Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants

Purpose: Genetic variants causing aberrant premessenger RNA splicing are increasingly being recognized as causal variants in genetic disorders. In this study, we devise standardized practices for polymerase chain reaction (PCR)-based RNA diagnostics using clinically accessible specimens (blood, fibroblasts, urothelia, biopsy). Methods: A total of 74 families with diverse monogenic conditions (31% prenatal-congenital onset, 47% early childhood, and 22% teenage-adult onset) were triaged into PCR-based RNA testing, with comparative RNA sequencing for 19 cases. Results: Informative RNA assay data were obtained for 96% of cases, enabling variant reclassification for 75% variants that can be used for genetic counseling (71%), to inform clinical care (32%) and prenatal counseling (41%). Variant-associated mis-splicing was highly reproducible for 28 cases with samples from ≥2 affected individuals or heterozygotes and 10 cases with ≥2 biospecimens. PCR amplicons encompassing another segregated heterozygous variant was vital for clinical interpretation of 22 of 79 variants to phase RNA splicing events and discern complete from partial mis-splicing. Conclusion: RNA diagnostics enabled provision of a genetic diagnosis for 64% of recruited cases. PCR-based RNA diagnostics has capacity to analyze 81.3% of clinically significant genes, with long amplicons providing an advantage over RNA sequencing to phase RNA splicing events. The Australasian Consortium for RNA Diagnostics (SpliceACORD) provide clinically-endorsed, standardized protocols and recommendations for interpreting RNA assay data

Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy.

Acknowledgements: We acknowledge H. Luque, L. Phillips, J. Casement, O. Magnuson, D. Nguyen and Y. Hu for technical support; R. García-Tercero and C. Díaz for sample collection; E. Zorio, M.E. Leach, D. Bharucha-Goebel, J. Dastgir and C. Konersman for clinical expertise and M. Gautel for helpful advice. We also thank CureCMD for their help in patient recruitment and the patients for donating their samples. The research leading to these results has received funding from the European Community’s Seventh Framework Program (FP7/2007-2013; 2012-305121) ‘Integrated European—omics research project for diagnosis and therapy in rare neuromuscular and neurodegenerative diseases (NEUROMICS)’ (to A. Töpf, V.S., I.T.Z. and F.M.); the European Union’s Horizon 2020 research and innovation program (Solve-RD project; 779257 to A. Töpf); Muscular Dystrophy UK and Muscular Dystrophy Association US (mda577346 to F.M.); Päulon Säätiö (to M. Savarese); Academy of Finland, Sigrid Juselius Foundation (to B.U.); core funding to the Sanger Institute by the Wellcome Trust (098051 and 206194 to E.M.B.-N., J.P. and N.W.); EURO-NMD and Fundación Gemio (to J.J.V., N.M. and P.M.); Intramural Research Grant (2-5, 29-4) for Neurological and Psychiatric Disorders of NCNP and AMED (JP20ek0109490h0001 to I.N.); Inserm, CNRS, University of Strasbourg, Labex INRT (ANR-10-LABX-0030 and ANR-10-IDEX-0002-02), France Génomique (ANR-10-INBS-09) and Fondation Maladies Rares for the ‘Myocapture’ sequencing project, AFM-Téléthon (22734), the European Joint program (EJPRD2019-126 IDOLS-G and ANR-19-RAR4-0002 to J.L., X.L. and V.B.); Intramural funds from the NIH National Institute of Neurological Disorders and Stroke (to C.G.B.); the Dutch Princess Beatrix Muscle Fund and the Dutch Spieren voor Spieren Muscle fund (to C.E.E.); PI16/00316 supported by the Instituto de Salud Carlos III (ISCIII), Madrid and the Generalitat Valenciana (grant PROMETEO/2019/075 to N.M.); Australian NHMRC Neil Hamilton Fairley Early Career Research Fellowship (GNT1090428 to E.C.O.); Starship Foundation A+7340 (to G.L.O.); Early Career Award from the Thrasher Research Fund (to S.S.); U54 HD090255 from the NIH Eunice Kennedy Shriver National Institute of Child Health and Human Development (to A.H.B.); Wellcome Center for Mitochondrial Research (203105/Z/16/Z), the Mitochondrial Disease Patient Cohort (UK; G0800674), the Medical Research Council International Center for Genomic Medicine in Neuromuscular Disease (MR/S005021/1), the Medical Research Council (MR/W019027/1), the Lily Foundation, Mito Foundation, the Pathological Society, the UK NIHR Biomedical Research Center for Ageing and Age-related Disease award to the Newcastle upon Tyne Foundation Hospitals NHS Trust and the UK NHS Highly Specialized Service for Rare Mitochondrial Disorders of Adults and Children (to R.W.T.). MYO–SEQ was funded by Sanofi Genzyme, Ultragenyx, LGMD2I Research Fund, Samantha J Brazzo Foundation, LGMD2D Foundation, Kurt+Peter Foundation, Muscular Dystrophy UK and Coalition to Cure Calpain 3. Sequencing and analysis for relevant families (Supplementary Note) were provided by the Broad Institute of MIT and Harvard Center for Mendelian Genomics (Broad CMG) and were funded by the National Human Genome Research Institute, the National Eye Institute and the National Heart, Lung and Blood Institute under grant UM1 HG008900 and the National Human Genome Research Institute under grants U01HG0011755 and R01 HG009141. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. DNA samples for NeurOmics and MYO–SEQ were provided by the John Walton Muscular Dystrophy Research Center Biobank. This facility is supported by the NIHR Newcastle Biomedical Research Center. Newcastle University’s Electron Microscopy Research Services and equipment Hitachi HT7800 120 kV TEM microscope are funded by BBSRC grant reference BB/R013942/1.Funder: Genzyme (Genzyme Corporation); doi: https://doi.org/10.13039/100004329Funder: Ultragenyx Pharmaceutical (Ultragenyx Pharmaceutical Inc.); doi: https://doi.org/10.13039/100013220Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)); doi: https://doi.org/10.13039/100011199; Grant(s): 2012-305121In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3-/-; ttn.1+/-) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases

Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy

In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3−/−; ttn.1+/−) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases.Peer reviewe

Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy.

