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Foncuberta ME, Monges S, Medina A, Lubieniecki F, Gravina LP. A novel deep intronic variant in the DMD gene causes Duchenne muscular dystrophy by pseudoexon activation encoding a nonsense codon. Gene 2024; 930:148862. [PMID: 39151676 DOI: 10.1016/j.gene.2024.148862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/30/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Dystrophinopathies are a group of neuromuscular disorders, inherited in an X-linked recessive manner, caused by pathogenic variants in the DMD gene. Copy number variation detection and next generation sequencing allow the detection of around 99 % of the pathogenic variants. However, some patients require mRNA studies from muscle biopsies to identify deep intronic pathogenic variants. Here, we report a child suspected of having Duchenne muscular dystrophy, with a muscle biopsy showing dystrophin deficiency, and negative molecular testing for deletions, duplications, and small variants. mRNA analysis from muscle biopsy revealed a pseudoexon activation that introduce a premature stop codon into the reading frame. gDNA sequencing allowed to identified a novel variant, c.832-186 T>G, which creates a cryptic donor splice site, recognizing the underlying mechanism causing the pseudoexon insertion. This case highlights the usefulness of the mRNA analysis from muscle biopsy when routine genetic testing is negative and clinical suspicion of dystrophinopathies remains the main clinical diagnosis suspicion.
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Affiliation(s)
- María Eugenia Foncuberta
- Laboratorio de Biología Molecular - Genética, Hospital de Pediatría Garrahan, Buenos Aires, Argentina.
| | - Soledad Monges
- Servicio de Neurología, Hospital de Pediatría Garrahan, Buenos Aires, Argentina
| | - Adriana Medina
- Laboratorio Biología Molecular - Hematogía y Oncología, Hospital de Pediatría Garrahan, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Servicio de Patología, Hospital de Pediatría Garrahan, Buenos Aires, Argentina
| | - Luis Pablo Gravina
- Laboratorio de Biología Molecular - Genética, Hospital de Pediatría Garrahan, Buenos Aires, Argentina
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2
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Poyatos-García J, Soblechero-Martín P, Liquori A, López-Martínez A, Maestre P, González-Romero E, Vázquez-Manrique RP, Muelas N, García-García G, Ohana J, Arechavala-Gomeza V, Vílchez JJ. Deletion of exons 45 to 55 in the DMD gene: from the therapeutic perspective to the in vitro model. Skelet Muscle 2024; 14:21. [PMID: 39354597 PMCID: PMC11443720 DOI: 10.1186/s13395-024-00353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 09/13/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUND Gene editing therapies in development for correcting out-of-frame DMD mutations in Duchenne muscular dystrophy aim to replicate benign spontaneous deletions. Deletion of 45-55 DMD exons (del45-55) was described in asymptomatic subjects, but recently serious skeletal and cardiac complications have been reported. Uncovering why a single mutation like del45-55 is able to induce diverse phenotypes and grades of severity may impact the strategies of emerging therapies. Cellular models are essential for this purpose, but their availability is compromised by scarce muscle biopsies. METHODS We introduced, as a proof-of-concept, using CRISPR-Cas9 edition, a del45-55 mimicking the intronic breakpoints harboured by a subset of patients of this form of dystrophinopathy (designing specific gRNAs), into a Duchenne patient's cell line. The edited cell line was characterized evaluating the dystrophin expression and the myogenic status. RESULTS Dystrophin expression was restored, and the myogenic defects were ameliorated in the edited myoblasts harbouring a specific del45-55. Besides confirming the potential of CRISPR-Cas9 to create tailored mutations (despite the low cleavage efficiency of our gRNAs) as a useful approach to generate in vitro models, we also generated an immortalized myoblast line derived from a patient with a specific del45-55. CONCLUSIONS Overall, we provide helpful resources to deepen into unknown factors responsible for DMD-pathophysiology.
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Affiliation(s)
- Javier Poyatos-García
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), CB23/07/00005, Madrid, Spain.
- University of Valencia, Valencia, Spain.
| | - Patricia Soblechero-Martín
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Alessandro Liquori
- Hematology Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
- Centre for Biomedical Network Research on Cancer (CIBERONC), CB16/12/00284, Madrid, Spain
| | - Andrea López-Martínez
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Pilar Maestre
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Elisa González-Romero
- Hematology Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Rafael P Vázquez-Manrique
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Health Research Institute Hospital La Fe, Valencia, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), U755, CB06/07/1030, Madrid, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, Valencia, Spain
| | - Nuria Muelas
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO- NMD), Hospital Universitari I Politècnic La Fe, Valencia, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), U763, CB06/05/0091, Madrid, Spain
| | - Gema García-García
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Health Research Institute Hospital La Fe, Valencia, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), U755, CB06/07/1030, Madrid, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, Valencia, Spain
| | - Jessica Ohana
- Centre de Recherche en Myologie, Sorbonne Université, INSERM, Institut de Myologie, Paris, 75013, France
| | - Virginia Arechavala-Gomeza
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Juan J Vílchez
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain.
- University of Valencia, Valencia, Spain.
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO- NMD), Hospital Universitari I Politècnic La Fe, Valencia, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), U763, CB06/05/0091, Madrid, Spain.
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3
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Pironon N, Bourrat E, Prost C, Chen M, Woodley DT, Titeux M, Hovnanian A. Splice modulation strategy applied to deep intronic variants in COL7A1 causing recessive dystrophic epidermolysis bullosa. Proc Natl Acad Sci U S A 2024; 121:e2401781121. [PMID: 39159368 PMCID: PMC11363305 DOI: 10.1073/pnas.2401781121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare and most often severe genetic disease characterized by recurrent blistering and erosions of the skin and mucous membranes after minor trauma, leading to major local and systemic complications. The disease is caused by loss-of-function variants in COL7A1 encoding type VII collagen (C7), the main component of anchoring fibrils, which form attachment structures stabilizing the cutaneous basement membrane zone. Alterations in C7 protein structure and/or expression lead to abnormal, rare or absent anchoring fibrils resulting in loss of dermal-epidermal adherence and skin blistering. To date, more than 1,200 distinct COL7A1 deleterious variants have been reported and 19% are splice variants. Here, we describe two RDEB patients for whom we identified two pathogenic deep intronic pathogenic variants in COL7A1. One of these variants (c.7795-97C > G) promotes the inclusion of a pseudoexon between exons 104 and 105 in the COL7A1 transcript, while the other causes partial or complete retention of intron 51. We used antisense oligonucleotide (ASO) mediated exon skipping to correct these aberrant splicing events in vitro. This led to increased normal mRNA splicing above 94% and restoration of C7 protein expression at a level (up to 56%) that should be sufficient to reverse the phenotype. This first report of exon skipping applied to counteract deep intronic variants in COL7A1 represents a promising therapeutic strategy for personalized medicine directed at patients with intronic variants at a distance of consensus splice sites.
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Affiliation(s)
- Nathalie Pironon
- Université Paris Cité, Inserm, UMR 1163, Institut Imagine, Laboratory of Genetic Skin Diseases, ParisF-75015, France
| | - Emmanuelle Bourrat
- Department of Dermatology, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint Louis, Paris, France
- Centre de référence des Maladies Génétiques à Expression Cutanée (MAGEC Nord Site Saint Louis), Hôpital Saint LouisF-75010, Paris, France
| | - Catherine Prost
- Hôpital Avicenne, Assistance Publique des Hôpitaux de Paris, BobignyF-93000, France
| | - Mei Chen
- Department of Dermatology, The Keck School of Medicine, University of Southern California, LA
| | - David T. Woodley
- Department of Dermatology, The Keck School of Medicine, University of Southern California, LA
| | - Matthias Titeux
- Université Paris Cité, Inserm, UMR 1163, Institut Imagine, Laboratory of Genetic Skin Diseases, ParisF-75015, France
| | - Alain Hovnanian
- Université Paris Cité, Inserm, UMR 1163, Institut Imagine, Laboratory of Genetic Skin Diseases, ParisF-75015, France
- Department of Genomic Medicine of Rare Diseases, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Necker-Enfants Malades, F-75015Paris, France
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4
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Baum ML, Wilton DK, Fox RG, Carey A, Hsu YHH, Hu R, Jäntti HJ, Fahey JB, Muthukumar AK, Salla N, Crotty W, Scott-Hewitt N, Bien E, Sabatini DA, Lanser TB, Frouin A, Gergits F, Håvik B, Gialeli C, Nacu E, Lage K, Blom AM, Eggan K, McCarroll SA, Johnson MB, Stevens B. CSMD1 regulates brain complement activity and circuit development. Brain Behav Immun 2024; 119:317-332. [PMID: 38552925 DOI: 10.1016/j.bbi.2024.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/29/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
Complement proteins facilitate synaptic elimination during neurodevelopmental pruning, but neural complement regulation is not well understood. CUB and Sushi Multiple Domains 1 (CSMD1) can regulate complement activity in vitro, is expressed in the brain, and is associated with increased schizophrenia risk. Beyond this, little is known about CSMD1 including whether it regulates complement activity in the brain or otherwise plays a role in neurodevelopment. We used biochemical, immunohistochemical, and proteomic techniques to examine the regional, cellular, and subcellular distribution as well as protein interactions of CSMD1 in the brain. To evaluate whether CSMD1 is involved in complement-mediated synapse elimination, we examined Csmd1-knockout mice and CSMD1-knockout human stem cell-derived neurons. We interrogated synapse and circuit development of the mouse visual thalamus, a process that involves complement pathway activity. We also quantified complement deposition on synapses in mouse visual thalamus and on cultured human neurons. Finally, we assessed uptake of synaptosomes by cultured microglia. We found that CSMD1 is present at synapses and interacts with complement proteins in the brain. Mice lacking Csmd1 displayed increased levels of complement component C3, an increased colocalization of C3 with presynaptic terminals, fewer retinogeniculate synapses, and aberrant segregation of eye-specific retinal inputs to the visual thalamus during the critical period of complement-dependent refinement of this circuit. Loss of CSMD1 in vivo enhanced synaptosome engulfment by microglia in vitro, and this effect was dependent on activity of the microglial complement receptor, CR3. Finally, human stem cell-derived neurons lacking CSMD1 were more vulnerable to complement deposition. These data suggest that CSMD1 can function as a regulator of complement-mediated synapse elimination in the brain during development.
