1
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Falzarano MS, Grilli A, Zia S, Fang M, Rossi R, Gualandi F, Rimessi P, El Dani R, Fabris M, Lu Z, Li W, Mongini T, Ricci F, Pegoraro E, Bello L, Barp A, Sansone VA, Hegde M, Roda B, Reschiglian P, Bicciato S, Selvatici R, Ferlini A. RNA-seq in DMD urinary stem cells recognized muscle-related transcription signatures and addressed the identification of atypical mutations by whole-genome sequencing. HGG ADVANCES 2022; 3:100054. [PMID: 35047845 PMCID: PMC8756543 DOI: 10.1016/j.xhgg.2021.100054] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Urinary stem cells (USCs) are a non-invasive, simple, and affordable cell source to study human diseases. Here we show that USCs are a versatile tool for studying Duchenne muscular dystrophy (DMD), since they are able to address RNA signatures and atypical mutation identification. Gene expression profiling of DMD individuals' USCs revealed a profound deregulation of inflammation, muscle development, and metabolic pathways that mirrors the known transcriptional landscape of DMD muscle and worsens following USCs' myogenic transformation. This pathogenic transcription signature was reverted by an exon-skipping corrective approach, suggesting the utility of USCs in monitoring DMD antisense therapy. The full DMD transcript profile performed in USCs from three undiagnosed DMD individuals addressed three splicing abnormalities, which were decrypted and confirmed as pathogenic variations by whole-genome sequencing (WGS). This combined genomic approach allowed the identification of three atypical and complex DMD mutations due to a deep intronic variation and two large inversions, respectively. All three mutations affect DMD gene splicing and cause a lack of dystrophin protein production, and one of these also generates unique fusion genes and transcripts. Further characterization of USCs using a novel cell-sorting technology (Celector) highlighted cell-type variability and the representation of cell-specific DMD isoforms. Our comprehensive approach to USCs unraveled RNA, DNA, and cell-specific features and demonstrated that USCs are a robust tool for studying and diagnosing DMD.
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Affiliation(s)
- Maria S Falzarano
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Andrea Grilli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy
| | | | | | - Rachele Rossi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Francesca Gualandi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Paola Rimessi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Reem El Dani
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Marina Fabris
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | | | - Wenyan Li
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Elena Pegoraro
- ERN Neuromuscular Center, Department of Neurosciences, Unit of Neurology, University of Padua, Padua 35122, Italy
| | - Luca Bello
- ERN Neuromuscular Center, Department of Neurosciences, Unit of Neurology, University of Padua, Padua 35122, Italy
| | - Andrea Barp
- The NEMO Clinical Center, Neurorehabilitation Unit, University of Milan, Milan 20162, Italy
| | - Valeria A Sansone
- The NEMO Clinical Center, Neurorehabilitation Unit, University of Milan, Milan 20162, Italy
| | - Madhuri Hegde
- PerkinElmer Genomics, 3950 Shackleford Rd., Ste. 195, Duluth, GA 30096, USA
| | - Barbara Roda
- Stem Sel s.r.l., Bologna 40127, Italy
- Department of Chemistry "G. Ciamician," University of Bologna, Bologna 40126, Italy
| | - Pierluigi Reschiglian
- Stem Sel s.r.l., Bologna 40127, Italy
- Department of Chemistry "G. Ciamician," University of Bologna, Bologna 40126, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy
| | - Rita Selvatici
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Alessandra Ferlini
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
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2
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Falzarano MS, Rossi R, Grilli A, Fang M, Osman H, Sabatelli P, Antoniel M, Lu Z, Li W, Selvatici R, Al-Khalili C, Gualandi F, Bicciato S, Torelli S, Ferlini A. Urine-Derived Stem Cells Express 571 Neuromuscular Disorders Causing Genes, Making Them a Potential in vitro Model for Rare Genetic Diseases. Front Physiol 2021; 12:716471. [PMID: 34744760 PMCID: PMC8565768 DOI: 10.3389/fphys.2021.716471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Neuromuscular disorders (NMDs) are a heterogeneous group of genetic diseases, caused by mutations in genes involved in spinal cord, peripheral nerve, neuromuscular junction, and muscle functions. To advance the knowledge of the pathological mechanisms underlying NMDs and to eventually identify new potential drugs paving the way for personalized medicine, limitations regarding the availability of neuromuscular disease-related biological samples, rarely accessible from patients, are a major challenge. Aim: We characterized urinary stem cells (USCs) by in-depth transcriptome and protein profiling to evaluate whether this easily accessible source of patient-derived cells is suitable to study neuromuscular genetic diseases, focusing especially on those currently involved in clinical trials. Methods: The global transcriptomics of either native or MyoD transformed USCs obtained from control individuals was performed by RNA-seq. The expression of 610 genes belonging to 16 groups of disorders (http://www.musclegenetable.fr/) whose mutations cause neuromuscular diseases, was investigated on the RNA-seq output. In addition, protein expression of 11 genes related to NMDs including COL6A, EMD, LMNA, SMN, UBA1, DYNC1H1, SOD1, C9orf72, DYSF, DAG1, and HTT was analyzed in native USCs by immunofluorescence and/or Western blot (WB). Results: RNA-seq profile of control USCs shows that 571 out of 610 genes known to be involved in NMDs, are expressed in USCs. Interestingly, the expression levels of the majority of NMD genes remain unmodified following USCs MyoD transformation. Most genes involved in the pathogenesis of all 16 groups of NMDs are well represented except for channelopathies and malignant hyperthermia related genes. All tested proteins showed high expression values, suggesting consistency between transcription and protein representation in USCs. Conclusion: Our data suggest that USCs are human cells, obtainable by non-invasive means, which might be used as a patient-specific cell model to study neuromuscular disease-causing genes and that they can be likely adopted for a variety of in vitro functional studies such as mutation characterization, pathway identification, and drug screening.
