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Grosz BR, Parmar JM, Ellis M, Bryen S, Simons C, Reis ALM, Stevanovski I, Deveson IW, Nicholson G, Laing N, Wallis M, Ravenscroft G, Kumar KR, Vucic S, Kennerson ML. A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing. J Peripher Nerv Syst 2024; 29:262-274. [PMID: 38860315 DOI: 10.1111/jns.12637] [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: 04/10/2024] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Loss-of-function variants in MME (membrane metalloendopeptidase) are a known cause of recessive Charcot-Marie-Tooth Neuropathy (CMT). A deep intronic variant, MME c.1188+428A>G (NM_000902.5), was identified through whole genome sequencing (WGS) of two Australian families with recessive inheritance of axonal CMT using the seqr platform. MME c.1188+428A>G was detected in a homozygous state in Family 1, and in a compound heterozygous state with a known pathogenic MME variant (c.467del; p.Pro156Leufs*14) in Family 2. AIMS We aimed to determine the pathogenicity of the MME c.1188+428A>G variant through segregation and splicing analysis. METHODS The splicing impact of the deep intronic MME variant c.1188+428A>G was assessed using an in vitro exon-trapping assay. RESULTS The exon-trapping assay demonstrated that the MME c.1188+428A>G variant created a novel splice donor site resulting in the inclusion of an 83 bp pseudoexon between MME exons 12 and 13. The incorporation of the pseudoexon into MME transcript is predicted to lead to a coding frameshift and premature termination codon (PTC) in MME exon 14 (p.Ala397ProfsTer47). This PTC is likely to result in nonsense mediated decay (NMD) of MME transcript leading to a pathogenic loss-of-function. INTERPRETATION To our knowledge, this is the first report of a pathogenic deep intronic MME variant causing CMT. This is of significance as deep intronic variants are missed using whole exome sequencing screening methods. Individuals with CMT should be reassessed for deep intronic variants, with splicing impacts being considered in relation to the potential pathogenicity of variants.
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Affiliation(s)
- Bianca R Grosz
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
| | - Jevin M Parmar
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Melina Ellis
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
| | - Samantha Bryen
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andre L M Reis
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Garth Nicholson
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Nigel Laing
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Gianina Ravenscroft
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Kishore R Kumar
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
- Translational Neurogenomics Group, Genomic and Inherited Disease Program, The Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Healthcare Campus, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales, Australia
| | - Steve Vucic
- The University of Sydney, Camperdown, New South Wales, Australia
- Brain and Nerve Research Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
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2
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Poudel BH, Fletcher S, Wilton SD, Aung-Htut M. Limb Girdle Muscular Dystrophy Type 2B (LGMD2B): Diagnosis and Therapeutic Possibilities. Int J Mol Sci 2024; 25:5572. [PMID: 38891760 PMCID: PMC11171558 DOI: 10.3390/ijms25115572] [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: 04/18/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Dysferlin is a large transmembrane protein involved in critical cellular processes including membrane repair and vesicle fusion. Mutations in the dysferlin gene (DYSF) can result in rare forms of muscular dystrophy; Miyoshi myopathy; limb girdle muscular dystrophy type 2B (LGMD2B); and distal myopathy. These conditions are collectively known as dysferlinopathies and are caused by more than 600 mutations that have been identified across the DYSF gene to date. In this review, we discuss the key molecular and clinical features of LGMD2B, the causative gene DYSF, and the associated dysferlin protein structure. We also provide an update on current approaches to LGMD2B diagnosis and advances in drug development, including splice switching antisense oligonucleotides. We give a brief update on clinical trials involving adeno-associated viral gene therapy and the current progress on CRISPR/Cas9 mediated therapy for LGMD2B, and then conclude by discussing the prospects of antisense oligomer-based intervention to treat selected mutations causing dysferlinopathies.
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Affiliation(s)
- Bal Hari Poudel
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; (B.H.P.); (S.F.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA 6009, Australia
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu 44618, Nepal
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; (B.H.P.); (S.F.); (S.D.W.)
