Identification and Validation of Hub Genes and Construction of miRNA-Gene and Transcription Factor-Gene Networks in Adipogenesis of Mesenchymal Stem Cells

Abstract

Background. Adipogenic differentiation stands as a crucial pathway in the range of differentiation options for mesenchymal stem cells (MSCs), carrying significant importance in the fields of regenerative medicine and the treatment of conditions such as obesity and osteoporosis. However, the exact mechanisms that control the adipogenic differentiation of MSCs are not yet fully understood. Materials and Methods. We procured datasets, namely GSE36923, GSE80614, GSE107789, and GSE113253, from the Gene Expression Omnibus database. These datasets enabled us to perform a systematic analysis, including the identification of differentially expressed genes (DEGs) pre- and postadipogenic differentiation in MSCs. Subsequently, we conducted an exhaustive analysis of DEGs common to all four datasets. To gain further insights, we subjected these overlapped DEGs to comprehensive gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses. Following the construction of protein–protein interaction (PPI) networks, we meticulously identified a cohort of hub genes pivotal to the adipogenic differentiation process and validated them using real-time quantitative polymerase chain reaction. Subsequently, we ventured into the construction of miRNA-gene and TF–gene interaction networks. Results. Our rigorous analysis revealed a total of 18 upregulated DEGs and 12 downregulated DEGs that consistently appeared across all four datasets. Notably, the peroxisome proliferator-activated receptor signaling pathway, regulation of lipolysis in adipocytes, and the adipocytokine signaling pathway emerged as the top-ranking pathways significantly implicated in the regulation of these DEGs. Subsequent to the construction of the PPI network, we identified and validated 10 key node genes, namely IL6, FABP4, ADIPOQ, LPL, PLIN1, RBP4, ACACB, NT5E, KRT19, and G0S2. Our endeavor to construct miRNA–gene interaction networks led to the discovery of the top 10 pivotal miRNAs, including hsa-mir-27a-3p, hsa-let-7b-5p, hsa-mir-1-3p, hsa-mir-124-3p, hsa-mir-155-5p, hsa-mir-16-5p, hsa-mir-101-3p, hsa-mir-21-3p, hsa-mir-146a-5p, and hsa-mir-148b-3p. Furthermore, the construction of TF–gene interaction networks revealed the top 10 critical TFs: ZNF501, ZNF512, YY1, EZH2, ZFP37, ZNF2, SOX13, MXD3, ELF3, and TFDP1. Conclusions. In summary, our comprehensive study has successfully unraveled the pivotal hub genes that govern the adipogenesis of MSCs. Moreover, the meticulously constructed miRNA-gene and TF–gene interaction networks are poised to significantly augment our comprehension of the intricacies underlying MSC adipogenic differentiation, thus providing a robust foundation for future advances in regenerative biology.