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Affiliation(s)
- Maria Sofia Falzarano
- UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Rachele Rossi
- UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara, Ferrara, Italy.,The Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Andrea Grilli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Mingyan Fang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Hana Osman
- UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara, Ferrara, Italy.,Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Patrizia Sabatelli
- CNR-Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza"- Unit of Bologna, Bologna, Italy.,Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manuela Antoniel
- CNR-Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza"- Unit of Bologna, Bologna, Italy.,Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Zhiyuan Lu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Wenyan Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Rita Selvatici
- UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Cristina Al-Khalili
- Department of Proteomics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Francesca Gualandi
- UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvia Torelli
- The Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, United Kingdom.,National Institute for Health Research, Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, United Kingdom
| | - Alessandra Ferlini
- UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara, Ferrara, Italy.,The Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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3
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Tomar S, Moorthy V, Sethi R, Chai J, Low PS, Hong STK, Lai PS. Mutational spectrum of dystrophinopathies in Singapore: Insights for genetic diagnosis and precision therapy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:230-244. [DOI: 10.1002/ajmg.c.31704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Vikaesh Moorthy
- Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Josiah Chai
- Department of Neurology, National Neuroscience Institute Singapore
| | - Poh Sim Low
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Stacey Tay Kiat Hong
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
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4
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Chauhan K, Kalam H, Dutt R, Kumar D. RNA Splicing: A New Paradigm in Host-Pathogen Interactions. J Mol Biol 2019; 431:1565-1575. [PMID: 30857970 DOI: 10.1016/j.jmb.2019.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/21/2022]
Abstract
RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pathologies including cancer. Emerging evidence suggests precise regulation of splicing as fundamental to normal well-being. In this context, infection-induced alternative splicing has emerged as a new pivot of host function, which pathogenic microbes can alter-directly or indirectly-to tweak the host immune responses against the pathogen. The implications of these findings are vast, and although not explored much in the case of pathogenic infections, we present here examples from splicing mediated regulation of immune responses across a variety of conditions and explore how this fascinating finding brings a new paradigm to host-pathogen interactions.
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Affiliation(s)
- Komal Chauhan
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Haroon Kalam
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ravi Dutt
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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5
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Wang L, Xu M, Li H, He R, Lin J, Zhang C, Zhu Y. Genotypes and Phenotypes of DMD Small Mutations in Chinese Patients With Dystrophinopathies. Front Genet 2019; 10:114. [PMID: 30833962 PMCID: PMC6388391 DOI: 10.3389/fgene.2019.00114] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 01/30/2019] [Indexed: 11/17/2022] Open
Abstract
Dystrophinopathies are a group of neuromuscular disorders resulting from mutations in DMD, including Duchenne muscular dystrophy (DMD), intermediate muscular dystrophy (IMD), and Becker muscular dystrophy (BMD). Herein, we present the characteristics of small mutations in Chinese patients with dystrophinopathies, and explore genotype–phenotype correlations. In our cohort, 115 patients with small mutations (18.49% of all patients) were included and DMD mutations were detected by either Sanger (53.91%) or next generation sequencing (46.09%). In total, 106 small mutations were detected, 28 of which (26.42%) had not been reported previously. The most common mutations were nonsense mutations (52.17%), followed by splicing (24.35%), frameshift (17.39%), and missense mutations (5.22%), in addition to a single untranslated region mutation (0.87%). We discovered distinct mutation characteristics in our patients, such as different positional distributions, indicating different exon skipping therapy strategies for small mutations in Chinese patients. Almost all patients (96.51%) with truncating or missense mutations, were covered by triple/double/single-exon skipping therapy; the most frequent single-exon skipping strategy was skipping exon 32, applicable for 8.51% of patients. Furthermore, splicing classification grades were correlated with phenotypes in nonsense mutations (P < 0.001), and serum creatinine levels differed significantly between DMD/IMD and BMD for patients ≤ 16 years old (P = 0.002). These observations can further aid prognostic judgment and guide treatment. In conclusion, the mutation characteristics and genotype–phenotype correlations in Chinese patients with dystrophinopathies and small mutations could provide insights into the molecular mechanisms of pathogenesis, diagnosis, and treatment designs.
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Affiliation(s)
- Liang Wang
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min Xu
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Li
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ruojie He
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinfu Lin
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng Zhang
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuling Zhu
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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6
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Szigyarto CAK, Spitali P. Biomarkers of Duchenne muscular dystrophy: current findings. Degener Neurol Neuromuscul Dis 2018; 8:1-13. [PMID: 30050384 PMCID: PMC6053903 DOI: 10.2147/dnnd.s121099] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Numerous biomarkers have been unveiled in the rapidly evolving biomarker discovery field, with an aim to improve the clinical management of disorders. In rare diseases, such as Duchenne muscular dystrophy, this endeavor has created a wealth of knowledge that, if effectively exploited, will benefit affected individuals, with respect to health care, therapy, improved quality of life and increased life expectancy. The most promising findings and molecular biomarkers are inspected in this review, with an aim to provide an overview of currently known biomarkers and the technological developments used. Biomarkers as cells, genetic variations, miRNAs, proteins, lipids and/or metabolites indicative of disease severity, progression and treatment response have the potential to improve development and approval of therapies, clinical management of DMD and patients’ life quality. We highlight the complexity of translating research results to clinical use, emphasizing the need for biomarkers, fit for purpose and describe the challenges associated with qualifying biomarkers for clinical applications.