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; (B.H.P.); (S.F.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA 6009, Australia
| | - May Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; (B.H.P.); (S.F.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA 6009, Australia
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3
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Cipriani V, Vestito L, Magavern EF, Jacobsen JO, Arno G, Behr ER, Benson KA, Bertoli M, Bockenhauer D, Bowl MR, Burley K, Chan LF, Chinnery P, Conlon P, Costa M, Davidson AE, Dawson SJ, Elhassan E, Flanagan SE, Futema M, Gale DP, García-Ruiz S, Corcia CG, Griffin HR, Hambleton S, Hicks AR, Houlden H, Houlston RS, Howles SA, Kleta R, Lekkerkerker I, Lin S, Liskova P, Mitchison H, Morsy H, Mumford AD, Newman WG, Neatu R, O'Toole EA, Ong AC, Pagnamenta AT, Rahman S, Rajan N, Robinson PN, Ryten M, Sadeghi-Alavijeh O, Sayer JA, Shovlin CL, Taylor JC, Teltsh O, Tomlinson I, Tucci A, Turnbull C, van Eerde AM, Ware JS, Watts LM, Webster AR, Westbury SK, Zheng SL, Caulfield M, Smedley D. Rare disease gene association discovery from burden analysis of the 100,000 Genomes Project data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.20.23300294. [PMID: 38196618 PMCID: PMC10775325 DOI: 10.1101/2023.12.20.23300294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
To discover rare disease-gene associations, we developed a gene burden analytical framework and applied it to rare, protein-coding variants from whole genome sequencing of 35,008 cases with rare diseases and their family members recruited to the 100,000 Genomes Project (100KGP). Following in silico triaging of the results, 88 novel associations were identified including 38 with existing experimental evidence. We have published the confirmation of one of these associations, hereditary ataxia with UCHL1 , and independent confirmatory evidence has recently been published for four more. We highlight a further seven compelling associations: hypertrophic cardiomyopathy with DYSF and SLC4A3 where both genes show high/specific heart expression and existing associations to skeletal dystrophies or short QT syndrome respectively; monogenic diabetes with UNC13A with a known role in the regulation of β cells and a mouse model with impaired glucose tolerance; epilepsy with KCNQ1 where a mouse model shows seizures and the existing long QT syndrome association may be linked; early onset Parkinson's disease with RYR1 with existing links to tremor pathophysiology and a mouse model with neurological phenotypes; anterior segment ocular abnormalities associated with POMK showing expression in corneal cells and with a zebrafish model with developmental ocular abnormalities; and cystic kidney disease with COL4A3 showing high renal expression and prior evidence for a digenic or modifying role in renal disease. Confirmation of all 88 associations would lead to potential diagnoses in 456 molecularly undiagnosed cases within the 100KGP, as well as other rare disease patients worldwide, highlighting the clinical impact of a large-scale statistical approach to rare disease gene discovery.
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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5
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Rufibach L, Berger K, Chakravorty S, Emmons S, Long L, Gibson G, Hegde M. Utilization of Targeted RNA-Seq for the Resolution of Variant Pathogenicity and Enhancement of Diagnostic Yield in Dysferlinopathy. J Pers Med 2023; 13:jpm13030520. [PMID: 36983702 PMCID: PMC10056012 DOI: 10.3390/jpm13030520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
For inherited diseases, obtaining a definitive diagnosis is critical for proper disease management, family planning, and participation in clinical trials. This can be challenging for dysferlinopathy due to the significant clinical overlap between the 30+ subtypes of limb–girdle muscular dystrophy (LGMD) and the large number of variants of unknown significance (VUSs) that are identified in the dysferlin gene, DYSF. We performed targeted RNA-Seq using a custom gene-panel in 77 individuals with a clinical/genetic suspicion of dysferlinopathy and evaluated all 111 identified DYSF variants according to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines. This evaluation identified 11 novel DYSF variants and allowed for the classification of 87 DYSF variants as pathogenic/likely pathogenic, 8 likely benign, while 16 variants remained VUSs. By the end of the study, 60 of the 77 cases had a definitive diagnosis of dysferlinopathy, which was a 47% increase in diagnostic yield over the rate at study onset. This data shows the ability of RNA-Seq to assist in variant pathogenicity classification and diagnosis of dysferlinopathy and is, therefore, a type of analysis that should be considered when DNA-based genetic analysis is not sufficient to provide a definitive diagnosis.
