1
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Etxaniz U, Marks I, Albin T, Diaz M, Bhardwaj R, Anderson A, Tyaglo O, Hoang T, Missinato MA, Svensson K, Badillo B, Kovach PR, Leung L, Cochran M, Kwon HW, Ahad Shah MN, Maruyama R, Yokota T, Doppalapudi VR, Darimont B, Younis H, Flanagan WM, Levin AA, Huang H, Karamanlidis G. AOC 1044 induces exon 44 skipping and restores dystrophin protein in preclinical models of Duchenne muscular dystrophy. Nucleic Acids Res 2025; 53:gkaf241. [PMID: 40183632 PMCID: PMC11969676 DOI: 10.1093/nar/gkaf241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 03/05/2025] [Accepted: 03/18/2025] [Indexed: 04/05/2025] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe disorder caused by mutations in the dystrophin gene, resulting in loss of functional dystrophin protein in muscle. While phosphorodiamidate morpholino oligomers (PMOs) are promising exon-skipping therapeutics aimed at restoring dystrophin expression, their effectiveness is often limited by poor muscle delivery. We developed AOC 1044, an antibody-oligonucleotide conjugate (AOC) that combines a PMO-targeting exon 44 with an antibody against the transferrin receptor (TfR1), enhancing delivery to muscle tissues for patients with DMD amenable to exon 44 skipping (DMD44). AOC 1044 induces dose-dependent exon 44 skipping and its mouse-active variant elicited dose-dependent dystrophin restoration in skeletal and cardiac muscle in a DMD mouse model. This treatment also reduced muscle damage, as evidenced by decreases in serum creatine kinase and key liver enzymes, suggesting that restored dystrophin is functionally active. In nonhuman primates, single or repeated AOC 1044 doses resulted in dose-dependent increases in PMO concentration and exon 44 skipping across a range of muscle tissues, including the heart. Collectively, these findings highlight AOC 1044 as a promising therapeutic candidate for patients with DMD44, offering improved muscle targeting and meaningful dystrophin restoration, with potential clinical benefits in reducing muscle degeneration.
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MESH Headings
- Animals
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/drug therapy
- Muscular Dystrophy, Duchenne/pathology
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/therapy
- Dystrophin/genetics
- Dystrophin/metabolism
- Exons
- Mice
- Disease Models, Animal
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/pathology
- Morpholinos
- Humans
- Mice, Inbred mdx
- Male
- Receptors, Transferrin/immunology
- Receptors, Transferrin/antagonists & inhibitors
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Affiliation(s)
- Usue Etxaniz
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Isaac Marks
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Tyler Albin
- Seawolf Therapeutics, 9880 Campus Point Drive, Suite 210, San Diego, CA 92121, United States
| | - Matthew Diaz
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Raghav Bhardwaj
- Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, United States
| | - Aaron Anderson
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Olecya Tyaglo
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Tiffany Hoang
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Maria Azzurra Missinato
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Kristoffer Svensson
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Ben Badillo
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Philip R Kovach
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Laura Leung
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Michael Cochran
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Hae Won Kwon
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Md Nur Ahad Shah
- Yokota Lab, Department of Medical Genetics, University of Alberta, Edmonton,T6G 2H, Canada
| | - Rika Maruyama
- Yokota Lab, Department of Medical Genetics, University of Alberta, Edmonton,T6G 2H, Canada
| | - Toshifumi Yokota
- Yokota Lab, Department of Medical Genetics, University of Alberta, Edmonton,T6G 2H, Canada
| | - Venkata R Doppalapudi
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Beatrice Darimont
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Husam S Younis
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - W Michael Flanagan
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Arthur A Levin
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Hanhua Huang
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
| | - Georgios Karamanlidis
- Avidity Biosciences, Inc., 10578 Science Drive, Suite 125, San Diego, CA 92121, United States
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2
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Oppeneer T, Qi Y, Henshaw J, Larimore K, Melton A, Puoliväli J, Carter C, Fant P, Brennan S, Wetzel LA, Sigg MA, Crawford BE, Magat J, Froelich S, Woloszynek JC, O'Neill CA. Targeting a Novel Site in Exon 51 with Antisense Oligonucleotides Induces Enhanced Exon Skipping in a Mouse Model of Duchenne Muscular Dystrophy. Nucleic Acid Ther 2025; 35:68-80. [PMID: 39916530 DOI: 10.1089/nat.2024.0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2025] Open
Abstract
Exon skipping with antisense oligonucleotides (ASOs) can correct disease-causing mutations of Duchenne muscular dystrophy (DMD) through RNA-targeted splice correction. This correction restores the reading frame and supports expression of near full-length dystrophin. First-generation exon 51-skipping ASOs targeted the same binding site, with limited clinical efficacy. We characterized a novel binding site within exon 51 that induced highly efficient exon skipping. A precursor ASO (AON-C12) and clinical ASO (BMN 351) were designed using 2'-O-methyl-modified phosphorothioate (2'OMePS) RNA and locked nucleic acids. hDMDdel52/mdx mice were given AON-C12 or BMN 351 for 13 weeks and evaluated for molecular and phenotypic correction of dystrophin deficiency. BMN 351 treatment induced durable, dose-dependent levels of exon skipping and dystrophin production in all muscles evaluated. In the heart, 8 weeks after the last BMN 351 dose at 18 mg/kg, exon-skipped transcripts remained at 44.3% of total, and dystrophin levels were 21.8% of wild type. BMN 351 reached higher tissue concentrations and percent exon skipping in the heart than a clinically relevant peptide-conjugated phosphorodiamidate morpholino oligomer comparator. BMN 351 also improved gait scores and clinical and anatomical muscle pathology parameters compared with vehicle-treated hDMDdel52/mdx mice. The pharmacologic activity and safety of BMN 351 warrant further nonclinical and clinical development.
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MESH Headings
- Animals
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/therapy
- Muscular Dystrophy, Duchenne/pathology
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/administration & dosage
- Exons/genetics
- Dystrophin/genetics
- Dystrophin/metabolism
- Mice
- Mice, Inbred mdx
- Disease Models, Animal
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscle, Skeletal/drug effects
- RNA Splicing
- Binding Sites
- Genetic Therapy
- Male
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Affiliation(s)
| | - Yulan Qi
- BioMarin Pharmaceutical Inc., San Rafael, CA, USA
| | | | | | | | | | | | - Pierluigi Fant
- Charles River Laboratories France Safety Assessment SAS, Saint-Germain-Nuelles, France
| | | | | | | | | | - Jenna Magat
- BioMarin Pharmaceutical Inc., San Rafael, CA, USA
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3
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Cochran M, Marks I, Albin T, Arias D, Kovach P, Darimont B, Huang H, Etxaniz U, Kwon HW, Shi Y, Diaz M, Tyaglo O, Levin A, Doppalapudi VR. Structure-Activity Relationship of Antibody-Oligonucleotide Conjugates: Evaluating Bioconjugation Strategies for Antibody-Phosphorodiamidate Morpholino Oligomer Conjugates for Drug Development. J Med Chem 2024; 67:14868-14884. [PMID: 39197837 PMCID: PMC11403617 DOI: 10.1021/acs.jmedchem.4c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2024]
Abstract
Antibody-oligonucleotide conjugates (AOCs) are promising treatments for Duchenne muscular dystrophy (DMD). They work via induction of exon skipping and restoration of dystrophin protein in skeletal and heart muscles. The structure-activity relationships (SARs) of AOCs comprising antibody-phosphorodiamidate morpholino oligomers (PMOs) depend on several aspects of their component parts. We evaluate the SAR of antimouse transferrin receptor 1 antibody (αmTfR1)-PMO conjugates: cleavable and noncleavable linkers, linker location on the PMO, and the impact of drug-to-antibody ratios (DARs) on plasma pharmacokinetics (PK), oligonucleotide delivery to tissues, and exon skipping. AOCs containing a stable linker with a DAR9.7 were the most effective PMO delivery vehicles in preclinical studies. We demonstrate that αmTfR1-PMO conjugates induce dystrophin protein restoration in the skeletal and heart muscles of mdx mice. Our results show that αmTfR1-PMO conjugates are a potentially effective approach for the treatment of DMD.