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Affiliation(s)
- Cristina Al-Khalili Szigyarto
- Division of Proteomics, School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden, .,Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden,
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands,
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7
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Falzarano MS, D'Amario D, Siracusano A, Massetti M, Amodeo A, La Neve F, Maroni CR, Mercuri E, Osman H, Scotton C, Armaroli A, Rossi R, Selvatici R, Crea F, Ferlini A. Duchenne Muscular Dystrophy Myogenic Cells from Urine-Derived Stem Cells Recapitulate the Dystrophin Genotype and Phenotype. Hum Gene Ther 2018; 27:772-783. [PMID: 27530229 DOI: 10.1089/hum.2016.079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A ready source of autologous myogenic cells is of vital importance for drug screening and functional genetic studies in Duchenne muscular dystrophy (DMD), a rare disease caused by a variety of dystrophin gene mutations. As stem cells (SCs) can be easily and noninvasively obtained from urine specimens, we set out to determine whether they could be myogenically induced and useful in DMD research. To this end, we isolated stem cells from the urine of two healthy donors and from one patient with DMD, and performed surface marker characterization, myogenic differentiation (MyoD), and then transfection with antisense oligoribonucleotides to test for exon skipping and protein restoration. We demonstrated that native urine-derived stem cells express the full-length dystrophin transcript, and that the dystrophin mutation was retained in the cells of the patient with DMD, although the dystrophin protein was detected solely in control cells after myogenic transformation according to the phenotype. Notably, we also showed that treatment with antisense oligoribonucleotide against dystrophin exon 44 induced skipping in both native and MyoD-transformed urine-derived stem cells in DMD, with a therapeutic transcript-reframing effect, as well as visible protein restoration in the latter. Hence MyoD-transformed cells may be a good myogenic model for studying dystrophin gene expression, and native urine stem cells could be used to study the dystrophin transcript, and both diagnostic procedures and splicing modulation therapies in both patients and control subjects, without invasive and costly collection methods. New, bankable bioproducts from urine stem cells, useful for prescreening studies and therapeutic applications alike, are also foreseeable after further, more in-depth characterization.
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Affiliation(s)
- Maria Sofia Falzarano
- 1 UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara , Ferrara, Italy
| | - Domenico D'Amario
- 2 Department of Cardiovascular Medicine, Catholic University of the Sacred Heart , Rome, Italy
| | - Andrea Siracusano
- 2 Department of Cardiovascular Medicine, Catholic University of the Sacred Heart , Rome, Italy
| | - Massimo Massetti
- 2 Department of Cardiovascular Medicine, Catholic University of the Sacred Heart , Rome, Italy
| | - Antonio Amodeo
- 3 Department of Cardiothoracic Surgery, Ospedale Bambino Gesù , Rome, Italy
| | - Federica La Neve
- 2 Department of Cardiovascular Medicine, Catholic University of the Sacred Heart , Rome, Italy
| | - Camilla Reina Maroni
- 2 Department of Cardiovascular Medicine, Catholic University of the Sacred Heart , Rome, Italy
| | - Eugenio Mercuri
- 4 Pediatric Neurology Unit, Catholic University, Rome , Italy
| | - Hana Osman
- 1 UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara , Ferrara, Italy
| | - Chiara Scotton
- 1 UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara , Ferrara, Italy
| | - Annarita Armaroli
- 1 UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara , Ferrara, Italy
| | - Rachele Rossi
- 1 UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara , Ferrara, Italy
| | - Rita Selvatici
- 1 UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara , Ferrara, Italy
| | - Filippo Crea
- 2 Department of Cardiovascular Medicine, Catholic University of the Sacred Heart , Rome, Italy
| | - Alessandra Ferlini
- 1 UOL (Unità Operativa Logistica) of Medical Genetics, University of Ferrara , Ferrara, Italy.,5 Neuromuscular Unit, Great Ormond Street Hospital, University College London , London, United Kingdom
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8
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Bates DO, Morris JC, Oltean S, Donaldson LF. Pharmacology of Modulators of Alternative Splicing. Pharmacol Rev 2017; 69:63-79. [PMID: 28034912 PMCID: PMC5226212 DOI: 10.1124/pr.115.011239] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
More than 95% of genes in the human genome are alternatively spliced to form multiple transcripts, often encoding proteins with differing or opposing function. The control of alternative splicing is now being elucidated, and with this comes the opportunity to develop modulators of alternative splicing that can control cellular function. A number of approaches have been taken to develop compounds that can experimentally, and sometimes clinically, affect splicing control, resulting in potential novel therapeutics. Here we develop the concepts that targeting alternative splicing can result in relatively specific pathway inhibitors/activators that result in dampening down of physiologic or pathologic processes, from changes in muscle physiology to altering angiogenesis or pain. The targets and pharmacology of some of the current inhibitors/activators of alternative splicing are demonstrated and future directions discussed.
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Affiliation(s)
- David O Bates
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Jonathan C Morris
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Sebastian Oltean
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Lucy F Donaldson
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
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9
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Park HJ, Jang H, Kim JH, Lee JH, Shin HY, Kim SM, Park KD, Yim SV, Lee JH, Choi YC. Discovery of pathogenic variants in a large Korean cohort of inherited muscular disorders. Clin Genet 2016; 91:403-410. [PMID: 27363342 DOI: 10.1111/cge.12826] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/06/2016] [Accepted: 06/17/2016] [Indexed: 01/31/2023]
Abstract
Inherited muscular disorders (IMDs) are clinically and genetically heterogeneous genetic disorders. We investigated the mutational spectrum and genotype-phenotype correlations in Korean patients with IMD. We developed a targeted panel of 69 known IMD genes and recruited a total of 209 Korean patients with IMD. Targeted capture sequencing identified 994 different variants. Among them, 98 variants were classified as pathogenic/likely pathogenic variants; 38 were novel variations. A total of 39 patients had the pathogenic/likely pathogenic variants. Among them, 75 (36%) patients were genetically confirmed, and 18 (9%) patients had one heterozygous variant of recessive myopathy. However, two genetically confirmed patients had an additional heterozygous variant of another recessive myopathy. Four patients with one heterozygous variant of a recessive myopathy showed different phenotypes, compared with the known phenotype of the identified gene. The major causative genes of Korean patients with IMDs were DMD (19 patients), COL6A1 (9), DYSF (9), GNE (7), LMNA (7), CAPN3 (6), and RYR1 (5). This study showed the mutational and clinical spectra in Korean patients with IMD and confirmed the usefulness of strategies utilizing targeted sequencing.