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Affiliation(s)
- Laura Rufibach
- Jain Foundation, Inc., Seattle, WA 98115, USA; (S.E.); (L.L.)
- Correspondence:
| | - Kiera Berger
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA; (K.B.); (G.G.)
| | - Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (S.C.); (M.H.)
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sarah Emmons
- Jain Foundation, Inc., Seattle, WA 98115, USA; (S.E.); (L.L.)
| | - Laurie Long
- Jain Foundation, Inc., Seattle, WA 98115, USA; (S.E.); (L.L.)
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA; (K.B.); (G.G.)
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (S.C.); (M.H.)
- PerkinElmer Genomics, Global Laboratory Services, Waltham, MA 02451, USA
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6
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Sun C, Xie Z, Cong L, Xu Y, Liu Z. An in-frame pseudoexon activation caused by a novel deep-intronic variant in the dysferlin gene. Ann Clin Transl Neurol 2023; 10:292-296. [PMID: 36542547 PMCID: PMC9930419 DOI: 10.1002/acn3.51716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
The precise detection and interpretation of pathogenic DYSF variants are sometimes challenging, largely due to rare deep-intronic splice-altering variants. Here, we report on the genetic diagnosis of a male patient with dysferlinopathy. He remained genetically unsolved after routine exonic detection approaches that only detected a novel heterozygous frameshift variant (c.407dup, p.Thr137Tyrfs*11) in DYSF exon 5. Via muscle-derived DYSF mRNA studies, we identified a novel deep-intronic DYSF variant in the other allele (c.1397 + 649C > T), which causing in-frame alterations in DYSF mRNA and protein structure and confirmed his genetic diagnosis of dysferlinopathy. Our study emphasizes the potential role of undetected deep-intronic splice-altering variants in monogenic diseases.
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Affiliation(s)
- Chengyue Sun
- Department of Neurology, Peking University People's Hospital, Beijing, 100044, China
| | - Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Lu Cong
- Department of Neurology, Peking University People's Hospital, Beijing, 100044, China
| | - Yan Xu
- Department of Neurology, Peking University People's Hospital, Beijing, 100044, China
| | - Zunjing Liu
- Department of Neurology, Peking University People's Hospital, Beijing, 100044, China
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7
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Antisense Morpholino-Based In Vitro Correction of a Pseudoexon-Generating Variant in the SGCB Gene. Int J Mol Sci 2022; 23:ijms23179817. [PMID: 36077211 PMCID: PMC9456520 DOI: 10.3390/ijms23179817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
Limb-girdle muscular dystrophies (LGMD) are clinically and genetically heterogenous presentations displaying predominantly proximal muscle weakness due to the loss of skeletal muscle fibers. Beta-sarcoglycanopathy (LGMDR4) results from biallelic molecular defects in SGCB and features pediatric onset with limb-girdle involvement, often complicated by respiratory and heart dysfunction. Here we describe a patient who presented at the age of 12 years reporting high creatine kinase levels and onset of cramps after strenuous exercise. Instrumental investigations, including a muscle biopsy, pointed towards a diagnosis of beta-sarcoglycanopathy. NGS panel sequencing identified two variants in the SGCB gene, one of which (c.243+1548T>C) was found to promote the inclusion of a pseudoexon between exons 2 and 3 in the SGCB transcript. Interestingly, we detected the same genotype in a previously reported LGMDR4 patient, deceased more than twenty years ago, who had escaped molecular diagnosis so far. After the delivery of morpholino oligomers targeting the pseudoexon in patient-specific induced pluripotent stem cells, we observed the correction of the physiological splicing and partial restoration of protein levels. Our findings prompt the analysis of the c.243+1548T>C variant in suspected LGMDR4 patients, especially those harbouring monoallelic SGCB variants, and provide a further example of the efficacy of antisense technology for the correction of molecular defects resulting in splicing abnormalities.
