RNA variant assessment using transactivation and transdifferentiation

• DOI: 10.1016/j.ajhg.2024.06.018
• Publication Date: 2024-07-30T15:10:49Z
• Authors: Emmylou C. Nicola...; Olivia Robinson; Christian Pflueger; Alison Gardner; Mark A. Corbett; Tarin Ritchie; Thessa Kroes; Clare L. van Eyk; Ingrid E. Scheffer; Michael S. Hildeb...; Jean-Vianney Barnier; Véronique Rousseau; David Genevieve; Virginie Haushalter; Amélie Piton; Anne-Sophie Denom...; Ange-Line Bruel; Sophie Nambot; Bertrand Isidor; John Grigg; Tina Gonzalez; Sondhya Ghedia; Rhett G. Marchant; Adam Bournazos; Wui-Kwan Wong; Richard I. Webster; Frances J. Evesson; Kristi J. Jones; Dimitar N. Azmanov; Christopher P. Ba...; Simon C. Barry; Gareth Baynam; Samuel F. Berkovic; John Christodoulou; David J. Coman; Sandra Cooper; Mark A. Corbett; Martin Delatycki; Tracy E. Dudding; Sue Fletcher; Alison E. Gardner; Jozef Gecz; Megan J. Higgins; Michael S. Hildeb...; Lachlan A. Jolly; Ryan Lister; Julie McGaughran; Christian Pflueger; Cathryn Poulton; Tony Roscioli; Ingrid Scheffer H...; Andrew H. Sinclair; Amanda B. Spurdle; Tiong Y. Tan; Clare L. van Eyk; Irina Voineagu; Sandra T. Cooper; Ryan Lister; Jozef Gecz; Lachlan A. Jolly
• Keywords: Transdifferentiation

Understanding the impact of splicing and nonsense variants on RNA is crucial for resolution variant classification as well their suitability precision medicine interventions. This primarily enabled through studies involving transcriptomics followed by targeted assays using isolated from clinically accessible tissues (CATs) such blood or skin affected individuals. Insufficient disease gene expression in CATs does however pose a major barrier to based investigations, which we show relevant 1,436 Mendelian genes. We term these "silent" genes (SMGs), largest portion (36%) are associated with neurological disorders. developed two approaches induce SMG human dermal fibroblasts (HDFs) overcome this limitation, including CRISPR-activation-based transactivation fibroblast-to-neuron transdifferentiation. Initial screens 40 SMGs stimulated our development highly multiplexed system culminating 6- 90,000-fold induction 20/20 (100%) tested HDFs. Transdifferentiation HDFs directly neurons led 193/516 (37.4%) implicated disease. The magnitude isoform diversity following either transdifferentiation was comparable tissues. apply and/or combined short- long-read sequencing investigate that USH2A, SCN1A, DMD, PAK3 have derived Transactivation represent rapid, scalable functional genomic solutions impacting patient cell context.