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Yuen M, Worgan L, Iwanski J, Pappas CT, Joshi H, Churko JM, Arbuckle S, Kirk EP, Zhu Y, Roscioli T, Gregorio CC, Cooper ST. Neonatal-lethal dilated cardiomyopathy due to a homozygous LMOD2 donor splice-site variant. Eur J Hum Genet 2022; 30:450-457. [PMID: 35082396 PMCID: PMC8989920 DOI: 10.1038/s41431-022-01043-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 12/29/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is characterized by cardiac enlargement and impaired ventricular contractility leading to heart failure. A single report identified variants in leiomodin-2 (LMOD2) as a cause of neonatally-lethal DCM. Here, we describe two siblings with DCM who died shortly after birth due to heart failure. Exome sequencing identified a homozygous LMOD2 variant in both siblings, (GRCh38)chr7:g.123656237G > A; NM_207163.2:c.273 + 1G > A, ablating the donor 5' splice-site of intron-1. Pre-mRNA splicing studies and western blot analysis on cDNA derived from proband cardiac tissue, MyoD-transduced proband skin fibroblasts and HEK293 cells transfected with LMOD2 gene constructs established variant-associated absence of canonically spliced LMOD2 mRNA and full-length LMOD2 protein. Immunostaining of proband heart tissue unveiled abnormally short actin-thin filaments. Our data are consistent with LMOD2 c.273 + 1G > A abolishing/reducing LMOD2 transcript expression by: (1) variant-associated perturbation in initiation of transcription due to ablation of the intron-1 donor; and/or (2) degradation of aberrant LMOD2 transcripts (resulting from use of alternative transcription start-sites or cryptic splice-sites) by nonsense-mediated decay. LMOD2 expression is critical for life and the absence of LMOD2 is associated with thin filament shortening and severe cardiac contractile dysfunction. This study describes the first splice-site variant in LMOD2 and confirms the role of LMOD2 variants in DCM.
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Affiliation(s)
- Michaela Yuen
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Westmead, NSW, Australia.
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia.
| | - Lisa Worgan
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Jessika Iwanski
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
| | - Christopher T Pappas
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
| | - Himanshu Joshi
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Jared M Churko
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
| | - Susan Arbuckle
- Department of Histopathology, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Edwin P Kirk
- New South Wales Health Pathology, Randwick Genomics Laboratory, Randwick, NSW, Australia
- School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Ying Zhu
- New South Wales Health Pathology, Randwick Genomics Laboratory, Randwick, NSW, Australia
| | - Tony Roscioli
- New South Wales Health Pathology, Randwick Genomics Laboratory, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, NSW, Australia
| | - Carol C Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, AZ, USA
| | - Sandra T Cooper
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- The Children's Medical Research Institute, Westmead, NSW, Australia
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Recessive DES cardio/myopathy without myofibrillar aggregates: intronic splice variant silences one allele leaving only missense L190P-desmin. Eur J Hum Genet 2019; 27:1267-1273. [PMID: 31024060 DOI: 10.1038/s41431-019-0393-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/04/2019] [Accepted: 03/19/2019] [Indexed: 01/08/2023] Open
Abstract
We establish autosomal recessive DES variants p.(Leu190Pro) and a deep intronic splice variant causing inclusion of a frameshift-inducing artificial exon/intronic fragment, as the likely cause of myopathy with cardiac involvement in female siblings. Both sisters presented in their twenties with slowly progressive limb girdle weakness, severe systolic dysfunction, and progressive, severe respiratory weakness. Desmin is an intermediate filament protein typically associated with autosomal dominant myofibrillar myopathy with cardiac involvement. However a few rare cases of autosomal recessive desminopathy are reported. In this family, a paternal missense p.(Leu190Pro) variant was viewed unlikely to be causative of autosomal dominant desminopathy, as the father and brothers carrying this variant were clinically unaffected. Clinical fit with a DES-related myopathy encouraged closer scrutiny of all DES variants, identifying a maternal deep intronic variant within intron-7, predicted to create a cryptic splice site, which segregated with disease. RNA sequencing and studies of muscle cDNA confirmed the deep intronic variant caused aberrant splicing of an artificial exon/intronic fragment into maternal DES mRNA transcripts, encoding a premature termination codon, and potently activating nonsense-mediate decay (92% paternal DES transcripts, 8% maternal). Western blot showed 60-75% reduction in desmin levels, likely comprised only of missense p.(Leu190Pro) desmin. Biopsy showed fibre size variation with increased central nuclei. Electron microscopy showed extensive myofibrillar disarray, duplication of the basal lamina, but no inclusions or aggregates. This study expands the phenotypic spectrum of recessive DES cardio/myopathy, and emphasizes the continuing importance of muscle biopsy for functional genomics pursuit of 'tricky' variants in neuromuscular conditions.
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Gonorazky H, Liang M, Cummings B, Lek M, Micallef J, Hawkins C, Basran R, Cohn R, Wilson MD, MacArthur D, Marshall CR, Ray PN, Dowling JJ. RNAseq analysis for the diagnosis of muscular dystrophy. Ann Clin Transl Neurol 2015; 3:55-60. [PMID: 26783550 PMCID: PMC4704476 DOI: 10.1002/acn3.267] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 10/25/2015] [Indexed: 12/19/2022] Open
Abstract
The precise genetic cause remains elusive in nearly 50% of patients with presumed neurogenetic disease, representing a significant barrier for clinical care. This is despite significant advances in clinical genetic diagnostics, including the application of whole‐exome sequencing and next‐generation sequencing‐based gene panels. In this study, we identify a deep intronic mutation in the DMD gene in a patient with muscular dystrophy using both conventional and RNAseq‐based transcriptome analyses. The implications of our data are that noncoding mutations likely comprise an important source of unresolved genetic disease and that RNAseq is a powerful platform for detecting such mutations.
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Affiliation(s)
- Hernan Gonorazky
- Division of Neurology Hospital for Sick Children Toronto Ontario Canada M5G A04; Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4
| | - Minggao Liang
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Beryl Cummings
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Monkol Lek
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Johann Micallef
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Cynthia Hawkins
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Raveen Basran
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Ronald Cohn
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Michael D Wilson
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Christian R Marshall
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Peter N Ray
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4; Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - James J Dowling
- Division of Neurology Hospital for Sick Children Toronto Ontario Canada M5G A04; Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
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