Dušan Lazić1*, Vladimir M. Jovanović2, Jelena Karanović1, Dušanka Savić-Pavićević1 and Bogdan Jovanović1
1 University of Belgrade-Faculty of Biology, Center for Human Molecular Genetics, Belgrade, Serbia;
2 Human Biology and Primate Evolution, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
dusan.lazic [at] bio.bg.ac.rs
Abstract
Myotonic dystrophy type 1 (DM1) is a rare, incurable multisystemic disease, with the main symptoms being skeletal muscle weakness, atrophy, and myotonia. It is caused by CTG expansion in the 3′ UTR of the DMPK gene whose RNA acquires toxic functions and sequesters MBNL proteins, resulting in globally altered RNA metabolism. Despite having many mouse models with different phenotypes, none of them has been able to fully recapitulate the phenotype and molecular pathogenesis of DM1. To map transcriptomic differences among various mouse DM1 models, we systematically analyzed gene expression in their skeletal muscles.
We retrieved all publicly available RNA-seq datasets from mouse models expressing expanded CTG repeats and Mbnl knockout models. Our workflow with unified parameters consisted of preprocessing, and differential gene expression analysis (DESeq2). Additionally, gene co-expression networks (WGCNA), were focused on the CTG repeat-expressing model that was most commonly used and had the largest number of biological replicates (HSALR), where network nodes were represented by a union of dysregulated genes from all analyzed datasets.
In models expressing CTG repeats, the average number of up- (787) and down-regulated (642) genes was greater compared to Mbnl knockouts (676 and 380; log2FC>1, padj>0.05). WGCNA recovered three modules of strongly co-expressed genes (adjacency>0.5). The turquoise module, sharply correlated with muscle type, was associated with extracellular space and muscle development. The midnightblue module consisted of Mup gene family members, while the brown module was associated with the immune response.
Our results revealed pathway changes in DM1 skeletal muscles, where immune pathways in muscle homeostasis and development are intriguing as molecular targets for further investigation. Furthermore, gene expression patterns separated Mbnl knockouts from models expressing CTG repeats, indicating the significance of mouse model choice for basic and preclinical research.
Keywords: Myotonic dystrophy type 1, comparative transcriptomics, mouse models, co-expression networks
Acknowledgment: This research was supported by the Science Fund of the Republic of Serbia, Grant number 7754217, READ-DM1