Analysis of Exon Skipping Applicability for Dysferlinopathies

Abstract

Exon skipping, mediated through antisense oligonucleotides (ASOs), is a promising approach to exclude pathogenic variants from the DYSF gene and treat dysferlinopathies. Understanding the applicability of various exon skipping strategies in the total patient population, an analysis not previously performed, can help guide researchers in prioritizing therapies with the broadest potential impact. Using data from the UMD-DYSF database, we evaluated all reported pathogenic variants in dysferlinopathy patients for the applicability of single- or double-exon skipping approaches to exclude the pathogenic variants while maintaining the open reading frame. A total of 61 theoretically applicable exon skipping strategies were identified, with the potential to address 90.0% of the pathogenic variants reported-44.6% through single-exon skipping and 45.3% through double-exon skipping. The most broadly applicable targets include exons 28 and 29 (9.0%), exons 27 and 28 (6.7%), and exons 50 and 51 (5.4%). While numerous theoretically applicable strategies were identified, it remains unclear if the truncated proteins produced through each exon skipping strategy will have improved functionality to alleviate patient symptoms. Further preclinical studies and clinical trials will be essential to determine the effectiveness of these therapies, potentially expanding access to disease-modifying treatments for dysferlinopathy patients.

Keywords: antisense oligonucleotide (ASO); applicability; dysferlinopathy; exon skipping.

Figure 1

A schematic representation of multi-exon skipping to exclude pathogenic variants in asymmetrical exons, flanked by differing intron phases, while preserving the reading frame to enable the production of a functional protein. (A) Without treatment, a nonsense mutation in exon 2 prevents the synthesis of a functional protein. (B) Skipping only exon 2 disrupts the reading frame, leading to a non-functional protein. (C) Skipping both exons 2 and 3 restores the reading frame, resulting in a truncated, yet functional, protein.

Figure 2

A visual representation of all 55 exons of the full-length dysferlin transcript and their respective intron phases (not to scale). Symmetrical exons are shown in light blue and asymmetrical exons are shown in dark blue.

Figure 3

A pie chart illustrating the overall theoretical applicability of single- and double-exon skipping to exclude pathogenic mutations and/or restore the reading frame, resulting in a truncated yet potentially functional dysferlin protein. This analysis is based on the pathogenic variants reported in the UMD-DYSF database. The ten most highly applicable targets are highlighted.