell
- Department of Pharmaceutical Sciences, Regis University School of Pharmacy, Denver, Colorado
| | - Daniel J. Berlau
- Department of Pharmaceutical Sciences, Regis University School of Pharmacy, Denver, Colorado
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48
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Østergaard ME, Jackson M, Low A, E Chappell A, G Lee R, Peralta RQ, Yu J, Kinberger GA, Dan A, Carty R, Tanowitz M, Anderson P, Kim TW, Fradkin L, Mullick AE, Murray S, Rigo F, Prakash TP, Bennett CF, Swayze EE, Gaus HJ, Seth PP. Conjugation of hydrophobic moieties enhances potency of antisense oligonucleotides in the muscle of rodents and non-human primates. Nucleic Acids Res 2020; 47:6045-6058. [PMID: 31076766 PMCID: PMC6614849 DOI: 10.1093/nar/gkz360] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/18/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
We determined the effect of attaching palmitate, tocopherol or cholesterol to PS ASOs and their effects on plasma protein binding and on enhancing ASO potency in the muscle of rodents and monkeys. We found that cholesterol ASO conjugates showed 5-fold potency enhancement in the muscle of rodents relative to unconjugated ASOs. However, they were toxic in mice and as a result were not evaluated in the monkey. In contrast, palmitate and tocopherol-conjugated ASOs showed enhanced potency in the skeletal muscle of rodents and modest enhancements in potency in the monkey. Analysis of the plasma-protein binding profiles of the ASO-conjugates by size-exclusion chromatography revealed distinct and species-specific differences in their association with plasma proteins which likely rationalizes their behavior in animals. Overall, our data suggest that modulating binding to plasma proteins can influence ASO activity and distribution to extra-hepatic tissues in a species-dependent manner and sets the stage to identify other strategies to enhance ASO potency in muscle tissues.
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Affiliation(s)
| | - Michaela Jackson
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Richard G Lee
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Rachel Q Peralta
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jinghua Yu
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Amy Dan
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Rick Carty
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael Tanowitz
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Patrick Anderson
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Tae-Won Kim
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Linda Fradkin
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Adam E Mullick
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Sue Murray
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - C Frank Bennett
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hans J Gaus
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
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49
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McMillan HJ, Amid A, Gonorazky H, Almobarak S, Campbell C. Drisapersen associated with elevated serum factor VIII levels in Duchenne muscular dystrophy. Neurology 2020; 94:538-540. [PMID: 32075891 DOI: 10.1212/wnl.0000000000009139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/14/2020] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hugh J McMillan
- From the Department of Pediatrics (H.J.M., A.A.), Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa; Department of Pediatrics (H.G.), Sick Kids Hospital, University of Toronto, Toronto; and Department of Pediatrics (S.A., C.C.), London Children's Hospital, University of Western Ontario, London, Ontario, Canada.
| | - Ali Amid
- From the Department of Pediatrics (H.J.M., A.A.), Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa; Department of Pediatrics (H.G.), Sick Kids Hospital, University of Toronto, Toronto; and Department of Pediatrics (S.A., C.C.), London Children's Hospital, University of Western Ontario, London, Ontario, Canada
| | - Hernan Gonorazky
- From the Department of Pediatrics (H.J.M., A.A.), Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa; Department of Pediatrics (H.G.), Sick Kids Hospital, University of Toronto, Toronto; and Department of Pediatrics (S.A., C.C.), London Children's Hospital, University of Western Ontario, London, Ontario, Canada
| | - Sulaiman Almobarak
- From the Department of Pediatrics (H.J.M., A.A.), Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa; Department of Pediatrics (H.G.), Sick Kids Hospital, University of Toronto, Toronto; and Department of Pediatrics (S.A., C.C.), London Children's Hospital, University of Western Ontario, London, Ontario, Canada
| | - Craig Campbell
- From the Department of Pediatrics (H.J.M., A.A.), Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa; Department of Pediatrics (H.G.), Sick Kids Hospital, University of Toronto, Toronto; and Department of Pediatrics (S.A., C.C.), London Children's Hospital, University of Western Ontario, London, Ontario, Canada
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50
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Zhao J, Kennedy SD, Berger KD, Turner DH. Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:1968-1984. [PMID: 31904966 DOI: 10.1021/acs.jctc.9b00912] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA and DNA are rapidly emerging as targets for therapeutics and as potential frameworks for nanotechnology. Accurate methods for predicting and designing structures and dynamics of nucleic acids would accelerate progress in these and other applications. Suitable approximations for modeling nucleic acids are being developed but require validation against disparate experimental observations. Here, nuclear magnetic resonance spectra for RNA and DNA single strands, CAAU and UCAAUC, are used as benchmarks to test molecular dynamics simulations with AMBER force fields OL3 and ROC-RNA for RNA and BSC1 for DNA. A detailed scheme for making comparisons is also presented. The results reflect recent progress in approximations and reveal remaining challenges.
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Affiliation(s)
- Jianbo Zhao
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| | - Scott D Kennedy
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.,Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Kyle D Berger
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.,Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
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