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Affiliation(s)
- Matthew L Baum
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; MD-PhD Program of Harvard & MIT, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel K Wilton
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel G Fox
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alanna Carey
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yu-Han H Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruilong Hu
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Henna J Jäntti
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jaclyn B Fahey
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Allie K Muthukumar
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nikkita Salla
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William Crotty
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Nicole Scott-Hewitt
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Bien
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David A Sabatini
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Toby B Lanser
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Arnaud Frouin
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick Gergits
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Chrysostomi Gialeli
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, S-214 28 Malmö, Sweden; Cardiovascular Research - Translational Studies Research Group, Department of Clinical Sciences, Lund University, S-214 28 Malmö, Sweden
| | - Eugene Nacu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anna M Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, S-214 28 Malmö, Sweden
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew B Johnson
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Beth Stevens
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, USA.
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5
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Szwec S, Kapłucha Z, Chamberlain JS, Konieczny P. Dystrophin- and Utrophin-Based Therapeutic Approaches for Treatment of Duchenne Muscular Dystrophy: A Comparative Review. BioDrugs 2024; 38:95-119. [PMID: 37917377 PMCID: PMC10789850 DOI: 10.1007/s40259-023-00632-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
Duchenne muscular dystrophy is a devastating disease that leads to progressive muscle loss and premature death. While medical management focuses mostly on symptomatic treatment, decades of research have resulted in first therapeutics able to restore the affected reading frame of dystrophin transcripts or induce synthesis of a truncated dystrophin protein from a vector, with other strategies based on gene therapy and cell signaling in preclinical or clinical development. Nevertheless, recent reports show that potentially therapeutic dystrophins can be immunogenic in patients. This raises the question of whether a dystrophin paralog, utrophin, could be a more suitable therapeutic protein. Here, we compare dystrophin and utrophin amino acid sequences and structures, combining published data with our extended in silico analyses. We then discuss these results in the context of therapeutic approaches for Duchenne muscular dystrophy. Specifically, we focus on strategies based on delivery of micro-dystrophin and micro-utrophin genes with recombinant adeno-associated viral vectors, exon skipping of the mutated dystrophin pre-mRNAs, reading through termination codons with small molecules that mask premature stop codons, dystrophin gene repair by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated genetic engineering, and increasing utrophin levels. Our analyses highlight the importance of various dystrophin and utrophin domains in Duchenne muscular dystrophy treatment, providing insights into designing novel therapeutic compounds with improved efficacy and decreased immunoreactivity. While the necessary actin and β-dystroglycan binding sites are present in both proteins, important functional distinctions can be identified in these domains and some other parts of truncated dystrophins might need redesigning due to their potentially immunogenic qualities. Alternatively, therapies based on utrophins might provide a safer and more effective approach.
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Affiliation(s)
- Sylwia Szwec
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Zuzanna Kapłucha
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Jeffrey S Chamberlain
- Department of Neurology, University of Washington School of Medicine, Seattle, WA, 98109-8055, USA
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Washington School of Medicine, Seattle, WA, 98109-8055, USA
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, 98109-8055, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109-8055, USA
| | - Patryk Konieczny
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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6
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de Sainte Agathe JM, Filser M, Isidor B, Besnard T, Gueguen P, Perrin A, Van Goethem C, Verebi C, Masingue M, Rendu J, Cossée M, Bergougnoux A, Frobert L, Buratti J, Lejeune É, Le Guern É, Pasquier F, Clot F, Kalatzis V, Roux AF, Cogné B, Baux D. SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation. Hum Genomics 2023; 17:7. [PMID: 36765386 PMCID: PMC9912651 DOI: 10.1186/s40246-023-00451-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
Abstract
SpliceAI is an open-source deep learning splicing prediction algorithm that has demonstrated in the past few years its high ability to predict splicing defects caused by DNA variations. However, its outputs present several drawbacks: (1) although the numerical values are very convenient for batch filtering, their precise interpretation can be difficult, (2) the outputs are delta scores which can sometimes mask a severe consequence, and (3) complex delins are most often not handled. We present here SpliceAI-visual, a free online tool based on the SpliceAI algorithm, and show how it complements the traditional SpliceAI analysis. First, SpliceAI-visual manipulates raw scores and not delta scores, as the latter can be misleading in certain circumstances. Second, the outcome of SpliceAI-visual is user-friendly thanks to the graphical presentation. Third, SpliceAI-visual is currently one of the only SpliceAI-derived implementations able to annotate complex variants (e.g., complex delins). We report here the benefits of using SpliceAI-visual and demonstrate its relevance in the assessment/modulation of the PVS1 classification criteria. We also show how SpliceAI-visual can elucidate several complex splicing defects taken from the literature but also from unpublished cases. SpliceAI-visual is available as a Google Colab notebook and has also been fully integrated in a free online variant interpretation tool, MobiDetails ( https://mobidetails.iurc.montp.inserm.fr/MD ).
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Affiliation(s)
- Jean-Madeleine de Sainte Agathe
- Département de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne Université, Paris, France.
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr/), Paris, France.
| | - Mathilde Filser
- Département de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne Université, Paris, France
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France
| | - Thomas Besnard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France
| | - Paul Gueguen
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr/), Paris, France
- Service de Génétique, Inserm U1253, CHRU de Tours, Tours, France
| | - Aurélien Perrin
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Charles Van Goethem
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Camille Verebi
- Service de Médecine Génomique, Maladies de Système et d'Organe, Fédération de Génétique et de Médecine Génomique, DMU BioPhyGen, APHP Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Marion Masingue
- Centre de référence des maladies neuromusculaires Nord/Est/Ile de France, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - John Rendu
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, Université Grenoble Alpes, Grenoble, France
| | - Mireille Cossée
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
- PhyMedExp, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
- PhyMedExp, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Laurent Frobert
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr/), Paris, France
| | - Julien Buratti
- Département de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne Université, Paris, France
| | - Élodie Lejeune
- Département de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne Université, Paris, France
| | - Éric Le Guern
- Département de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne Université, Paris, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr/), Paris, France
| | - Florence Pasquier
- Centre mémoire, Inserm U1172 DistALZ, Licend, Univ Lille, CHU Lille, 59000, Lille, France
| | - Fabienne Clot
- Département de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne Université, Paris, France
| | | | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
- INM, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Benjamin Cogné
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr/), Paris, France
- Nantes Université, CHU Nantes, Service de Génétique Médicale, 44000, Nantes, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
- INM, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
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7
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Clinical, muscle imaging, and genetic characteristics of dystrophinopathies with deep-intronic DMD variants. J Neurol 2023; 270:925-937. [PMID: 36319768 DOI: 10.1007/s00415-022-11432-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Phenotypic heterogeneity within or between families with a same deep-intronic splice-altering variant in the DMD gene has never been systematically analyzed. This study aimed to determine the phenotypic and genetic characteristics of patients with deep-intronic DMD variants. METHODS Of 1338 male patients with a suspected dystrophinopathy, 38 were confirmed to have atypical pathogenic DMD variants via our comprehensive genetic testing approach. Of the 38 patients, 30 patients from 22 unrelated families with deep-intronic DMD variants underwent a detailed clinical and imaging assessment. RESULTS Nineteen different deep-intronic DMD variants were identified in the 30 patients, including 15 with Duchenne muscular dystrophy (DMD), 14 with Becker muscular dystrophy (BMD), and one with X-linked dilated cardiomyopathy. Of the 19 variants, 15 were single-nucleotide variants, 2 were structural variants (SVs), and 2 were pure-intronic large-scale SVs causing aberrant inclusion of other protein-coding genes sequences into the mature DMD transcripts. The trefoil with single fruit sign was observed in 18 patients and the concentric fatty infiltration pattern was observed in 2 patients. Remarkable phenotypic heterogeneity was observed not only in skeletal but also cardiac muscle involvement in 2 families harboring a same deep-intronic variant. Different skeletal muscle involvement between families with a same variant was observed in 4 families. High inter-individual phenotypic heterogeneity was observed within two BMD families and one DMD family. CONCLUSIONS Our study first highlights the variable phenotypic expressivity of deep-intronic DMD variants and demonstrates a new class of deep-intronic DMD variants, i.e., pure-intronic SVs involving other protein-coding genes.
