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Abstract
Heritable cardiomyopathies are a class of heart diseases caused by variations in a number of genetic loci. Genetic variants on one allele lead to either a degraded protein, which causes a haploinsufficiency of that protein, or a nonfunctioning protein that subverts the molecular system within which the protein works. Over years, both of these mechanisms eventually lead to diseased heart tissue and symptoms of a failing heart. Most cardiomyopathy treatments repurpose heart failure drugs to manage these symptoms and avoid adverse outcomes. There are few therapies that correct the underlying pathogenic genetic or molecular mechanism. This review will reflect on this unmet clinical need in genetic cardiomyopathies and consider a variety of therapies that address the mechanism of disease rather than patient symptoms. These therapies are genetic, targeting a defective gene or transcript, or ameliorating a genetic insufficiency. However, there are also a number of small molecules under exploration that modulate downstream faulty protein products affected in cardiomyopathies.
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Affiliation(s)
- Giuliana G Repetti
- From the Department of Genetics, Harvard Medical School, Boston, MA (G.G.R., C.N.T., J.G.S., C.E.S.)
| | - Christopher N Toepfer
- From the Department of Genetics, Harvard Medical School, Boston, MA (G.G.R., C.N.T., J.G.S., C.E.S.)
- Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, United Kingdom (C.N.T.)
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA (C.N.T., C.E.S.)
| | - Jonathan G Seidman
- From the Department of Genetics, Harvard Medical School, Boston, MA (G.G.R., C.N.T., J.G.S., C.E.S.)
| | - Christine E Seidman
- From the Department of Genetics, Harvard Medical School, Boston, MA (G.G.R., C.N.T., J.G.S., C.E.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
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Nguyen KV. Potential epigenomic co-management in rare diseases and epigenetic therapy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:752-780. [PMID: 31079569 DOI: 10.1080/15257770.2019.1594893] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The purpose of this review is to highlight the impact of the alternative splicing process on human disease. Epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced. The recent progress in the field of epigenetics has important implications for the study of rare diseases. The role of epigenetics in rare diseases is a key issue in molecular physiology and medicine because not only rare diseases can benefit from epigenetic research, but can also provide useful principles for other common and complex disorders such as cancer, cardiovascular, type 2 diabetes, obesity, and neurological diseases. Predominantly, epigenetic modifications include DNA methylation, histone modification, and RNA-associated silencing. These modifications in the genome regulate numerous cellular activities. Disruption of epigenetic regulation process can contribute to the etiology of numerous diseases during both prenatal and postnatal life. Here, I discuss current knowledge about this matter including some current epigenetic therapies and future directions in the field by emphasizing on the RNA-based therapy via antisense oligonucleotides to correct splicing defects.
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Affiliation(s)
- Khue Vu Nguyen
- a Department of Medicine, Biochemical Genetics and Metabolism, The Mitochondrial and Metabolic Disease Center, School of Medicine, University of California, San Diego , San Diego , CA , USA.,b Department of Pediatrics, UC San Diego School of Medicine , La Jolla , CA , USA
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53
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Buijsen RAM, Toonen LJA, Gardiner SL, van Roon-Mom WMC. Genetics, Mechanisms, and Therapeutic Progress in Polyglutamine Spinocerebellar Ataxias. Neurotherapeutics 2019; 16:263-286. [PMID: 30607747 PMCID: PMC6554265 DOI: 10.1007/s13311-018-00696-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Autosomal dominant cerebellar ataxias (ADCAs) are a group of neurodegenerative disorders characterized by degeneration of the cerebellum and its connections. All ADCAs have progressive ataxia as their main clinical feature, frequently accompanied by dysarthria and oculomotor deficits. The most common spinocerebellar ataxias (SCAs) are 6 polyglutamine (polyQ) SCAs. These diseases are all caused by a CAG repeat expansion in the coding region of a gene. Currently, no curative treatment is available for any of the polyQ SCAs, but increasing knowledge on the genetics and the pathological mechanisms of these polyQ SCAs has provided promising therapeutic targets to potentially slow disease progression. Potential treatments can be divided into pharmacological and gene therapies that target the toxic downstream effects, gene therapies that target the polyQ SCA genes, and stem cell replacement therapies. Here, we will provide a review on the genetics, mechanisms, and therapeutic progress in polyglutamine spinocerebellar ataxias.
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Affiliation(s)
- Ronald A M Buijsen
- Department of Human Genetics, LUMC, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
| | - Lodewijk J A Toonen
- Department of Human Genetics, LUMC, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Sarah L Gardiner
- Department of Human Genetics, LUMC, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
- Department of Neurology, LUMC, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
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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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55
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Abstract
Two new studies refine our understanding of CRISPR-associated exon skipping and redefine its utility in engineering alternative splicing.
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Affiliation(s)
- Jordan L Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Program in Molecular Medicine, Department of Molecular, Cell and Cancer Biology, and Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Plantation Street, Worcester, MA, 01605, USA.
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Montazersaheb S, Hejazi MS, Nozad Charoudeh H. Potential of Peptide Nucleic Acids in Future Therapeutic Applications. Adv Pharm Bull 2018; 8:551-563. [PMID: 30607328 PMCID: PMC6311635 DOI: 10.15171/apb.2018.064] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
Peptide nucleic acids (PNA) are synthetic analog of DNA with a repeating N-(2-aminoethyl)-glycine peptide backbone connected to purine and pyrimidine nucleobases via a linker. Considering the unique properties of PNA, including resistance to enzymatic digestion, higher biostability combined with great hybridization affinity toward DNA and RNA, it has attracted great attention toward PNA- based technology as a promising approach for gene alteration. However, an important challenge in utilizing PNA is poor intracellular uptake. Therefore, some strategies have been developed to enhance the delivery of PNA in order to reach cognate site. Although PNAs primarily demonstrated to act as an antisense and antigene agents for inhibition of transcription and translation of target genes, more therapeutic applications such as splicing modulation and gene editing are also used to produce specific genome modifications. Hence, several approaches based on PNAs technology have been designed for these purposes. This review briefly presents the properties and characteristics of PNA as well as different gene modulation mechanisms. Thereafter, current status of successful therapeutic applications of PNA as gene therapeutic intervention in different research areas with special interest in medical application in particular, anti-cancer therapy are discussed. Then it focuses on possible use of PNA as anti-mir agent and PNA-based strategies against clinically important bacteria.
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Affiliation(s)
- Soheila Montazersaheb
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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57
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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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58
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Leigh F, Ferlini A, Biggar D, Bushby K, Finkel R, Morgenroth LP, Wagner KR. Neurology Care, Diagnostics, and Emerging Therapies of the Patient With Duchenne Muscular Dystrophy. Pediatrics 2018; 142:S5-S16. [PMID: 30275245 DOI: 10.1542/peds.2018-0333c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 11/24/2022] Open
Abstract
Duchenne muscular dystrophy is the most common form of childhood muscular dystrophy. A mutation in the DMD gene disrupts dystrophin (protein) production, causing damage to muscle integrity, weakness, loss of ambulation, and cardiopulmonary compromise by the second decade of life. Life expectancy has improved from mid-teenage years to mid-20s with the use of glucocorticoids and beyond the third decade with ventilator support and multidisciplinary care. However, Duchenne muscular dystrophy is associated with comorbidities and is a fatal disease. Glucocorticoids prolong ambulation, but their side effects are significant. Emerging investigational therapies have surfaced over the past decade and have rapidly been tested in clinical trials. Gene-specific strategies include nonsense readthrough, exon skipping, gene editing, utrophin modulation, and gene replacement. Other mechanisms include muscle regeneration, antioxidants, and antifibrosis and anti-inflammatory pathways. With potential therapies emerging, early diagnosis is needed to initiate treatment early enough to minimize morbidity and mortality. Newborn screening can be used to significantly improve early diagnosis, especially for gene-specific therapeutics.
