Unraveling the molecular etiology of Pompe disease using RNA sequencing

Pompe disease (glycogen storage disease II) is rare, recessive lysosomal storage disease (LSD) characterized by a deficiency in lysosomal acid alpha-glucosidase (GAA), leading to severe, eventually lethal muscular hypotonia affecting patients, as well as cardiomyopathy in the infantile form. However, little of the mechanism between the genetic etiology, and the muscular atrophy affecting patients is currently known.

In this study, RNASeq and miRNASeq were performed on fibroblasts from Pompe patients and healthy controls. These allowed us to identify miRNA-dependent differential gene expression, providing a more complete picture of the molecular disease mechanism. The differentially expressed genes dataset was subjected to a gene ontology (GO) analysis, and compared to known mRNA expression levels in different tissues affected in Pompe patients (e.g. cardiac and skeletal muscle).

In this dataset, 122 genes were identified as differentially expressed (DE) between both groups, of which 48 were downregulated and 74 upregulated. GO analysis revealed that a number of these genes are associated with or regulating muscle development and function, such as BEX1, PPARG and DES. Other DE genes are also involved in several signaling pathways, such as the ERK1/ERK2 cascade and Wnt signaling pathway.

miRNA sequencing revealed 12 differentially expressed miRNAs. Cross-referencing the predicted targets of these miRNAs with the mRNA DE genes list and performing GO analysis on them indicated a few pathways that are potentially affected in Pompe disease. Differential expression of genes such as UTRN and COL4A5, which are also targeted by a number of miRNAs in our results, suggests the involvement of the neuromuscular junction in the disease mechanism. Further studies on the role of DE genes in Pompe patients, and the associated pathways, can provide insight in the molecular mechanism for the muscular atrophy in Pompe patients.