Acknowledgements: We acknowledge H. Luque, L. Phillips, J. Casement, O. Magnuson, D. Nguyen and Y. Hu for technical support; R. García-Tercero and C. Díaz for sample collection; E. Zorio, M.E. Leach, D. Bharucha-Goebel, J. Dastgir and C. Konersman for clinical expertise and M. Gautel for helpful advice. We also thank CureCMD for their help in patient recruitment and the patients for donating their samples. The research leading to these results has received funding from the European Community’s Seventh Framework Program (FP7/2007-2013; 2012-305121) ‘Integrated European—omics research project for diagnosis and therapy in rare neuromuscular and neurodegenerative diseases (NEUROMICS)’ (to A. Töpf, V.S., I.T.Z. and F.M.); the European Union’s Horizon 2020 research and innovation program (Solve-RD project; 779257 to A. Töpf); Muscular Dystrophy UK and Muscular Dystrophy Association US (mda577346 to F.M.); Päulon Säätiö (to M. Savarese); Academy of Finland, Sigrid Juselius Foundation (to B.U.); core funding to the Sanger Institute by the Wellcome Trust (098051 and 206194 to E.M.B.-N., J.P. and N.W.); EURO-NMD and Fundación Gemio (to J.J.V., N.M. and P.M.); Intramural Research Grant (2-5, 29-4) for Neurological and Psychiatric Disorders of NCNP and AMED (JP20ek0109490h0001 to I.N.); Inserm, CNRS, University of Strasbourg, Labex INRT (ANR-10-LABX-0030 and ANR-10-IDEX-0002-02), France Génomique (ANR-10-INBS-09) and Fondation Maladies Rares for the ‘Myocapture’ sequencing project, AFM-Téléthon (22734), the European Joint program (EJPRD2019-126 IDOLS-G and ANR-19-RAR4-0002 to J.L., X.L. and V.B.); Intramural funds from the NIH National Institute of Neurological Disorders and Stroke (to C.G.B.); the Dutch Princess Beatrix Muscle Fund and the Dutch Spieren voor Spieren Muscle fund (to C.E.E.); PI16/00316 supported by the Instituto de Salud Carlos III (ISCIII), Madrid and the Generalitat Valenciana (grant PROMETEO/2019/075 to N.M.); Australian NHMRC Neil Hamilton Fairley Early Career Research Fellowship (GNT1090428 to E.C.O.); Starship Foundation A+7340 (to G.L.O.); Early Career Award from the Thrasher Research Fund (to S.S.); U54 HD090255 from the NIH Eunice Kennedy Shriver National Institute of Child Health and Human Development (to A.H.B.); Wellcome Center for Mitochondrial Research (203105/Z/16/Z), the Mitochondrial Disease Patient Cohort (UK; G0800674), the Medical Research Council International Center for Genomic Medicine in Neuromuscular Disease (MR/S005021/1), the Medical Research Council (MR/W019027/1), the Lily Foundation, Mito Foundation, the Pathological Society, the UK NIHR Biomedical Research Center for Ageing and Age-related Disease award to the Newcastle upon Tyne Foundation Hospitals NHS Trust and the UK NHS Highly Specialized Service for Rare Mitochondrial Disorders of Adults and Children (to R.W.T.). MYO–SEQ was funded by Sanofi Genzyme, Ultragenyx, LGMD2I Research Fund, Samantha J Brazzo Foundation, LGMD2D Foundation, Kurt+Peter Foundation, Muscular Dystrophy UK and Coalition to Cure Calpain 3. Sequencing and analysis for relevant families (Supplementary Note) were provided by the Broad Institute of MIT and Harvard Center for Mendelian Genomics (Broad CMG) and were funded by the National Human Genome Research Institute, the National Eye Institute and the National Heart, Lung and Blood Institute under grant UM1 HG008900 and the National Human Genome Research Institute under grants U01HG0011755 and R01 HG009141. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. DNA samples for NeurOmics and MYO–SEQ were provided by the John Walton Muscular Dystrophy Research Center Biobank. This facility is supported by the NIHR Newcastle Biomedical Research Center. Newcastle University’s Electron Microscopy Research Services and equipment Hitachi HT7800 120 kV TEM microscope are funded by BBSRC grant reference BB/R013942/1.Funder: Genzyme (Genzyme Corporation); doi: https://doi.org/10.13039/100004329Funder: Ultragenyx Pharmaceutical (Ultragenyx Pharmaceutical Inc.); doi: https://doi.org/10.13039/100013220Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)); doi: https://doi.org/10.13039/100011199; Grant(s): 2012-305121In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3-/-; ttn.1+/-) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases