miRNA-mRNA Network Regulation of Mesodermal Differentiation from Human Embryonic Stem Cells
YANG Jiwen, QUAN Yingyi, ZHANG Huan, WANG Yongyu*
The embryonic mesoderm cells can differentiate into different types of cells, such as cardiovascular, blood and muscle cells, and the hESCs (human embryonic stem cells)-inducecd mesoderm differentiation provides an important in vitro model to study the molecular mechanisms of differentiation for mesoderm and its derived cells. The expression of miRNA-regulated genes participates in mesoderm cell differentiation through a variety of signaling pathways. Although some regulatory mechanisms of the mesoderm cell differentiation have been revealed, they have not been fully elucidated. Especially, the systemic analysis of expression changes of genes and non-coding RNA, as well as their interaction network. To better understand the mesoderm differentiation mechanisms from hESCs, this study established a potential miRNA-mRNA regulatory network that participates in the mesoderm differentiation from hESCs by regulating multiple signal pathways through bioinformatic analysis. This study first applied second-generation sequencing technology (RNAseq) and microarray to detect and screen the differently expressed miRNAs and protein coding genes during the mesoderm cells differentiation from hESCs. Furthermore, GESA enrichment, GO annotation and KEGG enrichment analysis were performed. Finally, miRNA-mRNA regulatory network was established and key genes were screened, and further confirmed. As a result, a total of 287 and 739 differently expessed miRNAs and genes were identified, respectively. There are 13 064 target genes were predicted from 287 differentially expressed miRNAs. In total, 401 desired genes were obtained by the overlap of 13 064 target genes and 739 differentially expressed genes. GSEA and KEGG analysis showed that these changed genes were involved in many signaling pathways, including Wnt/β-catenin, TGF-β and Hippo signaling pathways. And the miRNA-mRNA regulatory network of the three key signaling pathways were further constructed, showing that 11 genes of Wnt/β-catenin pathway were targeted by 100 miRNAs, 7 genes of the TGF-β pathway were targeted by 59 miRNAs, and 10 genes of the Hippo pathway were targeted by 106 miRNAs. Finally, the expression of some key genes from these three pathways was verified by RT-qPCR. In summary, this study reveals that the Wnt/β-catenin, TGF-β and Hippo signaling pathways play an important regulatory role in the process of mesodermal differentiation from hESCs, which may form a complex network with various miRNA-mRNAs and precisely regulate the mesodermal cell differentiation.
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