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Affiliation(s)
- Michael Cochran
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Isaac Marks
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Tyler Albin
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Danny Arias
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Philip Kovach
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | | | - Hanhua Huang
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Usue Etxaniz
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Hae Won Kwon
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Yunyu Shi
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Matthew Diaz
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Olecya Tyaglo
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Arthur Levin
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
| | - Venkata Ramana Doppalapudi
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125, San Diego, California 92121, United States
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4
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Mora J, Palmer R, Wagner L, Wu B, Partridge M, Meena, Sonderegger I, Smeraglia J, Bivi N, Dakappagari N, Diebold S, Garofolo F, Grimaldi C, Kalina W, Kamerud J, Kar S, Marshall JC, Mayer C, Melton A, Merdek K, Nolan K, Picard S, Shao W, Seitzer J, Tanaka Y, Tounekti O, Vigil A, Walravens K, Xu J, Xu W, Xu Y, Yang L, Zhu L, Verthelyi D, Kubiak RJ, Coble K, Gupta S, Abhari MR, Richards S, Song Y, Ullmann M, Calderon B, Cludts I, Gunn GR, Gupta S, Ishii-Watabe A, Manangeeswaran M, Maxfield K, McCush F, O'Day C, Peng K, Poetzl J, Rasamoelisolo M, Saad OM, Scheibner K, Shubow S, Song S, Thacker S. 2023 White Paper on Recent Issues in Bioanalysis: ISR for ADA Assays, the Rise of dPCR vs qPCR, International Reference Standards for Vaccine Assays, Anti-AAV TAb Post-Dose Assessment, NanoString Validation, ELISpot as Gold Standard (Part 3 - Recommendations on Gene Therapy, Cell Therapy, Vaccines Immunogenicity & Technologies; Biotherapeutics Immunogenicity & Risk Assessment; ADA/NAb Assay/Reporting Harmonization). Bioanalysis 2024; 16:77-119. [PMID: 38389403 DOI: 10.4155/bio-2024-0024] [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: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
The 17th Workshop on Recent Issues in Bioanalysis (17th WRIB) took place in Orlando, FL, USA on June 19-23, 2023. Over 1000 professionals representing pharma/biotech companies, CROs, and multiple regulatory agencies convened to actively discuss the most current topics of interest in bioanalysis. The 17th WRIB included 3 Main Workshops and 7 Specialized Workshops that together spanned 1 week to allow an exhaustive and thorough coverage of all major issues in bioanalysis of biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on "EU IVDR 2017/746 Implementation and impact for the Global Biomarker Community: How to Comply with these NEW Regulations" and on "US FDA/OSIS Remote Regulatory Assessments (RRAs)" were the special features of the 17th edition. As in previous years, WRIB continued to gather a wide diversity of international, industry opinion leaders and regulatory authority experts working on both small and large molecules as well as gene, cell therapies and vaccines to facilitate sharing and discussions focused on improving quality, increasing regulatory compliance, and achieving scientific excellence on bioanalytical issues. This 2023 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2023 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations on Gene Therapy, Cell therapy, Vaccines and Biotherapeutics Immunogenicity. Part 1A (Mass Spectrometry Assays and Regulated Bioanalysis/BMV), P1B (Regulatory Inputs) and Part 2 (Biomarkers, IVD/CDx, LBA and Cell-Based Assays) are published in volume 16 of Bioanalysis, issues 8 and 9 (2024), respectively.
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Affiliation(s)
| | | | | | | | | | - Meena
- Stoke, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Joshua Xu
- US FDA, Jefferson, AR, USA
- Regenxbio, Rockville, MD, USA
| | | | | | - Lin Yang
- US FDA, Jefferson, AR, USA
- Regenxbio, Rockville, MD, USA
| | | | | | | | | | | | | | | | - Yuan Song
- Genentech, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - Kate Peng
- Genentech, South San Francisco, CA, USA
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5
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Hays A, Wissel M, Colletti K, Soon R, Azadeh M, Smith J, Doddareddy R, Chalfant M, Adamowicz W, Ramaswamy SS, Dholakiya SL, Guelman S, Gullick B, Durham J, Rennier K, Nagilla P, Muruganandham A, Diaz M, Tierney C, John K, Valentine J, Lockman T, Liu HY, Moritz B, Ouedraogo JP, Piche MS, Smet M, Murphy J, Koenig K, Zybura A, Vyhlidal C, Mercier J, Jani N, Kubista M, Birch D, Morse K, Johansson O. Recommendations for Method Development and Validation of qPCR and dPCR Assays in Support of Cell and Gene Therapy Drug Development. AAPS J 2024; 26:24. [PMID: 38316745 DOI: 10.1208/s12248-023-00880-9] [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: 09/04/2023] [Accepted: 12/06/2023] [Indexed: 02/07/2024] Open
Abstract
The emerging use of qPCR and dPCR in regulated bioanalysis and absence of regulatory guidance on assay validations for these platforms has resulted in discussions on lack of harmonization on assay design and appropriate acceptance criteria for these assays. Both qPCR and dPCR are extensively used to answer bioanalytical questions for novel modalities such as cell and gene therapies. Following cross-industry conversations on the lack of information and guidelines for these assays, an American Association of Pharmaceutical Scientists working group was formed to address these gaps by bringing together 37 industry experts from 24 organizations to discuss best practices to gain a better understanding in the industry and facilitate filings to health authorities. Herein, this team provides considerations on assay design, development, and validation testing for PCR assays that are used in cell and gene therapies including (1) biodistribution; (2) transgene expression; (3) viral shedding; (4) and persistence or cellular kinetics of cell therapies.
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Affiliation(s)
- Amanda Hays
- BioAgilytix Laboratories, Durham, North Carolina, USA.