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Affiliation(s)
- Fawn Leigh
- Massachusetts General Hospital and Harvard Medical School, Harvard University, Cambridge, Massachusetts; .,Seattle Children's Hospital, University of Washington, Seattle, Washington
| | | | - Doug Biggar
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Katharine Bushby
- John Walton Centre for Muscular Dystrophy Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | - Kathryn R Wagner
- Kennedy Krieger Institute, Baltimore, Maryland; and.,School of Medicine, Johns Hopkins University, Baltimore, Maryland
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59
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Shahnoor N, Siebers EM, Brown KJ, Lawlor MW. Pathological Issues in Dystrophinopathy in the Age of Genetic Therapies. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:105-126. [PMID: 30148687 DOI: 10.1146/annurev-pathmechdis-012418-012945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Dystrophinopathy is a class of genetic skeletal muscle disease characterized by myofiber degeneration and regeneration due to insufficient levels or functioning of dystrophin. Pathological evaluation for dystrophinopathy includes the identification of dystrophic skeletal muscle pathology and the immunohistochemical evaluation of dystrophin epitopes, but biopsies have become rare in recent years. However, the evaluation of dystrophin expression in the research setting has become critically important due to recent advances in genetic therapies, including exon skipping and gene therapy. Given the number of these therapies under evaluation in patients, it is likely that the traditional methods of evaluating dystrophinopathy will need to evolve in the near future. This review discusses current muscle biopsy diagnostic practices in dystrophinopathy and further focuses on how these practices have evolved in the context of therapeutic interventions for dystrophinopathy.
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Affiliation(s)
- Nazima Shahnoor
- Department of Pathology and Laboratory Medicine, and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; , ,
| | - Emily M Siebers
- Department of Pathology and Laboratory Medicine, and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; , ,
| | - Kristy J Brown
- Solid Biosciences, Inc., Cambridge, Massachusetts 02139, USA;
| | - Michael W Lawlor
- Department of Pathology and Laboratory Medicine, and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA; , ,
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60
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Gapinske M, Luu A, Winter J, Woods WS, Kostan KA, Shiva N, Song JS, Perez-Pinera P. CRISPR-SKIP: programmable gene splicing with single base editors. Genome Biol 2018; 19:107. [PMID: 30107853 PMCID: PMC6092781 DOI: 10.1186/s13059-018-1482-5] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/13/2018] [Indexed: 01/09/2023] Open
Abstract
CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes through targeted double-strand breaks in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for off-target mutations, technologies capable of introducing targeted changes with increased precision, such as single-base editors, are preferred. We present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program exon skipping by mutating target DNA bases within splice acceptor sites. Given its simplicity and precision, CRISPR-SKIP will be broadly applicable in gene therapy and synthetic biology.
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Affiliation(s)
- Michael Gapinske
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Alan Luu
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801-3080 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jackson Winter
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Wendy S. Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Kurt A. Kostan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Nikhil Shiva
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Jun S. Song
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801-3080 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Carle Illinois College of Medicine, Champaign, IL 61820 USA
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de Bruin D, Bossert N, Aartsma-Rus A, Bouwmeester D. Measuring DNA hybridization using fluorescent DNA-stabilized silver clusters to investigate mismatch effects on therapeutic oligonucleotides. J Nanobiotechnology 2018; 16:37. [PMID: 29622040 PMCID: PMC5887185 DOI: 10.1186/s12951-018-0361-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 03/21/2018] [Indexed: 01/07/2023] Open
Abstract
Background Short nucleic acid oligomers have found a wide range of applications in experimental physics, biology and medicine, and show potential for the treatment of acquired and genetic diseases. These applications rely heavily on the predictability of hybridization through Watson–Crick base pairing to allow positioning on a nanometer scale, as well as binding to the target transcripts, but also off-target binding to transcripts with partial homology. These effects are of particular importance in the development of therapeutic oligonucleotides, where off-target effects caused by the binding of mismatched sequences need to be avoided. Results We employ a novel method of probing DNA hybridization using optically active DNA-stabilized silver clusters (Ag-DNA) to measure binding efficiencies through a change in fluorescence intensity. In this way we can determine their location-specific sensitivity to individual mismatches in the sequence. The results reveal a strong dependence of the hybridization on the location of the mismatch, whereby mismatches close to the edges and center show a relatively minor impact. In parallel, we propose a simple model for calculating the annealing ratios of mismatched DNA sequences, which supports our experimental results. Conclusion The primary result shown in this work is a demonstration of a novel technique to measure DNA hybridization using fluorescent Ag-DNA. With this technique, we investigated the effect of mismatches on the hybridization efficiency, and found a significant dependence on the location of individual mismatches. These effects are strongly influenced by the length of the used oligonucleotides. The novel probe method based on fluorescent Ag-DNA functions as a reliable tool in measuring this behavior. As a secondary result, we formulated a simple model that is consistent with the experimental data. Electronic supplementary material The online version of this article (10.1186/s12951-018-0361-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Donny de Bruin
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands.
| | - Nelli Bossert
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands
| | | | - Dirk Bouwmeester
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands.,Department of Physics, University of California, Santa Barbara, CA, 93106, USA
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Thomas JD, Oliveira R, Sznajder ŁJ, Swanson MS. Myotonic Dystrophy and Developmental Regulation of RNA Processing. Compr Physiol 2018; 8:509-553. [PMID: 29687899 PMCID: PMC11323716 DOI: 10.1002/cphy.c170002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Myotonic dystrophy (DM) is a multisystemic disorder caused by microsatellite expansion mutations in two unrelated genes leading to similar, yet distinct, diseases. DM disease presentation is highly variable and distinguished by differences in age-of-onset and symptom severity. In the most severe form, DM presents with congenital onset and profound developmental defects. At the molecular level, DM pathogenesis is characterized by a toxic RNA gain-of-function mechanism that involves the transcription of noncoding microsatellite expansions. These mutant RNAs disrupt key cellular pathways, including RNA processing, localization, and translation. In DM, these toxic RNA effects are predominantly mediated through the modulation of the muscleblind-like and CUGBP and ETR-3-like factor families of RNA binding proteins (RBPs). Dysfunction of these RBPs results in widespread RNA processing defects culminating in the expression of developmentally inappropriate protein isoforms in adult tissues. The tissue that is the focus of this review, skeletal muscle, is particularly sensitive to mutant RNA-responsive perturbations, as patients display a variety of developmental, structural, and functional defects in muscle. Here, we provide a comprehensive overview of DM1 and DM2 clinical presentation and pathology as well as the underlying cellular and molecular defects associated with DM disease onset and progression. Additionally, fundamental aspects of skeletal muscle development altered in DM are highlighted together with ongoing and potential therapeutic avenues to treat this muscular dystrophy. © 2018 American Physiological Society. Compr Physiol 8:509-553, 2018.
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Affiliation(s)
- James D. Thomas
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Ruan Oliveira
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Łukasz J. Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Maurice S. Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
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63
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Randeree L, Eslick GD. Eteplirsen for paediatric patients with Duchenne muscular dystrophy: A pooled-analysis. J Clin Neurosci 2018; 49:1-6. [PMID: 29254734 DOI: 10.1016/j.jocn.2017.10.082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/23/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Duchenne Muscular Dystrophy is a paediatric disorder resulting from a defective dystrophin gene. It causes progressive loss of muscle fibres, muscle weakness, and eventually loss of ambulation during adolescence, with death due to respiratory or cardiovascular complications soon afterwards. The drug eteplirsen has received support from medical experts and parents of affected children, but the FDA has delayed their decision for approval of this drug. OBJECTIVE This study analysed the results of previous studies to assess the safety and efficacy of the eteplirsen, and is the first pooled-analysis of its kind. METHODS A literature search of electronic databases was performed. Only human studies using eteplirsen were eligible. RESULTS A total of four relevant clinical studies were identified. A pooled-analysis was performed using data relating to percentage dystrophin-positive fibres obtained from muscle biopsy, and the six-minute walk test (6 MWT). The average increase in percentage dystrophin-positive fibres after treatment with eteplirsen was 24.23% (range -4 to 78; SD 24.44%). The average rate of decline in distance walked was 65metres (range -335 to 83; SD 100.08 m). CONCLUSIONS Whether or not this increase in percentage dystrophin-positive fibres and distance walked is clinically significant is unclear, and there is therefore a need for more clinical trials.
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Affiliation(s)
- Liane Randeree
- The Whiteley-Martin Research Centre, Discipline of Surgery, The University of Sydney, Nepean Hospital, Penrith, New South Wales, Australia
| | - Guy D Eslick
- The Whiteley-Martin Research Centre, Discipline of Surgery, The University of Sydney, Nepean Hospital, Penrith, New South Wales, Australia.
