Investigating an Axonal Form of Charcot-Marie-Tooth Neuropathy Using Combined Transcriptomic and Genomic Analysis

Abstract

Charcot-Marie-Tooth disease (CMT) is an inherited peripheral neuropathy (IPN) that leads to the degeneration of the sensory and motor nerves of the peripheral nervous system. We previously reported a Polish family (CMT720) with an autosomal dominant form of axonal CMT. Five suggestive linkage loci were established in this family and all coding mutations in the suggestive linkage regions were excluded using whole genome sequencing (WGS). In this study, we hypothesised that CMT720 is caused by a noncoding mutation. To address the challenge of selecting and analysing noncoding variants, a multi-omics strategy was devised to determine variants worthwhile for future functional analysis. In this project, fine mapping linkage analysis supported two of the five suggestive linkage loci initially reported. By utilising both long and short read WGS and the telomere-to-telomere reference, a full spectrum of variants ranging from single base changes to structural variants were identified in CMT720 patients. Using the diverse set of benign variants from the draft human pangenome and targeting the suggestive linkage regions on chromosome 8 and 16 provided variant filtering power to identify a manageable number of noncoding variants for analysis. Transcriptome profiling of CMT720 patient fibroblasts identified dysregulated gene expression for four positional candidate genes (IRX6, ZNF704, BCL7C, PRRT2). Using publicly available epigenomics data, one of the selected noncoding single nucleotide variants was found to localise within a transcription factor binding site that may potentially cause downregulation of the positional candidate gene PRRT2.

Overall, this study has demonstrated the use of multi-omics analysis in combination with improved sequencing technologies and genomics resources as a powerful strategy to effectively interrogate the noncoding genome in unsolved IPNs.