Comparison of gene expression between human and mouse iPSC-derived cardiomyocytes for stem cell therapies of cardiovascular defects via bioinformatic analysis

Abstract

Abstract Background Preclinical studies have demonstrated the potential use of induced pluripotent stem cells (iPSCs) to treat cardiovascular disease (CVD). In vivo preclinical studies conducted on animal models (murine, porcine, guinea pig, etc.) have employed either syngeneic or human-derived iPSCs. However, no study has been carried out to investigate and report the key genetic differences between the human and animal-derived iPSCs. Our study analysed the gene expression profile and molecular pathway patterns underlying the differentiation of both human and mouse iPSCs to iPSC-cardiomyocytes (iPSC-CMs), and the differences between them via bioinformatic analysis. Method Data sets were downloaded from the Gene Expression Omnibus (GEO) database and included both human and mouse models, and the data for undifferentiated iPSCs and iPSC-CMs were isolated from each. Differentially expressed genes (DEGs) were screened and then analysed. The website g:Profiler was used to obtain the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Protein-protein interaction (PPI) networks of the DEGs were constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software. The subclusters were then extracted from the PPI network for further analysis. Results iPSC-derived cardiomyocytes expressed many genes related to vascular, endothelial, and smooth muscle repair in the human iPSC-CMs, and prevention of calcification in the mouse iPSC-CMs with clear differences in gene expression, which will affect how iPSCs act in research. Especially in the human iPSC-CMs, and also prevention of calcification processes in the mouse data. The identified differences in gene expression of iPSCs derived from the two species suggests that in vivo studies using mouse iPSC-CMs may not reflect those in humans. Conclusion The study provides new insights into the key genes related to the iPSCs, including genes related to angiogenesis, calcification, and striated muscle, endothelium, and bone formation. Moreover, the clear differences between both mouse and human-derived iPSCs have been identified, which could be used as new evidence and guidance for developing novel targeted therapy strategies to improve the therapeutic effects of iPSC treatment in cardiovascular defects.

Keywords

• Bioinformatics
• iPSCs
• Cardiomyocytes
• Enrichment analysis
• Cardiovascular disease