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Jain HV, Boehler JF, Nagaraju K, Beaucage SL. Synthesis, Characterization, and Function of an RNA-Based Transfection Reagent. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2018; 72:4.81.1-4.81.29. [PMID: 29927123 PMCID: PMC6020023 DOI: 10.1002/cpnc.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A synthetic 8-mer, amphipathic, trans-acting poly-2'-O-methyluridylic thiophosphate triester RNA element (2'-OMeUtaPS) can be prepared using solid-phase synthesis protocols. 2'-OMeUtaPS efficiently mediates the delivery of uncharged polyA-tailed phosphorodiamidate morpholino (PMO) sequences in HeLa pLuc 705 cells, as evidenced by flow cytometry measurements. In this cell line, 2'-OMeUtaPS-mediated transfection of an antisense polyA-tailed PMO sequence induces alternative splicing of an aberrant luciferase pre-mRNA splice site, leading to restoration of functional luciferase, as quantitatively measured using a typical luciferase assay. 2'-OMeUtaPS is also potent at delivering an uncharged antisense polyA-tailed PMO sequence in muscle cells of the mdx mouse model of muscular dystrophy; targeting the polyA-tailed PMO sequence against a splice site of the pre-mRNA encoding mutated dystrophin triggers an alternate splicing event that results in excision of the mutated exon (exon 23) from the pre-mRNA and production of functional dystrophin, as demonstrated by agarose gel electrophoresis. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Harsh V Jain
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
| | - Jessica F Boehler
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, District of Columbia
- The Institute for Biomedical Sciences, The George Washington University, Washington, District of Columbia
| | - Kanneboyina Nagaraju
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, District of Columbia
- Department of Pharmaceutical Sciences, Binghamton University, Binghamton, New York
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
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Shao L, Cui L, Lu J, Lang Y, Bottillo I, Zhao X. A novel mutation in exon 9 of Cullin 3 gene contributes to aberrant splicing in pseudohypoaldosteronism type II. FEBS Open Bio 2018; 8:461-469. [PMID: 29511623 PMCID: PMC5832971 DOI: 10.1002/2211-5463.12389] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/26/2017] [Accepted: 01/12/2018] [Indexed: 01/30/2023] Open
Abstract
Pseudohypoaldosteronism type II (PHAII) is a rare renal tubular disease that is inherited in an autosomal dominant manner. Mutations in four genes (WNK1,WNK4,CUL3, and KLHL3) have been identified to be responsible for this disease. Cullin 3 (CUL3) and KLHL3 are subunits of Cullin–RING E3 ubiquitin ligase complexes, and the serine–threonine kinases WNK1 and WNK4 are substrates of this ubiquitin ligase. For CUL3, all mutations associated with PHAII exclusively lead to exon 9 skipping. In this study, we identified a Chinese PHAII kindred caused by a novel synonymous mutation (c.1221A > G p.Glu407Glu) in CUL3, and explored its effects on exon 9 abnormal splicing through an in vitro splicing assay and study of the patients’ RNA. We obtained evidence that this synonymous mutation leads to complete exon 9 skipping, and in silico bioinformatics analysis demonstrated that the CUL3 c.1221A > G mutation might decrease the ratio of exonic splicing enhancers and silencers. This is the first report of PHAII in Chinese patients with a novel CUL3 mutation. Our findings add a novel pathogenic splicing variant to the CUL3 mutational spectrum and provide reference for further research on mechanisms of splicing modulation and development of potential therapeutic reagents for PHAII.
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Affiliation(s)
- Leping Shao
- Department of Nephrology The Affiliated Hospital of Qingdao University Qingdao China
| | - Li Cui
- Department of Nephrology The Affiliated Hospital of Qingdao University Qingdao China
| | - Jingru Lu
- Department of Nephrology The Affiliated Hospital of Qingdao University Qingdao China
| | - Yanhua Lang
- Department of Nephrology The Affiliated Hospital of Qingdao University Qingdao China
| | - Irene Bottillo
- Division of Medical Genetics Department of Molecular Medicine Sapienza University San Camillo-Forlanini Hospital Rome Italy
| | - Xiangzhong Zhao
- Central Laboratory The Affiliated Hospital of Qingdao University Qingdao China
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66
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Impact, Characterization, and Rescue of Pre-mRNA Splicing Mutations in Lysosomal Storage Disorders. Genes (Basel) 2018; 9:genes9020073. [PMID: 29415500 PMCID: PMC5852569 DOI: 10.3390/genes9020073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/19/2018] [Accepted: 01/31/2018] [Indexed: 11/16/2022] Open
Abstract
Lysosomal storage disorders (LSDs) represent a group of more than 50 severe metabolic diseases caused by the deficiency of specific lysosomal hydrolases, activators, carriers, or lysosomal integral membrane proteins, leading to the abnormal accumulation of substrates within the lysosomes. Numerous mutations have been described in each disease-causing gene; among them, about 5-19% affect the pre-mRNA splicing process. In the last decade, several strategies to rescue/increase normal splicing of mutated transcripts have been developed and LSDs represent excellent candidates for this type of approach: (i) most of them are inherited in an autosomic recessive manner and patients affected by late-onset (LO) phenotypes often retain a fair amount of residual enzymatic activity; thus, even a small recovery of normal splicing may be beneficial in clinical settings; (ii) most LSDs still lack effective treatments or are currently treated with extremely expensive approaches; (iii) in few LSDs, a single splicing mutation accounts for up to 40-70% of pathogenic alleles. At present, numerous preclinical studies support the feasibility of reverting the pathological phenotype by partially rescuing splicing defects in LSDs. This review provides an overview of the impact of splicing mutations in LSDs and the related therapeutic approaches currently under investigation in these disorders.
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67
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Lim KRQ, Yokota T. Quantitative Evaluation of Exon Skipping in Immortalized Muscle Cells In Vitro. Methods Mol Biol 2018; 1828:127-139. [PMID: 30171538 DOI: 10.1007/978-1-4939-8651-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Exon skipping through the use of antisense oligonucleotides (AOs) is currently one of the most promising approaches for treating Duchenne muscular dystrophy (DMD). While we now have a number of AO drug candidates in clinical trials, we are still faced with issues of poor or controversial efficacy in some of these drugs. This is the case with eteplirsen, an exon 51-skipping AO that is the first and only FDA-approved drug for DMD to date. Effective procedures must, therefore, be set up for the in vitro screening of potential AOs for DMD treatment. Here, we describe one such procedure using immortalized DMD patient-derived muscle cells. Aside from allowing for the quantitative evaluation of candidate AOs based on their exon skipping efficiency and dystrophin protein rescue levels, these immortalized cells are stable, pure, easy to grow, and not subject to confounding by senescence-related issues. This procedure enables a more reliable screening of AOs prior to their entry in clinical trials and greatly facilitates the search for more efficacious candidate exon skipping AOs for DMD treatment.
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Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada. .,The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
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68
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Cywoniuk P, Taylor K, Sznajder ŁJ, Sobczak K. Hybrid splicing minigene and antisense oligonucleotides as efficient tools to determine functional protein/RNA interactions. Sci Rep 2017; 7:17587. [PMID: 29242583 PMCID: PMC5730568 DOI: 10.1038/s41598-017-17816-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing is a complex process that provides a high diversity of proteins from a limited number of protein-coding genes. It is governed by multiple regulatory factors, including RNA-binding proteins (RBPs), that bind to specific RNA sequences embedded in a specific structure. The ability to predict RNA-binding regions recognized by RBPs using whole-transcriptome approaches can deliver a multitude of data, including false-positive hits. Therefore, validation of the global results is indispensable. Here, we report the development of an efficient and rapid approach based on a modular hybrid minigene combined with antisense oligonucleotides to enable verification of functional RBP-binding sites within intronic and exonic sequences of regulated pre-mRNA. This approach also provides valuable information regarding the regulatory properties of pre-mRNA, including the RNA secondary structure context. We also show that the developed approach can be used to effectively identify or better characterize the inhibitory properties of potential therapeutic agents for myotonic dystrophy, which is caused by sequestration of specific RBPs, known as muscleblind-like proteins, by mutated RNA with expanded CUG repeats.
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Affiliation(s)
- Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland
| | - Łukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland.,Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida,, Gainesville, Florida, 32610-3610, USA
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland.