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8
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Ivanova A, Smirnikhina S, Lavrov A. Dysferlinopathies: clinical and genetic variability. Clin Genet 2022; 102:465-473. [PMID: 36029111 DOI: 10.1111/cge.14216] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022]
Abstract
Dysferlinopathies are a clinically heterogeneous group of diseases caused by mutations in the DYSF gene encoding the dysferlin protein. Dysferlin is mostly expressed in muscle tissues and is localized in the sarcolemma, where it performs its main function of resealing and maintaining of the integrity of the cell membrane. At least four forms of dysferlinopathies have been described: Miyoshi myopathy, limb-girdle muscular dystrophy type 2B, distal myopathy with anterior tibial onset, and isolated hyperCKemia. Here we review the clinical features of different forms of dysferlinopathies and attempt to identify genotype-phenotype correlations. Because of the great clinical variability and rarety of the disease and mutations little is known, how different phenotypes develop as a result of different mutations. However missense mutations seem to induce more severe disease than LoF, which is typical for many muscle dystrophies. The role of several specific mutations and possible gene modifiers is also discussed in the paper.
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Affiliation(s)
- Alisa Ivanova
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, Russia
| | | | - Alexander Lavrov
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, Russia
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Folland C, Johnsen R, Gomez AB, Trajanoski D, Davis MR, Moore U, Straub V, Barresi R, Guglieri M, Hayhurst H, Schaefer AM, Laing NG, Lamont PJ, Ravenscroft G. Identification of a novel heterozygous DYSF variant in a large family with a dominantly-inherited dysferlinopathy. Neuropathol Appl Neurobiol 2022; 48:e12846. [PMID: 35962550 DOI: 10.1111/nan.12846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/29/2022] [Accepted: 08/07/2022] [Indexed: 11/27/2022]
Abstract
AIMS Dysferlinopathy is an autosomal recessive muscular dystrophy, caused by bi-allelic variants in the gene encoding dysferlin (DYSF). Onset typically occurs in the second to third decade and is characterised by slowly progressive skeletal muscle weakness and atrophy of the proximal and/or distal muscles of the four limbs. There are rare cases of symptomatic DYSF variant carriers. Here, we report a large family with a dominantly inherited hyperCKaemia and late-onset muscular dystrophy. METHODS AND RESULTS Genetic analysis identified a co-segregating novel DYSF variant [NM_003494.4:c.6207del p.(Tyr2070Metfs*4)]. No secondary variants in DYSF or other dystrophy-related genes were identified on whole genome sequencing and analysis of the proband's DNA. Skeletal muscle involvement was milder and later onset than typical dysferlinopathy presentations; these clinical signs manifested in four individuals, all between the fourth and sixth decades of life. All individuals heterozygous for the c.6207del variant had hyperCKaemia. Histological analysis of skeletal muscle biopsies across three generations showed clear dystrophic signs, including inflammatory infiltrates, regenerating myofibres, increased variability in myofibre size, and internal nuclei. Muscle magnetic resonance imaging revealed fatty replacement of muscle in two individuals. Western blot and immunohistochemical analysis of muscle biopsy demonstrated consistent reduction of dysferlin staining. Allele-specific quantitative PCR analysis of DYSF mRNA from patient muscle found that the variant, localised to the extreme C-terminus of dysferlin, does not activate post-transcriptional mRNA decay. CONCLUSIONS We propose that this inheritance pattern may be underappreciated and that other late-onset muscular dystrophy cases with mono-allelic DYSF variants, particularly C-terminal premature truncation variants, may represent dominant forms of disease.