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Segarra-Casas A, Domínguez-González C, Hernández-Laín A, Sanchez-Calvin MT, Camacho A, Rivas E, Campo-Barasoain A, Madruga M, Ortez C, Natera-de Benito D, Nascimento A, Codina A, Rodriguez MJ, Gallano P, Gonzalez-Quereda L. Genetic diagnosis of Duchenne and Becker muscular dystrophy through mRNA analysis: new splicing events. J Med Genet 2022; 60:615-619. [DOI: 10.1136/jmg-2022-108828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/27/2022] [Indexed: 12/24/2022]
Abstract
BackgroundUp to 7% of patients with Duchenne muscular dystrophy (DMD) or Becker muscular dystrophy (BMD) remain genetically undiagnosed after routine genetic testing. These patients are thought to carry deep intronic variants, structural variants or splicing alterations not detected through multiplex ligation-dependent probe amplification or exome sequencing.MethodsRNA was extracted from seven muscle biopsy samples of patients with genetically undiagnosed DMD/BMD after routine genetic diagnosis. RT-PCR of theDMDgene was performed to detect the presence of alternative transcripts. Droplet digital PCR and whole-genome sequencing were also performed in some patients.ResultsWe identified an alteration in the mRNA level in all the patients. We detected three pseudoexons inDMDcaused by deep intronic variants, two of them not previously reported. We also identified a chromosomal rearrangement between Xp21.2 and 8p22. Furthermore, we detected three exon skipping events with unclear pathogenicity.ConclusionThese findings indicate that mRNA analysis of theDMDgene is a valuable tool to reach a precise genetic diagnosis in patients with a clinical and anatomopathological suspicion of dystrophinopathy that remain genetically undiagnosed after routine genetic testing.
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9
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Poyatos‐García J, Martí P, Liquori A, Muelas N, Pitarch I, Martinez‐Dolz L, Rodríguez B, Gonzalez‐Quereda L, Damiá M, Aller E, Selva‐Gimenez M, Vilchez R, Diaz‐Manera J, Alonso‐Pérez J, Barcena JE, Jauregui A, Gámez J, Aladrén JA, Fernández A, Montolio M, Azorin I, Hervas D, Casasús A, Nieto M, Gallano P, Sevilla T, Vilchez JJ. Dystrophinopathy Phenotypes and Modifying Factors in DMD Exon 45-55 Deletion. Ann Neurol 2022; 92:793-806. [PMID: 35897138 PMCID: PMC9825930 DOI: 10.1002/ana.26461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Duchenne muscular dystrophy (DMD) exon 45-55 deletion (del45-55) has been postulated as a model that could treat up to 60% of DMD patients, but the associated clinical variability and complications require clarification. We aimed to understand the phenotypes and potential modifying factors of this dystrophinopathy subset. METHODS This cross-sectional, multicenter cohort study applied clinical and functional evaluation. Next generation sequencing was employed to identify intronic breakpoints and their impact on the Dp140 promotor, intronic long noncoding RNA, and regulatory splicing sequences. DMD modifiers (SPP1, LTBP4, ACTN3) and concomitant mutations were also assessed. Haplotypes were built using DMD single nucleotide polymorphisms. Dystrophin expression was evaluated via immunostaining, Western blotting, reverse transcription polymerase chain reaction (PCR), and droplet digital PCR in 9 muscle biopsies. RESULTS The series comprised 57 subjects (23 index) expressing Becker phenotype (28%), isolated cardiopathy (19%), and asymptomatic features (53%). Cognitive impairment occurred in 90% of children. Patients were classified according to 10 distinct index-case breakpoints; 4 of them were recurrent due to founder events. A specific breakpoint (D5) was associated with severity, but no significant effect was appreciated due to the changes in intronic sequences. All biopsies showed dystrophin expression of >67% and traces of alternative del45-57 transcript that were not deemed pathogenically relevant. Only the LTBP4 haplotype appeared associated the presence of cardiopathy among the explored extragenic factors. INTERPRETATION We confirmed that del45-55 segregates a high proportion of benign phenotypes, severe cases, and isolated cardiac and cognitive presentations. Although some influence of the intronic breakpoint position and the LTBP4 modifier may exist, the pathomechanisms responsible for the phenotypic variability remain largely unresolved. ANN NEUROL 2022;92:793-806.
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Affiliation(s)
- Javier Poyatos‐García
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Pilar Martí
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Alessandro Liquori
- Hematology Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Cancer (CIBERONC); CB16/12/00284MadridSpain
| | - Nuria Muelas
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain
| | - Inmaculada Pitarch
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Neuropediatric DepartmentUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Luis Martinez‐Dolz
- Cardiology DepartmentUniversity and Polytechnic La Fe Hospital, IIS La FeValenciaSpain,Centre for Biomedical Network Research on Cardiovascular Diseases (CIBERCV)ValenciaSpain
| | - Benjamin Rodríguez
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Lidia Gonzalez‐Quereda
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Maria Damiá
- Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Neuropediatric DepartmentUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Elena Aller
- Genetics UnitUniversitary and Polytechnic La Fe HospitalValenciaSpain
| | - Marta Selva‐Gimenez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Roger Vilchez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Jordi Diaz‐Manera
- Neuromuscular Disorders Unit, Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Hospital of Sant PauBarcelonaSpain,Autonomous University of BarcelonaBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U762, CB06/05/0030BarcelonaSpain
| | - Jorge Alonso‐Pérez
- Neuromuscular Disorders Unit, Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Hospital of Sant PauBarcelonaSpain,Autonomous University of BarcelonaBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U762, CB06/05/0030BarcelonaSpain
| | - José Eulalio Barcena
- Neuromuscular Section, Neurology ServiceCruces University HospitalBarakaldoSpain
| | - Amaia Jauregui
- Neuromuscular Section, Neurology ServiceCruces University HospitalBarakaldoSpain
| | - Josep Gámez
- Autonomous University of BarcelonaBarcelonaSpain,Neurology Department, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)GMA ClinicBarcelonaSpain
| | | | | | - Marisol Montolio
- Duchenne Parent Project SpainMadridSpain,Department of Cell Biology, Physiology, and Immunology, Faculty of BiologyBarcelonaSpain
| | - Inmaculada Azorin
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - David Hervas
- Department of Applied Statistics and Operations Research, and QualityPolytechnic University of ValenciaValenciaSpain
| | - Ana Casasús
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Marisa Nieto
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain
| | - Pia Gallano
- Genetics DepartmentIIB Sant Pau, Hospital of Sant PauBarcelonaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER)U705, U745, CB06/07/0011BarcelonaSpain
| | - Teresa Sevilla
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Department of MedicineUniversity of ValenciaValenciaSpain
| | - Juan Jesus Vilchez
- Neuromuscular and Ataxias Research GroupHealth Research Institute Hospital La Fe (IIS La Fe)ValenciaSpain,Centre for Biomedical Network Research on Rare Diseases (CIBERER); U763, CB06/05/0091ValenciaSpain,Neuromuscular Referral Center, European Reference Network on Rare Neuromuscular Diseases (ERN EURO‐NMD)Universitary and Polytechnic La Fe HospitalValenciaSpain,Department of MedicineUniversity of ValenciaValenciaSpain
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García-Cruz C, Aragón J, Lourdel S, Annan A, Roger JE, Montanez C, Vaillend C. Tissue- and cell-specific whole-transcriptome meta-analysis from brain and retina reveals differential expression of dystrophin complexes and new dystrophin spliced isoforms. Hum Mol Genet 2022; 32:659-676. [PMID: 36130212 PMCID: PMC9896479 DOI: 10.1093/hmg/ddac236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 02/07/2023] Open
Abstract
The large DMD gene encodes a group of dystrophin proteins in brain and retina, produced from multiple promoters and alternative splicing events. Dystrophins are core components of different scaffolding complexes in distinct cell types. Their absence may thus alter several cellular pathways, which might explain the heterogeneous genotype-phenotype relationships underlying central comorbidities in Duchenne muscular dystrophy (DMD). However, the cell-specific expression of dystrophins and associated proteins (DAPs) is still largely unknown. The present study provides a first RNA-Seq-based reference showing tissue- and cell-specific differential expression of dystrophins, splice variants and DAPs in mouse brain and retina. We report that a cell type may express several dystrophin complexes, perhaps due to expression in separate cell subdomains and/or subpopulations, some of which with differential expression at different maturation stages. We also identified new splicing events in addition to the common exon-skipping events. These include a new exon within intron 51 (E51b) in frame with the flanking exons in retina, as well as inclusions of intronic sequences with stop codons leading to the presence of transcripts with elongated exons 40 and/or 41 (E40e, E41e) in both retina and brain. PCR validations revealed that the new exons may affect several dystrophins. Moreover, immunoblot experiments using a combination of specific antibodies and dystrophin-deficient mice unveiled that the transcripts with stop codons are translated into truncated proteins lacking their C-terminus, which we called N-Dp427 and N-Dp260. This study thus uncovers a range of new findings underlying the complex neurobiology of DMD.
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Affiliation(s)
| | | | - Sophie Lourdel
- Institut des Neurosciences Paris Saclay, Université Paris-Saclay, CNRS, 91400 Saclay, France
| | - Ahrmad Annan
- Institut des Neurosciences Paris Saclay, Université Paris-Saclay, CNRS, 91400 Saclay, France
| | - Jérôme E Roger
- To whom correspondence should be addressed. E-mail: (C.V.); (C.M.); (J.E.R.)
| | - Cecilia Montanez
- To whom correspondence should be addressed. E-mail: (C.V.); (C.M.); (J.E.R.)
| | - Cyrille Vaillend
- To whom correspondence should be addressed. E-mail: (C.V.); (C.M.); (J.E.R.)
