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Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation
Human Genomics ( IF 4.5 ) Pub Date : 2020-11-25 , DOI: 10.1186/s40246-020-00293-1
Fatemeh Khodabandehloo 1 , Sara Taleahmad 2 , Reza Aflatoonian 3 , Farzad Rajaei 4 , Zahra Zandieh 5 , Marjan Nassiri-Asl 4 , Mohamadreza Baghaban Eslaminejad 2
Affiliation  

Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine applications. This study aims to evaluate the hub genes and key pathways of differentially expressed genes (DEGs) related to osteogenesis by bioinformatics analysis in three different days. The DEGs were derived from the three different days compared with day 0. Gene expression profiles of GSE37558 were obtained from the Gene Expression Omnibus (GEO) database. A total of 4076 DEGs were acquired on days 8, 12, and 25. Gene ontology (GO) enrichment analysis showed that the non-canonical Wnt signaling pathway and lipopolysaccharide (LPS)-mediated signaling pathway were commonly upregulated DEGs for all 3 days. KEGG pathway analysis indicated that the PI3K-Akt and focal adhesion were also commonly upregulated DEGs for all 3 days. Ten hub genes were identified by CytoHubba on days 8, 12, and 25. Then, we focused on the association of these hub genes with the Wnt pathways that had been enriched from the protein-protein interaction (PPI) by the Cytoscape plugin MCODE. These findings suggested further insights into the roles of the PI3K/AKT and Wnt pathways and their association with osteogenesis. In addition, the stem cell microenvironment via growth factors, extracellular matrix (ECM), IGF1, IGF2, LPS, and Wnt most likely affect osteogenesis by PI3K/AKT.

中文翻译:

微阵列分析鉴定成骨分化过程中差异基因表达的关键通路和相互作用网络

成人骨髓间充质干细胞 (BM-MSC) 是多能干细胞,可以分化为三个谱系。它们是基于细胞的治疗和再生医学应用的合适来源。本研究旨在通过生物信息学分析在三天内评估与成骨相关的差异表达基因(DEGs)的枢纽基因和关键通路。与第 0 天相比,DEG 来自三个不同的天数。 GSE37558 的基因表达谱是从基因表达综合 (GEO) 数据库中获得的。在第 8、12 和 25 天共获得 4076 个 DEG。基因本体 (GO) 富集分析表明,非经典 Wnt 信号通路和脂多糖 (LPS) 介导的信号通路在所有 3 天中普遍上调。KEGG 通路分析表明 PI3K-Akt 和粘着斑在所有 3 天内也是普遍上调的 DEG。CytoHubba 在第 8、12 和 25 天鉴定了 10 个中枢基因。然后,我们关注这些中枢基因与通过 Cytoscape 插件 MCODE 从蛋白质-蛋白质相互作用 (PPI) 中富集的 Wnt 通路的关联。这些发现表明对 PI3K/AKT 和 Wnt 通路的作用及其与成骨的关联有进一步的了解。此外,干细胞微环境通过生长因子、细胞外基质 (ECM)、IGF1、IGF2、LPS 和 Wnt 最有可能通过 PI3K/AKT 影响成骨。我们专注于这些枢纽基因与通过 Cytoscape 插件 MCODE 从蛋白质-蛋白质相互作用 (PPI) 中丰富的 Wnt 通路的关联。这些发现表明对 PI3K/AKT 和 Wnt 通路的作用及其与成骨的关联有进一步的了解。此外,干细胞微环境通过生长因子、细胞外基质 (ECM)、IGF1、IGF2、LPS 和 Wnt 最有可能通过 PI3K/AKT 影响成骨。我们专注于这些枢纽基因与通过 Cytoscape 插件 MCODE 从蛋白质-蛋白质相互作用 (PPI) 中丰富的 Wnt 通路的关联。这些发现表明对 PI3K/AKT 和 Wnt 通路的作用及其与成骨的关联有进一步的了解。此外,干细胞微环境通过生长因子、细胞外基质 (ECM)、IGF1、IGF2、LPS 和 Wnt 最有可能通过 PI3K/AKT 影响成骨。
更新日期:2020-11-25
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