Screening for genes, miRNAs and transcription factors of adipogenic differentiation and dedifferentiation of mesenchymal stem cells

BACKGROUND: The purpose of present study was to reveal the molecular mechanisms responsible for both adipogenic differentiation and dedifferentiation of mesenchymal stem cells (MSCs). METHODS: Microarray data GSE36923 were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between adipogenically differentiated cells vs undifferentiated bone marrow-derived MSCs, adipogenically differentiated cells vs dedifferentiated cells samples at day 7 and adipogenically differentiated cells vs dedifferentiated cells samples at day 35 were screened, and overlapped DEGs across the three groups were analyzed. The underlying functions of the upregulated and downregulated DEGs were investigated by Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The protein–protein interaction network was constructed, and hub genes were obtained subsequently. Hub genes were verified with GSE113253 dataset, and then miRNA-gene network and TF-gene network were constructed. RESULTS: A total of 284 upregulated DEGs and 376 downregulated DEGs overlapped across the three groups. PPAR signaling pathway, AMPK signaling pathway, insulin signaling pathway, carbon metabolism, pyruvate metabolism, fatty acid metabolism, regulation of lipolysis in adipocytes, biosynthesis of amino acids, citrate cycle (TCA cycle) and 2-Oxocarboxylic acid metabolism were the top 10 pathways involving in the upregulated DEGs, and graft-versus-host disease, allograft rejection, viral myocarditis, cell adhesion molecules, phagosome, type I diabetes mellitus, antigen processing and presentation, autoimmune thyroid disease, intestinal immune network for IgA production and rheumatoid arthritis were the top 10 pathways in downregulated DEGs. After validation, the 8 hub genes were IL6, PPARG, CCL2, FASN, CEBPA, ADIPOQ, FABP4 and LIPE. Ten key miRNAs were hsa-mir-27a-3p, hsa-mir-182-5p, hsa-mir-7-5p, hsa-mir-16-5p, hsa-mir-1-3p, hsa-mir-155-5p, hsa-mir-21-3p, hsa-mir-34a-5p, hsa-mir-27a-5p and hsa-mir-30c-5p, and 10 key TFs were TFDP1, GTF2A2, ZNF584, NRF1, ZNF512, NFRKB, CEBPG, KLF16, GLIS2 and MXD4. CONCLUSION: Our study constructed miRNA-gene network and TF-gene network involved in both adipogenic differentiation and dedifferentiation of MSCs, contributing to enhancing the efficiency of MSCs transplantation in soft tissue defect repair and developing more potent remedies for adipogenesis-related skeletal disorders. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13018-023-03514-0.