Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases
Por:
Segarra-Casas A, Domínguez-González C, Natera-de Benito D, Kapetanovic S, Hernández-Laín A, Estévez-Arias B, Llansó L, Ortez-Gonzalez CI, Jou-Munoz C, Martí-Carrera I, López-Marquez A, Rodríguez MJ, González-Mera L, Nedkova V, Fernández-Torrón R, Rodríguez-Santiago B, Jimenez-Mallebrera C, Juntas-Morales R, López-de Munain A, Surrallés J, Nascimento-Osorio A, Gallardo E, Olive-Valls M, Gallano P and González-Quereda L
Publicada:
1 jul 2025
Ahead of Print:
1 may 2025
Resumen:
ObjectiveApproximately half of patients with hereditary myopathies remain without a definitive genetic diagnosis after DNA next-generation sequencing (NGS). Here, we implemented transcriptome analysis of muscle biopsies as a complementary diagnostic tool for patients with muscle disease but no definitive genetic diagnosis after exome sequencing.MethodsIn total, 70 undiagnosed cases with suspected genetic muscular dystrophies or congenital myopathies were included in the study. Muscle RNAseq comprised the analysis of aberrant splicing, aberrant expression, and monoallelic expression. In addition, existing NGS data or variant calling from RNAseq were reanalyzed, and genome sequencing was performed in selected cases. Four aberrant splicing open-source tools were compared and assessed.ResultsRNAseq established a diagnosis in 10/70 patients (14.3%) by identifying aberrant transcripts produced by single nucleotide variants (7/10) or copy number variants (3/10). Reanalysis of NGS data allowed the diagnosis in 9/70 individuals (12.9%). Based on this cohort, FRASER was the tool that reported more splicing outlier events per sample while showing the highest accuracy (81.26%).ConclusionsWe demonstrate the utility of RNAseq in identifying causative variants in muscle diseases. Evaluation of four aberrant splicing tools allowed efficient identification of most pathogenic splicing events, obtaining a manageable number of candidate events for manual inspection, demonstrating feasibility for translation into a clinical setting. We also show how the integration of omic technologies reduces the turnaround time to identify causative variants.
Filiaciones:
Segarra-Casas A:
Join Research Unit on Genomic Medicine Universitat Autonòma de Barcelona-IR SANT PAU, Barcelona, Spain
Genetics Department, Institut de Recerca Sant Pau (IR SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
Genetics and Microbiology Department, Universitat Autonòma de Barcelona, Bellaterra, Spain
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Domínguez-González C:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Disorders Unit, Neurology Department, imas12 Research Institute, Hospital Universitario, Madrid, Spain
Natera-de Benito D:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
Applied Research in Neuromuscular Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
Kapetanovic S:
ALS and Neuromuscular Unit, Department of Neurology, Hospital Universitario Basurto, Bilbao, Spain
Nucleic Acid Therapeutics for Rare Diseases (NAT-RD), BioBizkaia Basque Health Research Institute (IIS BioBizkaia), Barakaldo, Spain
Hernández-Laín A:
Neuropathology Unit, imas12 Research Institute, Hospital Universitario 12 de Octubre, Madrid, Spain
Estévez-Arias B:
Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
Laboratory of Neurogenetics and Molecular Medicine, Center for Genomic Sciences in Medicine, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
Llansó L:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
Ortez-Gonzalez CI:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
Applied Research in Neuromuscular Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
Jou-Munoz C:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Applied Research in Neuromuscular Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
Martí-Carrera I:
Department of Pediatrics, Donostia University Hospital, San Sebastian, Spain
Pediatric Group, BioGipuzkoa Health Research Institute, San Sebastian, Spain
Department of Pediatrics, University of the Basque Country UPV/EHU, San Sebastian, Spain
López-Marquez A:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
Applied Research in Neuromuscular Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
Rodríguez MJ:
Genetics Department, Institut de Recerca Sant Pau (IR SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
González-Mera L:
Neuropathology Unit, Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
Nedkova V:
Neuropathology Unit, Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
Fernández-Torrón R:
Group of Neuromuscular Diseases, Donostia University Hospital, Biodonostia, BioGipuzkoa Health Research Institute, OSAKIDETZA, Donostia-San Sebastián, Spain