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11
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Qian W, Xia S, Yang X, Yu J, Guo B, Lin Z, Wei R, Mao M, Zhang Z, Zhao G, Bai J, Han Q, Wang Z, Luo Q. Complex Involvement of the Extracellular Matrix, Immune Effect, and Lipid Metabolism in the Development of Idiopathic Pulmonary Fibrosis. Front Mol Biosci 2022; 8:800747. [PMID: 35174208 PMCID: PMC8841329 DOI: 10.3389/fmolb.2021.800747] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/06/2021] [Indexed: 01/02/2023] Open
Abstract
Background and objective: Idiopathic pulmonary fibrosis (IPF) is an aggressive fibrotic pulmonary disease with spatially and temporally heterogeneous alveolar lesions. There are no early diagnostic biomarkers, limiting our understanding of IPF pathogenesis. Methods: Lung tissue from surgical lung biopsy of patients with early-stage IPF (n = 7), transplant-stage IPF (n = 2), and healthy controls (n = 6) were subjected to mRNA sequencing and verified by real-time quantitative PCR (RT-qPCR), immunohistochemistry, Western blot, and single-cell RNA sequencing (scRNA-Seq). Results: Three hundred eighty differentially expressed transcripts (DETs) were identified in IPF that were principally involved in extracellular matrix (ECM) remodeling, lipid metabolism, and immune effect. Of these DETs, 21 (DMD, MMP7, POSTN, ECM2, MMP13, FASN, FADS1, SDR16C5, ACAT2, ACSL1, CYP1A1, UGT1A6, CXCL13, CXCL5, CXCL14, IL5RA, TNFRSF19, CSF3R, S100A9, S100A8, and S100A12) were selected and verified by RT-qPCR. Differences in DMD, FASN, and MMP7 were also confirmed at a protein level. Analysis of scRNA-Seq was used to trace their cellular origin to determine which lung cells regulated them. The principal cell sources of DMD were ciliated cells, alveolar type I/II epithelial cells (AT cells), club cells, and alveolar macrophages (AMs); MMP7 derives from AT cells, club cells, and AMs, while FASN originates from AT cells, ciliated cells, and AMs. Conclusion: Our data revealed a comprehensive transcriptional mRNA profile of IPF and demonstrated that ECM remodeling, lipid metabolism, and immune effect were collaboratively involved in the early development of IPF.
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Affiliation(s)
- Weiping Qian
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Shu Xia
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Xiaoyun Yang
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiaying Yu
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bingpeng Guo
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Zhengfang Lin
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rui Wei
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Mengmeng Mao
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Ziyi Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Gui Zhao
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Junye Bai
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Qian Han
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
| | - Zhongfang Wang
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
| | - Qun Luo
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- National Clinical Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
- *Correspondence: Qian Han, ; Zhongfang Wang, ; Qun Luo,
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12
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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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13
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Ohlendieck K, Swandulla D. Complexity of skeletal muscle degeneration: multi-systems pathophysiology and organ crosstalk in dystrophinopathy. Pflugers Arch 2021; 473:1813-1839. [PMID: 34553265 PMCID: PMC8599371 DOI: 10.1007/s00424-021-02623-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Duchenne muscular dystrophy is a highly progressive muscle wasting disorder due to primary abnormalities in one of the largest genes in the human genome, the DMD gene, which encodes various tissue-specific isoforms of the protein dystrophin. Although dystrophinopathies are classified as primary neuromuscular disorders, the body-wide abnormalities that are associated with this disorder and the occurrence of organ crosstalk suggest that a multi-systems pathophysiological view should be taken for a better overall understanding of the complex aetiology of X-linked muscular dystrophy. This article reviews the molecular and cellular effects of deficiency in dystrophin isoforms in relation to voluntary striated muscles, the cardio-respiratory system, the kidney, the liver, the gastrointestinal tract, the nervous system and the immune system. Based on the establishment of comprehensive biomarker signatures of X-linked muscular dystrophy using large-scale screening of both patient specimens and genetic animal models, this article also discusses the potential usefulness of novel disease markers for more inclusive approaches to differential diagnosis, prognosis and therapy monitoring that also take into account multi-systems aspects of dystrophinopathy. Current therapeutic approaches to combat muscular dystrophy are summarised.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Co. Kildare, Maynooth, W23F2H6, Ireland.
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Co. Kildare, Maynooth, W23F2H6, Ireland.
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, 53115, Bonn, Germany.
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14
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Vieira LM, Jorge NAN, de Sousa JB, Setubal JC, Stadler PF, Walter MEMT. Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction. Front Oncol 2021; 11:681579. [PMID: 34178670 PMCID: PMC8222815 DOI: 10.3389/fonc.2021.681579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/22/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a heterogeneous cancer. Its treatment depends on its anatomical site and distinguishes between colon, rectum, and rectosigmoid junction cancer. This study aimed to identify diagnostic and prognostic biomarkers using networks of CRC-associated transcripts that can be built based on competing endogenous RNAs (ceRNA). METHODS RNA expression and clinical information data of patients with colon, rectum, and rectosigmoid junction cancer were obtained from The Cancer Genome Atlas (TCGA). The RNA expression profiles were assessed through bioinformatics analysis, and a ceRNA was constructed for each CRC site. A functional enrichment analysis was performed to assess the functional roles of the ceRNA networks in the prognosis of colon, rectum, and rectosigmoid junction cancer. Finally, to verify the ceRNA impact on prognosis, an overall survival analysis was performed. RESULTS The study identified various CRC site-specific prognosis biomarkers: hsa-miR-1271-5p, NRG1, hsa-miR-130a-3p, SNHG16, and hsa-miR-495-3p in the colon; E2F8 in the rectum and DMD and hsa-miR-130b-3p in the rectosigmoid junction. We also identified different biological pathways that highlight differences in CRC behavior at different anatomical sites, thus reinforcing the importance of correctly identifying the tumor site. CONCLUSIONS Several potential prognostic markers for colon, rectum, and rectosigmoid junction cancer were found. CeRNA networks could provide better understanding of the differences between, and common factors in, prognosis of colon, rectum, and rectosigmoid junction cancer.
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Affiliation(s)
- Lucas Maciel Vieira
- Departamento de Ciência da Computação, Instituto de Ciência Exatas, University of Brasília, Brasília, Brazil
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig, Germany
| | | | - João Batista de Sousa
- Division of Coloproctology, Department of Surgery, University of Brasília School of Medicine, Brasília, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig, Germany
- Max Planck Institute for Mathematics in the Science, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia
- Santa Fe Institute, Santa Fe, CA, United States
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15
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Luce L, Carcione M, Mazzanti C, Buonfiglio PI, Dalamón V, Mesa L, Dubrovsky A, Corderí J, Giliberto F. Theragnosis for Duchenne Muscular Dystrophy. Front Pharmacol 2021; 12:648390. [PMID: 34149409 PMCID: PMC8209366 DOI: 10.3389/fphar.2021.648390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Dystrophinopathies cover a spectrum of rare progressive X-linked muscle diseases, arising from DMD mutations. They are among the most common pediatric muscular dystrophies, being Duchenne muscular dystrophy (DMD) the most severe form. Despite the fact that there is still no cure for these serious diseases, unprecedented advances are being made for the development of therapies for DMD. Some of which are already conditionally approved: exon skipping and premature stop codon read-through. The present work aimed to characterize the mutational spectrum of DMD in an Argentinian cohort, to identify candidates for available pharmacogenetic treatments and finally, to conduct a comparative analysis of the Latin American (LA) frequencies of mutations amenable for available DMD therapies. We studied 400 patients with clinical diagnosis of dystrophinopathy, implementing a diagnostic molecular algorithm including: MLPA/PCR/Sanger/Exome and bioinformatics. We also performed a meta-analysis of LA's metrics for DMD available therapies. The employed algorithm resulted effective for the achievement of differential diagnosis, reaching a detection rate of 97%. Because of this, corticosteroid treatment was correctly indicated and validated in 371 patients with genetic confirmation of dystrophinopathy. Also, 20 were eligible for exon skipping of exon 51, 21 for exon 53, 12 for exon 45 and another 70 for premature stop codon read-through therapy. We determined that 87.5% of DMD patients will restore the reading frame with the skipping of only one exon. Regarding nonsense variants, UGA turned out to be the most frequent premature stop codon observed (47%). According to the meta-analysis, only four LA countries (Argentina, Brazil, Colombia and Mexico) provide the complete molecular algorithm for dystrophinopathies. We observed different relations among the available targets for exon skipping in the analyzed populations, but a more even proportion of nonsense variants (∼40%). In conclusion, this manuscript describes the theragnosis carried out in Argentinian dystrophinopathy patients. The implemented molecular algorithm proved to be efficient for the achievement of differential diagnosis, which plays a crucial role in patient management, determination of the standard of care and genetic counseling. Finally, this work contributes with the international efforts to characterize the frequencies and variants in LA, pillars of drug development and theragnosis.
