Comprehensive analysis of competing endogenous RNA network in Wilms tumor based on the TARGET database

Bo Guan; Feng Qi; Ye Tian

doi:10.21037/tau.2020.01.34

Comprehensive analysis of competing endogenous RNA network in Wilms tumor based on the TARGET database

Transl Androl Urol. 2020 Apr;9(2):473-484. doi: 10.21037/tau.2020.01.34.

Authors

Bo Guan¹, Feng Qi², Ye Tian¹

Affiliations

¹ Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China.
² Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.

Abstract

Background: Wilms tumor (WT) was the most common malignant tumor of urinary system in children. With the advances in gene sequencing, research of molecular mechanism of WT tumor was gradually increasing. However, few studies have explored the influence of competing endogenous RNA (ceRNA) in WT. Accordingly, we aimed to explore the mechanisms of ceRNA co-expression network in WT.

Methods: A total of 6 non-tumor controls and 127 WT patients' RNA-seq data combined with clinical data was acquired from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Differentially expressed lncRNA, miRNA and mRNA between WT tissues and normal tissues were analyzed using "edgeR" package in R software. Weighted gene co-expression network analysis (WGCNA) was utilized to construct the ceRNA co-expression network while Molecular Complex Detection (MCODE) algorithm was used to extract the pivotal sub-network. Function annotation of mRNA was performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Survival analysis was then conducted based on long-rank test and Kaplan-Meier curves using the survival package.

Results: By applying the "edgeR" package in R, the transcriptome expression data of 127 WT tissues with 6 normal tissues were normalized. Moreover, 146 DElncRNAs, 62 DEmiRNAs, 287 DEmRNAs of them were involved in ceRNA network after applying WGCNA. According to MCODE, we identified that the interactions between LINC002253 (lncRNA) and TRIM71 (mRNA) was mediated by hsa-mir-301a and hsa-mir-301b (miRNA). Furthermore, we detected 13 DElncRNAs which were significantly associated with the progression of WT.

Conclusions: We used WGCNA method to construct the WT ceRNA network for the first time. TRIM71 was identified to be the most closely related genes involved in hub sub-network by MCDOE, suggesting it might act as a new drug target and prognostic factor based on our comprehensive results.

Keywords: Therapeutically Applicable Research to Generate Effective Treatments (TARGET); Wilms tumor (WT); competitive endogenous RNA (ceRNA); lncRNA.