Clinicopathological-Associated Regulatory Network of Deregulated circRNAs in Hepatocellular Carcinoma

SIMPLE SUMMARY: Here, we present a novel strategy to identify key signatures of clinically-relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate the prognosis of HCC patients, by integrating clinicopathological features, circRNA and mRNA expression profiles. Five master circRNAs were identified and experimentally demonstrated to upregulate proliferate and promote transformation. Through further integration with miRNA-expression profiles, clinically-relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. The most up-regulated nodal-circRNA, circGPC3 was experimentally demonstrated to up-regulate cell-cycle, migration and invasion. circGPC3 was found to act as a sponge of miR-378a-3p to regulate ASPM expression and modulate cell transformation. These 5 nodal circRNAs has potential to be good prognostic biomarkers with good prognostic performance. circGPC3 has great potential to be a promising non-invasive prognostic biomarker for early HCC. We have thus demonstrated the robustness of bioinformatically-predicted master circRNAs in clinically-relevant, circRNA-mRNA networks, underscoring the important roles that these identified deregulated key/master circRNAs play in HCC. ABSTRACT: Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. Here, we present a novel strategy to identify key circRNA signatures of clinically relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate prognosis of HCC patients, by integrating clinic-pathological features, circRNA and mRNA expression profiles. Through further integration with miRNA expression profiles, clinically relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. At least five clinically relevant nodal-circRNAs, co-expressed with numerous genes, were identified from the circRNA-mRNA networks. These nodal circRNAs upregulated proliferation (except circRaly) and transformation in cells. The most upregulated nodal-circRNA, circGPC3, associated with higher-grade tumors and co-expressed with 33 genes, competes with 11 mRNAs for two shared miRNAs. circGPC3 was experimentally demonstrated to upregulate cell-cycle and migration/invasion in both transformed and non-transformed liver cell-lines. circGPC3 was further shown to act as a sponge of miR-378a-3p to regulate APSM (Abnormal spindle-like microcephaly associated) expression and modulate cell transformation. This study identifies 5 key nodal master circRNAs in a clinically relevant circRNA-centric network that are significantly associated with poorer prognosis of HCC patients and promotes tumorigenesis in cell-lines. The identification and characterization of these key circRNAs in clinically relevant circRNA-mRNA and ceRNA networks may facilitate the design of novel strategies targeting these important regulators for better HCC prognosis.