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Affiliation(s)
- Leonela Luce
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Micaela Carcione
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Chiara Mazzanti
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula I Buonfiglio
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) "Dr. Héctor N. Torres", CONICET, Buenos Aires, Argentina
| | - Viviana Dalamón
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) "Dr. Héctor N. Torres", CONICET, Buenos Aires, Argentina
| | - Lilia Mesa
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - Alberto Dubrovsky
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - José Corderí
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - Florencia Giliberto
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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16
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Santin R, Vieira IA, Nunes JC, Benevides ML, Quadros F, Brusius-Facchin AC, Macedo G, Bertoni APS. A novel DMD intronic alteration: a potentially disease-causing variant of an intermediate muscular dystrophy phenotype. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2021; 40:93-100. [PMID: 34355126 PMCID: PMC8290513 DOI: 10.36185/2532-1900-048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Pathogenic germline variants in DMD gene, which encodes the well-known cytoskeletal protein named dystrophin, are associated with a wide range of dystrophinopathies disorders, such as Duchenne muscular dystrophy (DMD, severe form), Becker muscular dystrophy (BMD, mild form) and intermediate muscular dystrophy (IMD). Muscle biopsy, immunohistochemistry, molecular (multiplex ligation-dependent probe amplification (MLPA)/next-generation sequencing (NGS) and Sanger methods) and in silico analyses were performed in order to identify alterations in DMD gene and protein in a patient with a clinical manifestation and with high creatine kinase levels. Herein, we described a previously unreported intronic variant in DMD and reduced dystrophin staining in the muscle biopsy. This novel DMD variant allele, c.9649+4A>T that was located in a splice donor site within intron 66. Sanger sequencing analysis from maternal DNA showed the presence of both variant c.9649+4A>T and wild-type (WT) DMD alleles. Different computational tools suggested that this nucleotide change might affect splicing through a WT donor site disruption, occurring in an evolutionarily conserved region. Indeed, we observed that this novel variant, could explain the reduced dystrophin protein levels and discontinuous sarcolemmal staining in muscle biopsy, which suggests that c.9649+4A>T allele may be re-classified as pathogenic in the future. Our data show that the c.9649+4A>T intronic sequence variant in the DMD gene may be associated with an IMD phenotype and our findings reinforce the importance of a more precise diagnosis combining muscle biopsy, molecular techniques and comprehensive in silico approaches in the clinical cases with negative results for conventional genetic analysis.
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Affiliation(s)
- Ricardo Santin
- Santa Casa de Misericórdia de Porto Alegre, (ISCMPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Igor Araujo Vieira
- Programa de Pós Graduação em Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Jean Costa Nunes
- Neurodiagnostic Brazil - Floranópolis, Santa Catarina (SC), Brazil
- Departmento de Patologia, Universidade Federal de Santa Catarina (UFSC), Hospital Polydoro Ernani de São Thiago, SC, Brazil
| | - Maria Luiza Benevides
- Departmento de Neurologia, Hospital Governador Celso Ramos, Santa Catarina (SC), Brazil
| | - Fernanda Quadros
- Santa Casa de Misericórdia de Porto Alegre, (ISCMPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Carolina Brusius-Facchin
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriel Macedo
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Paula Santin Bertoni
- Departamento de Ciências Básicas da Saúde and Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
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17
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Brogna C, Coratti G, Rossi R, Neri M, Messina S, Amico AD, Bruno C, Lucibello S, Vita G, Berardinelli A, Magri F, Ricci F, Pedemonte M, Mongini T, Battini R, Bello L, Pegoraro E, Baranello G, Politano L, Comi GP, Sansone VA, Albamonte E, Donati A, Bertini E, Goemans N, Previtali S, Bovis F, Pane M, Ferlini A, Mercuri E. The nonsense mutation stop+4 model correlates with motor changes in Duchenne muscular dystrophy. Neuromuscul Disord 2021; 31:479-488. [PMID: 33773883 DOI: 10.1016/j.nmd.2021.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 10/22/2022]
Abstract
The aim was to assess 3-year longitudinal data using 6MWT in 26 ambulant boys affected by DMD carrying nonsense mutations and to compare their results to other small mutations. We also wished to establish, within the nonsense mutations group, patterns of change according to several variables. Patients with nonsense mutations were categorized according to the stop codon type newly created by the mutation and also including the adjacent 5' (upstream) and 3' (downstream) nucleotides. No significant difference was found between nonsense mutations and other small mutations (p > 0.05) on the 6MWT. Within the nonsense mutations group, there was no difference in 6MWT when the patients were subdivided according to: Type of stop codon, frame status of exons involved, protein domain affected. In contrast, there was a difference when the stop codon together with the 3' adjacent nucleotide ("stop+4 model") was considered (p < 0.05) with patients with stop codon TGA and 3' adjacent nucleotide G (TGAG) having a more rapid decline. Our finding suggest that the stop+4 model may help in predicting functional changes. This data will be useful at the time of interpreting the long term follow up of patients treated with Ataluren that are becoming increasingly available.
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Affiliation(s)
- Claudia Brogna
- Pediatric Neurology, Università Cattolica del Sacro Cuore, Rome, Italy; Centro Clinico Nemo, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, Rome 00152, Italy
| | - Giorgia Coratti
- Pediatric Neurology, Università Cattolica del Sacro Cuore, Rome, Italy; Centro Clinico Nemo, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, Rome 00152, Italy
| | - Rachele Rossi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Marcella Neri
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Sonia Messina
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy; Nemo SUD Clinical Center, University Hospital "G. Martino", Messina, Italy
| | - Adele D' Amico
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Claudio Bruno
- Center of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Simona Lucibello
- Pediatric Neurology, Università Cattolica del Sacro Cuore, Rome, Italy; Centro Clinico Nemo, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, Rome 00152, Italy
| | - Gianluca Vita
- Nemo SUD Clinical Center, University Hospital "G. Martino", Messina, Italy
| | - Angela Berardinelli
- Child Neurology and Psychiatry Unit, ''Casimiro Mondino'' Foundation, Pavia, Italy
| | - Francesca Magri
- Department of Pathophysiology and Transplantation, Fondazione IRCCS Ca' Grande Ospedale Maggiore Policlinico, Dino Ferrari Center, , University of Milan, Milan, Italy
| | - Federica Ricci
- Neuromuscular Center, AOU Città della Salute e della Scienza, University of Torino, Italy
| | - Marina Pedemonte
- Center of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Tiziana Mongini
- Neuromuscular Center, AOU Città della Salute e della Scienza, University of Torino, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, Stella Maris Institute, Pisa, Italy; Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Luca Bello
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Elena Pegoraro
- Department of Neurosciences, University of Padua, Padua, Italy
| | | | - Luisa Politano
- Cardiomiologia e Genetica Medica, Dipartimento di Medicina Sperimentale, Università della Campania Luigi Vanvitelli, Napoli, Italy
| | - Giacomo P Comi
- Department of Pathophysiology and Transplantation, Fondazione IRCCS Ca' Grande Ospedale Maggiore Policlinico, Dino Ferrari Center, , University of Milan, Milan, Italy
| | - Valeria A Sansone
- The NEMO Center in Milan, Neurorehabilitation Unit, University of Milan, ASST Niguarda Hospital, Milan, Italy
| | - Emilio Albamonte
- The NEMO Center in Milan, Neurorehabilitation Unit, University of Milan, ASST Niguarda Hospital, Milan, Italy
| | - Alice Donati
- Metabolic Unit, A. Meyer Children's Hospital, Florence, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Nathalie Goemans
- Department of Child Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Stefano Previtali
- Neuromuscular Repair Unit, Inspe and Division of Neuroscience, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Bovis
- Department of Health Sciences (DISSAL), University of Genova, Genoa, Italy
| | - Marika Pane
- Pediatric Neurology, Università Cattolica del Sacro Cuore, Rome, Italy; Centro Clinico Nemo, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, Rome 00152, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Eugenio Mercuri
- Pediatric Neurology, Università Cattolica del Sacro Cuore, Rome, Italy; Centro Clinico Nemo, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, Rome 00152, Italy.
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18
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Saint-Martin C, Cauchois-Le Mière M, Rex E, Soukarieh O, Arnoux JB, Buratti J, Bouvet D, Frébourg T, Gaildrat P, Shyng SL, Bellanné-Chantelot C, Martins A. Functional characterization of ABCC8 variants of unknown significance based on bioinformatics predictions, splicing assays, and protein analyses: Benefits for the accurate diagnosis of congenital hyperinsulinism. Hum Mutat 2021; 42:408-420. [PMID: 33410562 DOI: 10.1002/humu.24164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/06/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022]
Abstract
ABCC8 encodes the SUR1 subunit of the β-cell ATP-sensitive potassium channel whose loss of function causes congenital hyperinsulinism (CHI). Molecular diagnosis is critical for optimal management of CHI patients. Unfortunately, assessing the impact of ABCC8 variants on RNA splicing remains very challenging as this gene is poorly expressed in leukocytes. Here, we performed bioinformatics analysis and cell-based minigene assays to assess the impact on splicing of 13 ABCC8 variants identified in 20 CHI patients. Next, channel properties of SUR1 proteins expected to originate from minigene-detected in-frame splicing defects were analyzed after ectopic expression in COSm6 cells. Out of the analyzed variants, seven induced out-of-frame splicing defects and were therefore classified as recessive pathogenic, whereas two led to skipping of in-frame exons. Channel functional analysis of the latter demonstrated their pathogenicity. Interestingly, the common rs757110 SNP increased exon skipping in our system suggesting that it may act as a disease modifier factor. Our strategy allowed determining the pathogenicity of all selected ABCC8 variants, and CHI-inheritance pattern for 16 out of the 20 patients. This study highlights the value of combining RNA and protein functional approaches in variant interpretation and reveals the minigene splicing assay as a new tool for CHI molecular diagnostics.
