Identiﬁcation of potential key genes associated with termination phase of rat liver regeneration through microarray analysis
1Department of Hepatobiliary Surgery, Secondary Aﬃliated Hospital of Chongqing Medical University, 400010 Chongqing, China
Submitted: 28 January 2021 Accepted: 12 March 2021
Online publish date: 18 June 2021
† These authors contributed equally.
Background and objective: Liver regeneration (LR) is a complex process inﬂuenced by various genes and pathways, the majority of the of research on LR focus on the initiation and proliferation phase while studies on termination phase is lacking. We aimed to identify potential genes and reveal the underlying the molecular mechanisms involved in the precise regulation of liver size during the termination phase of LR.
Materials and methods: We obtained the rat liver tissue gene datasets (GSE63742) collected following partial hepatectomy (PH) from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI), from which, this study screened the late stage LR samples (7 days post-PH) using the R/Bioconductor packages for the identiﬁcation of differentially expressed genes (DEGs). Afterwards, we performed enrichment analysis using the database for annotation visualization and integrated discovery (DAVID) online tool. Moreover, the Search Tool for the Retrieval of Interacting proteins (STRING) database was employed to construct protein-protein interaction (PPI) networks based on those identiﬁed DEGs; the PPI network was then used by Cytoscape software to predict hub genes and nodes. Animal experimentation (Rat PH model) was performed to acquire liver tissues which were then used for western blot analysis to verify our results.
Results: The present study identiﬁed together 74 signiﬁcant DEGs, among which, 51 showed up-regulation while 23 presented as down-regulated. As revealed by KEGG pathway enrichment analysis, DEGs were mostly related to pathways such as retinol metabolism, steroid hormone synthesis, transforming growth factor-β (TGF-β) and mitogen-activated protein kinase (MAPK) signaling. In addition, as suggested by GO enrichment analysis, DEGs were mostly related to the cyclooxygenase P450 pathway, negative regulation of Notch signaling pathway, aromatase activity, steroid hydroxylase activity, exosomes, and extracellular domain. Analyses based on STRING database and Cytoscape software identiﬁed genes like Ste2 and Btg2 as the hub genes in the termination stage LR. The obtained results were conﬁrmed by Western blot analysis.
Conclusions: Taken together, the microarray analysis in this study suggests that DEGs such as Ste2 and Btg2 are the hub genes, which are associated with the regulation of termination stage LR, while the molecular mechanisms are possibly related to the MAPK and TGF-β signal transduction pathways.
Liver regeneration; Differentially expressed genes; Enrichment analysis; Protein-protein interaction networks
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