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

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.

Figure 1

Heatmap of differentially expressed RNAs between WT and normal tissues. (A) LncRNAs; (B) miRNAs; (C) mRNAs. WT, Wilms tumor.

Figure 2

Volcano plot of differentially expressed lncRNAs (A); miRNA (B) and mRNAs (C). The red point in the plot represents up-regulated RNAs and blue point represents down-regulated RNAs. FC, fold change; FDR, false discovery rate.

Figure 3

The ceRNA network of lncRNA-miRNA-mRNA in WT constructed from Cytoscape software. Red diamonds indicate IncRNAs, blue polygon indicate miRNA and green oval indicate mRNA. The comprehensive lines or colors represented the underlying interactions among them in WT. ceRNA, competing endogenous RNA; WT, Wilms tumor.

Figure 4

Identification of hub subnetwork. (A) LINC002253 (lncRNA) was interacted with TRIM71 (mRNA) mediated by hsa-mir-301a and hsa-mir-301b (miRNA); (B) Pearson’s correlation coefficient between LINC002253 and TRIM71; (C) Kaplan-Meier survival curves of TRIM71.

Figure 5

The enriched GO terms drawn in GOplot package reveals the potential biological mechanisms that the DEmRNAs might be involved in. FC, fold change; GO, Gene Ontology.

Figure 6

Top 8 enriched KEGG pathways of DEmRNAs involved in the ceRNA network. KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 7

Kaplan-Meier survival curves of top 6 DElncRNAs associated with overall survival in WT. WT, Wilms tumor.