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69
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Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:199-214. [PMID: 29499933 PMCID: PMC5862129 DOI: 10.1016/j.omtn.2017.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 01/16/2023]
Abstract
Oligonucleotide gene therapy has shown great promise for the treatment of muscular dystrophies. Nevertheless, the selective delivery to affected muscles has shown to be challenging because of their high representation in the body and the high complexity of their cell membranes. Current trials show loss of therapeutic molecules to non-target tissues leading to lower target efficacy. Therefore, strategies that increase uptake efficiency would be particularly compelling. To address this need, we applied a cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment) approach and identified a skeletal muscle-specific RNA aptamer. A01B RNA aptamer preferentially internalizes in skeletal muscle cells and exhibits decreased affinity for off-target cells. Moreover, this in vitro selected aptamer retained its functionality in vivo, suggesting a potential new approach for targeting skeletal muscles. Ultimately, this will aid in the development of targeted oligonucleotide therapies against muscular dystrophies.
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70
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Jain HV, Boehler JF, Verthelyi D, Nagaraju K, Beaucage SL. An amphipathic trans-acting phosphorothioate RNA element delivers an uncharged phosphorodiamidate morpholino sequence in mdx mouse myotubes. RSC Adv 2017; 7:42519-42528. [PMID: 28989703 PMCID: PMC5625301 DOI: 10.1039/c7ra04247g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
An efficient method for the delivery of uncharged polyA-tailed phosphorodiamidate morpholino sequences (PMO) in mammalian cells consists of employing a synthetic 8-mer amphipathic trans-acting poly-2'-O-methyluridylic thiophosphate triester element (2'-OMeUtaPS) as a transfection reagent. Unlike the dTtaPS DNA-based element, this RNA element is potent at delivering polyA-tailed PMO sequences to HeLa pLuc 705 cells or to myotube muscle cells. However, much like dTtaPS, the 2'-OMeUtaPS-mediated internalization of PMO sequences occurs through an energy-dependent mechanism; macropinocytosis appears to be the predominant endocytic pathway used for cellular uptake. The transfected PMO sequences induce alternate splicing of either the pre-mRNA encoding luciferase in HeLa pLuc 705 cells or the excision of exon 23 from the pre-mRNA encoding dystrophin in myotube muscle cells of the mdx mouse model of muscular dystrophy with an efficiency comparable to that of commercial cationic lipid reagents but without detrimental cytotoxicity.
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Affiliation(s)
- H V Jain
- Division of Biotechnology Review and Research IV, CDER, FDA, 10903 New Hampshire Avenue, Silver Spring, Maryland 20933, USA
| | - J F Boehler
- Research Center for Genetic Medicine, Children's National Medical Center, 111 Michigan Avenue, NW Washington, DC 20010, USA
- The Institute for Biomedical Sciences, The George Washington University, Washington, DC 20037, USA
| | - D Verthelyi
- Division of Biotechnology Review and Research III, CDER, FDA, 10903 New Hampshire Avenue, Silver Spring, Maryland 20933, USA
| | - K Nagaraju
- Research Center for Genetic Medicine, Children's National Medical Center, 111 Michigan Avenue, NW Washington, DC 20010, USA
- Department of Pharmaceutical Sciences, AB-G34, Binghamton University, P.O. Box 6000, Binghamton, New York 13902, USA
| | - S L Beaucage
- Division of Biotechnology Review and Research IV, CDER, FDA, 10903 New Hampshire Avenue, Silver Spring, Maryland 20933, USA
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71
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Morihiro K, Kasahara Y, Obika S. Biological applications of xeno nucleic acids. MOLECULAR BIOSYSTEMS 2017; 13:235-245. [PMID: 27827481 DOI: 10.1039/c6mb00538a] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Xeno nucleic acids (XNAs) are a group of chemically modified nucleic acid analogues that have been applied to various biological technologies such as antisense oligonucleotides, siRNAs and aptamers.
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Affiliation(s)
- Kunihiko Morihiro
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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72
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Al-Zaidy SA, Lloyd-Puryear M, Kennedy A, Lopez V, Mendell JR. A Roadmap to Newborn Screening for Duchenne Muscular Dystrophy. Int J Neonatal Screen 2017; 3:8. [PMID: 31588416 PMCID: PMC6777346 DOI: 10.3390/ijns3020008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is the most common childhood form of muscular dystrophy, with an estimated frequency of 1:5000 live births. The impact of the disease presents as early as infancy with significant developmental delays, and ultimately loss of ambulation and respiratory insufficiency. Glucocorticoids are the only pharmacological agents known to alter the natural progression of the disease by prolonging ambulation, reducing scoliosis, and assisted ventilation. Introduction of therapy at an early age may halt the muscle pathology in DMD. In anticipation of the potentially disease-modifying products that are reaching regulatory review, Parent Project Muscular Dystrophy (PPMD) formally initiated a national Duchenne Newborn Screening (DNBS) effort in December 2014 to build public health infrastructure for newborn screening (NBS) for Duchenne in the United States. The effort includes a formalized national Duchenne Newborn Screening Steering Committee, six related Working Groups, a Duchenne Screening Test Development Project led by PerkinElmer, a program with the American College of Medical Genetic and Genomics' Newborn Screening Translation Research Network (NBSTRN), and collaborations with other Duchenne partners and federal agencies involved in NBS. We herein review the organization and effort of the U.S. DNBS program to develop the evidence supporting the implementation of NBS for DMD.
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Affiliation(s)
- Samiah A. Al-Zaidy
- Department of Pediatrics, Divisions of Neurology and Neuromuscular at Nationwide Children’s Hospital, Columbus, 43205 OH, USA
| | | | - Annie Kennedy
- Parent Project Muscular Dystrophy, Hackensack, 07601 NJ, USA
| | - Veronica Lopez
- Mark Krueger & Associates, Inc., New York, 10175 NY, USA
| | - Jerry R. Mendell
- Department of Pediatrics, Divisions of Neurology and Neuromuscular at Nationwide Children’s Hospital, Columbus, 43205 OH, USA
- Center for Gene Therapy, Research Institute, Nationwide Children’s Hospital, Columbus, 43205 OH, USA
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73
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Alfano LN, Miller NF, Berry KM, Yin H, Rolf KE, Flanigan KM, Mendell JR, Lowes LP. The 100-meter timed test: Normative data in healthy males and comparative pilot outcome data for use in Duchenne muscular dystrophy clinical trials. Neuromuscul Disord 2017; 27:452-457. [DOI: 10.1016/j.nmd.2017.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 01/12/2017] [Accepted: 02/15/2017] [Indexed: 11/27/2022]
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Applications of antisense oligonucleotides for the treatment of inherited retinal diseases. Curr Opin Ophthalmol 2017; 28:260-266. [PMID: 28151748 DOI: 10.1097/icu.0000000000000363] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW Over the last years, antisense oligonucleotides (AONs) have gained attention as a therapeutic tool for the treatment of ocular diseases such as cytomegalovirus retinitis, keratitis-induced corneal neovascularization, and inherited retinal diseases (IRDs). In this review, we summarize the recent key findings, and describe the challenges and opportunities that lie ahead to translate AON-based therapies to the clinic, in particular for IRDs. RECENT FINDINGS The efficacy of AONs to restore splice defects and cellular phenotypes associated with a common mutation in CEP290 was demonstrated in patient-derived optic cups and in a transgenic mouse model, respectively. In addition, allele-specific knockdown of a mutant RHO allele resulted in a delay of photoreceptor cell death and functional preservation of these cells in a transgenic rat model. SUMMARY As demonstrated by several preclinical efficacy studies, AON-based therapy is moving to the clinic for the treatment of some genetic subtypes of IRD. More insights into the delivery of these molecules, the duration of the therapeutic effect, and potential off-target effects will be essential to further shape the transition to the clinic and reveal the true potential of AON-based therapy for retinal diseases.
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Abstract
Most of the human genome encodes RNAs that do not code for proteins. These non-coding RNAs (ncRNAs) may affect normal gene expression and disease progression, making them a new class of targets for drug discovery. Because their mechanisms of action are often novel, developing drugs to target ncRNAs will involve equally novel challenges. However, many potential problems may already have been solved during the development of technologies to target mRNA. Here, we discuss the growing field of ncRNA - including microRNA, intronic RNA, repetitive RNA and long non-coding RNA - and assess the potential and challenges in their therapeutic exploitation.