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Affiliation(s)
- Cécile Saint-Martin
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Marine Cauchois-Le Mière
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Emily Rex
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Omar Soukarieh
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Jean-Baptiste Arnoux
- Department of Inherited Metabolic Disease, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Julien Buratti
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Delphine Bouvet
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Thierry Frébourg
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | | | - Alexandra Martins
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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19
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Schneider AFE, Aartsma-Rus A. Developments in reading frame restoring therapy approaches for Duchenne muscular dystrophy. Expert Opin Biol Ther 2020; 21:343-359. [PMID: 33074029 DOI: 10.1080/14712598.2021.1832462] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Exon skipping compounds restoring the dystrophin transcript reading frame have received regulatory approval for Duchenne muscular dystrophy (DMD). Recently, focus shifted to developing compounds to skip additional exons, improving delivery to skeletal muscle, and to genome editing, to restore the reading frame on DNA level. AREAS COVERED We outline developments for reading frame restoring approaches, challenges of mutation specificity, and optimizing delivery. Also, we highlight ongoing efforts to better detect exon skipping therapeutic effects in clinical trials. Searches on relevant terms were performed, focusing on recent publications (<3 years). EXPERT OPINION Currently, 3 AONS are approved. Whether dystrophin levels are sufficient to slowdown disease progression needs to be confirmed. Enhancing AON uptake by muscles is currently under investigation. Gene editing is an alternative, but one that involves practical and ethical concerns. Given the field's momentum, we believe the efficiency of frame-restoring approaches will improve.
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Affiliation(s)
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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20
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EMQN best practice guidelines for genetic testing in dystrophinopathies. Eur J Hum Genet 2020; 28:1141-1159. [PMID: 32424326 PMCID: PMC7608854 DOI: 10.1038/s41431-020-0643-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 02/04/2023] Open
Abstract
Dystrophinopathies are X-linked diseases, including Duchenne muscular dystrophy and Becker muscular dystrophy, due to DMD gene variants. In recent years, the application of new genetic technologies and the availability of new personalised drugs have influenced diagnostic genetic testing for dystrophinopathies. Therefore, these European best practice guidelines for genetic testing in dystrophinopathies have been produced to update previous guidelines published in 2010.These guidelines summarise current recommended technologies and methodologies for analysis of the DMD gene, including testing for deletions and duplications of one or more exons, small variant detection and RNA analysis. Genetic testing strategies for diagnosis, carrier testing and prenatal diagnosis (including non-invasive prenatal diagnosis) are then outlined. Guidelines for sequence variant annotation and interpretation are provided, followed by recommendations for reporting results of all categories of testing. Finally, atypical findings (such as non-contiguous deletions and dual DMD variants), implications for personalised medicine and clinical trials and incidental findings (identification of DMD gene variants in patients where a clinical diagnosis of dystrophinopathy has not been considered or suspected) are discussed.
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21
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Slusher AL, Kim JJJ, Ludlow AT. The Role of Alternative RNA Splicing in the Regulation of hTERT, Telomerase, and Telomeres: Implications for Cancer Therapeutics. Cancers (Basel) 2020; 12:E1514. [PMID: 32531916 PMCID: PMC7352778 DOI: 10.3390/cancers12061514] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative RNA splicing impacts the majority (>90%) of eukaryotic multi-exon genes, expanding the coding capacity and regulating the abundance of gene isoforms. Telomerase (hTERT) is a key example of a gene that is alternatively spliced during human fetal development and becomes dysregulated in nearly all cancers. Approximately 90% of human tumors use telomerase to synthesize de novo telomere repeats and obtain telomere-dependent cellular immortality. Paradigm shifting data indicates that hTERT alternative splicing, in addition to transcription, plays an important role in the regulation of active telomerase in cells. Our group and others are pursuing the basic science studies to progress this emerging area of telomerase biology. Recent evidence demonstrates that switching splicing of hTERT from the telomerase activity producing full-length hTERT isoform to alternatively spliced, non-coding isoforms may be a novel telomerase inhibition strategy to prevent cancer growth and survival. Thus, the goals of this review are to detail the general roles of telomerase in cancer development, explore the emerging regulatory mechanisms of alternative RNA splicing of the hTERT gene in various somatic and cancer cell types, define the known and potential roles of hTERT splice isoforms in cancer cell biology, and provide insight into new treatment strategies targeting hTERT in telomerase-positive cancers.
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Affiliation(s)
| | | | - Andrew T. Ludlow
- School of Kinesiology, University of Michigan, Ann Arbor, MI 48109, USA; (A.L.S.); (J.J.K.)
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22
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Neri M, Rossi R, Trabanelli C, Mauro A, Selvatici R, Falzarano MS, Spedicato N, Margutti A, Rimessi P, Fortunato F, Fabris M, Gualandi F, Comi G, Tedeschi S, Seia M, Fiorillo C, Traverso M, Bruno C, Giardina E, Piemontese MR, Merla G, Cau M, Marica M, Scuderi C, Borgione E, Tessa A, Astrea G, Santorelli FM, Merlini L, Mora M, Bernasconi P, Gibertini S, Sansone V, Mongini T, Berardinelli A, Pini A, Liguori R, Filosto M, Messina S, Vita G, Toscano A, Vita G, Pane M, Servidei S, Pegoraro E, Bello L, Travaglini L, Bertini E, D'Amico A, Ergoli M, Politano L, Torella A, Nigro V, Mercuri E, Ferlini A. The Genetic Landscape of Dystrophin Mutations in Italy: A Nationwide Study. Front Genet 2020; 11:131. [PMID: 32194622 PMCID: PMC7063120 DOI: 10.3389/fgene.2020.00131] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/03/2020] [Indexed: 12/11/2022] Open
Abstract
Dystrophinopathies are inherited diseases caused by mutations in the dystrophin (DMD) gene for which testing is mandatory for genetic diagnosis, reproductive choices and eligibility for personalized trials. We genotyped the DMD gene in our Italian cohort of 1902 patients (BMD n = 740, 39%; DMD n =1162, 61%) within a nationwide study involving 11 diagnostic centers in a 10-year window (2008–2017). In DMD patients, we found deletions in 57%, duplications in 11% and small mutations in 32%. In BMD, we found deletions in 78%, duplications in 9% and small mutations in 13%. In BMD, there are a higher number of deletions, and small mutations are more frequent than duplications. Among small mutations that are generally frequent in both phenotypes, 44% of DMD and 36% of BMD are nonsense, thus, eligible for stop codon read-through therapy; 63% of all out-of-frame deletions are eligible for single exon skipping. Patients were also assigned to Italian regions and showed interesting regional differences in mutation distribution. The full genetic characterization in this large, nationwide cohort has allowed us to draw several correlations between DMD/BMD genotype landscapes and mutation frequency, mutation types, mutation locations along the gene, exon/intron architecture, and relevant protein domain, with effects on population genetic characteristics and new personalized therapies.
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Affiliation(s)
- Marcella Neri
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Rachele Rossi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Cecilia Trabanelli
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Antonio Mauro
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Rita Selvatici
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Maria Sofia Falzarano
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Noemi Spedicato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alice Margutti
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Paola Rimessi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Fortunato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Marina Fabris
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Francesca Gualandi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Giacomo Comi
- Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Silvana Tedeschi
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Seia
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Fiorillo
- Paediatric Neurology and Muscular Diseases Unit, University of Genoa and G. Gaslini Institute, Genoa, Italy
| | - Monica Traverso
- Paediatric Neurology and Muscular Diseases Unit, University of Genoa and G. Gaslini Institute, Genoa, Italy
| | - Claudio Bruno
- Center of Translational and Experimental Myology, IRCCS Gaslini, Genova, Italy
| | - Emiliano Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | | | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Milena Cau
- Laboratory of Genetics and Genomics, Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
| | - Monica Marica
- Clinica Pediatrica e Malattie Rare, Brotzu, Cagliari, Italy
| | - Carmela Scuderi
- Unit of Neuromuscular Diseases, Oasi Research Institute-IRCCS, Troina, Italy
| | - Eugenia Borgione
- Unit of Neuromuscular Diseases, Oasi Research Institute-IRCCS, Troina, Italy
| | - Alessandra Tessa
- Department of Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Guia Astrea
- Department of Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | | | - Luciano Merlini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Pia Bernasconi
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Sara Gibertini
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valeria Sansone
- Neurorehabilitation Unit, Department Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Tiziana Mongini
- Neuromuscular Center, AOU Città della Salute e della Scienza, University of Turin, Turin, Italy
| | - Angela Berardinelli
- Child Neurology and Psychiatry Unit, "Casimiro Mondino" Foundation, Pavia, Italy
| | - Antonella Pini
- Child Neurology Unit, IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Rocco Liguori
- Department of Biomedical and Neuro Motor Sciences, University of Bologna, Bologna, Italy
| | - Massimiliano Filosto
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonia Messina
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Gianluca Vita
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Antonio Toscano
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Giuseppe Vita
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Marika Pane
- Centro Clinico Nemo, Policlinico A. Gemelli, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Serenella Servidei
- UOC Neurofisiopatologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Elena Pegoraro
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Luca Bello
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Adele D'Amico
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Manuela Ergoli
- Cardiomiology and Medical Genetics, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Luisa Politano
- Cardiomiology and Medical Genetics, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Eugenio Mercuri
- Centro Clinico Nemo, Policlinico A. Gemelli, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Pediatric Neurology, Catholic University, Rome, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy.,Dubowitz Neuromuscular Unit, Institute of Child Health, University College London, London, United Kingdom
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Exon skipping induced by nonsense/frameshift mutations in DMD gene results in Becker muscular dystrophy. Hum Genet 2020; 139:247-255. [PMID: 31919629 PMCID: PMC6981323 DOI: 10.1007/s00439-019-02107-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/27/2019] [Indexed: 01/13/2023]
Abstract
Duchenne muscular dystrophy (DMD) is caused by a nonsense or frameshift mutation in the DMD gene, while its milder form, Becker muscular dystrophy (BMD) is caused by an in-frame deletion/duplication or a missense mutation. Interestingly, however, some patients with a nonsense mutation exhibit BMD phenotype, which is mostly attributed to the skipping of the exon containing the nonsense mutation, resulting in in-frame deletion. This study aims to find BMD cases with nonsense/frameshift mutations in DMD and to investigate the exon skipping rate of those nonsense/frameshift mutations. We searched for BMD cases with nonsense/frameshift mutations in DMD in the Japanese Registry of Muscular Dystrophy. For each DMD mutation identified, we constructed minigene plasmids containing one exon with/without a mutation and its flanking intronic sequence. We then introduced them into HeLa cells and measured the skipping rate of transcripts of the minigene by RT-qPCR. We found 363 cases with a nonsense/frameshift mutation in DMD gene from a total of 1497 dystrophinopathy cases in the registry. Among them, 14 had BMD phenotype. Exon skipping rates were well correlated with presence or absence of dystrophin, suggesting that 5% exon skipping rate is critical for the presence of dystrophin in the sarcolemma, leading to milder phenotypes. Accurate quantification of the skipping rate is important in understanding the exact functions of the nonsense/frameshift mutations in DMD and for interpreting the phenotypes of the BMD patients.
