Identification of KHSRP-Regulated RNAs in Esophageal Cancer by Integrated Bioinformatics Analysis.

Publisher: Mary Ann Liebert, Inc Country of Publication: United States NLM ID: 9605408 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1557-8852 (Electronic) Linking ISSN: 10849785 NLM ISO Abbreviation: Cancer Biother Radiopharm Subsets: MEDLINE

Original Publication: Larchmont, NY : Mary Ann Liebert, Inc., c1996-

Esophageal Neoplasms/*genetics ; MicroRNAs/*genetics ; RNA, Long Noncoding/*genetics ; RNA-Binding Proteins/*genetics ; Trans-Activators/*genetics; Cell Cycle Proteins/genetics ; Computational Biology ; Databases, Genetic ; Gene Expression Regulation, Neoplastic ; Humans ; Protein Serine-Threonine Kinases/genetics ; Proto-Oncogene Proteins/genetics ; RNA, Messenger ; Survivin/genetics ; Up-Regulation ; Polo-Like Kinase 1

Background: The objective of this study was to identify key molecules that included long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs involved in esophageal cancer with KH-type splicing regulatory protein (KHSRP) knockdown. Materials and Methods: GSE99422 and GSE99423 from Gene Expression Omnibus database were extracted. After differentially expressed analysis of miRNAs, lncRNAs, and mRNAs, the lncRNAs-mRNAs interaction was obtained. Then the protein-protein interaction (PPI) network and module analyses were performed for differentially expressed mRNAs (DEmRNAs). Combined with miRWalk tool and DIANA-LncBase tool, regulating relationship between differentially expressed miRNAs (DEmiRNAs) and DEmRNAs/DElncRNAs were predicted. Finally, mRNA-miRNA-lncRNA regulatory network construction was established by Cytoscape software. Finally, the key genes were validated based on the Gene Expression Profiling Interactive Analysis ( GEPIA) database. Results: Totally, 2,027 DEmiRNAs, 3,480 DElncRNAs, and 18,293 DEmRNAs were screened. The PPI network included 399 nodes and 1671 interaction pairs, and two function models (Cluster 1 and Cluster 2) were separately identified. The PLK1 was a hub in the Cluster 1, which mainly enriched in the function of nuclear division. Then the competing endogenous RNA (ceRNA) network was constructed with 20 miRNAs, 66 lncRNA, and 202 mRNA. Here, lncRNA RP11-159D12.2 might function as a ceRNA in regulating BIRC5 expression of esophagus cancer through competitively binding to hsa-miR-4430. BIRC5 was mainly enriched in the function of mitotic nuclear division. Besides, the expression of BIRC5 and PLK1 genes was upregulated in tumor tissues compared with normal controls. Also, the correlation analysis showed that the key genes ( BIRC5 and PLK1 ) were validated to be positively correlated with KHSRP. Conclusions: PLK1 , BIRC5 , hsa-miR-4430, and lncRNA RP11-159D12.2 were likely to be associated with esophageal cancer development.

Keywords: ceRNA network; differentially expressed analysis; esophagus cancer; functional enrichment analysis; protein–protein interaction network analysis

0 (BIRC5 protein, human)
0 (Cell Cycle Proteins)
0 (KHSRP protein, human)
0 (MicroRNAs)
0 (Proto-Oncogene Proteins)
0 (RNA, Long Noncoding)
0 (RNA, Messenger)
0 (RNA-Binding Proteins)
0 (Survivin)
0 (Trans-Activators)
EC 2.7.11.1 (Protein Serine-Threonine Kinases)

Date Created: 20200717 Date Completed: 20211130 Latest Revision: 20231213

20240105

10.1089/cbr.2020.3745

32673063