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Radziwonik-Fraczyk W, Elert-Dobkowska E, Karpinski M, Pilch J, Ziora-Jakutowicz K, Kubalska J, Szczesniak D, Stepniak I, Zaremba J, Sulek A. Next generation sequencing panel as an effective approach to genetic testing in patients with a highly variable phenotype of neuromuscular disorders. Neurogenetics 2024; 25:233-247. [PMID: 38758368 PMCID: PMC11249508 DOI: 10.1007/s10048-024-00762-y] [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: 03/19/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
Neuromuscular disorders (NMDs) include a wide range of diseases affecting the peripheral nervous system. The genetic diagnoses are increasingly obtained with using the next generation sequencing (NGS). We applied the custom-design targeted NGS panel including 89 genes, together with genotyping and multiplex ligation-dependent probe amplification (MLPA) to identify a genetic spectrum of NMDs in 52 Polish patients. As a result, the genetic diagnosis was determined by NGS panel in 29 patients so its diagnostic utility is estimated at 55.8%. The most pathogenic variants were found in CLCN1, followed by CAPN3, SCN4A, and SGCA genes. Genotyping of myotonic dystrophy type 1 and 2 (DM1 and DM2) as a secondary approach has been performed. The co-occurrence of CAPN3 and CNBP mutations in one patient as well as DYSF and CNBP mutations in another suggests possibly more complex inheritance as well as expression of a phenotype. In 7 individuals with single nucleotide variant found in NGS testing, the MLPA of the CAPN3 gene was performed detecting the deletion encompassing exons 2-8 in the CAPN3 gene in one patient, confirming recessive limb-girdle muscular dystrophy type 1 (LGMDR1). Thirty patients obtained a genetic diagnosis (57.7%) after using NGS testing, genotyping and MLPA analysis. The study allowed for the identification of 27 known and 4 novel pathogenic/likely pathogenic variants and variants of uncertain significance (VUS) associated with NMDs.In conclusion, the diagnostic approach with diverse molecular techniques enables to broaden the mutational spectrum and maximizes the diagnostic yield. Furthermore, the co-occurrence of DM2 and LGMD has been detected in 2 individuals.
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Affiliation(s)
| | | | | | - Jacek Pilch
- Department of Pediatric Neurology, Medical University of Silesia, Katowice, Poland
| | | | - Jolanta Kubalska
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Dominika Szczesniak
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Iwona Stepniak
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Jacek Zaremba
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Anna Sulek
- Faculty of Medicine, Lazarski University, Warsaw, Poland.
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Aguti S, Gallus GN, Bianchi S, Salvatore S, Rubegni A, Berti G, Formichi P, De Stefano N, Malandrini A, Lopergolo D. Novel Biomarkers for Limb Girdle Muscular Dystrophy (LGMD). Cells 2024; 13:329. [PMID: 38391941 PMCID: PMC10886967 DOI: 10.3390/cells13040329] [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: 12/15/2023] [Revised: 01/22/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
OBJECTIVE To identify novel biomarkers as an alternative diagnostic tool for limb girdle muscular dystrophy (LGMD). BACKGROUND LGMD encompasses a group of muscular dystrophies characterized by proximal muscles weakness, elevated CK levels and dystrophic findings on muscle biopsy. Heterozygous CAPN3 mutations are associated with autosomal dominant LGMD-4, while biallelic mutations can cause autosomal recessive LGMD-1. Diagnosis is currently often based on invasive methods requiring muscle biopsy or blood tests. In most cases Western blotting (WB) analysis from muscle biopsy is essential for a diagnosis, as muscle samples are currently the only known tissues to express the full-length CAPN3 isoform. METHODS We analyzed CAPN3 in a cohort including 60 LGMD patients. Selected patients underwent a complete neurological examination, electromyography, muscle biopsy, and skin biopsies for primary fibroblasts isolation. The amount of CAPN3 was evaluated by WB analysis in muscle and skin tissues. The total RNA isolated from muscle, fibroblast and urine was processed, and cDNA was used for qualitative analysis. The expression of CAPN3 was investigated by qRT-PCR. The CAPN3 3D structure has been visualized and analyzed using PyMOL. RESULTS Among our patients, seven different CAPN3 mutations were detected, of which two were novel. After sequencing CAPN3 transcripts from fibroblast and urine, we detected different CAPN3 isoforms surprisingly including the full-length transcript. We found comparable protein levels from fibroblasts and muscle tissue; in particular, patients harboring a novel CAPN3 mutation showed a 30% reduction in protein compared to controls from both tissues. CONCLUSIONS Our findings showed for the first time the presence of the CAPN3 full-length transcript in urine and skin samples. Moreover, we demonstrated surprisingly comparable CAPN3 protein levels between muscle and skin samples, thus allowing us to hypothesize the use of skin biopsy and probably of urine samples as an alternative less invasive method to assess the amount of CAPN3 when molecular diagnosis turns out to be inconclusive.
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Affiliation(s)
- Sara Aguti
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
| | - Gian Nicola Gallus
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
| | - Silvia Bianchi
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
| | - Simona Salvatore
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
| | - Anna Rubegni
- Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Gianna Berti
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
| | - Patrizia Formichi
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
| | - Nicola De Stefano
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
| | - Alessandro Malandrini
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
| | - Diego Lopergolo
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (S.A.); (G.N.G.); (S.B.); (S.S.); (G.B.); (P.F.); (N.D.S.); (A.M.)
