Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions

As a novel class of noncoding RNAs, circular RNAs (circRNAs) have been reported to play a role in various biological processes. Some circRNAs may serve as microRNA (miRNA) sponges, regulating transcription or splicing. Herein, we investigated the expression profiles and interactions of miRNAs/isomiRs and circRNAs in male patients with esophageal cancer. We found that some miRNA genes generated two deregulated miRNA products (miR-#-5p and miR-#-3p), and these products were consistently abnormally expressed. Some circRNAs were predicted to be miRNA sponges for specific miRNAs. Some of these typically showed opposing expression patterns in cancer tissues: one upregulated and the other downregulated. Although fewer miRNAs were predicted to interact with circRNAs, the number of predicted interactions would be substantially increased if detailed isomiRs were involved. High sequence similarity across multiple isomiRs suggested that they might interact with circRNAs, similar to the interaction of homologous miRNAs with circRNAs. At the isomiR level, due to the characteristics of the sequences and expression patterns involved, the cross-talk between different ncRNAs is complicated despite simplification of the isomiRs involved through clustering. We expect that our results may provide methods for further study of the cross-talk among ncRNAs and elucidate their biological roles in human diseases.