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Affiliation(s)
- H J Park
- Department of Neurology, Mokdong Hospital, Ewha Womans University School of Medicine, Seoul, Korea.,Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - H Jang
- Department of Chemistry, Yonsei University, Seoul, Korea
| | - J H Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, Korea
| | - J H Lee
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - H Y Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - S M Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - K D Park
- Department of Neurology, Mokdong Hospital, Ewha Womans University School of Medicine, Seoul, Korea
| | - S-V Yim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, Korea
| | - J H Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Y-C Choi
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
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10
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Fattahi Z, Kalhor Z, Fadaee M, Vazehan R, Parsimehr E, Abolhassani A, Beheshtian M, Zamani G, Nafissi S, Nilipour Y, Akbari M, Kahrizi K, Kariminejad A, Najmabadi H. Improved diagnostic yield of neuromuscular disorders applying clinical exome sequencing in patients arising from a consanguineous population. Clin Genet 2016; 91:386-402. [DOI: 10.1111/cge.12810] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Z. Fattahi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - Z. Kalhor
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - M. Fadaee
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - R. Vazehan
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - E. Parsimehr
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - A. Abolhassani
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - M. Beheshtian
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - G. Zamani
- Department of NeurologyTehran University of Medical Sciences Tehran Iran
| | - S. Nafissi
- Department of Pediatric Neurology, Pediatrics Center of Excellence, Children's Medical CenterTehran University of Medical Sciences Tehran Iran
| | - Y. Nilipour
- Pediatric Pathology Research Center, Mofid Children HospitalShahid Beheshti University of Medical Sciences Tehran Iran
| | - M.R. Akbari
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Women's College Research InstituteWomen's College Hospital Toronto Canada
- Dalla Lana School of Public HealthUniversity of Toronto Toronto Canada
| | - K. Kahrizi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - A. Kariminejad
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - H. Najmabadi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
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11
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New variants, challenges and pitfalls in DMD genotyping: implications in diagnosis, prognosis and therapy. J Hum Genet 2014; 59:454-64. [DOI: 10.1038/jhg.2014.54] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 06/02/2014] [Accepted: 06/06/2014] [Indexed: 01/17/2023]
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12
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Biodistribution and molecular studies on orally administered nanoparticle-AON complexes encapsulated with alginate aiming at inducing dystrophin rescue in mdx mice. BIOMED RESEARCH INTERNATIONAL 2013; 2013:527418. [PMID: 24392452 PMCID: PMC3874323 DOI: 10.1155/2013/527418] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
We have previously demonstrated that intraperitoneal injections of 2'-O-methyl-phosphorothioate (2'OMePS) antisense oligoribonucleotides adsorbed onto a cationic core-shell nanoparticles (NPs), termed ZM2, provoke dystrophin restoration in the muscles of mdx mice. The aim of the present work was to evaluate the oral route as an alternative way of administration for ZM2-antisense oligoribonucleotides complexes. The biodistribution and elimination of nanoparticles were evaluated after single and multiple oral doses of IR-dye conjugated nanoparticles. Labeled nanoparticles were tracked in vivo as well as in tissue cryosections, urines and feces by Odyssey infrared imaging system, and revealed a permanence in the intestine and abdominal lymph nodes for 72 hours to 7 days before being eliminated. We subsequently tested alginate-free and alginate-encapsulated ZM2-antisense oligoribonucleotides (AON) complexes orally administered 2 and 3 times per week, respectively, in mdx mice for a total of 12 weeks. Treatment with alginate ZM2-AON induced a slight dystrophin rescue in diaphragm and intestine smooth muscles, while no dystrophin was detected in alginate-free ZM2-AON treated mice. These data encourage further experiments on oral administration testing of NP and AON complexes, possibly translatable in oligoribonucleotides-mediated molecular therapies.
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13
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Anthony K, Feng L, Arechavala-Gomeza V, Guglieri M, Straub V, Bushby K, Cirak S, Morgan J, Muntoni F. Exon skipping quantification by quantitative reverse-transcription polymerase chain reaction in Duchenne muscular dystrophy patients treated with the antisense oligomer eteplirsen. Hum Gene Ther Methods 2013; 23:336-45. [PMID: 23075107 DOI: 10.1089/hgtb.2012.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Restoration of the open reading frame of the DMD gene and dystrophin protein production in Duchenne muscular dystrophy (DMD) can be achieved by exon skipping using antisense oligomers (AOs) targeted to splicing elements. Several such RNA-based gene therapy approaches are in clinical development in which all studies to date have assessed AO efficacy by semiquantitative nested reverse-transcription polymerase chain reaction (RT-PCR). Precise evaluation of dystrophin protein levels is complex and hindered by the large size and low abundance of dystrophin; thus an accurate and standardized measurement of DMD exon skipping at the RNA level remains important to assess and compare patient responses in DMD exon skipping clinical trials. Here we describe the development of a Taqman quantitative (q)RT-PCR assay to quantify exon skipping and highlight its use to determine the levels of exon skipping in DMD patients treated intramuscularly with a morpholino AO to skip exon 51, eteplirsen (AVI-4658). The muscle biopsies of these patients were previously thoroughly characterized, providing a valuable benchmark for the evaluation of novel methodology. We demonstrate that levels of dystrophin protein restoration, and thus patient response, correlate accurately with the RNA level. Furthermore, this sensitive assay detects revertant exon 51 skipped fibers in untreated biopsies, providing an important baseline to precisely quantify treatment success. This study represents the first quantitative assessment of exon skipping in a clinical trial setting. We present a standardized and reproducible method to assess patient response that will complement protein studies in future preclinical and clinical exon skipping-based gene therapy studies for DMD.
