# Comparative Analysis of Splicing Alterations in Three Muscular Dystrophies

## TL;DR

This study compares splicing changes in three muscular dystrophies to identify disease-specific and shared patterns that could serve as biomarkers.

## Contribution

The paper provides a comparative analysis of splicing alterations across three muscular dystrophies using RNA-sequencing data.

## Key findings

- All three myopathies showed upregulation of alternative splicing factors and downregulation of constitutive splicing factors.
- DM1 exhibited more intron retention and alternative exon usage, while FSHD showed more exon skipping.
- Missplicing events were only partially shared between the three myopathies.

## Abstract

Background/Objectives: Missplicing caused by toxic DMPK-mRNA is described as a hallmark of myotonic dystrophy type 1 (DM1). Yet, there is an expressional misregulation of additional splicing factors described in DM1, and missplicing has been observed in other myopathies. Here, we compare the expressional misregulation of splicing factors and the resulting splicing profiles between three different hereditary myopathies. Methods: We used publicly available RNA-sequencing datasets for the three muscular dystrophies—DM1, facioscapulohumeral muscular dystrophy (FSHD) and Emery–Dreifuss muscular dystrophy (EDMD)—to compare the splicing factor expression and missplicing genome-wide using DESeq2 and MAJIQ. Results: Upregulation of alternative splicing factors and downregulation of constitutive splicing factors were detected for all three myopathies, but to different degrees. Correspondingly, the missplicing events were mostly alternative exon usage and skipping events. In DM1, most events were alternative exon usage and intron retention, while exon skipping was prevalent in FSHD, with EDMD being in between the two other myopathies in terms of splice factor regulation as well as missplicing. Accordingly, the missplicing events were only partially shared between these three myopathies, sometimes with the same locus being spliced differently. Conclusions: This indicates a combination of primary (toxic RNA) and more downstream effects (splicing factor expression) resulting in the DM1 missplicing phenotype. Furthermore, this analysis allows the distinction between disease-specific missplicing and general myopathic splicing alteration to be used as biomarkers.