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RNA sequencing identifies gene expression profile changes associated with β-estradiol treatment in U2OS osteosarcoma cells

Authors Chen B, Liu Z, Zhang J, Wang H, Yu B

Received 22 February 2017

Accepted for publication 27 May 2017

Published 11 July 2017 Volume 2017:10 Pages 3421—3427

DOI https://doi.org/10.2147/OTT.S135396

Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Narasimha Reddy Parine

Peer reviewer comments 2

Editor who approved publication: Dr Tohru Yamada

Bin Chen, Zude Liu, Jidong Zhang, Hantao Wang, Bo Yu

Department of Orthopedic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China

Abstract: This study was conducted to identify gene expression profile changes associated with β-estradiol (E2) treatment in U2OS osteosarcoma cells by high-throughput RNA sequencing (RNA-seq). Two U2OS cell samples treated with E2 (15 µmol/L) and two untreated control U2OS cell samples were subjected to RNA-seq. Differentially expressed genes (DEGs) between the groups were identified, and main biological process enrichment was performed using gene ontology (GO) analysis. A protein–protein interaction (PPI) network was constructed using Cytoscape based on the Human Protein Reference Database. Finally, NFKB1 expression was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). The map ratios of the four sequenced samples were >65%. In total, 128 upregulated and 92 downregulated DEGs were identified in E2 samples. After GO enrichment, the downregulated DEGs, such as AKT1, were found to be mainly enriched in cell cycle processes, whereas the upregulated DEGs, such as NFKB1, were involved in the regulation of gene expression. Moreover, AKT1 (degree =117) and NFKB1 (degree =72) were key nodes with the highest degrees in the PPI network. Similarly, the results of qRT-PCR confirmed that E2 upregulated NFKB1 expression. The results suggest that E2 upregulates the expression of NFKB1, ATF7IP, and HDAC5, all of which are involved in the regulation of gene expression and transcription, but downregulates that of TCF7L2, ALCAM, and AKT, which are involved in Wnt receptor signaling through β-catenin and morphogenesis in U2OS osteosarcoma cells.

Keywords:
differentially expressed genes, Wnt receptor signaling, β-catenin, protein-protein interaction network

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