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Affiliation(s)
- Karen Anthony
- Dubowitz Neuromuscular Centre, UCL Institute of Child Health, London, WC1N 1EH, United Kingdom
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14
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Havens MA, Duelli DM, Hastings ML. Targeting RNA splicing for disease therapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2013; 4:247-66. [PMID: 23512601 PMCID: PMC3631270 DOI: 10.1002/wrna.1158] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Splicing of pre-messenger RNA into mature messenger RNA is an essential step for the expression of most genes in higher eukaryotes. Defects in this process typically affect cellular function and can have pathological consequences. Many human genetic diseases are caused by mutations that cause splicing defects. Furthermore, a number of diseases are associated with splicing defects that are not attributed to overt mutations. Targeting splicing directly to correct disease-associated aberrant splicing is a logical approach to therapy. Splicing is a favorable intervention point for disease therapeutics, because it is an early step in gene expression and does not alter the genome. Significant advances have been made in the development of approaches to manipulate splicing for therapy. Splicing can be manipulated with a number of tools including antisense oligonucleotides, modified small nuclear RNAs (snRNAs), trans-splicing, and small molecule compounds, all of which have been used to increase specific alternatively spliced isoforms or to correct aberrant gene expression resulting from gene mutations that alter splicing. Here we describe clinically relevant splicing defects in disease states, the current tools used to target and alter splicing, specific mutations and diseases that are being targeted using splice-modulating approaches, and emerging therapeutics.
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Affiliation(s)
- Mallory A. Havens
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science. North Chicago, IL, 60064, USA. No conflicts of interest
| | - Dominik M. Duelli
- Department of Cellular and Molecular Pharmacology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA. No conflicts of interest
| | - Michelle L. Hastings
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science. North Chicago, IL, 60064, USA, Phone: 847-578-8517 Fax: 847-578-3253. No conflicts of interest
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15
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Douglas AGL, Wood MJA. Splicing therapy for neuromuscular disease. Mol Cell Neurosci 2013; 56:169-85. [PMID: 23631896 PMCID: PMC3793868 DOI: 10.1016/j.mcn.2013.04.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 12/25/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) and spinal muscular atrophy (SMA) are two of the most common inherited neuromuscular diseases in humans. Both conditions are fatal and no clinically available treatments are able to significantly alter disease course in either case. However, by manipulation of pre-mRNA splicing using antisense oligonucleotides, defective transcripts from the DMD gene and from the SMN2 gene in SMA can be modified to once again produce protein and restore function. A large number of in vitro and in vivo studies have validated the applicability of this approach and an increasing number of preliminary clinical trials have either been completed or are under way. Several different oligonucleotide chemistries can be used for this purpose and various strategies are being developed to facilitate increased delivery efficiency and prolonged therapeutic effect. As these novel therapeutic compounds start to enter the clinical arena, attention must also be drawn to the question of how best to facilitate the clinical development of such personalised genetic therapies and how best to implement their provision.
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Affiliation(s)
- Andrew G L Douglas
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
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16
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Gualandi F, Manzati E, Sabatelli P, Passarelli C, Bovolenta M, Pellegrini C, Perrone D, Squarzoni S, Pegoraro E, Bonaldo P, Ferlini A. Antisense-induced messenger depletion corrects a COL6A2 dominant mutation in Ullrich myopathy. Hum Gene Ther 2012; 23:1313-8. [PMID: 22992134 DOI: 10.1089/hum.2012.109] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Collagen VI gene mutations cause Ullrich and Bethlem muscular dystrophies. Pathogenic mutations frequently have a dominant negative effect, with defects in collagen VI chain secretion and assembly. It is agreed that, conversely, collagen VI haploinsufficiency has no pathological consequences. Thus, RNA-targeting approaches aimed at preferentially inactivating the mutated COL6 messenger may represent a promising therapeutic strategy. By in vitro studies we obtained the preferential depletion of the mutated COL6A2 messenger, by targeting a common single-nucleotide polymorphism (SNP), cistronic with a dominant COL6A2 mutation. We used a 2'-O-methyl phosphorothioate (2'OMePS) antisense oligonucleotide covering the SNP within exon 3, which is out of frame. Exon 3 skipping has the effect of depleting the mutated transcript via RNA nonsense-mediated decay, recovering the correct collagen VI secretion and restoring the ability to form an interconnected microfilament network into the extracellular matrix. This novel RNA modulation approach to correcting dominant mutations may represent a therapeutic strategy potentially applicable to a great variety of mutations and diseases.
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Affiliation(s)
- Francesca Gualandi
- Section of Medical Genetics, Department of Medical Science, University of Ferrara, 44121 Ferrara, Italy.
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17
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Persistent dystrophin protein restoration 90 days after a course of intraperitoneally administered naked 2'OMePS AON and ZM2 NP-AON complexes in mdx mice. J Biomed Biotechnol 2012; 2012:897076. [PMID: 23091362 PMCID: PMC3471065 DOI: 10.1155/2012/897076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/25/2012] [Accepted: 06/14/2012] [Indexed: 11/18/2022] Open
Abstract
In Duchenne muscular dystrophy, the exon-skipping approach has obtained proof of concept in animal models, myogenic cell cultures, and following local and systemic administration in Duchenne patients. Indeed, we have previously demonstrated that low doses (7.5 mg/Kg/week) of 2′-O-methyl-phosphorothioate antisense oligoribonucleotides (AONs) adsorbed onto ZM2 nanoparticles provoke widespread dystrophin restoration 7 days after intraperitoneal treatment in mdx mice. In this study, we went on to test whether this dystrophin restoration was still measurable 90 days from the end of the same treatment. Interestingly, we found that both western blot and immunohistochemical analysis (up to 7% positive fibres) were still able to detect dystrophin protein in the skeletal muscles of ZM2-AON-treated mice at this time, and the level of exon-23 skipping could still be assessed by RT real-time PCR (up to 10% of skipping percentage). In contrast, the protein was undetectable by western blot analysis in the skeletal muscles of mdx mice treated with an identical dose of naked AON, and the percentage of dystrophin-positive fibres and exon-23 skipping were reminiscent of those of untreated mdx mice. Our data therefore demonstrate the long-term residual efficacy of this systemic low-dose treatment and confirm the protective effect nanoparticles exert on AON molecules.