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Affiliation(s)
- Masayuki Matsui
- Departments of Pharmacology and Biochemistry, UT Southwestern, Dallas, Texas 75390-9041, USA
| | - David R Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern, Dallas, Texas 75390-9041, USA
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76
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Suñé-Pou M, Prieto-Sánchez S, Boyero-Corral S, Moreno-Castro C, El Yousfi Y, Suñé-Negre JM, Hernández-Munain C, Suñé C. Targeting Splicing in the Treatment of Human Disease. Genes (Basel) 2017; 8:genes8030087. [PMID: 28245575 PMCID: PMC5368691 DOI: 10.3390/genes8030087] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 02/07/2023] Open
Abstract
The tightly regulated process of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is a key mechanism in the regulation of gene expression. Defects in this regulatory process affect cellular functions and are the cause of many human diseases. Recent advances in our understanding of splicing regulation have led to the development of new tools for manipulating splicing for therapeutic purposes. Several tools, including antisense oligonucleotides and trans-splicing, have been developed to target and alter splicing to correct misregulated gene expression or to modulate transcript isoform levels. At present, deregulated AS is recognized as an important area for therapeutic intervention. Here, we summarize the major hallmarks of the splicing process, the clinical implications that arise from alterations in this process, and the current tools that can be used to deliver, target, and correct deficiencies of this key pre-mRNA processing event.
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Affiliation(s)
- Marc Suñé-Pou
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
- Drug Development Service, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII, s/n 08028 Barcelona, Spain.
| | - Silvia Prieto-Sánchez
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Sofía Boyero-Corral
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Cristina Moreno-Castro
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Younes El Yousfi
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Josep Mª Suñé-Negre
- Drug Development Service, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Avda. Joan XXIII, s/n 08028 Barcelona, Spain.
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
| | - Carlos Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain.
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Delalande O, Czogalla A, Hubert JF, Sikorski A, Le Rumeur E. Dystrophin and Spectrin, Two Highly Dissimilar Sisters of the Same Family. Subcell Biochem 2017; 82:373-403. [PMID: 28101868 DOI: 10.1007/978-3-319-49674-0_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dystrophin and Spectrin are two proteins essential for the organization of the cytoskeleton and for the stabilization of membrane cells. The comparison of these two sister proteins, and with the dystrophin homologue utrophin, enables us to emphasise that, despite a similar topology with common subdomains and a common structural basis of a three-helix coiled-coil, they show a large range of dissimilarities in terms of genetics, cell expression and higher level structural organisation. Interactions with cellular partners, including proteins and membrane phospholipids, also show both strikingly similar and very different behaviours. The differences between dystrophin and spectrin are also illustrated by the large variety of pathological anomalies emerging from the dysfunction or the absence of these proteins, showing that they are keystones in their function of providing a scaffold that sustains cell structure.
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Affiliation(s)
- Olivier Delalande
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France.
| | - Aleksander Czogalla
- Biotechnology Faculty, Department of Cytobiochemistry, University of Wrocław, ul. joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Jean-François Hubert
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France
| | - Aleksander Sikorski
- Biotechnology Faculty, Department of Cytobiochemistry, University of Wrocław, ul. joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Elisabeth Le Rumeur
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France
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Nakamura A, Shiba N, Miyazaki D, Nishizawa H, Inaba Y, Fueki N, Maruyama R, Echigoya Y, Yokota T. Comparison of the phenotypes of patients harboring in-frame deletions starting at exon 45 in the Duchenne muscular dystrophy gene indicates potential for the development of exon skipping therapy. J Hum Genet 2016; 62:459-463. [PMID: 27974813 DOI: 10.1038/jhg.2016.152] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/10/2016] [Accepted: 11/10/2016] [Indexed: 01/07/2023]
Abstract
Exon skipping therapy has recently received attention for its ability to convert the phenotype of lethal Duchenne muscular dystrophy (DMD) to a more benign form, Becker muscular dystrophy (BMD), by correcting the open reading frame. This therapy has mainly focused on a hot-spot (exons 45-55) mutation in the DMD gene. Exon skipping of an entire stretch of exons 45-55 is an approach applicable to 46.9% of DMD patients. However, the resulting phenotype is not yet fully understood. Here we examined the clinical profiles of 24 patients with BMD resulting from deletions starting at exon 45. The Δ45-55 group ranged in age from 2 to 87 years; no mortality was observed, and one patient was ambulatory at 79 years of age. The age at which patients became wheelchair-bound in the Δ45-48 group (18-88 years old) was approximately 50 years. Cardiomyopathy was well controlled by pharmaceuticals in both deletion groups. In contrast, the Δ45-47 and Δ45-49 groups exhibited more severe phenotypes than those with other mutations: the age at which patients in the Δ45-49 group became wheelchair-bound was around 30-40 years. Our study shows that clinical severity differs between each hot-spot deletion.
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Affiliation(s)
- Akinori Nakamura
- Third Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan.,Department of Neurology, National Hospital Organization, Matsumoto Medical Center, Matsumoto, Japan
| | - Naoko Shiba
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Daigo Miyazaki
- Third Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | | | - Yuji Inaba
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Noboru Fueki
- Division of Rehabilitation, Nagano Children's Hospital, Azumino, Japan
| | - Rika Maruyama
- Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yusuke Echigoya
- Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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Kralovicova J, Moreno PM, Cross NC, Pêgo AP, Vorechovsky I. Antisense Oligonucleotides Modulating Activation of a Nonsense-Mediated RNA Decay Switch Exon in the ATM Gene. Nucleic Acid Ther 2016; 26:392-400. [PMID: 27658045 PMCID: PMC5105335 DOI: 10.1089/nat.2016.0635] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/25/2016] [Indexed: 12/28/2022] Open
Abstract
ATM (ataxia-telangiectasia, mutated) is an important cancer susceptibility gene that encodes a key apical kinase in the DNA damage response pathway. ATM mutations in the germ line result in ataxia-telangiectasia (A-T), a rare genetic syndrome associated with hypersensitivity to double-strand DNA breaks and predisposition to lymphoid malignancies. ATM expression is limited by a tightly regulated nonsense-mediated RNA decay (NMD) switch exon (termed NSE) located in intron 28. In this study, we identify antisense oligonucleotides that modulate NSE inclusion in mature transcripts by systematically targeting the entire 3.1-kb-long intron. Their identification was assisted by a segmental deletion analysis of transposed elements, revealing NSE repression upon removal of a distant antisense Alu and NSE activation upon elimination of a long terminal repeat transposon MER51A. Efficient NSE repression was achieved by delivering optimized splice-switching oligonucleotides to embryonic and lymphoblastoid cells using chitosan-based nanoparticles. Together, these results provide a basis for possible sequence-specific radiosensitization of cancer cells, highlight the power of intronic antisense oligonucleotides to modify gene expression, and demonstrate transposon-mediated regulation of NSEs.
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Affiliation(s)
- Jana Kralovicova
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Pedro M.D. Moreno
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Engenharia Biomédica (INEB), Universidade do Porto, Porto, Portugal
| | - Nicholas C.P. Cross
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Wessex Regional Genetics Laboratory, Salisbury Hospital, Salisbury, United Kingdom
| | - Ana Paula Pêgo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Engenharia Biomédica (INEB), Universidade do Porto, Porto, Portugal
- Faculdade de Engenharia and Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Igor Vorechovsky
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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80
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Kaplan JC. Clin d’œil du Dinosaure émérite. Med Sci (Paris) 2016; 32 Hors série n°2:57-59. [PMID: 27869079 DOI: 10.1051/medsci/201632s217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aux États-Unis, les associations de familles de DMD sont montées au créneau pour demander l’agrément par la FDA de la première molécule induisant un saut d’exon thérapeutique. Fait sans précédent et méritant un Clin d’œil, elles ont obtenu satifsfaction.
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81
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Casaca-Carreira J, Temel Y, Larrakoetxea I, Jahanshahi A. Distribution and Penetration of Intracerebroventricularly Administered 2'OMePS Oligonucleotide in the Mouse Brain. Nucleic Acid Ther 2016; 27:4-10. [PMID: 27753537 DOI: 10.1089/nat.2016.0642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antisense oligonucleotide (AON) therapy is emerging as a potential treatment strategy for neurodegenerative diseases, such as spinal muscular atrophy, Huntington's disease, and amyotrophic lateral sclerosis. AONs function at the cellular level by, for example, direct interference with the expression of gene products or the molecular activation of neuroprotective pathways. However, AON therapy faces a major obstacle limiting its clinical application for central nervous system (CNS) disorders: the blood-brain barrier. Systemic administration of AONs leads to rapid clearance and breakdown of its molecules in the periphery. One way to overcome this obstacle is intracerebroventricular (ICV) delivery of the therapeutics directly to cerebrospinal fluid (CSF). Given the particular molecular structure of oligonucleotides, the (pharmaco) kinetic and distribution pattern of these compounds in the brain are yet to be clarified. In this study, 2'OMePS oligonucleotide delivered through ICV into CSF reached the most key structures in the brain. The distribution of this oligonucleotide differed when comparing specific brain structures and cell groups. After 48 h post-infusion, the distribution of the oligonucleotide reached its maximum and was found intracellularly in many key brain structures. These findings help understanding the kinetic and distribution pattern of 2'OMePS oligonucleotide in the brain and will direct more rational and effective use of ICV drug delivery and unleash its full therapeutic potential in managing CNS diseases.
