Predictive identification of DECs with potential ceRNA functionality
Many prior investigations have illuminated the ability of specific circRNAs to function as ceRNAs, binding to miRNAs in a sequence-specific behavior and thereby inhibiting their expression or function. As such, we next predicted the potential miRNA targets of identified DECs using miRanda-based customized software developed by OG-Biotech based upon known sequence complementarity between DECs and miRNAs, which then facilitated the construction of a circRNA network incorporating 87 DECs and their putative target miRNAs (Fig. 7). The majority of circRNAs in this network were predicted to interact with more than 10 miRNAs, while hsa_circ_0015733 was predicted to bind to 10 miRNAs. Notably, hsa_circ_0005076, hsa_circ_0005044, hsa_circ_0008699, hsa_circ_0007120, hsa_circ_0062021, hsa_circ_0000699, hsa_circ_0002520, hsa_circ_0009130, hsa_circ_0004617, hsa_circ_0061782, hsa_circ_0056567, hsa_circ_0040827, and hsa_circ_0008410 were predicted to harbor binding sites for hundreds of different miRNAs.
The potency of a given ceRNA interaction is dependent upon the number of miRNAs, with circRNAs and miRNAs competing for target binding in a complex intracellular environment. To identify potential circRNA-miRNA-mRNA regulatory networks, we utilized the miRTarBase database in conjunction with Functional MTI analysis. Cytoscape software was used to generate six circRNA-miRNA-mRNA networks for the RT-qPCR-validated circRNAs (Fig. 8).