| | - Mark Wissel
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | - Russell Soon
- BioMarin Pharmaceutical Inc., Novato, California, USA
| | - Mitra Azadeh
- Ultragenyx Pharmaceutical Inc., Novato, Calfornia, USA
| | | | | | | | - Wendy Adamowicz
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | | | | | | | - Bryan Gullick
- BioAgilytix Laboratories, Durham, North Carolina, USA
| | | | | | - Pruthvi Nagilla
- Asher Biotherapeutics, Inc., South San Francisco, California, USA
| | | | - Manisha Diaz
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | | | | | - Timothy Lockman
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | - Hsing-Yin Liu
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | | | | | | | - Jacqueline Murphy
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Kaylyn Koenig
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Agnes Zybura
- Labcorp Drug Development, Greenfield, Indiana, USA
| | - Carrie Vyhlidal
- KCAS Bioanalytical and Biomarker Services, Shawnee, Kansas, USA
| | | | - Niketa Jani
- BioAgilytix Laboratories, Boston, Massachusetts, USA
| | - Mikael Kubista
- Institute of Biotechnology Czech Academy of Sciences, Prague, Czech Republic
| | - Donald Birch
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Karlin Morse
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
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6
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McDonald C, Camino E, Escandon R, Finkel RS, Fischer R, Flanigan K, Furlong P, Juhasz R, Martin AS, Villa C, Sweeney HL. Draft Guidance for Industry Duchenne Muscular Dystrophy, Becker Muscular Dystrophy, and Related Dystrophinopathies - Developing Potential Treatments for the Entire Spectrum of Disease. J Neuromuscul Dis 2024; 11:499-523. [PMID: 38363616 DOI: 10.3233/jnd-230219] [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] [Indexed: 02/17/2024]
Abstract
Background Duchenne muscular dystrophy (DMD) and related dystrophinopathies are neuromuscular conditions with great unmet medical needs that require the development of effective medical treatments. Objective To aid sponsors in clinical development of drugs and therapeutic biological products for treating DMD across the disease spectrum by integrating advancements, patient registries, natural history studies, and more into a comprehensive guidance. Methods This guidance emerged from collaboration between the FDA, the Duchenne community, and industry stakeholders. It entailed a structured approach, involving multiple committees and boards. From its inception in 2014, the guidance underwent revisions incorporating insights from gene therapy studies, cardiac function research, and innovative clinical trial designs. Results The guidance provides a deeper understanding of DMD and its variants, focusing on patient engagement, diagnostic criteria, natural history, biomarkers, and clinical trials. It underscores patient-focused drug development, the significance of dystrophin as a biomarker, and the pivotal role of magnetic resonance imaging in assessing disease progression. Additionally, the guidance addresses cardiomyopathy's prominence in DMD and the burgeoning field of gene therapy. Conclusions The updated guidance offers a comprehensive understanding of DMD, emphasizing patient-centric approaches, innovative trial designs, and the importance of biomarkers. The focus on cardiomyopathy and gene therapy signifies the evolving realm of DMD research. It acts as a crucial roadmap for sponsors, potentially leading to improved treatments for DMD.
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Affiliation(s)
| | - Eric Camino
- Parent Project Muscular Dystrophy, Washington, DC, USA
| | - Rafael Escandon
- DGBI Consulting, LLC, Bainbridge Island, Washington, DC, USA
| | | | - Ryan Fischer
- Parent Project Muscular Dystrophy, Washington, DC, USA
| | - Kevin Flanigan
- Center for Experimental Neurotherapeutics, Department of Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pat Furlong
- Parent Project Muscular Dystrophy, Washington, DC, USA
| | - Rose Juhasz
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Ann S Martin
- Parent Project Muscular Dystrophy, Washington, DC, USA
| | - Chet Villa
- Trinity Health Michigan, Grand Rapids, MI, USA
| | - H Lee Sweeney
- Cincinnati Children's Hospital Medical Center within the UC Department of Pediatrics, Cincinnati, OH, USA
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7
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Barman SD, Frimand Z, De Morree A. Absolute Quantification of mRNA Isoforms in Adult Stem Cells Using Microfluidic Digital PCR. Bio Protoc 2023; 13:e4811. [PMID: 37719075 PMCID: PMC10501916 DOI: 10.21769/bioprotoc.4811] [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: 01/27/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 09/19/2023] Open
Abstract
Adult stem cells play key roles in homeostasis and tissue repair. These cells are regulated by a tight control of transcriptional programs. For example, muscle stem cells (MuSCs), located beneath the basal lamina, exist in the quiescent state but can transition to an activated, proliferative state upon injury. The control of MuSC state depends on the expression levels of myogenic transcription factors. Recent studies revealed the presence of different mRNA isoforms, with distinct biological regulation. Quantifying the exact expression levels of the mRNA isoforms encoding these myogenic transcription factors is therefore key to understanding how MuSCs switch between cell states. Previously, quantitative real-time polymerase chain reaction (qRT-PCR) has been used to quantify RNA expression levels. However, qRT-PCR depends on large amounts of RNA input and only measures relative abundance. Here, we present a protocol for the absolute quantification of mRNA isoforms using microfluidic digital PCR (mdPCR). Primary MuSCs isolated from individual skeletal muscles (gastrocnemius and masseter) are lysed, and their RNA is reverse-transcribed into cDNA and copied into double-stranded DNA. Following exonuclease I digestion to remove remaining single-stranded DNA, the samples are loaded onto a mdPCR chip with TaqMan probes targeting the mRNA isoforms of interest, whereupon target molecules are amplified in nanoliter chambers. We demonstrate that mdPCR can give exact molecule counts per cell for mRNA isoforms encoding the myogenic transcription factor Pax3. This protocol enables the absolute quantification of low abundant mRNA isoforms in a fast, precise, and reliable way.
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Affiliation(s)
| | - Zofija Frimand
- Department of Biomedicine, Aarhus University, Central Jutland, Denmark
| | - Antoine De Morree
- Department of Biomedicine, Aarhus University, Central Jutland, Denmark
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8
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Hu N, Kim E, Antoury L, Wheeler TM. Correction of Clcn1 alternative splicing reverses muscle fiber type transition in mice with myotonic dystrophy. Nat Commun 2023; 14:1956. [PMID: 37029100 PMCID: PMC10082032 DOI: 10.1038/s41467-023-37619-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
In myotonic dystrophy type 1 (DM1), deregulated alternative splicing of the muscle chloride channel Clcn1 causes myotonia, a delayed relaxation of muscles due to repetitive action potentials. The degree of weakness in adult DM1 is associated with increased frequency of oxidative muscle fibers. However, the mechanism for glycolytic-to-oxidative fiber type transition in DM1 and its relationship to myotonia are uncertain. Here we cross two mouse models of DM1 to create a double homozygous model that features progressive functional impairment, severe myotonia, and near absence of type 2B glycolytic fibers. Intramuscular injection of an antisense oligonucleotide for targeted skipping of Clcn1 exon 7a corrects Clcn1 alternative splicing, increases glycolytic 2B levels to ≥ 40% frequency, reduces muscle injury, and improves fiber hypertrophy relative to treatment with a control oligo. Our results demonstrate that fiber type transitions in DM1 result from myotonia and are reversible, and support the development of Clcn1-targeting therapies for DM1.
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Affiliation(s)
- Ningyan Hu
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eunjoo Kim
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Layal Antoury
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thurman M Wheeler
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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9
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Poyatos‐García J, Martí P, Liquori A, Muelas N, Pitarch I, Martinez‐Dolz L, Rodríguez B, Gonzalez‐Quereda L, Damiá M, Aller E, Selva‐Gimenez M, Vilchez R, Diaz‐Manera J, Alonso‐Pérez J, Barcena JE, Jauregui A, Gámez J, Aladrén JA, Fernández A, Montolio M, Azorin I, Hervas D, Casasús A, Nieto M, Gallano P, Sevilla T, Vilchez JJ. Dystrophinopathy Phenotypes and Modifying Factors in DMD Exon 45-55 Deletion. Ann Neurol 2022; 92:793-806. [PMID: 35897138 PMCID: PMC9825930 DOI: 10.1002/ana.26461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Duchenne muscular dystrophy (DMD) exon 45-55 deletion (del45-55) has been postulated as a model that could treat up to 60% of DMD patients, but the associated clinical variability and complications require clarification. We aimed to understand the phenotypes and potential modifying factors of this dystrophinopathy subset. METHODS This cross-sectional, multicenter cohort study applied clinical and functional evaluation. Next generation sequencing was employed to identify intronic breakpoints and their impact on the Dp140 promotor, intronic long noncoding RNA, and regulatory splicing sequences. DMD modifiers (SPP1, LTBP4, ACTN3) and concomitant mutations were also assessed. Haplotypes were built using DMD single nucleotide polymorphisms. Dystrophin expression was evaluated via immunostaining, Western blotting, reverse transcription polymerase chain reaction (PCR), and droplet digital PCR in 9 muscle biopsies. RESULTS The series comprised 57 subjects (23 index) expressing Becker phenotype (28%), isolated cardiopathy (19%), and asymptomatic features (53%). Cognitive impairment occurred in 90% of children. Patients were classified according to 10 distinct index-case breakpoints; 4 of them were recurrent due to founder events. A specific breakpoint (D5) was associated with severity, but no significant effect was appreciated due to the changes in intronic sequences. All biopsies showed dystrophin expression of >67% and traces of alternative del45-57 transcript that were not deemed pathogenically relevant. Only the LTBP4 haplotype appeared associated the presence of cardiopathy among the explored extragenic factors. INTERPRETATION We confirmed that del45-55 segregates a high proportion of benign phenotypes, severe cases, and isolated cardiac and cognitive presentations. Although some influence of the intronic breakpoint position and the LTBP4 modifier may exist, the pathomechanisms responsible for the phenotypic variability remain largely unresolved. ANN NEUROL 2022;92:793-806.
