دورية أكاديمية
RNA variant assessment using transactivation and transdifferentiation.
| العنوان: | RNA variant assessment using transactivation and transdifferentiation. |
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| المؤلفون: | Nicolas-Martinez EC; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia., Robinson O; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia., Pflueger C; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia., Gardner A; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia., Corbett MA; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia., Ritchie T; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia., Kroes T; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia., van Eyk CL; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia., Scheffer IE; Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia., Hildebrand MS; Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia., Barnier JV; Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France., Rousseau V; Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France., Genevieve D; Montpellier University, Inserm U1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics Department, Montpellier Hospital, Montpellier, France., Haushalter V; Genetic Diagnosis Laboratory, Strasbourg University Hospital, Strasbourg, France., Piton A; Genetic Diagnosis Laboratory, Strasbourg University Hospital, Strasbourg, France., Denommé-Pichon AS; CRMRs 'Anomalies du Développement et syndromes malformatifs' et 'Déficiences Intellectuelles de causes rares', Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD 'Génétique des Anomalies du Développement,' FHU-TRANSLAD, University of Burgundy, Dijon, France., Bruel AL; CRMRs 'Anomalies du Développement et syndromes malformatifs' et 'Déficiences Intellectuelles de causes rares', Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD 'Génétique des Anomalies du Développement,' FHU-TRANSLAD, University of Burgundy, Dijon, France., Nambot S; CRMRs 'Anomalies du Développement et syndromes malformatifs' et 'Déficiences Intellectuelles de causes rares', Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD 'Génétique des Anomalies du Développement,' FHU-TRANSLAD, University of Burgundy, Dijon, France., Isidor B; CRMRs 'Anomalies du Développement et syndromes malformatifs' et 'Déficiences Intellectuelles de causes rares', Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD 'Génétique des Anomalies du Développement,' FHU-TRANSLAD, University of Burgundy, Dijon, France., Grigg J; Speciality of Ophthalmology, Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia., Gonzalez T; Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW 2065, Australia., Ghedia S; Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW 2065, Australia., Marchant RG; Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia., Bournazos A; Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia., Wong WK; Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia; Department of Paediatric Neurology, Children's Hospital at Westmead, Sydney, NSW 2000, Australia., Webster RI; Department of Paediatric Neurology, Children's Hospital at Westmead, Sydney, NSW 2000, Australia., Evesson FJ; Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia., Jones KJ; Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia; Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, NSW 2000, Australia., Cooper ST; Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia., Lister R; Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia., Gecz J; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia. Electronic address: jozef.gecz@adelaide.edu.au., Jolly LA; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia. Electronic address: lachlan.jolly@adelaide.edu.au. |
| مؤلفون مشاركون: | PERSYST Investigator Team |
| المصدر: | American journal of human genetics [Am J Hum Genet] 2024 Aug 08; Vol. 111 (8), pp. 1673-1699. Date of Electronic Publication: 2024 Jul 30. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Cell Press Country of Publication: United States NLM ID: 0370475 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1537-6605 (Electronic) Linking ISSN: 00029297 NLM ISO Abbreviation: Am J Hum Genet Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2008- : [Cambridge, MA] : Cell Press Original Publication: Baltimore, American Society of Human Genetics. |
| مواضيع طبية MeSH: | Cell Transdifferentiation*/genetics , Fibroblasts*/metabolism , Fibroblasts*/cytology , Transcriptional Activation* , Neurons*/metabolism , Neurons*/cytology, Humans ; RNA/genetics ; RNA/metabolism ; CRISPR-Cas Systems |
| مستخلص: | Understanding the impact of splicing and nonsense variants on RNA is crucial for the resolution of variant classification as well as their suitability for precision medicine interventions. This is primarily enabled through RNA studies involving transcriptomics followed by targeted assays using RNA isolated from clinically accessible tissues (CATs) such as blood or skin of affected individuals. Insufficient disease gene expression in CATs does however pose a major barrier to RNA based investigations, which we show is relevant to 1,436 Mendelian disease genes. We term these "silent" Mendelian genes (SMGs), the largest portion (36%) of which are associated with neurological disorders. We developed two approaches to induce SMG expression in human dermal fibroblasts (HDFs) to overcome this limitation, including CRISPR-activation-based gene transactivation and fibroblast-to-neuron transdifferentiation. Initial transactivation screens involving 40 SMGs stimulated our development of a highly multiplexed transactivation system culminating in the 6- to 90,000-fold induction of expression of 20/20 (100%) SMGs tested in HDFs. Transdifferentiation of HDFs directly to neurons led to expression of 193/516 (37.4%) of SMGs implicated in neurological disease. The magnitude and isoform diversity of SMG expression following either transactivation or transdifferentiation was comparable to clinically relevant tissues. We apply transdifferentiation and/or gene transactivation combined with short- and long-read RNA sequencing to investigate the impact that variants in USH2A, SCN1A, DMD, and PAK3 have on RNA using HDFs derived from affected individuals. Transactivation and transdifferentiation represent rapid, scalable functional genomic solutions to investigate variants impacting SMGs in the patient cell and genomic context. Competing Interests: Declaration of interests S.T.C. has no paid advisory roles to declare. S.T.C. is a volunteer member of ClinGen Expert Panels: Muscular Dystrophies and Myopathies GCEP and Limb Girdle Muscular Dystrophy VCEP. S.T.C. is named inventor of intellectual property (IP) relating to novel methods and biomarkers to identify DNA variants that alter pre-messenger RNA splicing: (1) PCT no. 2018904348 and (2) Australian Patent no. 2019379868. PCT no. 2019900836. This IP is unrelated to the data and outcomes described within this manuscript. (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.) |
| فهرسة مساهمة: | Investigator: DN Azmanov; CP Barnett; SC Barry; G Baynam; SF Berkovic; J Christodoulou; DJ Coman; S Cooper; MA Corbett; M Delatycki; TE Dudding; S Fletcher; AE Gardner; J Gecz; MJ Higgins; MS Hildebrand; LA Jolly; R Lister; J McGaughran; C Pflueger; C Poulton; T Roscioli; IS Hamish S Scott; AH Sinclair; AB Spurdle; TY Tan; CL van Eyk; I Voineagu |
| المشرفين على المادة: | 63231-63-0 (RNA) |
| تواريخ الأحداث: | Date Created: 20240731 Date Completed: 20240809 Latest Revision: 20240809 |
| رمز التحديث: | 20240812 |
| DOI: | 10.1016/j.ajhg.2024.06.018 |
| PMID: | 39084224 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1537-6605 |
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| DOI: | 10.1016/j.ajhg.2024.06.018 |