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Affiliation(s)
- Chiara Folland
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Russell Johnsen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Australia
| | - Adriana Botero Gomez
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Daniel Trajanoski
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Ursula Moore
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Michela Guglieri
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Hannah Hayhurst
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Andrew M Schaefer
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Nigel G Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | | | - Gianina Ravenscroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Perth, WA, Australia
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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11
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Matsuo M. Antisense Oligonucleotide-Mediated Exon-skipping Therapies: Precision Medicine Spreading from Duchenne Muscular Dystrophy. JMA J 2021; 4:232-240. [PMID: 34414317 PMCID: PMC8355726 DOI: 10.31662/jmaj.2021-0019] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/13/2021] [Indexed: 11/12/2022] Open
Abstract
In 1995, we were the first to propose antisense oligonucleotide (ASO)-mediated exon-skipping therapy for the treatment of Duchenne muscular dystrophy (DMD), a noncurable, progressive muscle-wasting disease. DMD is caused by deletion mutations in one or more exons of the DMD gene that shift the translational reading frame and create a premature stop codon, thus prohibiting dystrophin production. The therapy aims to correct out-of-frame mRNAs to produce in-frame transcripts by removing an exon during splicing, with the resumption of dystrophin production. As this treatment is recognized as the most promising, many extensive studies have been performed to develop ASOs that induce the skipping of DMD exons. In 2016, an ASO designed to skip exon 51 was first approved by the Food and Drug Administration, which accelerated studies on the use of ASOs to treat other monogenic diseases. The ease of mRNA editing by ASO-mediated exon skipping has resulted in the further application of exon-skipping therapy to nonmonogenic diseases, such as diabetes mellites. Recently, this precision medicine strategy was drastically transformed for the emergent treatment of only one patient with one ASO, which represents a future aspect of ASO-mediated exon-skipping therapy for extremely rare diseases. Herein, the invention of ASO-mediated exon-skipping therapy for DMD and the current applications of ASO-mediated exon-skipping therapies are reviewed, and future perspectives on this therapeutic strategy are discussed. This overview will encourage studies on ASO-mediated exon-skipping therapy and will especially contribute to the development of treatments for noncurable diseases.
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Affiliation(s)
- Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Department of Physical Rehabilitation and Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Japan
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12
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Zhu F, Zhang F, Hu L, Liu H, Li Y. Integrated Genome and Transcriptome Sequencing to Solve a Neuromuscular Puzzle: Miyoshi Muscular Dystrophy and Early Onset Primary Dystonia in Siblings of the Same Family. Front Genet 2021; 12:672906. [PMID: 34276779 PMCID: PMC8283672 DOI: 10.3389/fgene.2021.672906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/23/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Neuromuscular disorders (NMD), many of which are hereditary, affect muscular function. Due to advances in high-throughput sequencing technologies, the diagnosis of hereditary NMDs has dramatically improved in recent years. METHODS AND RESULTS In this study, we report an family with two siblings exhibiting two different NMD, Miyoshi muscular dystrophy (MMD) and early onset primary dystonia (EOPD). Whole exome sequencing (WES) identified a novel monoallelic frameshift deletion mutation (dysferlin: c.4404delC/p.I1469Sfs∗17) in the Dysferlin gene in the index patient who suffered from MMD. This deletion was inherited from his unaffected father and was carried by his younger sister with EOPD. However, immunostaining staining revealed an absence of dysferlin expression in the proband's muscle tissue and thus suggested the presence of the second underlying mutant allele in dysferlin. Using integrated RNA sequencing (RNA-seq) and whole genome sequencing (WGS) of muscle tissue, a novel deep intronic mutation in dysferlin (dysferlin: c.5341-415A > G) was discovered in the index patient. This mutation caused aberrant mRNA splicing and inclusion of an additional pseudoexon (PE) which we termed PE48.1. This PE was inherited from his unaffected mother. PE48.1 inclusion altered the Dysferlin sequence, causing premature termination of translation. CONCLUSION Using integrated genome and transcriptome sequencing, we discovered hereditary MMD and EOPD affecting two siblings of same family. Our results added further weight to the combined use of RNA-seq and WGS as an important method for detection of deep intronic gene mutations, and suggest that integrated sequencing assays are an effective strategy for the diagnosis of hereditary NMDs.