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Affiliation(s)
- João Casaca-Carreira
- 1 Department of Neurosurgery, Maastricht University Medical Center , Maastricht, the Netherlands .,2 Department of Neuroscience, Maastricht University Medical Center , Maastricht, the Netherlands .,3 European Graduate School of Neuroscience (EURON) , Maastricht, the Netherlands
| | - Yasin Temel
- 1 Department of Neurosurgery, Maastricht University Medical Center , Maastricht, the Netherlands .,2 Department of Neuroscience, Maastricht University Medical Center , Maastricht, the Netherlands .,3 European Graduate School of Neuroscience (EURON) , Maastricht, the Netherlands
| | | | - Ali Jahanshahi
- 1 Department of Neurosurgery, Maastricht University Medical Center , Maastricht, the Netherlands .,2 Department of Neuroscience, Maastricht University Medical Center , Maastricht, the Netherlands .,3 European Graduate School of Neuroscience (EURON) , Maastricht, the Netherlands
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82
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Miller CM, Harris EN. Antisense Oligonucleotides: Treatment Strategies and Cellular Internalization. RNA & DISEASE 2016; 3:e1393. [PMID: 28374018 PMCID: PMC5376066 DOI: 10.14800/rd.1393] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The clinical applicaton of antisense oligonucleotides (ASOs) is becoming more of a reality as several drugs have been approved for the treatment of human disorders and many others are in various phases in development and clinical trials. ASOs are short DNA/RNA oligos which are heavily modified to increase their stability in biological fluids and retain the properties of creating RNA-RNA and DNA-RNA duplexes that knock-down or correct genetic expression. This review outlines several strategies that ASOs utilize for the treatment of various congenital diseases and syndromes that develop with aging. In addition, we discuss some of the mechanisms for specific non-targeted ASO internalization within cells.
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Affiliation(s)
- Colton M. Miller
- Department of Biochemistry, University of Nebraska - Lincoln, 1901 Vine St. Lincoln NE 68588 USA
| | - Edward N. Harris
- Department of Biochemistry, University of Nebraska - Lincoln, 1901 Vine St. Lincoln NE 68588 USA
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83
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Jain HV, Beaucage SL. An Amphipathic trans-Acting Phosphorothioate DNA Element Delivers Uncharged PNA and PMO Nucleic Acid Sequences in Mammalian Cells. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2016; 64:4.69.1-4.69.22. [PMID: 27516815 PMCID: PMC4976944 DOI: 10.1002/0471142700.nc0469s64] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An innovative approach to the delivery of uncharged peptide nucleic acids (PNAs) and phosphorodiamidate morpholino (PMO) oligomers in mammalian cells is described and consists of extending the sequence of those oligomers with a short PNA-polyA or PMO-polyA tail. Recognition of the polyA-tailed PNA or PMO oligomers by an amphipathic trans-acting polythymidylic thiophosphate triester element (dTtaPS) results in efficient internalization of those oligomers in several cell lines. The authors' findings indicate that cellular uptake of the oligomers occurs through an energy-dependent mechanism and macropinocytosis appears to be the predominant endocytic pathway used for internalization. The functionality of the internalized oligomers is demonstrated by alternate splicing of the pre-mRNA encoding luciferase in HeLa pLuc 705 cells. Amphipathic phosphorothioate DNA elements may represent a unique class of cellular transporters for robust delivery of uncharged nucleic acid sequences in live mammalian cells. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Harsh V Jain
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
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84
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Xu L, Park KH, Zhao L, Xu J, El Refaey M, Gao Y, Zhu H, Ma J, Han R. CRISPR-mediated Genome Editing Restores Dystrophin Expression and Function in mdx Mice. Mol Ther 2016; 24:564-569. [PMID: 26449883 PMCID: PMC4786912 DOI: 10.1038/mt.2015.192] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/05/2015] [Indexed: 12/13/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a degenerative muscle disease caused by genetic mutations that lead to the disruption of dystrophin in muscle fibers. There is no curative treatment for this devastating disease. Clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) has emerged as a powerful tool for genetic manipulation and potential therapy. Here we demonstrate that CRIPSR-mediated genome editing efficiently excised a 23-kb genomic region on the X-chromosome covering the mutant exon 23 in a mouse model of DMD, and restored dystrophin expression and the dystrophin-glycoprotein complex at the sarcolemma of skeletal muscles in live mdx mice. Electroporation-mediated transfection of the Cas9/gRNA constructs in the skeletal muscles of mdx mice normalized the calcium sparks in response to osmotic shock. Adenovirus-mediated transduction of Cas9/gRNA greatly reduced the Evans blue dye uptake of skeletal muscles at rest and after downhill treadmill running. This study provides proof evidence for permanent gene correction in DMD.
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Affiliation(s)
- Li Xu
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Ki Ho Park
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Lixia Zhao
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Jing Xu
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Mona El Refaey
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Yandi Gao
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Hua Zhu
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Jianjie Ma
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Renzhi Han
- Department of Surgery, Davis Heart and Lung Research Institute, Biomedical Sciences Graduate Program, Biophysics Graduate Program, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
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85
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Correcting the NLRP3 inflammasome deficiency in macrophages from autoimmune NZB mice with exon skipping antisense oligonucleotides. Immunol Cell Biol 2016; 94:520-4. [PMID: 26833024 DOI: 10.1038/icb.2016.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 12/22/2022]
Abstract
Inflammasomes are molecular complexes activated by infection and cellular stress, leading to caspase-1 activation and subsequent interleukin-1β (IL-1β) processing and cell death. The autoimmune NZB mouse strain does not express NLRP3, a key inflammasome initiator mediating responses to a wide variety of stimuli including endogenous danger signals, environmental irritants and a range of bacterial, fungal and viral pathogens. We have previously identified an intronic point mutation in the Nlrp3 gene from NZB mice that generates a splice acceptor site. This leads to inclusion of a pseudoexon that introduces an early termination codon and is proposed to be the cause of NLRP3 inflammasome deficiency in NZB cells. Here we have used exon skipping antisense oligonucleotides (AONs) to prevent aberrant splicing of Nlrp3 in NZB macrophages, and this restored both NLRP3 protein expression and NLRP3 inflammasome activity. Thus, the single point mutation leading to aberrant splicing is the sole cause of NLRP3 inflammasome deficiency in NZB macrophages. The NZB mouse provides a model for addressing a splicing defect in macrophages and could be used to further investigate AON design and delivery of AONs to macrophages in vivo.
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86
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Iyombe-Engembe JP, Ouellet DL, Barbeau X, Rousseau J, Chapdelaine P, Lagüe P, Tremblay JP. Efficient Restoration of the Dystrophin Gene Reading Frame and Protein Structure in DMD Myoblasts Using the CinDel Method. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e283. [PMID: 26812655 PMCID: PMC5012554 DOI: 10.1038/mtna.2015.58] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 12/10/2015] [Indexed: 12/18/2022]
Abstract
The CRISPR/Cas9 system is a great revolution in biology. This technology allows the modification of genes in vitro and in vivo in a wide variety of living organisms. In most Duchenne muscular dystrophy (DMD) patients, expression of dystrophin (DYS) protein is disrupted because exon deletions result in a frame shift. We present here the CRISPR-induced deletion (CinDel), a new promising genome-editing technology to correct the DMD gene. This strategy is based on the use of two gRNAs targeting specifically exons that precede and follow the patient deletion in the DMD gene. This pair of gRNAs induced a precise large additional deletion leading to fusion of the targeted exons. Using an adequate pair of gRNAs, the deletion of parts of these exons and the intron separating them restored the DMD reading frame in 62% of the hybrid exons in vitro in DMD myoblasts and in vivo in electroporated hDMD/mdx mice. Moreover, adequate pairs of gRNAs also restored the normal spectrin-like repeat of the dystrophin rod domain; such restoration is not obtained by exon skipping or deletion of complete exons. The expression of an internally deleted DYS protein was detected following the formation of myotubes by the unselected, treated DMD myoblasts. Given that CinDel induces permanent reparation of the DMD gene, this treatment would not have to be repeated as it is the case for exon skipping induced by oligonucleotides.
