Integrated analysis using ToppMiR uncovers altered miRNA– mRNA regulatory networks in pediatric hepatocellular carcinoma—A pilot study

Abstract

Abstract Background Pediatric hepatocellular carcinoma (HCC) is a group of liver cancers whose mechanisms behind their pathogenesis and progression are poorly understood. Aim We aimed to identify alterations in the expression of miRNAs and their putative target mRNAs in not only tumor tissues of patients with pediatric HCC but also in corresponding non‐tumorous background livers by using liver tissues without underlying liver disease as a control. Methods and results We performed a small‐scale miRNA and mRNA profiling of pediatric HCC (consisting of fibrolamellar carcinoma [FLC] and non‐FLC HCC) and paired liver tissues to identify miRNAs whose expression levels differed significantly from control livers without underlying liver disease. ToppMiR was used to prioritize both miRNAs and their putative target mRNAs in a gene‐annotation network, and the mRNA profile was used to refine the prioritization. Our analysis generated prioritized lists of miRNAs and mRNAs from the following three sets of analyses: (a) pediatric HCC versus control; (b) FLC versus control; and (c) corresponding non‐tumorous background liver tissues from the same patients with pediatric HCC versus control. No liver disease liver tissues were used as the control group for all analyses. Many miRNAs whose expressions were deregulated in pediatric HCC were consistent with their roles in adult HCC and/or other non‐hepatic cancers. Our gene ontology analysis of target mRNAs revealed enrichment of biological processes related to the sustenance and propagation of cancer and significant downregulation of metabolic processes. Conclusion Our pilot study indicates that alterations in miRNA–mRNA networks were detected in not only tumor tissues but also corresponding non‐tumorous liver tissues from patients with pediatric HCC, suggesting multi‐faceted roles of miRNAs in disease progression. Our results may lead to novel hypotheses for future large‐scale studies.

Keywords

• miRNA
• pediatric hepatocellular carcinoma
• RNA sequencing
• ToppMiR