Comparative transcriptome analysis of muscular dystrophy models Large(myd), Dmd(mdx)/Large(myd) and Dmd(mdx): what makes them different?

Abstract

Muscular dystrophies (MD) are a clinically and genetically heterogeneous group of Mendelian diseases. The underlying pathophysiology and phenotypic variability in each form are much more complex, suggesting the involvement of many other genes. Thus, here we studied the whole genome expression profile in muscles from three mice models for MD, at different time points: Dmd(mdx) (mutation in dystrophin gene), Large(myd-/-) (mutation in Large) and Dmd(mdx)/Large(myd-/-) (both mutations). The identification of altered biological functions can contribute to understand diseases and to find prognostic biomarkers and points for therapeutic intervention. We identified a substantial number of differentially expressed genes (DEGs) in each model, reflecting diseases' complexity. The main biological process affected in the three strains was immune system, accounting for the majority of enriched functional categories, followed by degeneration/regeneration and extracellular matrix remodeling processes. The most notable differences were in 21-day-old Dmd(mdx), with a high proportion of DEGs related to its regenerative capacity. A higher number of positive embryonic myosin heavy chain (eMyHC) fibers confirmed this. The new Dmd(mdx)/Large(myd-/-) model did not show a highly different transcriptome from the parental lineages, with a profile closer to Large(myd-/-), but not bearing the same regenerative potential as Dmd(mdx). This is the first report about transcriptome profile of a mouse model for congenital MD and Dmd(mdx)/Large(myd). By comparing the studied profiles, we conclude that alterations in biological functions due to the dystrophic process are very similar, and that the intense regeneration in Dmd(mdx) involves a large number of activated genes, not differentially expressed in the other two strains.

Figure 1

(a) Number of DEGs in the three lineages in relation to wild type. (b) Venn diagrams showing overlapping DEGs between three ages of each mouse lineage. The total number of genes with differential expression in the lineage was calculated considering only those with expressions values >±1.0.

Figure 2

Venn diagrams showing overlapping DEGs between the three dystrophic models. (a) DEGs grouped by lineage. The gray area highlights the genes shared by all animals. (b) DEGs grouped by age. The grey areas highlight the genes specific of each age.

Figure 3

Fold-change values of eight selected significantly upregulated genes over time shared by the three lineages.

Figure 4

Enriched functional categories. Pie charts representing the enriched GO terms upregulated in all mice studied.

Figure 5

Enriched functional categories. Pie charts representing the enriched GO terms upregulated in all mice studied, excluding immune system and inflammation category.

Figure 6

Proportion of positive eMyHC myofibers. (a) Percentage of positive fibers in the muscle of studied mice over time. (b) Representative images of eMyHC staining in muscles sections from 21-day-old animals.