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100 Siena, Italy
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Tomforde M, Steinbach M, Haack TB, Kuhlenbäumer G. Family and literature analysis demonstrates phenotypic effect of two variants in the calpain-3 gene. Neurogenetics 2023; 24:273-278. [PMID: 37589857 PMCID: PMC10545561 DOI: 10.1007/s10048-023-00728-6] [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: 04/27/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Both, recessive (LGMD R1) and dominant (LGMD D4) inheritance occur in calpain 3-related muscular dystrophy. We report a family with calpain-related muscular dystrophy caused by two known variants in the calpain 3 gene (CAPN3, NM_000070.3; (I) c.700G>A, p.Gly234Arg and (II) c.1746-20C>G, p.?). Three family members are compound heterozygous and exhibit a relatively homogeneous phenotype characterized by progressive proximal weakness starting in the third to fourth decade of life in the shoulder girdle and spreading to the legs. Two family members affected only by the p.Gly234Arg heterozygous missense variants show a different phenotype characterized by severe exertional myalgia without overt pareses. We conclude that in our family, the missense variant causes a severe myalgic phenotype without pareses that is aggravated by the second intronic variant and put these findings in the context of previous studies of the same variants.
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Affiliation(s)
- Maike Tomforde
- Department of Neurology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Meike Steinbach
- Department of Neurology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Gregor Kuhlenbäumer
- Department of Neurology, University Medical Center Schleswig-Holstein, Kiel, Germany.
- Department of Neurology, Kiel University, Arnold-Heller Str. 3, D-24105, Kiel, Germany.
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Kalyta K, Stelmaszczyk W, Szczęśniak D, Kotuła L, Dobosz P, Mroczek M. The Spectrum of the Heterozygous Effect in Biallelic Mendelian Diseases-The Symptomatic Heterozygote Issue. Genes (Basel) 2023; 14:1562. [PMID: 37628614 PMCID: PMC10454578 DOI: 10.3390/genes14081562] [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: 06/26/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Heterozygous carriers of pathogenic/likely pathogenic variants in autosomal recessive disorders seem to be asymptomatic. However, in recent years, an increasing number of case reports have suggested that mild and unspecific symptoms can occur in some heterozygotes, as symptomatic heterozygotes have been identified across different disease types, including neurological, neuromuscular, hematological, and pulmonary diseases. The symptoms are usually milder in heterozygotes than in biallelic variants and occur "later in life". The status of symptomatic heterozygotes as separate entities is often disputed, and alternative diagnoses are considered. Indeed, often only a thin line exists between dual, dominant, and recessive modes of inheritance and symptomatic heterozygosity. Interestingly, recent population studies have found global disease effects in heterozygous carriers of some genetic variants. What makes the few heterozygotes symptomatic, while the majority show no symptoms? The molecular basis of this phenomenon is still unknown. Possible explanations include undiscovered deep-splicing variants, genetic and environmental modifiers, digenic/oligogenic inheritance, skewed methylation patterns, and mutational burden. Symptomatic heterozygotes are rarely reported in the literature, mainly because most did not undergo the complete diagnostic procedure, so alternative diagnoses could not be conclusively excluded. However, despite the increasing accessibility to high-throughput technologies, there still seems to be a small group of patients with mild symptoms and just one variant of autosomes in biallelic diseases. Here, we present some examples, the current state of knowledge, and possible explanations for this phenomenon, and thus argue against the existing dominant/recessive classification.
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Affiliation(s)
- Kateryna Kalyta
- School of Life Sciences, FHNW—University of Applied Sciences, 4132 Muttenz, Switzerland;
| | - Weronika Stelmaszczyk
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK;
| | - Dominika Szczęśniak
- Institute of Psychiatry and Neurology in Warsaw, Genetics Department, 02-957 Warsaw, Poland;
| | - Lidia Kotuła
- Department of Genetics, Medical University, 20-080 Lublin, Poland;
| | - Paula Dobosz
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland;
| | - Magdalena Mroczek
- University Hospital Basel, University of Basel, 4031 Basel, Switzerland
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Andoni Urtizberea J, Malfatti E, Carlier PG. [The Second Baltic School of Neuromyology]. Med Sci (Paris) 2022; 38 Hors série n° 1:49-51. [PMID: 36649638 DOI: 10.1051/medsci/2022183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The second edition of the Baltic School of Neuromyology took place on August 26-27, 2022 in Riga (Latvia), in a somewhat peculiar atmosphere given the international situation. An opportunity for the authors to measure the accomplishments made by their Baltic counterparts in the diagnosis and management of neuromuscular disorders, a successful although challenging venture, which led to the integration of three Baltic neuromuscular reference centers to the European Reference Network Euro-NMD. Beyond this form of consecration, and even though a lot remains to be achieved, notably in the field of muscle histopathology, various Baltic teams showed truly remarkable pieces of clinical research that will be useful to the whole myology community worldwide.
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Affiliation(s)
| | - Edoardo Malfatti
- Centre de référence neuromusculaire, CHU Henri Mondor, Créteil, France
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