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Affiliation(s)
- Javier Poyatos‐García
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Pilar Martí
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Alessandro Liquori
- Hematology Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Cancer (CIBERONC); CB16/12/00284MadridSpain
| | - Nuria Muelas
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain
| | - Inmaculada Pitarch
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Neuropediatric DepartmentUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Luis Martinez‐Dolz
- Cardiology DepartmentUniversity and Polytechnic La Fe Hospital, IIS La FeValenciaSpain,Centre for Biomedical Network Research on Cardiovascular Diseases (CIBERCV)ValenciaSpain
| | - Benjamin Rodríguez
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Lidia Gonzalez‐Quereda
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Maria Damiá
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Neuropediatric DepartmentUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Elena Aller
- Genetics UnitUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Marta Selva‐Gimenez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Roger Vilchez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Jordi Diaz‐Manera
- Neuromuscular Disorders Unit, Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Hospital of Sant PauBarcelonaSpain,Autonomous University of BarcelonaBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U762, CB06/05/0030BarcelonaSpain
| | - Jorge Alonso‐Pérez
- Neuromuscular Disorders Unit, Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Hospital of Sant PauBarcelonaSpain,Autonomous University of BarcelonaBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U762, CB06/05/0030BarcelonaSpain
| | - José Eulalio Barcena
- Neuromuscular Section, Neurology ServiceCruces University HospitalBarakaldoSpain
| | - Amaia Jauregui
- Neuromuscular Section, Neurology ServiceCruces University HospitalBarakaldoSpain
| | - Josep Gámez
- Autonomous University of BarcelonaBarcelonaSpain,Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)GMA ClinicBarcelonaSpain
| | | | | | - Marisol Montolio
- Duchenne Parent Project SpainMadridSpain,Department of Cell Biology, Physiology, and Immunology, Faculty of BiologyBarcelonaSpain
| | - Inmaculada Azorin
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - David Hervas
- Department of Applied Statistics and Operations Research, and QualityPolytechnic University of ValenciaValenciaSpain
| | - Ana Casasús
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Marisa Nieto
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Pia Gallano
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Teresa Sevilla
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Department of MedicineUniversity of ValenciaValenciaSpain
| | - Juan Jesus Vilchez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Department of MedicineUniversity of ValenciaValenciaSpain
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10
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Cohen SA, Bar-Am O, Fuoco C, Saar G, Gargioli C, Seliktar D. In vivo restoration of dystrophin expression in mdx mice using intra-muscular and intra-arterial injections of hydrogel microsphere carriers of exon skipping antisense oligonucleotides. Cell Death Dis 2022; 13:779. [PMID: 36085138 PMCID: PMC9463190 DOI: 10.1038/s41419-022-05166-0] [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: 08/10/2021] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 01/21/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a genetic disease caused by a mutation in the X-linked Dytrophin gene preventing the expression of the functional protein. Exon skipping therapy using antisense oligonucleotides (AONs) is a promising therapeutic strategy for DMD. While benefits of AON therapy have been demonstrated, some challenges remain before this strategy can be applied more comprehensively to DMD patients. These include instability of AONs due to low nuclease resistance and poor tissue uptake. Delivery systems have been examined to improve the availability and stability of oligonucleotide drugs, including polymeric carriers. Previously, we showed the potential of a hydrogel-based polymeric carrier in the form of injectable PEG-fibrinogen (PF) microspheres for delivery of chemically modified 2'-O-methyl phosphorothioate (2OMePs) AONs. The PF microspheres proved to be cytocompatible and provided sustained release of the AONs for several weeks, causing increased cellular uptake in mdx dystrophic mouse cells. Here, we further investigated this delivery strategy by examining in vivo efficacy of this approach. The 2OMePS/PEI polyplexes loaded in PF microspheres were delivered by intramuscular (IM) or intra-femoral (IF) injections. We examined the carrier biodegradation profiles, AON uptake efficiency, dystrophin restoration, and muscle histopathology. Both administration routes enhanced dystrophin restoration and improved the histopathology of the mdx mice muscles. The IF administration of the microspheres improved the efficacy of the 2OMePS AONs over the IM administration. This was demonstrated by a higher exon skipping percentage and a smaller percentage of centered nucleus fibers (CNF) found in H&E-stained muscles. The restoration of dystrophin expression found for both IM and IF treatments revealed a reduced dystrophic phenotype of the treated muscles. The study concludes that injectable PF microspheres can be used as a carrier system to improve the overall therapeutic outcomes of exon skipping-based therapy for treating DMD.
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Affiliation(s)
- Shani Attias Cohen
- grid.6451.60000000121102151Faculty of Biomedical Engineering, Technion–Israel Institute of Technology, Haifa, Israel
| | - Orit Bar-Am
- grid.6451.60000000121102151Faculty of Biomedical Engineering, Technion–Israel Institute of Technology, Haifa, Israel
| | - Claudia Fuoco
- grid.6530.00000 0001 2300 0941Department of Biology, Rome University Tor Vergata, Rome, Italy
| | - Galit Saar
- grid.6451.60000000121102151Biomedical Core Facility, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Cesare Gargioli
- grid.6530.00000 0001 2300 0941Department of Biology, Rome University Tor Vergata, Rome, Italy
| | - Dror Seliktar
- grid.6451.60000000121102151Faculty of Biomedical Engineering, Technion–Israel Institute of Technology, Haifa, Israel
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11
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Sagath L, Lehtokari VL, Wallgren-Pettersson C, Pelin K, Kiiski K. A custom ddPCR method for the detection of copy number variations in the nebulin triplicate region. PLoS One 2022; 17:e0267793. [PMID: 35576196 PMCID: PMC9109913 DOI: 10.1371/journal.pone.0267793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
The human genome contains repetitive regions, such as segmental duplications, known to be prone to copy number variation. Segmental duplications are highly identical and homologous sequences, posing a specific challenge for most mutation detection methods. The giant nebulin gene is expressed in skeletal muscle. It harbors a large segmental duplication region composed of eight exons repeated three times, the so-called triplicate region. Mutations in nebulin are known to cause nemaline myopathy and other congenital myopathies. Using our custom targeted Comparative Genomic Hybridization arrays, we have previously shown that copy number variations in the nebulin triplicate region are pathogenic when the copy number of the segmental duplication block deviates two or more copies from the normal number, which is three per allele. To complement our Comparative Genomic Hybridization arrays, we have established a custom Droplet Digital PCR method for the detection of copy number variations within the nebulin triplicate region. The custom Droplet Digital PCR assays allow sensitive, rapid, high-throughput, and cost-effective detection of copy number variations within this region and is ready for implementation a screening method for disease-causing copy number variations of the nebulin triplicate region. We suggest that Droplet Digital PCR may also be used in the study and diagnostics of other segmental duplication regions of the genome.