CIBERNED Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas-Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), Madrid, Spain
Neurosciences Area, Department of Internal Medicine, Faculty of Medicine, University of Deusto, San Sebastian-Bilbao, Spain
Rodríguez-Santiago B:
Join Research Unit on Genomic Medicine Universitat Autonòma de Barcelona-IR SANT PAU, Barcelona, Spain
Genetics Department, Institut de Recerca Sant Pau (IR SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
Genetics and Microbiology Department, Universitat Autonòma de Barcelona, Bellaterra, Spain
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Jimenez-Mallebrera C:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
Applied Research in Neuromuscular Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
Juntas-Morales R:
Neuromuscular Diseases Unit, European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Department of Neurology, Vall D'hebron University Hospital, Barcelona, Spain
López-de Munain A:
Group of Neuromuscular Diseases, Donostia University Hospital, Biodonostia, BioGipuzkoa Health Research Institute, OSAKIDETZA, Donostia-San Sebastián, Spain
CIBERNED Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas-Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), Madrid, Spain
Neurosciences Area, Department of Internal Medicine, Faculty of Medicine, University of Deusto, San Sebastian-Bilbao, Spain
Group of Neurosciences, Department of Neurosciences, University of the Basque Country UPV-EHU, Donostia-San Sebastián, Spain
Surrallés J:
Join Research Unit on Genomic Medicine Universitat Autonòma de Barcelona-IR SANT PAU, Barcelona, Spain
Genetics Department, Institut de Recerca Sant Pau (IR SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
Genetics and Microbiology Department, Universitat Autonòma de Barcelona, Bellaterra, Spain
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Nascimento-Osorio A:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
Applied Research in Neuromuscular Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
Gallardo E:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
Olive-Valls M:
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
Gallano P:
Join Research Unit on Genomic Medicine Universitat Autonòma de Barcelona-IR SANT PAU, Barcelona, Spain
Genetics Department, Institut de Recerca Sant Pau (IR SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
González-Quereda L:
Join Research Unit on Genomic Medicine Universitat Autonòma de Barcelona-IR SANT PAU, Barcelona, Spain
Genetics Department, Institut de Recerca Sant Pau (IR SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
Genetics and Microbiology Department, Universitat Autonòma de Barcelona, Bellaterra, Spain
Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
Univ Autonoma Barcelona IR St PAU, Join Res Unit Genom Med, Barcelona,
Spain
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Genet Dept,
Barcelona, Spain
Univ Autonoma Barcelona, Genet & Microbiol Dept, Bellaterra, Spain
Inst Salud Carlos III, Ctr Biomed Network Res Rare Dis CIBERER, Madrid,
Hosp Univ, Imas12 Res Inst, Neurol Dept, Neuromuscular Disorders Unit,
Madrid, Spain
Hosp St Joan Deu, Dept Neurol, Neuromuscular Unit, Barcelona, Spain
Inst Recerca St Joan Deu, Appl Res Neuromuscular Dis, Barcelona, Spain
Hosp Univ Basurto, Dept Neurol, ALS & Neuromuscular Unit, Bilbao, Spain
BioBizkaia Basque Hlth Res Inst IIS BioBizkaia, Nucl Acid Therapeut Rare
Dis NAT RD, Baracaldo, Spain
Hosp Univ 12 Octubre, Imas12 Res Inst, Neuropathol Unit, Madrid, Spain
Inst Recerca St Joan Deu, Ctr Genom Sci Med, Lab Neurogenet & Mol Med,
Hosp Santa Creu & Sant Pau, Inst Recerca St Pau IR SANT PAU, Dept
Neurol, Neuromuscular Dis Unit, Barcelona, Spain
Hosp St Joan Deu, Dept Pathol, Barcelona, Spain
Donostia Univ Hosp, Dept Pediat, San Sebastian, Spain
BioGipuzkoa Hlth Res Inst, Pediat Grp, San Sebastian, Spain
Univ Basque Country UPV EHU, Dept Pediat, San Sebastian, Spain
Univ Barcelona, Fac Biol, Dept Genet Microbiol & Stat, Barcelona, Spain
Hosp Bellvitge Princeps Espanya, IDIBELL, Dept Pathol, Neuropathol Unit,
Lhospitalet De Llobregat, Barcelona, Spain
Hosp Bellvitge Princeps Espanya, IDIBELL, Dept Neurol, Neuromuscular
Unit, Lhospitalet De Llobregat, Barcelona, Spain
Donostia Univ Hosp, BioGipuzkoa Hlth Res Inst, Grp Neuromuscular Dis,
Biodonostia,OSAKIDETZA, Donostia San Sebastian, Spain
Inst Salud Carlos III, CIBERNED Ctr Invest Biomed Red Enfermedades
Neurod, CIBER, CIBERNED,ISCIII, Madrid, Spain
Univ Deusto, Fac Med, Dept Internal Med, Neurosci Area, San Sebastian
Bilbao, Spain
Vall Dhebron Univ Hosp, Dept Neurol, Neuromuscular Dis Unit, European
Reference Network Rare Neuromuscular Dis,, Barcelona, Spain
Univ Basque Country UPV EHU, Dept Neurosci, Grp Neurosci, Donostia San
Sebastian, Spain
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