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Affiliation(s)
- Feng Zhu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengxiao Zhang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lizhi Hu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haowen Liu
- Department of Neurology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yahua Li
- Department of Respiratory Medicine, The Third Hospital of Hebei Medical University, Shijiazhuang, China
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13
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Zhang H, Li Y, Cheng Q, Chen X, Yu Q, Li Z. Abnormal Expression of Dysferlin in Blood Monocytes Supports Primary Dysferlinopathy in Patients Confirmed by Genetic Analyses. Front Neurol 2021; 11:540098. [PMID: 33613410 PMCID: PMC7890250 DOI: 10.3389/fneur.2020.540098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Objective: Dysferlin deficiency causes dysferlinopathy. This study aimed to expand the mutational spectrum of dysferlinopathies, to further study one case with diagnostic ambiguity, and to identify the diagnostic value of dysferlin expression in total peripheral blood mononuclear cells (PBMC). Methods: The clinical and molecular profiles of dysferlinopathies in eight Chinese patients were evaluated. We also conducted magnetic resonance imaging (6/8) and determined dysferlin protein expression in muscle (7/8) and PBMC (3/8). Results: Nine of the 13 DYSF mutations identified were novel. One patient was homozygous for the Gln111Ter mutation by genomic DNA sequencing but was found to be heterozygous by sequencing of cDNA from total PBMC. A daughter of this patient did not carry any Gln111Ter mutation. Abnormal muscle MRI with predominant involvement of the medial gastrocnemius and soleus muscle was observed in 5/6 patients. Dysferlin levels were significantly reduced (immunohistochemistry/immunoblot) or absent (immunohistochemistry) in muscle and total PBMC (26–39%) for most patients. Sarcoplasmic accumulation of dysferlin was detected in one patient. Conclusion: Genomic DNA sequencing detects frequent homozygous mutations, while fewer heterozygous mutations in cDNA are detected after posttranscription. Total PBMC may serve as an alternative to confirm diagnosis and to guide further testing in dysferlinopathies. Our results contribute to the mutational spectrum of dysferlinopathies.
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Affiliation(s)
- Huili Zhang
- Department of Neurology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yaqin Li
- Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qiusheng Cheng
- Department of Neurology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xi Chen
- Department of Neurology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qiuxia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ze Li
- Department of Neurology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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14
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Chakravorty S, Nallamilli BRR, Khadilkar SV, Singla MB, Bhutada A, Dastur R, Gaitonde PS, Rufibach LE, Gloster L, Hegde M. Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent. Front Neurol 2020; 11:559327. [PMID: 33250842 PMCID: PMC7674836 DOI: 10.3389/fneur.2020.559327] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Objective: Inherited myopathies comprise more than 200 different individually rare disease-subtypes, but when combined together they have a high prevalence of 1 in 6,000 individuals across the world. Our goal was to determine for the first time the clinical- and gene-variant spectrum of genetic myopathies in a substantial cohort study of the Indian subcontinent. Methods: In this cohort study, we performed the first large clinical exome sequencing (ES) study with phenotype correlation on 207 clinically well-characterized inherited myopathy-suspected patients from the Indian subcontinent with diverse ethnicities. Results: Clinical-correlation driven definitive molecular diagnosis was established in 49% (101 cases; 95% CI, 42–56%) of patients with the major contributing pathogenicity in either of three genes, GNE (28%; GNE-myopathy), DYSF (25%; Dysferlinopathy), and CAPN3 (19%; Calpainopathy). We identified 65 variant alleles comprising 37 unique variants in these three major genes. Seventy-eight percent of the DYSF patients were homozygous for the detected pathogenic variant, suggesting the need for carrier-testing for autosomal-recessive disorders like Dysferlinopathy that are common in India. We describe the observed clinical spectrum of myopathies including uncommon and rare subtypes in India: Sarcoglycanopathies (SGCA/B/D/G), Collagenopathy (COL6A1/2/3), Anoctaminopathy (ANO5), telethoninopathy (TCAP), Pompe-disease (GAA), Myoadenylate-deaminase-deficiency-myopathy (AMPD1), myotilinopathy (MYOT), laminopathy (LMNA), HSP40-proteinopathy (DNAJB6), Emery-Dreifuss-muscular-dystrophy (EMD), Filaminopathy (FLNC), TRIM32-proteinopathy (TRIM32), POMT1-proteinopathy (POMT1), and Merosin-deficiency-congenital-muscular-dystrophy-type-1 (LAMA2). Thirteen patients harbored pathogenic variants in >1 gene and had unusual clinical features suggesting a possible role of synergistic-heterozygosity/digenic-contribution to disease presentation and progression. Conclusions: Application of clinically correlated ES to myopathy diagnosis has improved our understanding of the clinical and genetic spectrum of different subtypes and their overlaps in Indian patients. This, in turn, will enhance the global gene-variant-disease databases by including data from developing countries/continents for more efficient clinically driven molecular diagnostics.
