Comprehensive analysis of circRNA expression patterns in small hepatocellular carcinoma by integrating circRNA and gene expression data

Circular RNA (circRNA) is a novel type of non-coding RNA molecule with covalently closed loop structures and may be involved in the regulation of gene expression in a post-transcriptional manner. Recent studies indicated that circRNA played important roles as microRNA sponges, in pre-mRNA splicing, and in the pathogenesis of human diseases. However, the expression patterns of circRNAs and their cognate linear RNAs in the tissues of small hepatocellular carcinoma are still unknown. This paper describes the expression profiles of circRNA and genes in hepatic tissues taken from patient with small hepatocellular carcinomas, to develop a further understanding of the relationship between circRNAs and their cognate linear RNAs in human disease. Hepatic tissues were taken from patients before liver transplantation, including tumorous tissues and non-tumorous tissues that were distant from the tumorous tissues. The circRNA arrays identified 931 circRNAs and the gene expression arrays identified 19367 genes differentially expressed in tumorous tissues, of which 296 circRNAs were detected as co-expressing with their cognate linear RNA. For the changes in the expression trends, 205 circRNAs and their cognate linear RNAs were found to be similar, and 91 circRNAs and their cognate linear RNAs were found to be different. The results of the arrays were confirmed by quantitative real-time PCR. Functional annotation revealed that the genes coexpressing circRNAs and linear RNAs were involved in cell differentiation, growth, and cellular signaling networks, and some of the genes were also identified as cancer-related genes in the literature. This work indicates that some circRNAs are derived from a special splicing pattern of cancer-related genes, and that others may serve as potential diagnosis biomarkers involved in post-transcriptional regulation in the pathogenesis of small hepatocellular carcinomas.