Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A

• Published in: bioRxiv
• Main Authors: Stergachis, Andrew B, Blue, Elizabeth E, Gillentine, Madelyn A, Wang, Lee-Kai, Schwarze, Ulrike, Cortés, Adriana Sedeño, Ranchalis, Jane, Allworth, Aimee, Bland, Austin E, Chanprasert, Sirisak, Chen, Jingheng, Doherty, Daniel, Folta, Andrew B, Glass, Ian, Horike-Pyne, Martha, Huang, Alden Y, Khan, Alyna T, Leppig, Kathleen A, Miller, Danny E, Mirzaa, Ghayda, Parhin, Azma, Raskind, Wendy, Rosenthal, Elisabeth A, Sheppeard, Sam, Strohbehn, Samuel, Sybert, Virginia P, Tran, Thao T, Wener, Mark, Byers, Peter H, Nelson, Stanley F, Bamshad, Michael J, Dipple, Katrina M, Jarvik, Gail P, Hoppins, Suzanne, Hisama, Fuki M
• Format: Journal Article Paper
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 07.02.2023; Cold Spring Harbor Laboratory
• Edition: 1.1
• Subjects: Charcot-Marie-Tooth disease; Fibroblasts; Genetics; Mitochondria; mRNA turnover; Neuropathy; Nonsense-mediated mRNA decay; Open reading frames
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2023.02.07.526487

Transcript sequencing of patient derived samples has been shown to improve the diagnostic yield for solving cases of likely Mendelian disorders, yet the added benefit of full-length long-read transcript sequencing is largely unexplored. We applied short-read and full-length isoform cDNA sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis. We identified an intronic homozygous c.600-31T>G variant that disrupts a branch point critical for intron 6 spicing. Full-length long-read isoform cDNA sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates five distinct altered splicing transcripts. All five altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length transcripts are still produced, this branch point variant results in deficient MFN2 protein levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A). This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.