Identification of key genes and transcription factors in aging mesenchymal stem cells by DNA microarray data

Abstract Background Mesenchymal stem cells (MSCs) are multipotent cells that can be widely used in stem cell therapy. However, few studies have revealed the potential mechanisms of the changes in aging MSC. Materials and methods In this study, microarray data GSE35955 was downloaded from the Gene Expression Omnibus database. Then limma package in R was used to filtrate differentially expressed genes (DEGs), Transcription factors (TFs) were predicted by DCGL package. After predicting TFs, protein-protein interaction (PPI) network and TF-mediated transcriptional regulation network were constructed. The functional and pathway enrichment analysis of screened DEGs, hub genes and TFs were conducted by the DAVID. Results Totally 156 up-regulated DEGs and 343 down-regulated DEGs were obtained. 6 hub genes ( CTNNB1 , PPP2R1A , FYN , MAPK1 , PIK3C2A and EP300 ) were obtained from PPI network. 11 TFs ( CREB1 , CUX1 , EGR1 , EP300 , FOXC1 , HSF2 , MEF2A , PLAU , SP1 , STAT1 and USF1 ) for DEGs were predicted and 2 highly scored co-expression relationships ( EP300-PPP2R1A and STAT1 - FOXC1 ) were acquired from the TF-mediated transcriptional regulation network. Conclusions The discovery of the hub genes, TFs and pathways might contribute to the understanding of genetic and molecular functions of aging-related changes in MSC. Further validation studies on genes and TFs such as CTNNB1 , FYN , PPP2R1A , MAPK1 , EP300 and related biological processes and pathways, including adherens junction, DNA damage caused from oxidative stress, attribution of telomere, MSC differentiation and epigenetic regulation, are urgent for clinical prevention and treatment.