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Affiliation(s)
- Samya Chakravorty
- Emory University Department of Pediatrics, Atlanta, GA, United States.,Emory University Department of Human Genetics, Atlanta, GA, United States.,Division of Neurosciences, Children's Healthcare of Atlanta, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - Satish Vasant Khadilkar
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | - Madhu Bala Singla
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | | | - Rashna Dastur
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | - Pradnya Satish Gaitonde
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | | | - Logan Gloster
- Emory University Department of Pediatrics, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Madhuri Hegde
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,PerkinElmer Genomics, Global Laboratory Services, Waltham, MA, United States
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15
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Lee SJ, Choi E, Shin S, Park J. Genetically confirmed limb-girdle muscular dystrophy type 2B with DYSF mutation using gene panel sequencing: A case report. Medicine (Baltimore) 2020; 99:e20810. [PMID: 32664072 PMCID: PMC7360247 DOI: 10.1097/md.0000000000020810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RATIONALE The limb-girdle muscular dystrophies (LGMDs) are a heterogeneous group of disorders characterized by progressive proximal muscle weakness and have more than 30 different subtypes linked to specific gene loci, which manifest as highly overlapping and heterogeneous phenotypes. PATIENT CONCERNS A 59-year-old male presented for evaluation of progressive muscle weakness since his late twenties. When he was 38 years old, he had muscle weakness in the upper extremities and had a waddling gait, hyper lordosis of lower back, and anterior pelvic tilt. His gait disturbance and muscle weakness slowly progressed. When he was 55 years old, he could not walk at all and had to use a wheelchair for ambulation. DIAGNOSIS Next-generation sequencing using a custom target capture-based gene panel including specific genes responsible for muscular dystrophy was performed. As a result, the proband was genetically diagnosed as LGMD type 2B, carrying 2 compound heterozygous mutations (NM_003494.3:c.1663C>T, p.Arg555Trp; rs377735262 and NM_003494.3:c.2997G>T, p.Trp999Cys; rs28937581) of the DYSF gene. INTERVENTIONS Physical and occupational therapy were prescribed properly for the first time Bracing and assistive devices were adapted specifically to the patient's deficiencies to preserve mobility and function and prevent contractures. OUTCOMES The patient with LGMD has periodic assessments of physical and occupational therapy for the prevention and management of comorbidities. However, in the 3 years after the gene panel sequencing diagnoses, his weakness was slowly progress and the patient still could not walk. LESSONS Gene panel sequencing allows for the correct recognition of different LGMD subtypes, improving timely treatment, management, and enrolment of molecularly diagnosed individuals in clinical trials.
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Affiliation(s)
| | - Eunseok Choi
- Department of Physical Medicine and Rehabilitation
| | - Soyoung Shin
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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16
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Izumi R, Takahashi T, Suzuki N, Niihori T, Ono H, Nakamura N, Katada S, Kato M, Warita H, Tateyama M, Aoki Y, Aoki M. The genetic profile of dysferlinopathy in a cohort of 209 cases: Genotype-phenotype relationship and a hotspot on the inner DysF domain. Hum Mutat 2020; 41:1540-1554. [PMID: 32400077 DOI: 10.1002/humu.24036] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/27/2022]
Abstract
Dysferlinopathy is a group of autosomal recessive muscular dystrophies caused by variants in the dysferlin gene (DYSF), with variable proximal and distal muscle involvement. We performed DYSF gene analyses of 200 cases suspected of having dysferlinopathy (Cohort 1), and identified diagnostic variants in 129/200 cases, including 19 novel variants. To achieve a comprehensive genetic profile of dysferlinopathy, we analyzed the variant data from 209 affected cases from unrelated 209 families, including 80 previously diagnosed and 129 newly diagnosed cases (Cohort 2). Among the 90 types of variants identified in 209 cases, the NM_003494.3: c.2997G>T; p.Trp999Cys, was the most frequent (96/420; 22.9%), followed by c.1566C>G; p.Tyr522* (45/420; 10.7%) on an allele base. p.Trp999Cys was found in 70/209 cases (33.5%), including 20/104 cases (19.2%) with the Miyoshi muscular phenotype and 43/82 cases (52.4%) with the limb-girdle phenotype. In the analysis of missense variants, p.Trp992Arg, p.Trp999Arg, p.Trp999Cys, p.Ser1000Phe, p.Arg1040Trp, and p.Arg1046His were located in the inner DysF domain, representing in 113/160 missense variants (70.6%). This large cohort highlighted the frequent missense variants located in the inner DysF domain as a hotspot for missense variants among our cohort of 209 cases (>95%, Japanese) and hinted at their potential as targets for future therapeutic strategies.