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Affiliation(s)
- Jean-Paul Iyombe-Engembe
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
| | - Dominique L Ouellet
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
| | - Xavier Barbeau
- Department of Chemistry, Université Laval, Quebec City, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec City, Québec, Canada
| | - Joël Rousseau
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
| | - Pierre Chapdelaine
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
| | - Patrick Lagüe
- Department of Chemistry, Université Laval, Quebec City, Québec, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec City, Québec, Canada
| | - Jacques P Tremblay
- Centre de Recherche du Centre Hospitalier, Universitaire de Québec, Neurosciences Axis, Quebec City, Québec, Canada
- Faculty of Medicine, Department of Molecular Medicine, Université Laval, Quebec City, Québec, Canada
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87
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Buck HM. Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/jbpc.2016.71003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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88
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Gene therapy in monogenic congenital myopathies. Methods 2015; 99:91-8. [PMID: 26454198 DOI: 10.1016/j.ymeth.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/10/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022] Open
Abstract
Current treatment options for patients with monogenetic congenital myopathies (MCM) ameliorate the symptoms of the disorder without resolving the underlying cause. However, gene therapies are being developed where the mutated or deficient gene target is replaced. Preclinical findings in animal models appear promising, as illustrated by gene replacement for X-linked myotubular myopathy (XLMTM) in canine and murine models. Prospective applications and approaches to gene replacement therapy, using these disorders as examples, are discussed in this review.
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89
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Hornum M, Kumar P, Podsiadly P, Nielsen P. Increasing the Stability of DNA:RNA Duplexes by Introducing Stacking Phenyl-Substituted Pyrazole, Furan, and Triazole Moieties in the Major Groove. J Org Chem 2015; 80:9592-602. [PMID: 26334359 DOI: 10.1021/acs.joc.5b01577] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Consecutive incorporations of our previously published thymidine analogue, 5-(1-phenyl-1H-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W in oligonucleotides, has demonstrated significant duplex-stabilizing properties due to its efficient staking properties in the major groove of DNA:RNA duplexes. The corresponding 2'-deoxycytidine analogue is not as well-accommodated in duplexes, however, due to its clear preference for the ring-flipped coplanar conformation. In our present work, we have used ab initio calculations to design two new building blocks, 5-(5-phenylfuran-2-yl)-2'-deoxycytidine monomer Y and 5-(1-phenyl-1H-pyrazol-3-yl)-2'-deoxycytidine monomer Z, that emulate the conformation of W. These monomers were synthesized by Suzuki-Miyaura couplings, and the pyrazole moiety was obtained in a cycloaddition from N-phenylsydnone. We show that the novel analogues Y and Z engage in efficient stacking either with themselves or with W due to a better overlap of the aromatic moieties. Importantly, we demonstrate that this translates into very thermally stable DNA:RNA duplexes, thus making Y and especially Z good candidates for improving the binding affinities of oligonucleotide-based therapeutics. Since we now have both efficiently stacking T and C analogues in hand, any purine rich stretch can be effectively targeted using these simple analogues. Notably, we show that the introduction of the aromatic rings in the major groove does not significantly change the helical geometry.
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Affiliation(s)
- Mick Hornum
- Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark
| | - Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark
| | - Patricia Podsiadly
- Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark
| | - Poul Nielsen
- Nucleic Acid Center, Department of Physics, Chemistry & Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark
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90
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Early pathogenesis of Duchenne muscular dystrophy modelled in patient-derived human induced pluripotent stem cells. Sci Rep 2015; 5:12831. [PMID: 26290039 PMCID: PMC4642533 DOI: 10.1038/srep12831] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 05/11/2015] [Indexed: 12/30/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a progressive and fatal muscle degenerating disease caused by a dystrophin deficiency. Effective suppression of the primary pathology observed in DMD is critical for treatment. Patient-derived human induced pluripotent stem cells (hiPSCs) are a promising tool for drug discovery. Here, we report an in vitro evaluation system for a DMD therapy using hiPSCs that recapitulate the primary pathology and can be used for DMD drug screening. Skeletal myotubes generated from hiPSCs are intact, which allows them to be used to model the initial pathology of DMD in vitro. Induced control and DMD myotubes were morphologically and physiologically comparable. However, electric stimulation of these myotubes for in vitro contraction caused pronounced calcium ion (Ca2+) influx only in DMD myocytes. Restoration of dystrophin by the exon-skipping technique suppressed this Ca2+ overflow and reduced the secretion of creatine kinase (CK) in DMD myotubes. These results suggest that the early pathogenesis of DMD can be effectively modelled in skeletal myotubes induced from patient-derived iPSCs, thereby enabling the development and evaluation of novel drugs.
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91
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Nancy MM, Nora RM, Rebeca MC. Peptidic tools applied to redirect alternative splicing events. Peptides 2015; 67:1-11. [PMID: 25748022 DOI: 10.1016/j.peptides.2015.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/05/2015] [Accepted: 02/26/2015] [Indexed: 01/25/2023]
Abstract
Peptides are versatile and attractive biomolecules that can be applied to modulate genetic mechanisms like alternative splicing. In this process, a single transcript yields different mature RNAs leading to the production of protein isoforms with diverse or even antagonistic functions. During splicing events, errors can be caused either by mutations present in the genome or by defects or imbalances in regulatory protein factors. In any case, defects in alternative splicing have been related to several genetic diseases including muscular dystrophy, Alzheimer's disease and cancer from almost every origin. One of the most effective approaches to redirect alternative splicing events has been to attach cell-penetrating peptides to oligonucleotides that can modulate a single splicing event and restore correct gene expression. Here, we summarize how natural existing and bioengineered peptides have been applied over the last few years to regulate alternative splicing and genetic expression. Under different genetic and cellular backgrounds, peptides have been shown to function as potent vehicles for splice correction, and their therapeutic benefits have reached clinical trials and patenting stages, emphasizing the use of regulatory peptides as an exciting therapeutic tool for the treatment of different genetic diseases.
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Affiliation(s)
- Martínez-Montiel Nancy
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Rosas-Murrieta Nora
- Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Martínez-Contreras Rebeca
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Mexico.
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92
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Jain HV, Verthelyi D, Beaucage SL. Amphipathic trans-acting phosphorothioate DNA elements mediate the delivery of uncharged nucleic acid sequences in mammalian cells. RSC Adv 2015. [DOI: 10.1039/c5ra12038a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Amphipathic trans-acting phosphorothioate DNA elements deliver PNA and PMO oligomers in mammalian cells.
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Affiliation(s)
- H. V. Jain
- Division of Biotechnology Review and Research IV
- CDER
- FDA
- Maryland 20933
- USA
| | - D. Verthelyi
- Division of Biotechnology Review and Research III
- CDER
- FDA
- Maryland 20933
- USA
| | - S. L. Beaucage
- Division of Biotechnology Review and Research IV
- CDER
- FDA
- Maryland 20933
- USA
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93
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Shabanpoor F, McClorey G, Saleh AF, Järver P, Wood MJA, Gait MJ. Bi-specific splice-switching PMO oligonucleotides conjugated via a single peptide active in a mouse model of Duchenne muscular dystrophy. Nucleic Acids Res 2014; 43:29-39. [PMID: 25468897 PMCID: PMC4288157 DOI: 10.1093/nar/gku1256] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The potential for therapeutic application of splice-switching oligonucleotides (SSOs) to modulate pre-mRNA splicing is increasingly evident in a number of diseases. However, the primary drawback of this approach is poor cell and in vivo oligonucleotide uptake efficacy. Biological activities can be significantly enhanced through the use of synthetically conjugated cationic cell penetrating peptides (CPPs). Studies to date have focused on the delivery of a single SSO conjugated to a CPP, but here we describe the conjugation of two phosphorodiamidate morpholino oligonucleotide (PMO) SSOs to a single CPP for simultaneous delivery and pre-mRNA targeting of two separate genes, exon 23 of the Dmd gene and exon 5 of the Acvr2b gene, in a mouse model of Duchenne muscular dystrophy. Conjugations of PMOs to a single CPP were carried out through an amide bond in one case and through a triazole linkage (‘click chemistry’) in the other. The most active bi-specific CPP–PMOs demonstrated comparable exon skipping levels for both pre-mRNA targets when compared to individual CPP–PMO conjugates both in cell culture and in vivo in the mdx mouse model. Thus, two SSOs with different target sequences conjugated to a single CPP are biologically effective and potentially suitable for future therapeutic exploitation.