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18
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Bovolenta M, Erriquez D, Valli E, Brioschi S, Scotton C, Neri M, Falzarano MS, Gherardi S, Fabris M, Rimessi P, Gualandi F, Perini G, Ferlini A. The DMD locus harbours multiple long non-coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms. PLoS One 2012; 7:e45328. [PMID: 23028937 PMCID: PMC3448672 DOI: 10.1371/journal.pone.0045328] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 08/20/2012] [Indexed: 11/18/2022] Open
Abstract
The 2.2 Mb long dystrophin (DMD) gene, the largest gene in the human genome, corresponds to roughly 0.1% of the entire human DNA sequence. Mutations in this gene cause Duchenne muscular dystrophy and other milder X-linked, recessive dystrophinopathies. Using a custom-made tiling array, specifically designed for the DMD locus, we identified a variety of novel long non-coding RNAs (lncRNAs), both sense and antisense oriented, whose expression profiles mirror that of DMD gene. Importantly, these transcripts are intronic in origin and specifically localized to the nucleus and are transcribed contextually with dystrophin isoforms or primed by MyoD-induced myogenic differentiation. Furthermore, their forced ectopic expression in both human muscle and neuronal cells causes a specific and negative regulation of endogenous dystrophin full length isoforms and significantly down-regulate the activity of a luciferase reporter construct carrying the minimal promoter regions of the muscle dystrophin isoform. Consistent with this apparently repressive role, we found that, in muscle samples of dystrophinopathic female carriers, lncRNAs expression levels inversely correlate with those of muscle full length DMD isoforms. Overall these findings unveil an unprecedented complexity of the transcriptional pattern of the DMD locus and reveal that DMD lncRNAs may contribute to the orchestration and homeostasis of the muscle dystrophin expression pattern by either selective targeting and down-modulating the dystrophin promoter transcriptional activity.
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Affiliation(s)
- Matteo Bovolenta
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Daniela Erriquez
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Emanuele Valli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Simona Brioschi
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Chiara Scotton
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Marcella Neri
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Maria Sofia Falzarano
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Samuele Gherardi
- Department of Pharmacy and Biotechnology, Health Sciences and Technologies – Interdepartmental Center for Industrial Research (HST-ICIR), University of Bologna, Bologna, Italy
| | - Marina Fabris
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Paola Rimessi
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Francesca Gualandi
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, Health Sciences and Technologies – Interdepartmental Center for Industrial Research (HST-ICIR), University of Bologna, Bologna, Italy
| | - Alessandra Ferlini
- Department of Medical Science, Section of Medical Genetics, University of Ferrara, Ferrara, Italy
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19
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Bovolenta M, Scotton C, Falzarano MS, Gualandi F, Ferlini A. Rapid, comprehensive analysis of the dystrophin transcript by a custom micro-fluidic exome array. Hum Mutat 2012; 33:572-81. [DOI: 10.1002/humu.22017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 12/20/2011] [Indexed: 11/08/2022]
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20
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Abstract
Antisense-mediated exon skipping to restore the disrupted dystrophin reading frame is currently in clinical trials for Duchenne muscular dystrophy. This chapter describes the rationale of this approach and gives an overview of in vitro and in vivo experiments with antisense oligonucleotides and antisense genes. Finally, an overview of clinical trials is given and outstanding questions and hurdles are discussed.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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21
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Abstract
Antisense oligonucleotide (AON)-mediated exon skipping is a therapeutic approach for subsets of Duchenne muscular dystrophy (DMD) patients to ameliorate the severe DMD phenotype. Several groups have successfully induced exon skipping by AONs to reframe the mRNA in various patients carrying deletions, and phase I/II clinical trials are ongoing. The approach is based on targeting specific splicing motifs, both exonic and located on the exon borders, thus interfering with the spliceosome assembly by steric hindrance. Evaluation of the effectiveness of treatment with AONs in cells, animal models, and humans requires a sensitive, specific, and highly reproducible method. We have developed a real-time PCR-based protocol that uses the probe-based approach to recognize specific sequences internal to the target exon (exon-specific real-time assay). The methods for this protocol are described in this chapter.
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Affiliation(s)
- Alessandra Ferlini
- Section of Medical Genetics, Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy.
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22
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Adkin CF, Meloni PL, Fletcher S, Adams AM, Muntoni F, Wong B, Wilton SD. Multiple exon skipping strategies to by-pass dystrophin mutations. Neuromuscul Disord 2011; 22:297-305. [PMID: 22182525 PMCID: PMC3488593 DOI: 10.1016/j.nmd.2011.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 10/10/2011] [Accepted: 10/11/2011] [Indexed: 11/24/2022]
Abstract
Manipulation of dystrophin pre-mRNA processing offers the potential to overcome mutations in the dystrophin gene that would otherwise lead to Duchenne muscular dystrophy. Dystrophin mutations will require the removal of one or more exons to restore the reading frame and in some cases, multiple exon skipping strategies exist to restore dystrophin expression. However, for some small intra-exonic mutations, a third strategy, not applicable to whole exon deletions, may be possible. The removal of only one frame-shifting exon flanking the mutation-carrying exon may restore the reading frame and allow synthesis of a functional dystrophin isoform, providing that no premature termination codons are encountered. For these mutations, the removal of only one exon offers a simpler, cheaper and more feasible alternative approach to the dual exon skipping that would otherwise be considered. We present strategies to by-pass intra-exonic dystrophin mutations that clearly demonstrate the importance of tailoring exon skipping strategies to specific patient mutations.