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Affiliation(s)
- Rumiko Izumi
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toshiaki Takahashi
- Department of Neurology, National Hospital Organization Sendai-Nishitaga Hospital, Sendai, Japan
| | - Naoki Suzuki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroya Ono
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurology, National Hospital Organization Iwate Hospital, Ichinoseki, Japan
| | - Naoko Nakamura
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shinichi Katada
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masaaki Kato
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hitoshi Warita
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Maki Tateyama
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurology, National Hospital Organization Iwate Hospital, Ichinoseki, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
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17
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Patsali P, Mussolino C, Ladas P, Floga A, Kolnagou A, Christou S, Sitarou M, Antoniou MN, Cathomen T, Lederer CW, Kleanthous M. The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements. J Clin Med 2019; 8:jcm8111959. [PMID: 31766235 PMCID: PMC6912506 DOI: 10.3390/jcm8111959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022] Open
Abstract
The common IVSI-110 (G>A) β-thalassemia mutation is a paradigm for intronic disease-causing mutations and their functional repair by non-homologous end joining-mediated disruption. Such mutation-specific repair by disruption of aberrant regulatory elements (DARE) is highly efficient, but to date, no systematic analysis has been performed to evaluate disease-causing mutations as therapeutic targets. Here, DARE was performed in highly characterized erythroid IVSI-110(G>A) transgenic cells and the disruption events were compared with published observations in primary CD34+ cells. DARE achieved the functional correction of β-globin expression equally through the removal of causative mutations and through the removal of context sequences, with disruption events and the restriction of indel events close to the cut site closely resembling those seen in primary cells. Correlation of DNA-, RNA-, and protein-level findings then allowed the extrapolation of findings to other mutations by in silico analyses for potential repair based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9, Cas12a, and transcription activator-like effector nuclease (TALEN) platforms. The high efficiency of DARE and unexpected freedom of target design render the approach potentially suitable for 14 known thalassemia mutations besides IVSI-110(G>A) and put it forward for several prominent mutations causing other inherited diseases. The application of DARE, therefore, has a wide scope for sustainable personalized advanced therapy medicinal product development for thalassemia and beyond.
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Affiliation(s)
- Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center–University of Freiburg, 79106 Freiburg, Germany; (C.M.); (T.C.)
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Petros Ladas
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
| | - Argyro Floga
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
| | - Annita Kolnagou
- Thalassemia Clinic Paphos, Paphos General Hospital, 8100 Paphos, Cyprus;
| | - Soteroula Christou
- Thalassemia Clinic Nicosia, Archbishop Makarios III Hospital, 1474 Nicosia, Cyprus;
| | - Maria Sitarou
- Thalassemia Clinic Larnaca, Larnaca General Hospital, 6301 Larnaca, Cyprus;
| | - Michael N. Antoniou
- Department of Medical and Molecular Genetics, King’s College London, London SE1 9RT, UK;
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center–University of Freiburg, 79106 Freiburg, Germany; (C.M.); (T.C.)
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Carsten Werner Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
- Correspondence: ; Tel.: +357-22-392-764
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
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