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Affiliation(s)
- Fazel Shabanpoor
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Graham McClorey
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Amer F Saleh
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Peter Järver
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Michael J Gait
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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94
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MLPA based detection of mutations in the dystrophin gene of 180 Polish families with Duchenne/Becker muscular dystrophy. Neurol Neurochir Pol 2014; 48:416-22. [DOI: 10.1016/j.pjnns.2014.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 10/03/2014] [Accepted: 10/15/2014] [Indexed: 11/17/2022]
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95
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96
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Siva K, Covello G, Denti MA. Exon-skipping antisense oligonucleotides to correct missplicing in neurogenetic diseases. Nucleic Acid Ther 2014; 24:69-86. [PMID: 24506781 DOI: 10.1089/nat.2013.0461] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alternative splicing is an important regulator of the transcriptome. However, mutations may cause alteration of splicing patterns, which in turn leads to disease. During the past 10 years, exon skipping has been looked upon as a powerful tool for correction of missplicing in disease and progress has been made towards clinical trials. In this review, we discuss the use of antisense oligonucleotides to correct splicing defects through exon skipping, with a special focus on diseases affecting the nervous system, and the latest stage achieved in its progress.
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Affiliation(s)
- Kavitha Siva
- 1 Center for Integrative Biology (CIBIO), University of Trento , Trento, Italy
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97
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Falzarano MS, Passarelli C, Ferlini A. Nanoparticle delivery of antisense oligonucleotides and their application in the exon skipping strategy for Duchenne muscular dystrophy. Nucleic Acid Ther 2014; 24:87-100. [PMID: 24506782 DOI: 10.1089/nat.2013.0450] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antisense therapy is a powerful tool for inducing post-transcriptional modifications and thereby regulating target genes associated with disease. There are several classes of antisense oligonucleotides (AONs) with therapeutic use, such as double-stranded RNAs (interfering RNAs, utilized for gene silencing, and single-stranded AONs with various chemistries, which are useful for antisense targeting of micro-RNAs and mRNAs. In particular, the use of AONs for exon skipping, by targeting pre-mRNA, is proving to be a highly promising therapy for some genetic disorders like Duchenne muscular dystrophy and spinal muscular atrophy. However, AONs are unable to cross the plasma membrane unaided, and several other obstacles still remain to be overcome, in particular their instability due to their nuclease sensitivity and their lack of tissue specificity. Various drug delivery systems have been explored to improve the bioavailability of nucleic acids, and nanoparticles (NPs) have been suggested as potential vectors for DNA/RNA. This review describes the recent progress in AON conjugation with natural and synthetic delivery systems, and provides an overview of the efficacy of NP-AON complexes as an exon-skipping treatment for Duchenne muscular dystrophy.
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Affiliation(s)
- Maria Sofia Falzarano
- 1 Section of Microbiology and Medical Genetics, Department of Medical Sciences, University of Ferrara , Ferrara, Italy
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98
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Widespread genome transcription: new possibilities for RNA therapies. Biochem Biophys Res Commun 2014; 452:294-301. [PMID: 25193698 DOI: 10.1016/j.bbrc.2014.08.139] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 08/25/2014] [Indexed: 12/15/2022]
Abstract
Comprehensive analysis of mammalian transcriptomes has surprisingly revealed that a major fraction of the RNAs produced by mammalian cells and tissues is comprised of long non-coding RNAs (lncRNAs). Such RNAs were previously disregarded as useless, but recent functional studies have revealed that they have multiple regulatory functions. A large subset of these lncRNAs are antisense to protein-coding genes; such RNAs are particularly attractive to researchers because their functions are better understood than other lncRNAs and their action can be easily modulated and engineered by modifying the antisense region. We discuss various aspects of regulation by antisense RNAs and other small nucleic acids and the challenges to bring these technologies to gene therapy. Despite several remaining issues related to delivery, RNA stability, side effects, and toxicity, the field is moving quickly towards future biotechnological and health applications. Therapies based on lncRNAs may be the key to increased cell-specificity of future gene therapies.
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99
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Ji X, Zhang J, Xu Y, Long F, Sun W, Liu X, Chen Y, Jiang W. MLPA Application in Clinical Diagnosis of DMD/BMD in Shanghai. J Clin Lab Anal 2014; 29:405-11. [PMID: 25131993 DOI: 10.1002/jcla.21787] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/21/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Duchenne and Becker muscular dystrophy (DMD/BMD) are X-linked recessive disorders caused by mutation in dystrophin gene. We reported 3-year clinic experience from a single hospital in Shanghai using multiplex ligation dependent probe amplification (MLPA) assay to detect DMD mutations. METHODS Four hundred and fifty-one males and 184 females, who were clinically diagnosed as DMD/BMD patients or carriers at our hospital's outpatient clinic, were collected and performed with MLPA to detect DMD gene mutations. RESULTS Seventeen novel mutation points not reported in the Leiden Muscular Dystrophy pages were identified in this study. We found that the most frequent deletion spots ranged from exon45 to exon52, and exon2, exon19 were the two most frequently detected duplication spots. CONCLUSION The results of our study confirmed MLPA as an efficient clinical method for detecting DMD gene mutations in DMD/BMD patients. Single exon mutation detected by MLPA should be verified by other methods, and we should emphasize that only precise clinical molecular diagnosis can lead to the feasibility of prenatal diagnosis.
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Affiliation(s)
- Xing Ji
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jingmin Zhang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yan Xu
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Fei Long
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wei Sun
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xiaoqin Liu
- Shanghai Institute for Pediatric Research, Shanghai, China.,Department of Neurology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingwei Chen
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenting Jiang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
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100
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Kralovicova J, Lages A, Patel A, Dhir A, Buratti E, Searle M, Vorechovsky I. Optimal antisense target reducing INS intron 1 retention is adjacent to a parallel G quadruplex. Nucleic Acids Res 2014; 42:8161-73. [PMID: 24944197 PMCID: PMC4081105 DOI: 10.1093/nar/gku507] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Splice-switching oligonucleotides (SSOs) have been widely used to inhibit exon usage
but antisense strategies that promote removal of entire introns to increase
splicing-mediated gene expression have not been developed. Here we show reduction of
INS intron 1 retention by SSOs that bind transcripts derived from
a human haplotype expressing low levels of proinsulin. This haplotype is tagged by a
polypyrimidine tract variant rs689 that decreases the efficiency of
intron 1 splicing and increases the relative abundance of mRNAs with extended 5'
untranslated region (5' UTR), which curtails translation. Co-expression of
haplotype-specific reporter constructs with SSOs bound to splicing regulatory motifs
and decoy splice sites in primary transcripts revealed a motif that significantly
reduced intron 1-containing mRNAs. Using an antisense microwalk at a single
nucleotide resolution, the optimal target was mapped to a splicing silencer
containing two pseudoacceptor sites sandwiched between predicted RNA guanine (G)
quadruplex structures. Circular dichroism spectroscopy and nuclear magnetic resonance
of synthetic G-rich oligoribonucleotide tracts derived from this region showed
formation of a stable parallel 2-quartet G-quadruplex on the 3' side of the antisense
retention target and an equilibrium between quadruplexes and stable hairpin-loop
structures bound by optimal SSOs. This region interacts with heterogeneous nuclear
ribonucleoproteins F and H that may interfere with conformational transitions
involving the antisense target. The SSO-assisted promotion of weak intron removal
from the 5' UTR through competing noncanonical and canonical RNA structures may
facilitate development of novel strategies to enhance gene expression.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Ana Lages
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Alpa Patel
- University of Nottingham, School of Chemistry, Centre for Biomolecular Sciences, Nottingham NG7 2RD, UK
| | | | | | - Mark Searle
- University of Nottingham, School of Chemistry, Centre for Biomolecular Sciences, Nottingham NG7 2RD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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