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Dofash LNH, Monahan GV, Servián-Morilla E, Rivas E, Faiz F, Sullivan P, Oates E, Clayton J, Taylor RL, Davis MR, Beilharz T, Laing NG, Cabrera-Serrano M, Ravenscroft G. A KLHL40 3' UTR splice-altering variant causes milder NEM8, an under-appreciated disease mechanism. Hum Mol Genet 2023; 32:1127-1136. [PMID: 36322148 DOI: 10.1093/hmg/ddac272] [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] [Received: 06/10/2022] [Revised: 10/04/2022] [Accepted: 10/29/2022] [Indexed: 12/23/2022] Open
Abstract
Nemaline myopathy 8 (NEM8) is typically a severe autosomal recessive disorder associated with variants in the kelch-like family member 40 gene (KLHL40). Common features include fetal akinesia, fractures, contractures, dysphagia, respiratory failure and neonatal death. Here, we describe a 26-year-old man with relatively mild NEM8. He presented with hypotonia and bilateral femur fractures at birth, later developing bilateral Achilles' contractures, scoliosis, and elbow and knee contractures. He had walking difficulties throughout childhood and became wheelchair bound from age 13 after prolonged immobilization. Muscle magnetic resonance imaging at age 13 indicated prominent fat replacement in his pelvic girdle, posterior compartments of thighs and vastus intermedius. Muscle biopsy revealed nemaline bodies and intranuclear rods. RNA sequencing and western blotting of patient skeletal muscle indicated significant reduction in KLHL40 mRNA and protein, respectively. Using gene panel screening, exome sequencing and RNA sequencing, we identified compound heterozygous variants in KLHL40; a truncating 10.9 kb deletion in trans with a likely pathogenic variant (c.*152G > T) in the 3' untranslated region (UTR). Computational tools SpliceAI and Introme predicted the c.*152G > T variant created a cryptic donor splice site. RNA-seq and in vitro analyses indicated that the c.*152G > T variant induces multiple de novo splicing events that likely provoke nonsense mediated decay of KLHL40 mRNA explaining the loss of mRNA expression and protein abundance in the patient. Analysis of 3' UTR variants in ClinVar suggests variants that introduce aberrant 3' UTR splicing may be underrecognized in Mendelian disease. We encourage consideration of this mechanism during variant curation.
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Affiliation(s)
- Lein N H Dofash
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Gavin V Monahan
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Emilia Servián-Morilla
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, Sevilla 41013, Spain
| | - Eloy Rivas
- Department of Pathology, Hospital Universitario Virgen del Rocío Sevilla, Sevilla 41013, Spain
| | - Fathimath Faiz
- Diagnostic Genomics, PathWest, Nedlands, WA 6009, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Emily Oates
- School of Biotechnology & Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2033, Australia
| | - Joshua Clayton
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Rhonda L Taylor
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Mark R Davis
- Diagnostic Genomics, PathWest, Nedlands, WA 6009, Australia
| | - Traude Beilharz
- Development and Stem Cells Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 Victoria, Australia
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Macarena Cabrera-Serrano
- Department of Neurology, Neuromuscular Unit and Instituto de Biomedicina de Sevilla/CSIC, Hospital Universitario Virgen del Rocío, Sevilla 41013, Spain
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia
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Bankoti K, Generotti C, Hwa T, Wang L, O'Malley BW, Li D. Advances and challenges in adeno-associated viral inner-ear gene therapy for sensorineural hearing loss. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 21:209-236. [PMID: 33850952 PMCID: PMC8010215 DOI: 10.1016/j.omtm.2021.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There is growing attention and effort focused on treating the root cause of sensorineural hearing loss rather than managing associated secondary characteristic features. With recent substantial advances in understanding sensorineural hearing-loss mechanisms, gene delivery has emerged as a promising strategy for the biological treatment of hearing loss associated with genetic dysfunction. There are several successful and promising proof-of-principle examples of transgene deliveries in animal models; however, there remains substantial further progress to be made in these avenues before realizing their clinical application in humans. Herein, we review different aspects of development, ongoing preclinical studies, and challenges to the clinical transition of transgene delivery of the inner ear toward the restoration of lost auditory and vestibular function.
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Affiliation(s)
- Kamakshi Bankoti
- Department of Otorhinolaryngology, Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charles Generotti
- Department of Otorhinolaryngology, Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tiffany Hwa
- Department of Otorhinolaryngology, Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lili Wang
- Department of Medicine, Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bert W O'Malley
- Department of Otorhinolaryngology, Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daqing Li
- Department of Otorhinolaryngology, Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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