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Affiliation(s)
- Carl F Adkin
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Perth, WA 6009, Australia
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23
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Sanaker PS, Toompuu M, McClorey G, Bindoff LA. Antisense oligonucleotide corrects splice abnormality in hereditary myopathy with lactic acidosis. Gene 2011; 494:231-6. [PMID: 22155317 DOI: 10.1016/j.gene.2011.11.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 11/11/2011] [Accepted: 11/14/2011] [Indexed: 02/01/2023]
Abstract
Hereditary myopathy with lactic acidosis (HML) (OMIM #255125) presents in childhood with exercise intolerance and muscle pain on trivial exercise, lactic acidosis, dyspnoea, palpitations, and rhabdomyolysis which can be fatal. The disease is recessively inherited and caused by a deep intronic, single base transition in the iron-sulfur cluster scaffold, ISCU gene that causes retention of a pseudoexon and introduction of a premature termination codon. IscU protein deficiency causes secondary defects in several iron-sulfur dependant proteins, including enzymes involved in aerobic energy metabolism. We have shown in a previous study that the splice abnormality affects skeletal muscle more than other tissues, leading to the purely muscular phenotype. Antisense oligonucleotides (AOs) have been able to redirect mRNA splicing in a number of disease models, and show promise in clinical studies. We designed 2'O-methyl phosphorothioate AOs targeting either splice site of the detrimental HML pseudoexon. The acceptor site AO effectively redirected splicing towards the normal state in cultured muscle fibroblasts, whilst the donor site AO promoted pseudoexon inclusion in both patient and control cells. Our results show that AO therapy seems feasible in HML, but care must be taken to avoid adverse splicing effects.
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24
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Malueka RG, Yagi M, Awano H, Lee T, Dwianingsih EK, Nishida A, Takeshima Y, Matsuo M. Antisense oligonucleotide induced dystrophin exon 45 skipping at a low half-maximal effective concentration in a cell-free splicing system. Nucleic Acid Ther 2011; 21:347-53. [PMID: 21967521 DOI: 10.1089/nat.2011.0310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Antisense oligonucleotides (AOs) can facilitate the expression of internally deleted dystrophin in dystrophin-deficient Duchenne muscular dystrophy (DMD) by correcting the reading frame of the pre-mRNA with AO-mediated exon skipping. An antisense 18-mer 2'-O-methyl RNA/ethylene-bridged nucleic acid chimera AO targeting exon 45 of the dystrophin gene, AO85, can induce exon 45 skipping efficiently in cultured cells. AO85 is expected to facilitate dystrophin expression in 8%-9% of all DMD patients. Here, we examined the kinetics of AO85-mediated exon 45 skipping in a cell-free splicing system. In vitro transcribed pre-mRNAs containing dystrophin exon 45 and part of its flanking introns within a hybrid minigene were incubated with HeLa cell nuclear extract, and the resultant mRNAs were amplified by semiquantitative reverse transcriptase-polymerase chain reaction. Time-course analysis revealed that the splicing process fitted well to first order kinetics. Addition of AO85 produced an extra spliced product, deleting exon 45 (Δexon 45), indicating AO85-mediated exon 45 skipping. Production of Δexon 45 increased linearly with increasing concentrations of AO85, reaching a maximum of nearly 80% of the transcripts. The half-maximal effective concentration (EC(50)) of AO85 was 58.0 nM. The percentage of Δexon 45 among the transcripts decreased inversely with the pre-mRNA concentration; Lineweaver-Burk plotting revealed a competitive fashion of AO85 action. The low EC(50) indicates high potential of AO85 for clinical application.
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25
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Magri F, Del Bo R, D'Angelo MG, Govoni A, Ghezzi S, Gandossini S, Sciacco M, Ciscato P, Bordoni A, Tedeschi S, Fortunato F, Lucchini V, Cereda M, Corti S, Moggio M, Bresolin N, Comi GP. Clinical and molecular characterization of a cohort of patients with novel nucleotide alterations of the Dystrophin gene detected by direct sequencing. BMC MEDICAL GENETICS 2011; 12:37. [PMID: 21396098 PMCID: PMC3061890 DOI: 10.1186/1471-2350-12-37] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 03/11/2011] [Indexed: 01/13/2023]
Abstract
Background Duchenne and Becker Muscular dystrophies (DMD/BMD) are allelic disorders caused by mutations in the dystrophin gene, which encodes a sarcolemmal protein responsible for muscle integrity. Deletions and duplications account for approximately 75% of mutations in DMD and 85% in BMD. The implementation of techniques allowing complete gene sequencing has focused attention on small point mutations and other mechanisms underlying complex rearrangements. Methods We selected 47 patients (41 families; 35 DMD, 6 BMD) without deletions and duplications in DMD gene (excluded by multiplex ligation-dependent probe amplification and multiplex polymerase chain reaction analysis). This cohort was investigated by systematic direct sequence analysis to study sequence variation. We focused our attention on rare mutational events which were further studied through transcript analysis. Results We identified 40 different nucleotide alterations in DMD gene and their clinical correlates; altogether, 16 mutations were novel. DMD probands carried 9 microinsertions/microdeletions, 19 nonsense mutations, and 7 splice-site mutations. BMD patients carried 2 nonsense mutations, 2 splice-site mutations, 1 missense substitution, and 1 single base insertion. The most frequent stop codon was TGA (n = 10 patients), followed by TAG (n = 7) and TAA (n = 4). We also analyzed the molecular mechanisms of five rare mutational events. They are two frame-shifting mutations in the DMD gene 3'end in BMD and three novel splicing defects: IVS42: c.6118-3C>A, which causes a leaky splice-site; c.9560A>G, which determines a cryptic splice-site activation and c.9564-426 T>G, which creates pseudoexon retention within IVS65. Conclusion The analysis of our patients' sample, carrying point mutations or complex rearrangements in DMD gene, contributes to the knowledge on phenotypic correlations in dystrophinopatic patients and can provide a better understanding of pre-mRNA maturation defects and dystrophin functional domains. These data can have a prognostic relevance and can be useful in directing new therapeutic approaches, which rely on a precise definition of the genetic defects as well as their molecular consequences.
