Comparative transcriptome analysis of the global circular RNAs expression profiles between SHEE and SHEEC cell lines

Abstract

Esophageal squamous cell carcinoma (ESCC) is widely regarded as one of the most lethal types of cancer around the world. The fact that early detection of ESCC could dramatically improve the treatment outcome of the patients has sparked considerable interest in searching for reliable and accurate diagnostic biomarkers. Recently, circular RNAs (circRNA) have emerged as a new type of non-coding RNAs with significant RNase resistance, wide abundance and remarkable internal diversity. There is also increasing evidence suggesting that circRNAs could be implicated in the pathogenesis of cancer and other diseases. In this study, we performed a comparative analysis of the global circRNA expression profiles in normal and malignant esophageal epithelial cell lines by a combination of RNA sequencing and bioinformatics analysis. We identified 813 significantly up-regulated and 445 down-regulated circRNA candidates, of which 32 were subsequently validated by quantitative real-time reverse transcription polymerase chain reaction analysis. The differentially expressed circRNAs were found to be associated with pathways involved in metabolism, cell apoptosis, proliferation and migration, which are commonly altered in cancer cells. Based on the obtained data, we constructed a circRNA-miRNA interaction network, in which circRNA9927-NBEAL1 represented the biggest node. Our study could lay the groundwork for further investigation concerning the pathological roles of circRNAs in ESCC.

Keywords: SHEE; SHEEC; Transcriptome; circular RNAs; miRNA.

Figure 1

Genomic distribution of the detected SHEEC (A) and SHEE (B) circRNAs. Exonic, intronic and intergenic circRNAs are colored in red, green and blue, respectively.

Figure 2

GO enrichment analysis of the differentially expressed circRNA candidates between SHEEC and SHEE cells.

Figure 3

KEGG enrichment analysis of the differentially expressed circRNA candidates. Enrichment scores are graphed on a logarithmic scale.

Figure 4

Construction of the circRNA-miRNA interaction network.

Figure 5

CircRNA-miRNA network showing the interactions between all the circRNAs putatively involved in the PI3K/Akt signaling pathway and their miRNA targets.

Figure 6

qRT-PCR validation of the 26 most up-regulated and the six most down-regulated circRNAs. In each instance, the fold enrichment score was calculated as a ratio of the expression level of the circRNA candidate in SHEEC cells to that in SHEE cells and graphed on a logarithmic scale. Data obtained by qRT-PCR and RNA sequencing were illustrated in the form of red and blue columns, respectively.