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More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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25
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Zhu Y, Deng H, Chen X, Li H, Yang C, Li S, Pan X, Tian S, Feng S, Tan X, Matsuo M, Zhang Z. Skipping of an exon with a nonsense mutation in the DMD gene is induced by the conversion of a splicing enhancer to a splicing silencer. Hum Genet 2019; 138:771-785. [DOI: 10.1007/s00439-019-02036-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/29/2019] [Indexed: 01/23/2023]
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26
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Dominov JA, Uyan Ö, McKenna‐Yasek D, Nallamilli BRR, Kergourlay V, Bartoli M, Levy N, Hudson J, Evangelista T, Lochmuller H, Krahn M, Rufibach L, Hegde M, Brown RH. Correction of pseudoexon splicing caused by a novel intronic dysferlin mutation. Ann Clin Transl Neurol 2019; 6:642-654. [PMID: 31019989 PMCID: PMC6469257 DOI: 10.1002/acn3.738] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 01/12/2019] [Accepted: 01/21/2019] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Dysferlin is a large transmembrane protein that functions in critical processes of membrane repair and vesicle fusion. Dysferlin-deficiency due to mutations in the dysferlin gene leads to muscular dystrophy (Miyoshi myopathy (MM), limb girdle muscular dystrophy type 2B (LGMD2B), distal myopathy with anterior tibial onset (DMAT)), typically with early adult onset. At least 416 pathogenic dysferlin mutations are known, but for approximately 17% of patients, one or both of their pathogenic variants remain undefined following standard exon sequencing methods that interrogate exons and nearby flanking intronic regions but not the majority of intronic regions. METHODS We sequenced RNA from myogenic cells to identify a novel dysferlin pathogenic variant in two affected siblings that previously had only one disease-causing variant identified. We designed antisense oligonucleotides (AONs) to bypass the effects of this mutation on RNA splicing. RESULTS We identified a new pathogenic point mutation deep within dysferlin intron 50i. This intronic variant causes aberrant mRNA splicing and inclusion of an additional pseudoexon (PE, we term PE50.1) within the mature dysferlin mRNA. PE50.1 inclusion alters the protein sequence, causing premature translation termination. We identified this mutation in 23 dysferlinopathy patients (seventeen families), revealing it to be one of the more prevalent dysferlin mutations. We used AON-mediated exon skipping to correct the aberrant PE50.1 splicing events in vitro, which increased normal mRNA production and significantly restored dysferlin protein expression. INTERPRETATION Deep intronic mutations can be a common underlying cause of dysferlinopathy, and importantly, could be treatable with AON-based exon-skipping strategies.
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Affiliation(s)
- Janice A. Dominov
- Department of NeurologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
| | - Özgün Uyan
- Department of NeurologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
| | - Diane McKenna‐Yasek
- Department of NeurologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
| | - Babi Ramesh Reddy Nallamilli
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgia
- Present address:
Perkin Elmer GenomicsWalthamMassachusetts
| | - Virginie Kergourlay
- Marseille Medical Genetics ‐ Translational NeuromyologyAix‐Marseille UnivINSERMMMGMarseilleFrance
| | - Marc Bartoli
- Marseille Medical Genetics ‐ Translational NeuromyologyAix‐Marseille UnivINSERMMMGMarseilleFrance
| | - Nicolas Levy
- Marseille Medical Genetics ‐ Translational NeuromyologyAix‐Marseille UnivINSERMMMGMarseilleFrance
- Département de Génétique MédicaleAPHMHôpital Timone EnfantsMarseilleFrance
| | - Judith Hudson
- Northern Molecular Genetics ServiceNewcastle upon TyneUnited Kingdom
| | - Teresinha Evangelista
- Newcastle University John Walton Centre for Muscular Dystrophy ResearchMRC Centre for Neuromuscular DiseasesInstitute of Genetic MedicineNewcastle upon TyneUnited Kingdom
| | - Hanns Lochmuller
- Newcastle University John Walton Centre for Muscular Dystrophy ResearchMRC Centre for Neuromuscular DiseasesInstitute of Genetic MedicineNewcastle upon TyneUnited Kingdom
- Department of Neuropediatrics and Muscle DisordersFaculty of MedicineMedical Center–University of FreiburgFreiburgGermany
- Centro Nacional de Análisis Genómico (CNAG‐CRG)Center for Genomic RegulationBarcelona Institute of Science and Technology (BIST)BarcelonaCataloniaSpain
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaCanada
- Division of NeurologyDepartment of MedicineThe Ottawa HospitalOttawaCanada
| | - Martin Krahn
- Marseille Medical Genetics ‐ Translational NeuromyologyAix‐Marseille UnivINSERMMMGMarseilleFrance
- Département de Génétique MédicaleAPHMHôpital Timone EnfantsMarseilleFrance
| | | | - Madhuri Hegde
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgia
| | - Robert H. Brown
- Department of NeurologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
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27
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Zhang Y, Yang W, Wen G, Wu Y, Jing Z, Li D, Tang M, Liu G, Wei X, Zhong Y, Li Y, Deng Y. Application whole exome sequencing for the clinical molecular diagnosis of patients with Duchenne muscular dystrophy; identification of four novel nonsense mutations in four unrelated Chinese DMD patients. Mol Genet Genomic Med 2019; 7:e622. [PMID: 30938079 PMCID: PMC6503051 DOI: 10.1002/mgg3.622] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/19/2019] [Accepted: 02/11/2019] [Indexed: 12/17/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) is the most common form of inherited muscular dystrophy. Germline mutations in dystrophin (DMD) gene cause DMD, with a X‐linked recessive mode of inheritance. Patients with DMD are usually characterized by weakness of muscle, usually started since childhood and gradually the patient will unable to stand and walk. Methods In our present study, we identified four unrelated Chinese patients with DMD from four Chinese families. Whole exome sequencing was performed for genetic molecular analysis for these probands. Results Whole exome sequencing and confirmatory Sanger sequencing identified four novel nonsense mutations in these four unrelated Chinese patients, respectively. All these four mutations lead to the formation of a truncated DMD protein by formation of a premature stop codon. According to the variant interpretation guidelines of American College of Medical Genetics and Genomics (ACMG), these four novel nonsense mutations are categorized as “likely pathogenic” variants. Conclusion Our present finding not only identified four novel loss‐of‐function mutations in dystrophin (DMD) gene but also strongly emphasized the significance of whole exome sequencing as the most efficient way of identifying the candidate genes and mutations which enables us for easy and rapid clinical diagnosis, follow‐up, and management of DMD patients.
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Affiliation(s)
- Yan Zhang
- Department of Pathology, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, P.R. China
| | - Weikang Yang
- Department of Prevention and health care, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Guoming Wen
- Department of Outpatient, Shenzhen Longhua District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Yanxia Wu
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Zhiliang Jing
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Dazhou Li
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Minshan Tang
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Guanglong Liu
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Xuxuan Wei
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
| | - Yan Zhong
- Department of Pathology, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, P.R. China
| | - Yanhua Li
- Department of Pathology, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, P.R. China
| | - Yongjian Deng
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, P.R. China
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28
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Zhang K, Yang X, Lin G, Han Y, Li J. Molecular genetic testing and diagnosis strategies for dystrophinopathies in the era of next generation sequencing. Clin Chim Acta 2019; 491:66-73. [PMID: 30660698 DOI: 10.1016/j.cca.2019.01.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 12/14/2022]
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive, inherited neuromuscular disorders, caused by pathogenic variants in the dystrophin gene that encodes the dystrophin protein. A number of mutations have been identified in the past years, producing dystrophin diversity and resulting in mild to severe phenotypes in patients. Mutations in the dystrophin gene can be characterized by laboratory testing to confirm a clinical diagnosis of DMD/BMD. Traditional genetic diagnostic strategy for DMD/BMD involves the initial detection of large mutations, followed by the detection of smaller mutations, where two or more analytical methods are employed. With the development of next generation sequencing (NGS) technology, comprehensive mutational screening for all variant types can be performed on a single platform in patients and carriers, although further optimization and validation are required. Furthermore, the discovery of cell-free fetal DNA (cffDNA) in maternal plasma provides basis for noninvasive prenatal diagnosis of DMD/BMD. Here, we discuss the correlation between genotype and phenotype, the current methods of molecular genetic testing and genetic diagnostic strategy for probands and female carriers of DMD/BMD, the diagnostic ability of a comprehensive targeted NGS strategy and the possibility of it replacing conventional methods.
