A computationally constructed ceRNA interaction network based on a comparison of the SHEE and SHEEC cell lines

Abstract

Long non-coding RNAs (lncRNAs) play critical and complicated roles in the regulation of various biological processes, including chromatin modification, transcription and post-transcriptional processing. Interestingly, some lncRNAs serve as miRNA "sponges" that inhibit interaction with miRNA targets in post-transcriptional regulation. We constructed a putative competing endogenous RNA (ceRNA) network by integrating lncRNA, miRNA and mRNA expression based on high-throughput RNA sequencing and microarray data to enable a comparison of the SHEE and SHEEC cell lines. Using Targetscan and miRanda bioinformatics algorithms and miRTarbase microRNA-target interactions database, we established that 51 miRNAs sharing 13,623 MREs with 2260 genes and 82 lncRNAs were involved in this ceRNA network. Through a biological function analysis, the ceRNA network appeared to be primarily involved in cell proliferation, apoptosis, the cell cycle, invasion and metastasis. Functional pathway analyses demonstrated that the ceRNA network potentially modulated multiple signaling pathways, such as the MAPK, Ras, HIF-1, Rap1, and PI3K/Akt signaling pathways. These results might provide new clues to better understand the regulation of the ceRNA network in cancer.

Keywords: SHEE; SHEEC; ceRNA; lncRNA; miRNA.

Fig. 1

A heatmap of differentially expressed miRNAs depicting miRNAs differentially expressed in the SHEE and SHEEC cell lines with a fold-change >2.0 and p < 0.05

Fig. 2

The ceRNA network. Cadmium green nodes represent miRNAs; fuchsia nodes represent genes; bright pink nodes represent lncRNAs

Fig. 3

The GO enrichment analysis of the ceRNA network

Fig. 4

The significantly enriched KEGG terms of the ceRNA network

Fig. 5

PI3K/Akt signaling pathway. The PI3K/Akt signaling pathway was the most significantly enriched biological function within the ceRNA-regulated target genes. Red nodes represent genes within the ceRNA network

Fig. 6

The ceRNA network modulates the PI3K/Akt signaling pathway. Cadmium green nodes represent miRNAs; fuchsia nodes represent genes; bright pink nodes represent lncRNAs