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Affiliation(s)
- Lydia Sagath
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- * E-mail: , (LS); (KK)
| | - Vilma-Lotta Lehtokari
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Carina Wallgren-Pettersson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Katarina Pelin
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kirsi Kiiski
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- * E-mail: , (LS); (KK)
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12
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Lambrescu I, Popa A, Manole E, Ceafalan LC, Gaina G. Application of Droplet Digital PCR Technology in Muscular Dystrophies Research. Int J Mol Sci 2022; 23:ijms23094802. [PMID: 35563191 PMCID: PMC9099497 DOI: 10.3390/ijms23094802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Although they are considered rare disorders, muscular dystrophies have a strong impact on people’s health. Increased disease severity with age, frequently accompanied by the loss of ability to walk in some people, and the lack of treatment, have directed the researchers towards the development of more effective therapeutic strategies aimed to improve the quality of life and life expectancy, slow down the progression, and delay the onset or convert a severe phenotype into a milder one. Improved understanding of the complex pathology of these diseases together with the tremendous advances in molecular biology technologies has led to personalized therapeutic procedures. Different approaches that are currently under extensive investigation require more efficient, sensitive, and less invasive methods. Due to its remarkable analytical sensitivity, droplet digital PCR has become a promising tool for accurate measurement of biomarkers that monitor disease progression and quantification of various therapeutic efficiency and can be considered a tool for non-invasive prenatal diagnosis and newborn screening. Here, we summarize the recent applications of droplet digital PCR in muscular dystrophy research and discuss the factors that should be considered to get the best performance with this technology.
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Affiliation(s)
- Ioana Lambrescu
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Alexandra Popa
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Animal Production and Public Health, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 050097 Bucharest, Romania
| | - Emilia Manole
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Laura Cristina Ceafalan
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Correspondence: ; Tel.: +40-21-319-2732
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13
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López-Martínez A, Soblechero-Martín P, Arechavala-Gomeza V. Evaluation of Exon Skipping and Dystrophin Restoration in In Vitro Models of Duchenne Muscular Dystrophy. Methods Mol Biol 2022; 2434:217-233. [PMID: 35213020 PMCID: PMC9703204 DOI: 10.1007/978-1-0716-2010-6_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Several exon skipping antisense oligonucleotides (eteplirsen, golodirsen, viltolarsen, and casimersen) have been approved for the treatment of Duchenne muscular dystrophy, but many more are in development targeting an array of different DMD exons. Preclinical screening of the new oligonucleotide sequences is routinely performed using patient-derived cell cultures, and evaluation of their efficacy may be performed at RNA and/or protein level. While several methods to assess exon skipping and dystrophin expression in cell culture have been developed, the choice of methodology often depends on the availability of specific research equipment.In this chapter, we describe and indicate the relevant bibliography of all the methods that may be used in this evaluation and describe in detail the protocols routinely followed at our institution, one to evaluate the efficacy of skipping at RNA level (nested PCR) and the other the restoration of protein expression (myoblot ), which provide good results using equipment largely available to most research laboratories.
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Affiliation(s)
- Andrea López-Martínez
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Patricia Soblechero-Martín
- Neuromuscular Disorders, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Osakidetza Basque Health Service, Bilbao-Basurto Integrated Health Organisation, Basurto University Hospital, Clinical Laboratory Service, Bilbao, Spain
| | - Virginia Arechavala-Gomeza
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
- Neuromuscular Disorders Research Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.
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14
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Therapeutic Prospects of Exon Skipping for Epidermolysis Bullosa. Int J Mol Sci 2021; 22:ijms222212222. [PMID: 34830104 PMCID: PMC8621297 DOI: 10.3390/ijms222212222] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Epidermolysis bullosa is a group of genetic skin conditions characterized by abnormal skin (and mucosal) fragility caused by pathogenic variants in various genes. The disease severity ranges from early childhood mortality in the most severe types to occasional acral blistering in the mildest types. The subtype and severity of EB is linked to the gene involved and the specific variants in that gene, which also determine its mode of inheritance. Current treatment is mainly focused on symptomatic relief such as wound care and blister prevention, because truly curative treatment options are still at the preclinical stage. Given the current level of understanding, the broad spectrum of genes and variants underlying EB makes it impossible to develop a single treatment strategy for all patients. It is likely that many different variant-specific treatment strategies will be needed to ultimately treat all patients. Antisense-oligonucleotide (ASO)-mediated exon skipping aims to counteract pathogenic sequence variants by restoring the open reading frame through the removal of the mutant exon from the pre-messenger RNA. This should lead to the restored production of the protein absent in the affected skin and, consequently, improvement of the phenotype. Several preclinical studies have demonstrated that exon skipping can restore protein production in vitro, in skin equivalents, and in skin grafts derived from EB-patient skin cells, indicating that ASO-mediated exon skipping could be a viable strategy as a topical or systemic treatment. The potential value of exon skipping for EB is supported by a study showing reduced phenotypic severity in patients who carry variants that result in natural exon skipping. In this article, we review the substantial progress made on exon skipping for EB in the past 15 years and highlight the opportunities and current challenges of this RNA-based therapy approach. In addition, we present a prioritization strategy for the development of exon skipping based on genomic information of all EB-involved genes.
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15
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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16
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Jin P, Gao X, Wang M, Qian Y, Yang J, Yang Y, Xu Y, Xu Y, Dong M. Case Report: Identification of Maternal Low-Level Mosaicism in the Dystrophin Gene by Droplet Digital Polymerase Chain Reaction. Front Genet 2021; 12:686993. [PMID: 34276787 PMCID: PMC8280780 DOI: 10.3389/fgene.2021.686993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 04/27/2021] [Indexed: 01/12/2023] Open
Abstract
Germline mosaicism should be suspected when the same de novo mutations are identified in a second pregnancy with asymptomatic parents. Our study aims to find a feasible approach to reveal the existence of germline mosaicism. Multiplex Ligation-dependent Probe Amplification was performed on a Duchenne muscular dystrophy affected pedigree to detect deletion mutations. Then gap-polymerase chain reaction was performed to amplify the breakpoints junction sequence. Droplet digital polymerase chain reaction was utilized to identify the mutation frequencies in healthy parents. The same deletion in the exon 51 of the dystrophin gene, which was 50,035 bp in size, was detected in the proband and the fetus but not in their parents. Droplet digital polymerase chain reaction analysis of peripheral blood samples revealed mutant alleles of 3.53% in maternal blood cells. We here report a case of maternal low-level mosaicism confirmed by droplet digital polymerase chain reaction in peripheral blood samples, which reveals the existence of germline mosaicism. Gap-polymerase chain reaction combined with droplet digital polymerase chain reaction provide insights into the detection of germline mosaicism.
