Investigation of hub genes involved in diabetic nephropathy using biological informatics methods
ANNALS OF TRANSLATIONAL MEDICINE
Authors: Li, Zhanting; Liu, Jianxin; Wang, Weiwei; Zhao, Yunchun; Yang, Dengfeng; Geng, Xiaodong
Abstract
Background: The aim of this study was to find genes with significantly aberrant expression in diabetic nephropathy (DINT) and determine their underlying mechanisms. Methods: GSE30528 and GSE1009 were obtained by querying the Gene Expression Omnibus (GEO) database. The difference in target gene expression between normal renal tissues and kidney tissues in patients with DN was screened by using the GEO2R tool. Using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database, differentially expressed genes (DEGs) were analysed by Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Then, the protein-protein interactions (PPIs) of DEGs were analyzed by Cytoscape with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the hub genes in this PPI network were recognized by centrality analysis. Results: There were 110 genes with significant expression differences between normal and DN tissues. The differences in gene expression involved many functions and expression pathways, such as the formation of the extracellular matrix and the construction of the extracellular domain. The correlation analysis and subgroup analysis of 14 hub genes and the clinical characteristics of DN showed that CTGF, ALB, PDPN, FLT1, IGF1, WT1, GJA1, IGFBP2, FGF9, BMP2, FGF1, BMP7, VEGFA, and TGFBR3 may be involved in the progression of DN. Conclusions: We confirmed the differentially expressed hub genes and other genes which may be the novel biomarker and target candidates in DNT.
MGP Promotes Colon Cancer Proliferation by Activating the NF-kappa B Pathway through Upregulation of the Calcium Signaling Pathway
MOLECULAR THERAPY-ONCOLYTICS
Authors: Li, Xueqing; Wei, Rui; Wang, Mizhu; Ma, Li; Zhang, Zheng; Chen, Lei; Guo, Qingdong; Guo, Shuilong; Zhu, Shengtao; Zhang, Shutian; Min, Li
Abstract
Matrix Gla protein (MGP), an extracellular matrix protein, is mainly associated with the inhibition of calcification in skeleton, coronary artery, and kidney, and more recently it has also been implicated in cancer. However, the biological function of MGP inside cancer cells and its role in colon cancer (CC) remain largely unknown. MGP expression and its association with clinicopathologic characteristics in CC were analyzed by immunohistochemistry and verified by Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets. The effects of MGP on CC cell proliferation were evaluated via knockdown and overexpression experiments in vitro. Mechanisms of MGP in CC were explored by western blots, quantitative real-time PCR, Fluo-3 AM staining, Rhod-2 AM staining, immunofluorescence, and other techniques. Our study confirmed that MGP was upregulated in different stages of CC and associated with a worse prognosis. MGP could enrich intracellular free Ca2+ concentration and promote nuclear factor kappa B (NF-kappa B)/p65 phosphorylation, activating the expression of c-MYC, ICAM-1, and VEGFA. Furthermore, the reduction of intracellular free Ca(2+ )concentration and the subsequent growth inhibition effect on CC cells induced by small interfering RNA targeting MGP (siMGP) could be rescued by a higher calcium concentration environment. Therefore, MGP promotes the growth and proliferation of CC cells by enriching intracellular calcium concentration and activating the NF-kappa B pathway, and it could serve as a potential prognostic biomarker in CC patients.