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Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Xin Yang
- The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong 264000, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.
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29
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Hinkle ER, Wiedner HJ, Black AJ, Giudice J. RNA processing in skeletal muscle biology and disease. Transcription 2019; 10:1-20. [PMID: 30556762 DOI: 10.1080/21541264.2018.1558677] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing.
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Affiliation(s)
- Emma R Hinkle
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Hannah J Wiedner
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Adam J Black
- b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Jimena Giudice
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA.,c McAllister Heart Institute , University of North Carolina , Chapel Hill , USA
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30
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Aartsma-Rus A, Hegde M, Ben-Omran T, Buccella F, Ferlini A, Gallano P, Howell RR, Leturcq F, Martin AS, Potulska-Chromik A, Saute JA, Schmidt WM, Sejersen T, Tuffery-Giraud S, Uyguner ZO, Witcomb LA, Yau S, Nelson SF. Evidence-Based Consensus and Systematic Review on Reducing the Time to Diagnosis of Duchenne Muscular Dystrophy. J Pediatr 2019; 204:305-313.e14. [PMID: 30579468 DOI: 10.1016/j.jpeds.2018.10.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/27/2018] [Accepted: 10/24/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine/School of Biological Sciences, Georgia Institute of Technology/Perkin Elmer Genetics, Atlanta, GA
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | | | | | - Pia Gallano
- U705 CIBERER, Servei de Genetica, Hospital de Sant Pau, Barcelona, Spain
| | | | - France Leturcq
- Department of Genetics and Molecular Biology, Hospitalier Universitaire Paris Centre, Cochin Hospital, Paris, France
| | - Ann S Martin
- Parent Project Muscular Dystrophy, Hackensack, NJ
| | | | - Jonas A Saute
- Medical Genetics and Neurology Services, Hospital de Clinicas de Porto Alegre/Internal Medicine Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Wolfgang M Schmidt
- Neuromuscular Research Department, Medical University of Vienna, Vienna, Austria
| | - Thomas Sejersen
- Department of Women's and Children's Health, Karolinska Institute/Astrid Lindgrens Barnsjukhus, Karolinska University Hospital, Stockholm, Sweden
| | - Sylvie Tuffery-Giraud
- Laboratory of Rare Genetic Diseases (LGMR), University of Montpellier, Montpellier, France
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | | | - Shu Yau
- Viapath Analytics, Guy's Hospital, London, United Kingdom
| | - Stanley F Nelson
- Department of Human Genetics, University of California, Los Angeles, CA.
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31
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Multiple Exon Skipping in the Duchenne Muscular Dystrophy Hot Spots: Prospects and Challenges. J Pers Med 2018; 8:jpm8040041. [PMID: 30544634 PMCID: PMC6313462 DOI: 10.3390/jpm8040041] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/24/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD), a fatal X-linked recessive disorder, is caused mostly by frame-disrupting, out-of-frame deletions in the dystrophin (DMD) gene. Antisense oligonucleotide-mediated exon skipping is a promising therapy for DMD. Exon skipping aims to convert out-of-frame mRNA to in-frame mRNA and induce the production of internally-deleted dystrophin as seen in the less severe Becker muscular dystrophy. Currently, multiple exon skipping has gained special interest as a new therapeutic modality for this approach. Previous retrospective database studies represented a potential therapeutic application of multiple exon skipping. Since then, public DMD databases have become more useful with an increase in patient registration and advances in molecular diagnosis. Here, we provide an update on DMD genotype-phenotype associations using a global DMD database and further provide the rationale for multiple exon skipping development, particularly for exons 45–55 skipping and an emerging therapeutic concept, exons 3–9 skipping. Importantly, this review highlights the potential of multiple exon skipping for enabling the production of functionally-corrected dystrophin and for treating symptomatic patients not only with out-of-frame deletions but also those with in-frame deletions. We will also discuss prospects and challenges in multiple exon skipping therapy, referring to recent progress in antisense chemistry and design, as well as disease models.
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32
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Abstract
Alternative splicing is a well-studied gene regulatory mechanism that produces biological diversity by allowing the production of multiple protein isoforms from a single gene. An involvement of alternative splicing in the key biological signalling Hippo pathway is emerging and offers new therapeutic avenues. This review discusses examples of alternative splicing in the Hippo pathway, how deregulation of these processes may contribute to disease and whether these processes offer new potential therapeutic targets.
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33
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Wilson K, Faelan C, Patterson-Kane JC, Rudmann DG, Moore SA, Frank D, Charleston J, Tinsley J, Young GD, Milici AJ. Duchenne and Becker Muscular Dystrophies: A Review of Animal Models, Clinical End Points, and Biomarker Quantification. Toxicol Pathol 2017; 45:961-976. [PMID: 28974147 DOI: 10.1177/0192623317734823] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are neuromuscular disorders that primarily affect boys due to an X-linked mutation in the DMD gene, resulting in reduced to near absence of dystrophin or expression of truncated forms of dystrophin. Some newer therapeutic interventions aim to increase sarcolemmal dystrophin expression, and accurate dystrophin quantification is critical for demonstrating pharmacodynamic relationships in preclinical studies and clinical trials. Current challenges with measuring dystrophin include the variation in protein expression within individual muscle fibers and across whole muscle samples, the presence of preexisting dystrophin-positive revertant fibers, and trace amounts of residual dystrophin. Immunofluorescence quantification of dystrophin can overcome many of these challenges, but manual quantification of protein expression may be complicated by variations in the collection of images, reproducible scoring of fluorescent intensity, and bias introduced by manual scoring of typically only a few high-power fields. This review highlights the pathology of DMD and BMD, discusses animal models of DMD and BMD, and describes dystrophin biomarker quantitation in DMD and BMD, with several image analysis approaches, including a new automated method that evaluates protein expression of individual muscle fibers.
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Affiliation(s)
- Kristin Wilson
- 1 Flagship Biosciences, Inc., Westminster, Colorado, USA
| | - Crystal Faelan
- 1 Flagship Biosciences, Inc., Westminster, Colorado, USA
| | | | | | - Steven A Moore
- 2 Department of Pathology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Diane Frank
- 3 Sarepta Therapeutics, Inc., Cambridge, Massachusetts, USA
| | - Jay Charleston
- 3 Sarepta Therapeutics, Inc., Cambridge, Massachusetts, USA
| | - Jon Tinsley
- 4 Summit Therapeutics, Abingdon, United Kingdom
| | - G David Young
- 1 Flagship Biosciences, Inc., Westminster, Colorado, USA
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34
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Gonçalves A, Oliveira J, Coelho T, Taipa R, Melo-Pires M, Sousa M, Santos R. Exonization of an Intronic LINE-1 Element Causing Becker Muscular Dystrophy as a Novel Mutational Mechanism in Dystrophin Gene. Genes (Basel) 2017; 8:genes8100253. [PMID: 28972564 PMCID: PMC5664103 DOI: 10.3390/genes8100253] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022] Open
Abstract
A broad mutational spectrum in the dystrophin (DMD) gene, from large deletions/duplications to point mutations, causes Duchenne/Becker muscular dystrophy (D/BMD). Comprehensive genotyping is particularly relevant considering the mutation-centered therapies for dystrophinopathies. We report the genetic characterization of a patient with disease onset at age 13 years, elevated creatine kinase levels and reduced dystrophin labeling, where multiplex-ligation probe amplification (MLPA) and genomic sequencing failed to detect pathogenic variants. Bioinformatic, transcriptomic (real time PCR, RT-PCR), and genomic approaches (Southern blot, long-range PCR, and single molecule real-time sequencing) were used to characterize the mutation. An aberrant transcript was identified, containing a 103-nucleotide insertion between exons 51 and 52, with no similarity with the DMD gene. This corresponded to the partial exonization of a long interspersed nuclear element (LINE-1), disrupting the open reading frame. Further characterization identified a complete LINE-1 (~6 kb with typical hallmarks) deeply inserted in intron 51. Haplotyping and segregation analysis demonstrated that the mutation had a de novo origin. Besides underscoring the importance of mRNA studies in genetically unsolved cases, this is the first report of a disease-causing fully intronic LINE-1 element in DMD, adding to the diversity of mutational events that give rise to D/BMD.
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Affiliation(s)
- Ana Gonçalves
- Unidade de Genética Molecular, Centro de Genética Médica Dr. Jacinto Magalhães, Centro Hospitalar do Porto, 4050-106 Porto, Portugal.
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal.
| | - Jorge Oliveira
- Unidade de Genética Molecular, Centro de Genética Médica Dr. Jacinto Magalhães, Centro Hospitalar do Porto, 4050-106 Porto, Portugal.
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal.
| | - Teresa Coelho
- Serviço de Neurofisiologia, Departamento de Neurociências, Centro Hospitalar do Porto, 4099-001 Porto, Portugal.
| | - Ricardo Taipa
- Unidade de Neuropatologia, Centro Hospitalar do Porto, 4099-001 Porto, Portugal.
| | - Manuel Melo-Pires
- Unidade de Neuropatologia, Centro Hospitalar do Porto, 4099-001 Porto, Portugal.
| | - Mário Sousa
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal.
- Departamento de Microscopia, Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal.
- Centro de Genética da Reprodução Prof. Alberto Barros, 4050-313 Porto, Portugal.
| | - Rosário Santos
- Unidade de Genética Molecular, Centro de Genética Médica Dr. Jacinto Magalhães, Centro Hospitalar do Porto, 4050-106 Porto, Portugal.
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal.
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal.
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