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Affiliation(s)
- Pengzhen Jin
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Xiaoyang Gao
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Miaomiao Wang
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yeqing Qian
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Jingjin Yang
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yanmei Yang
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yuqing Xu
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yanfei Xu
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Minyue Dong
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China
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17
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Yavas A, Weij R, van Putten M, Kourkouta E, Beekman C, Puoliväli J, Bragge T, Ahtoniemi T, Knijnenburg J, Hoogenboom ME, Ariyurek Y, Aartsma-Rus A, van Deutekom J, Datson N. Detailed genetic and functional analysis of the hDMDdel52/mdx mouse model. PLoS One 2020; 15:e0244215. [PMID: 33362201 PMCID: PMC7757897 DOI: 10.1371/journal.pone.0244215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/07/2020] [Indexed: 01/30/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe, progressive neuromuscular disorder caused by reading frame disrupting mutations in the DMD gene leading to absence of functional dystrophin. Antisense oligonucleotide (AON)-mediated exon skipping is a therapeutic approach aimed at restoring the reading frame at the pre-mRNA level, allowing the production of internally truncated partly functional dystrophin proteins. AONs work in a sequence specific manner, which warrants generating humanized mouse models for preclinical tests. To address this, we previously generated the hDMDdel52/mdx mouse model using transcription activator like effector nuclease (TALEN) technology. This model contains mutated murine and human DMD genes, and therefore lacks mouse and human dystrophin resulting in a dystrophic phenotype. It allows preclinical evaluation of AONs inducing the skipping of human DMD exons 51 and 53 and resulting in restoration of dystrophin synthesis. Here, we have further characterized this model genetically and functionally. We discovered that the hDMD and hDMDdel52 transgene is present twice per locus, in a tail-to-tail-orientation. Long-read sequencing revealed a partial deletion of exon 52 (first 25 bp), and a 2.3 kb inversion in intron 51 in both copies. These new findings on the genomic make-up of the hDMD and hDMDdel52 transgene do not affect exon 51 and/or 53 skipping, but do underline the need for extensive genetic analysis of mice generated with genome editing techniques to elucidate additional genetic changes that might have occurred. The hDMDdel52/mdx mice were also evaluated functionally using kinematic gait analysis. This revealed a clear and highly significant difference in overall gait between hDMDdel52/mdx mice and C57BL6/J controls. The motor deficit detected in the model confirms its suitability for preclinical testing of exon skipping AONs for human DMD at both the functional and molecular level.
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Affiliation(s)
- Alper Yavas
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rudie Weij
- BioMarin Nederland BV, Leiden, The Netherlands
| | - Maaike van Putten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | - Timo Bragge
- Charles River Discovery Services, Kuopio, Finland
| | | | - Jeroen Knijnenburg
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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18
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Datson NA, Bijl S, Janson A, Testerink J, van den Eijnde R, Weij R, Puoliväli J, Lehtimäki K, Bragge T, Ahtoniemi T, van Deutekom JC. Using a State-of-the-Art Toolbox to Evaluate Molecular and Functional Readouts of Antisense Oligonucleotide-Induced Exon Skipping in mdx Mice. Nucleic Acid Ther 2020; 30:50-65. [PMID: 31821107 PMCID: PMC7049912 DOI: 10.1089/nat.2019.0824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe childhood muscle disease primarily caused by the lack of functional dystrophin at the muscle fiber membranes. Multiple therapeutic approaches are currently in (pre)clinical development, aimed at restoring expression of (truncated) dystrophin. Key questions in this phase relate to route of drug administration, dose regimen, and levels of dystrophin required to improve muscle function. A series of studies applying antisense oligonucleotides (AONs) in the mdx mouse model for DMD has been reported over the last two decades, claiming a variable range of exon skipping and increased dystrophin levels correlated to some functional improvement. The aim of this study was to compare the efficacy of subcutaneous (SC) versus intravenous (IV) dosing routes of an mdx-specific AON at both the molecular and functional level, using state-of-the-art quantitative technologies, including digital droplet polymerase chain reaction, capillary Western immunoassay, magnetic resonance imaging, and automated kinematic analysis. The majority of all readouts we quantified, both molecular and functional, showed that IV dosing of the AON had a more pronounced beneficial effect than SC dosing in mdx mice. Last, but not least, the more quantitative molecular and functional data obtained in this study suggest that low levels of dystrophin protein of at least 2.5% of wild type may already have a beneficial effect on muscle leakiness and may improve motor performance of mdx mice.
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Affiliation(s)
| | | | | | | | | | - Rudie Weij
- BioMarin Nederland BV, Leiden, the Netherlands
| | | | | | - Timo Bragge
- Charles River Discovery Research Services, Kuopio, Finland
| | - Toni Ahtoniemi
- Charles River Discovery Research Services, Kuopio, Finland
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19
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Komaki H, Nagata T, Saito T, Masuda S, Takeshita E, Sasaki M, Tachimori H, Nakamura H, Aoki Y, Takeda S. Systemic administration of the antisense oligonucleotide NS-065/NCNP-01 for skipping of exon 53 in patients with Duchenne muscular dystrophy. Sci Transl Med 2019; 10:10/437/eaan0713. [PMID: 29669851 DOI: 10.1126/scitranslmed.aan0713] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 11/17/2017] [Indexed: 12/12/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a lethal hereditary muscle disease caused by mutations in the gene encoding the muscle protein dystrophin. These mutations result in a shift in the open reading frame leading to loss of the dystrophin protein. Antisense oligonucleotides (ASOs) that induce exon skipping correct this frame shift during pre-mRNA splicing and partially restore dystrophin expression in mouse and dog models. We conducted a phase 1, open-label, dose-escalation clinical trial to determine the safety, pharmacokinetics, and activity of NS-065/NCNP-01, a morpholino ASO that enables skipping of exon 53. Ten patients with DMD (6 to 16 years old), carrying mutations in the dystrophin gene whose reading frame would be restored by exon 53 skipping, were administered NS-065/NCNP-01 at doses of 1.25, 5, or 20 mg/kg weekly for 12 weeks. The primary endpoint was safety; the secondary endpoints were pharmacokinetics and successful exon skipping. No severe adverse drug reactions were observed, and no treatment discontinuation occurred. Muscle biopsy samples were taken before and after treatment and compared by reverse transcription polymerase chain reaction (RT-PCR), immunofluorescence, and Western blotting to assess the amount of exon 53 skipping and dystrophin expression. NS-065/NCNP-01 induced exon 53 skipping in dystrophin-encoding mRNA in a dose-dependent manner and increased the dystrophin/spectrin ratio in 7 of 10 patients. Furthermore, the amount of exon skipping correlated with the maximum drug concentration in plasma (Cmax) and the area under the concentration-time curve in plasma (AUC0-t ). These results indicate that NS-065/NCNP-01 has a favorable safety profile and promising pharmacokinetics warranting further study in a phase 2 clinical trial.
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Affiliation(s)
- Hirofumi Komaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Tetsuya Nagata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Takashi Saito
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Satoru Masuda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Hisateru Tachimori
- Department of Mental Health Administration, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Harumasa Nakamura
- Translational Medical Center, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, Japan.
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20
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Kourkouta E, Weij R, González-Barriga A, Mulder M, Verheul R, Bosgra S, Groenendaal B, Puoliväli J, Toivanen J, van Deutekom JCT, Datson NA. Suppression of Mutant Protein Expression in SCA3 and SCA1 Mice Using a CAG Repeat-Targeting Antisense Oligonucleotide. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:601-614. [PMID: 31394429 PMCID: PMC6695277 DOI: 10.1016/j.omtn.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 10/26/2022]
Abstract
Spinocerebellar ataxia type 3 (SCA3) and type 1 (SCA1) are dominantly inherited neurodegenerative disorders that are currently incurable. Both diseases are caused by a CAG-repeat expansion in exon 10 of the Ataxin-3 and exon 8 of the Ataxin-1 gene, respectively, encoding an elongated polyglutamine tract that confers toxic properties to the resulting proteins. We have previously shown lowering of the pathogenic polyglutamine protein in Huntington's disease mouse models using (CUG)7, a CAG repeat-targeting antisense oligonucleotide. Here we evaluated the therapeutic capacity of (CUG)7 for SCA3 and SCA1, in vitro in patient-derived cell lines and in vivo in representative mouse models. Repeated intracerebroventricular (CUG)7 administration resulted in a significant reduction of mutant Ataxin-3 and Ataxin-1 proteins throughout the brain of SCA3 and SCA1 mouse models, respectively. Furthermore, in both a SCA3 patient cell line and the MJD84.2 mouse model, (CUG)7 induced formation of a truncated Ataxin-3 protein species lacking the polyglutamine stretch, likely arising from (CUG)7-mediated exon 10 skipping. In contrast, skipping of exon 8 of Ataxin-1 did not significantly contribute to the Ataxin-1 protein reduction observed in (CUG)7-treated SCA1154Q/2Q mice. These findings support the therapeutic potential of a single CAG repeat-targeting AON for the treatment of multiple polyglutamine disorders.
