Lightning Talk and Poster Presentation GENEMAPPERS 2024

Integrated transcriptomic and genomic analysis to investigate an axonal form of Charcot-Marie-Tooth disease (#9)

Dora Yasar 1 2 , Bianca Grosz 1 2 , Melina Ellis 1 , Anthony Cutrupi 1 2 , Gonzalo Perez-Siles 1 2 , Chris Record 3 , Georgina Samaha 4 , Giorgia Mori 4 , Tracy Chew 4 , Chiara Folland 5 6 , Gina Ravenscroft 5 6 , Ira Deveson 7 , Sanju Chintalaphani 7 , Igor Stevanovski 7 , Andrzej Kochanski 8 , Mary Reilly 3 , Steve Vucic 9 , Marina Kennerson 1 2 10
  1. Northcott Neuroscience Laboratory, ANZAC Research Institute, SLHD, Concord, NSW, Australia
  2. Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
  3. Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, United Kingdom
  4. Australian Biocommons, Sydney Informatics Hub, The University of Sydney, Sydney, NSW, Australia
  5. Centre of Medical Research, University of Western Australia, Nedlands , WA, Australia
  6. Harry Perkins Institute of Medical Research, Perth, WA, Australia
  7. Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
  8. Neuromuscular Unit, Mossakowski Medical Research Institute , Polish Academy of Sciences, Warsaw, Poland
  9. Brain and Nerve Research Centre, Concord Hospital, Sydney, NSW, Australia
  10. Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia

Background: Charcot-Marie-Tooth disease (CMT) is an incurable inherited neuropathy affecting the motor and sensory neurons of the peripheral nervous system. We are investigating a Polish family with autosomal dominant axonal CMT. After both whole-exome and whole-genome sequencing (WGS), genome wide coding mutations and intragenic mutations in known CMT2 genes were excluded. We therefore hypothesize that the pathogenic mutation is non-coding, and causes disease by either disrupting gene regulation, causing pathogenic splicing, or forming aberrant gene fusions. To focus the search for non-coding mutations, linkage analysis was performed which mapped two candidate linkage peaks to chromosomes 8 and 16. Methods: RNA sequencing was performed on patient and control fibroblasts to identify candidate genes. Both long- and short-read WGS was aligned to the T2T reference. Structural variants (SV), repeat expansions (RE), SNVs and indels localising to the linkage regions were then called. To identify and exclude benign variants, short-read WGS data was genotyped against the human Pangenome draft using PanGenie. Variants that could impact short (±250kb either side of dysregulated genes) or long range (>250 kb) gene interactions were assessed using ENCODE and publicly available promoter capture Hi-C data. Results: The 3 dysregulated candidate genes identified in the chromosome 8 linkage region, and 3 of the 7 found in the chromosome 16 linkage region were prioritized and analysed for associated mutations. No abnormal transcripts, SVs or REs segregated with the affected individuals. Two extremely rare non-coding SNVs in regulatory regions with the potential to disrupt two chromosome 16 candidate genes were identified and include iroquois homeobox 3 (IRX3) and proline-rich transmembrane protein 2 (PRRT2). Conclusion: Our transcriptome guided analysis is a powerful strategy to identify non-coding variants likely to be pathogenic. In absence of coding mutations, thorough interrogation of non-coding genome for variants is critical for diagnosing unsolved cases of inherited neuropathy.