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Affiliation(s)
- Francesca Magri
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Foundation Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
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26
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Wilton SD, Fletcher S. Novel compounds for the treatment of Duchenne muscular dystrophy: emerging therapeutic agents. APPLICATION OF CLINICAL GENETICS 2011; 4:29-44. [PMID: 23776365 PMCID: PMC3681176 DOI: 10.2147/tacg.s8762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The identification of dystrophin and the causative role of mutations in this gene in Duchenne and Becker muscular dystrophies (D/BMD) was expected to lead to timely development of effective therapies. Despite over 20 years of research, corticosteroids remain the only available pharmacological treatment for DMD, although significant benefits and extended life have resulted from advances in the clinical care and management of DMD individuals. Effective treatment of DMD will require dystrophin restitution in skeletal, cardiac, and smooth muscles and nonmuscle tissues; however, modulation of muscle loss and regeneration has the potential to play an important role in altering the natural history of DMD, particularly in combination with other treatments. Emerging biological, molecular, and small molecule therapeutics are showing promise in ameliorating this devastating disease, and it is anticipated that regulatory environments will need to display some flexibility in order to accommodate the new treatment paradigms.
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Affiliation(s)
- Steve D Wilton
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Crawley, Perth, WA, Australia
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27
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Forrest S, Meloni PL, Muntoni F, Kim J, Fletcher S, Wilton SD. Personalized exon skipping strategies to address clustered non-deletion dystrophin mutations. Neuromuscul Disord 2011; 20:810-6. [PMID: 20817455 DOI: 10.1016/j.nmd.2010.07.276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 07/12/2010] [Accepted: 07/27/2010] [Indexed: 11/30/2022]
Abstract
Antisense oligomer induced exon skipping is showing promise as a therapy to reduce the severity of Duchenne muscular dystrophy. To date, the focus has been on excluding single exons flanking frame-shifting deletions in the dystrophin gene. However, a third of all Duchenne muscular dystrophy causing mutations are more subtle DNA changes. Thirty nine dystrophin exons are potentially frame-shifting and mutations in these will require the targeted removal of exon blocks to generate in-frame transcripts. We report that clustered non-deletion mutations in the dystrophin gene respond differently to different antisense oligomer preparations targeting the same dual exon block, the removal of which bypasses the mutation and restores the open reading-frame. The personalized nature of the responses to antisense oligomer application presents additional challenges to the induction of multi-exon skipping with a single oligomer preparation.
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Affiliation(s)
- Sarah Forrest
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Perth, WA 6009, Australia
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28
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Abstract
A milestone of molecular medicine is the identification of dystrophin gene mutation as the cause of Duchenne muscular dystrophy (DMD). Over the last 2 decades, major advances in dystrophin biology and gene delivery technology have created an opportunity to treat DMD with gene therapy. Remarkable success has been achieved in treating dystrophic mice. Several gene therapy strategies, including plasmid transfer, exon skipping, and adeno-associated virus-mediated microdystrophin therapy, have entered clinical trials. However, therapeutic benefit has not been realized in DMD patients. Bridging the gap between mice and humans is no doubt the most pressing issue facing DMD gene therapy now. In contrast to mice, dystrophin-deficient dogs are genetically and phenotypically similar to human patients. Preliminary gene therapy studies in the canine model may offer critical insights that cannot be obtained from murine studies. It is clear that the canine DMD model may represent an important link between mice and humans. Unfortunately, our current knowledge of dystrophic dogs is limited, and the full picture of disease progression remains to be clearly defined. We also lack rigorous outcome measures (such as in situ force measurement) to monitor therapeutic efficacy in dystrophic dogs. Undoubtedly, maintaining a dystrophic dog colony is technically demanding, and the cost of dog studies cannot be underestimated. A carefully coordinated effort from the entire DMD community is needed to make the best use of the precious dog resource. Successful DMD gene therapy may depend on valid translational studies in dystrophin-deficient dogs.
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Affiliation(s)
- Dongsheng Duan
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
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Aartsma-Rus A, den Dunnen JT, van Ommen GJB. New insights in gene-derived therapy: the example of Duchenne muscular dystrophy. Ann N Y Acad Sci 2010; 1214:199-212. [PMID: 21121926 DOI: 10.1111/j.1749-6632.2010.05836.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The two therapeutic approaches currently most advanced in clinical trials for Duchenne muscular dystrophy are antisense-mediated exon skipping and forced read-through of premature stop codons. Interestingly, these approaches target the gene product rather than the gene itself. This review will explain the rationale and current state of affairs of these approaches and will then discuss how these gene-derived therapies might also be applicable to other diseases.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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Lu QL, Yokota T, Takeda S, Garcia L, Muntoni F, Partridge T. The status of exon skipping as a therapeutic approach to duchenne muscular dystrophy. Mol Ther 2010; 19:9-15. [PMID: 20978473 DOI: 10.1038/mt.2010.219] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is associated with mutations in the dystrophin gene that disrupt the open reading frame whereas the milder Becker's form is associated with mutations which leave an in-frame mRNA transcript that can be translated into a protein that includes the N- and C- terminal functional domains. It has been shown that by excluding specific exons at, or adjacent to, frame-shifting mutations, open reading frame can be restored to an out-of-frame mRNA, leading to the production of a partially functional Becker-like dystrophin protein. Such targeted exclusion can be achieved by administration of oligonucleotides that are complementary to sequences that are crucial to normal splicing of the exon into the transcript. This principle has been validated in mouse and canine models of DMD with a number of variants of oligonucleotide analogue chemistries and by transduction with adeno-associated virus (AAV)-small nuclear RNA (snRNA) reagents encoding the antisense sequence. Two different oligonucleotide agents are now being investigated in human trials for splicing out of exon 51 with some early indications of success at the biochemical level.
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Affiliation(s)
- Qi-Long Lu
- McColl-Lockwood Laboratory for Muscular Dystrophy Research, Neuromuscular/ALS Center, Carolinas Medical Center, Charlotte, North Carolina, USA
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