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Affiliation(s)
| | - Rudie Weij
- BioMarin Nederland BV, Leiden, the Netherlands
| | | | | | | | | | | | | | - Jussi Toivanen
- Charles River Discovery Research Services, Kuopio, Finland
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21
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Antoury L, Hu N, Darras B, Wheeler TM. Urine mRNA to identify a novel pseudoexon causing dystrophinopathy. Ann Clin Transl Neurol 2019; 6:1106-1112. [PMID: 31211175 PMCID: PMC6562067 DOI: 10.1002/acn3.777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/20/2019] [Indexed: 11/16/2022] Open
Abstract
In muscular dystrophies, identification of pathogenic pseudoexons involves sequencing of the target gene cDNA derived from muscle mRNA. Here we use a urine “liquid biopsy,” droplet digital PCR, and sequencing of PCR products to identify a novel cryptic splice site in DMD intron 67 that causes dystrophinopathy. Pseudoexon inclusion is 35% in urine cells, 34% in urine extracellular RNA (exRNA), and 54% in muscle biopsy tissue, but absent in serum exRNA. Our results suggest that cryptic splice site use varies depending on the RNA source, and that urine RNA has the potential to substitute for muscle biopsies to identify DMD pseudoexons.
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Affiliation(s)
- Layal Antoury
- Department of Neurology Massachusetts General Hospital Boston Massachusetts.,Harvard Medical School Boston Massachusetts
| | - Ningyan Hu
- Department of Neurology Massachusetts General Hospital Boston Massachusetts.,Harvard Medical School Boston Massachusetts
| | - Basil Darras
- Harvard Medical School Boston Massachusetts.,Department of Neurology Boston Children's Hospital Boston Massachusetts
| | - Thurman M Wheeler
- Department of Neurology Massachusetts General Hospital Boston Massachusetts.,Harvard Medical School Boston Massachusetts
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22
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Hiller M, Spitali P, Datson N, Aartsma-Rus A. Exon 51 Skipping Quantification by Digital Droplet PCR in del52hDMD/mdx Mice. Methods Mol Biol 2019; 1828:249-262. [PMID: 30171546 DOI: 10.1007/978-1-4939-8651-4_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a severe, neuromuscular disorder caused by mutations in the DMD gene, precluding synthesis of functional dystrophin protein. Antisense oligonucleotide (AON)-mediated exon skipping has been developed as a method to restore the reading frame, which allows the synthesis of internally truncated, but partially functional dystrophin proteins, as found in the less severe Becker muscular dystrophy (BMD). This approach is species specific, since AONs targeting human exons often will not have full homology to mouse exons. As such, mouse models with mutations in the murine Dmd gene are of limited use to study human specific AONs in vivo. However, our del52hDMD/mdx mouse model contains mutated copies of both the mouse (nonsense mutation in exon 23) and human (deletion of exon 52) dystrophin-encoding genes. This model allows for testing effects of treatment with human specific exon 51 or 53 targeting AONs on RNA, protein, histological, and functional levels. Therefore, the model can be used to optimize human specific AONs, e.g., by comparing dystrophin protein and exon skipping levels.Absolute quantification of exon skipping levels can be obtained by digital droplet PCR (ddPCR). This method compartmentalizes samples into thousands of droplets that represent individual micro PCR reactions, and can be either positive or negative after amplification depending on whether there was a template molecule present or not. This allows for precise determination of the copy numbers of template molecules. The protocol described here uses probes binding to exon-exon junctions (EEJs) of human DMD transcripts with and without skipping of exon 51. We report that this method is specific for human transcripts so that exon skipping levels can be quantified accurately by ddPCR in del52hDMD/mdx mice.
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Affiliation(s)
- Monika Hiller
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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23
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Direct Reprogramming of Human DMD Fibroblasts into Myotubes for In Vitro Evaluation of Antisense-Mediated Exon Skipping and Exons 45-55 Skipping Accompanied by Rescue of Dystrophin Expression. Methods Mol Biol 2019; 1828:141-150. [PMID: 30171539 DOI: 10.1007/978-1-4939-8651-4_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Antisense oligonucleotide-mediated exon skipping is a promising therapeutic approach for the treatment of various genetic diseases and a therapy which has gained significant traction in recent years following FDA approval of new antisense-based drugs. Exon skipping for Duchenne muscular dystrophy (DMD) works by modulating dystrophin pre-mRNA splicing, preventing incorporation of frame-disrupting exons into the final mRNA product while maintaining the open reading frame, to produce a shortened-yet-functional protein as seen in milder Becker muscular dystrophy (BMD) patients. Exons 45-55 skipping in dystrophin is potentially applicable to approximately 47% of DMD patients because many mutations occur within this "mutation hotspot." In addition, patients naturally harboring a dystrophin exons 45-55 in-frame deletion mutation have an asymptomatic or exceptionally mild phenotype compared to shorter in-frame deletion mutations in this region. As such, exons 45-55 skipping could transform the DMD phenotype into an asymptomatic or very mild BMD phenotype and rescue nearly a half of DMD patients. In addition, this strategy is potentially applicable to some BMD patients as well, who have in-frame deletion mutations in this region. As the degree of exon skipping correlates with therapeutic outcomes, reliable measurements of exon skipping efficiencies are essential to the development of novel antisense-mediated exon skipping therapeutics. In the case of DMD, researchers have often relied upon human muscle fibers obtained from muscle biopsies for testing; however, this method is highly invasive and patient myofibers can display limited proliferative ability. To overcome these challenges, researchers can generate myofibers from patient fibroblast cells by transducing the cells with a viral vector containing MyoD, a myogenic regulatory factor. Here, we describe a methodology for assessing dystrophin exons 45-55 multiple skipping efficiency using antisense oligonucleotides in human muscle cells derived from DMD patient fibroblast cells.
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24
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Rocha CSJ. Antisense Oligonucleotides for Splice Modulation: Assessing Splice Switching Efficacy. Methods Mol Biol 2019; 2036:73-90. [PMID: 31410791 DOI: 10.1007/978-1-4939-9670-4_4] [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] [Indexed: 06/10/2023]
Abstract
Today, there are emerging numbers of oligonucleotide therapies being approved by the governmental authorities. These types of therapies present a different mode of action when compared to the traditional small molecules, acting at the RNA level instead of the protein level. In drug development, drug potency is defined by the drug affinity to the target biomolecule (target engagement), together with the ability to initiate a response at the molecular, cellular, tissue, or system level (efficacy). In oligonucleotide therapies, affinity and efficacy can be both easily evaluated by gene expression analysis. Although more advanced techniques can be used, this chapter presents a protocol to evaluate splice switching oligonucleotide efficacy that can be easily applied in a molecular biology laboratory without the need of advanced equipment. It describes all steps from sample preparation to data analysis.
