High throughput analysis to identify key gene molecules that inhibit adipogenic differentiation and promote osteogenic differentiation of human mesenchymal stem cells

The present study investigated the key genes, which cause switch from adipogenic to osteogenic differentiation of human mesenchymal stem cells (hMSCs). The transcriptomic profile of hMSCs samples were collected from Array Express database. Differential expression network was constructed by calculating the Pearson's correlation coefficient and ranked according to their topological features. The top 5% genes with degree ≥2 were selected as ego genes. Following the KEGG pathway enrichment analysis and the relevant miRNAs prediction, the miRNA-mRNA-pathway networks were constructed by combining the miRNA-mRNA pairs and mRNA-pathway pairs together. In total, we obtained 84, 119, 94 and 97 ego-genes in B, BI, BT and BTI groups, and DLGAP5, DLGAP5, NUSAP1 and NDC80 were the ego-genes with the highest z-score of each group, respectively. Beginning from each ego-gene, we identified 2 significant ego-modules with gene size ≥4 in group BI, and the ego-genes were PBK and NCOA3, respectively. Through KEGG pathway analysis, we found that most of the pathways enriched by ego-genes were associated with gene replication and repair, and cell proliferation. According to the miRNA prediction results, we found that some of the predicted miRNAs have been validated to be the regulatory miRNAs of these corresponding mRNAs. Finally we constructed a miRNA-mRNA-pathway network by integrating the miRNA-mRNA and mRNA-pathway pairs together. The constructed network gives us a more comprehensive understanding of the mechanism of osteogenic differentiation of hMSCs.