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Affiliation(s)
- Cristina S J Rocha
- Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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25
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Hiller M, Falzarano MS, Garcia-Jimenez I, Sardone V, Verheul RC, Popplewell L, Anthony K, Ruiz-Del-Yerro E, Osman H, Goeman JJ, Mamchaoui K, Dickson G, Ferlini A, Muntoni F, Aartsma-Rus A, Arechavala-Gomeza V, Datson NA, Spitali P. A multicenter comparison of quantification methods for antisense oligonucleotide-induced DMD exon 51 skipping in Duchenne muscular dystrophy cell cultures. PLoS One 2018; 13:e0204485. [PMID: 30278058 PMCID: PMC6168132 DOI: 10.1371/journal.pone.0204485] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 09/10/2018] [Indexed: 12/20/2022] Open
Abstract
Background Duchenne muscular dystrophy is a lethal disease caused by lack of dystrophin. Skipping of exons adjacent to out-of-frame deletions has proven to restore dystrophin expression in Duchenne patients. Exon 51 has been the most studied target in both preclinical and clinical settings and the availability of standardized procedures to quantify exon skipping would be advantageous for the evaluation of preclinical and clinical data. Objective To compare methods currently used to quantify antisense oligonucleotide–induced exon 51 skipping in the DMD transcript and to provide guidance about the method to use. Methods Six laboratories shared blinded RNA samples from Duchenne patient-derived muscle cells treated with different amounts of exon 51 targeting antisense oligonucleotide. Exon 51 skipping levels were quantified using five different techniques: digital droplet PCR, single PCR assessed with Agilent bioanalyzer, nested PCR with agarose gel image analysis by either ImageJ or GeneTools software and quantitative real-time PCR. Results Differences in mean exon skipping levels and dispersion around the mean were observed across the different techniques. Results obtained by digital droplet PCR were reproducible and showed the smallest dispersion. Exon skipping quantification with the other methods showed overestimation of exon skipping or high data variation. Conclusions Our results suggest that digital droplet PCR was the most precise and quantitative method. The quantification of exon 51 skipping by Agilent bioanalyzer after a single round of PCR was the second-best choice with a 2.3-fold overestimation of exon 51 skipping levels compared to digital droplet PCR.
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Affiliation(s)
- Monika Hiller
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Iker Garcia-Jimenez
- Neuromuscular Disorders Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Valentina Sardone
- Dubowitz Neuromuscular Centre, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Linda Popplewell
- Centre of Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, London, United Kingdom
| | - Karen Anthony
- Dubowitz Neuromuscular Centre, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
- Faculty of Health and Society, University of Northampton, Northampton, United Kingdom
| | | | - Hana Osman
- UOL of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Jelle J. Goeman
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kamel Mamchaoui
- INSERM, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - George Dickson
- Centre of Biomedical Sciences, School of Biological Sciences, Royal Holloway University of London, London, United Kingdom
| | | | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
- MRC Centre for Neuromuscular Diseases, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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26
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Antoury L, Hu N, Balaj L, Das S, Georghiou S, Darras B, Clark T, Breakefield XO, Wheeler TM. Analysis of extracellular mRNA in human urine reveals splice variant biomarkers of muscular dystrophies. Nat Commun 2018; 9:3906. [PMID: 30254196 PMCID: PMC6156576 DOI: 10.1038/s41467-018-06206-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 08/22/2018] [Indexed: 12/18/2022] Open
Abstract
Urine contains extracellular RNA (exRNA) markers of urogenital cancers. However, the capacity of genetic material in urine to identify systemic diseases is unknown. Here we describe exRNA splice products in human urine as a source of biomarkers for the two most common forms of muscular dystrophies, myotonic dystrophy (DM) and Duchenne muscular dystrophy (DMD). Using a training set, RT-PCR, droplet digital PCR, and principal component regression, we identify ten transcripts that are spliced differently in urine exRNA from patients with DM type 1 (DM1) as compared to unaffected or disease controls, form a composite biomarker, and develop a predictive model that is 100% accurate in our independent validation set. Urine also contains mutation-specific DMD mRNAs that confirm exon-skipping activity of the antisense oligonucleotide drug eteplirsen. Our results establish that urine mRNA splice variants can be used to monitor systemic diseases with minimal or no clinical effect on the urinary tract.
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Affiliation(s)
- Layal Antoury
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ningyan Hu
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sofia Georghiou
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Basil Darras
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Tim Clark
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Xandra O Breakefield
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Thurman M Wheeler
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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27
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Van Der Steen N, Mentens Y, Ramael M, Leon LG, Germonpré P, Ferri J, Gandara DR, Giovannetti E, Peters GJ, Pauwels P, Rolfo C. Double Trouble: A Case Series on Concomitant Genetic Aberrations in NSCLC. Clin Lung Cancer 2018; 19:35-41. [PMID: 28757336 DOI: 10.1016/j.cllc.2017.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 01/03/2023]
Abstract
Several oncogenic drivers have been identified in non-small cell lung cancer. Targeted therapies for these aberrations have already been successfully developed and implemented in clinical practice. Owing to improved sensitivity in genetic testing, more and more tumors with multiple driver mutations are identified, resulting in dilemmas for treating physicians whether and which targeted therapy to use. In this case series, we provide an overview of patients with intrinsic double mutations in oncogenic drivers and their reported response to targeted therapies, with a focus on epidermal growth factor receptor, anaplastic lymphoma kinase, cMET, and Kirsten rat sarcoma viral oncogene. We also include an unpublished case report on a patient with an epidermal growth factor receptor L858R and cMET exon 14 skipping.
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Affiliation(s)
- Nele Van Der Steen
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Antwerp, Belgium; Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Yves Mentens
- Department of Pneumology, AZ Herentals, Herentals, Belgium
| | - Marc Ramael
- Department of Pathology, AZ Herentals, Herentals, Belgium; Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Leticia G Leon
- Cancer Pharmacology Lab, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
| | - Paul Germonpré
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium; Department of Pneumology, AZ Maria Middelares, Ghent, Belgium
| | - Jose Ferri
- Phase I - Early Clinical Trials Unit, Oncology Department, Antwerp University Hospital, Antwerp, Belgium
| | - David R Gandara
- Department of Medicine, University of California Davis Cancer Center, Sacramento, CA
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands; Cancer Pharmacology Lab, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
| | - Godefridus J Peters
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium; Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
| | - Christian Rolfo
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium; Phase I - Early Clinical Trials Unit, Oncology Department, Antwerp University Hospital, Antwerp, Belgium.
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Jirka SMG, 't Hoen PAC, Diaz Parillas V, Tanganyika-de Winter CL, Verheul RC, Aguilera B, de Visser PC, Aartsma-Rus AM. Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy. Mol Ther 2017; 26:132-147. [PMID: 29103911 PMCID: PMC5763161 DOI: 10.1016/j.ymthe.2017.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 10/03/2017] [Accepted: 10/05/2017] [Indexed: 01/16/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe, progressive muscle wasting disorder caused by reading frame disrupting mutations in the DMD gene. Exon skipping is a therapeutic approach for DMD. It employs antisense oligonucleotides (AONs) to restore the disrupted open reading frame, allowing the production of shorter, but partly functional dystrophin protein as seen in less severely affected Becker muscular dystrophy patients. To be effective, AONs need to be delivered and effectively taken up by the target cells, which can be accomplished by the conjugation of tissue-homing peptides. We performed phage display screens using a cyclic peptide library combined with next generation sequencing analyses to identify candidate muscle-homing peptides. Conjugation of the lead peptide to 2'-O-methyl phosphorothioate AONs enabled a significant, 2-fold increase in delivery and exon skipping in all analyzed skeletal and cardiac muscle of mdx mice and appeared well tolerated. While selected as a muscle-homing peptide, uptake was increased in liver and kidney as well. The homing capacity of the peptide may have been overruled by the natural biodistribution of the AON. Nonetheless, our results suggest that the identified peptide has the potential to facilitate delivery of AONs and perhaps other compounds to skeletal and cardiac muscle.
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Affiliation(s)
- Silvana M G Jirka
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | | | | | | | | | | | - Annemieke M Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands.
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Gil BM, Valero D. NUEVAS TECNOLOGÍAS PARA EL DIAGNÓSTICO GENÉTICO. REVISTA MÉDICA CLÍNICA LAS CONDES 2017. [DOI: 10.1016/j.rmclc.2017.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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