A New Network-Based Strategy for Predicting the Potential miRNA-mRNA Interactions in Tumorigenesis

In silico Methods for Identification of Potential Therapeutic Targets

At the initial stage of drug discovery, identifying novel targets with maximal efficacy and minimal side effects can improve the success rate and portfolio value of drug discovery projects while simultaneously reducing cycle time and cost. However, harnessing the full potential of big data to narrow the range of plausible targets through existing computational methods remains a key issue in this field. This paper reviews two categories of in silico methods—comparative genomics and network-based methods—for finding potential therapeutic targets among cellular functions based on understanding their related biological processes. In addition to describing the principles, databases, software, and applications, we discuss some recent studies and prospects of the methods. While comparative genomics is mostly applied to infectious diseases, network-based methods can be applied to infectious and non-infectious diseases. Nonetheless, the methods often complement each other in their advantages and disadvantages. The information reported here guides toward improving the application of big data-driven computational methods for therapeutic target discovery.

Graphical abstract

MicroRNA Alteration in Developing Rat Oligodendrocyte Precursor Cells Induced by Hypoxia-Ischemia

microRNAs (miRNAs) are involved in the pathogenesis of white matter injury (WMI). However, their roles in developing rat brains under hypoxia-ischemia (HI) insult remain unknown. Here, we examined the expression profiles of miRNAs in oligodendrocyte precursor cells using microarray analysis. We identified 162 miRNAs and only 6 were differentially regulated in HI compared with sham. Next, we used these 6 miRNAs and 525 extensively changed coding genes (fold change absolute: FC(abs) ≥2, p < 0.05) to establish the coexpression network, the result revealed that only 3 miRNAs (miR-142-3p, miR-466b-5p, and miR-146a-5p) have differentially expressed targeted mRNAs. RT-PCR analysis showed that the expression of the miRNAs was consistent with the microarray analysis. Further gene ontology and KEGG pathway analysis of the targets of these 3 miRNAs indicated that they were largely associated with neural activity. Furthermore, we found that 2 of the 3 miRNAs, miR-142-3p, and miR-466b-5p, have the same target gene, Capn6, an antiapoptotic gene that is tightly regulated in the pathogenesis of neurological diseases. Collectively, we have shown that a number of miRNAs change in oligodendrocyte precursor cells in response to HI insult in developing brains, and miR-142-3p/miR-466b-5p/Capn6 pathway might affect the pathogenesis of WMI, providing us new clues for the diagnosis and therapy for WMI.

Impact of miRNA-mRNA Profiling and Their Correlation on Medulloblastoma Tumorigenesis

Medulloblastoma (MB) is a clinically challenging, childhood brain tumor with a diverse genetic makeup and differential miRNA profile. Aiming to identify deregulated miRNAs in MB, the miRNA expression profile of human MB samples was compared to that of normal cerebellar tissues. As a result, 8 upregulated and 64 downregulated miRNAs were identified in MB samples. Although various algorithms have been developed to predict the interaction between miRNA-mRNA pairs, the complexity and fidelity of miRNA-mRNA remain a concern. Therefore, to identify the signatures of miRNA-mRNA interactions essential for MB pathogenesis, miRNA profiling, RNA sequencing, and ingenuity pathway analysis (IPA) were performed in the same primary human MB samples. Further, when miR-217 was inhibited, a significant upregulation of predicted target genes SIRT1, ROBO1, FOXO3, and SMAD7 in HDMB03 cells was observed, confirming the validity of our approach. Functional analysis revealed that the inhibition of miR-217 in HDMB03 cells suppresses colony formation, migration, invasion, promoted apoptosis, and arrested cell population in S phase, indicating that manipulation of miR-217 may have a therapeutic potential for MB patients. Therefore, our study provides an essential platform for future investigations of specific miRNAs responsible for MB pathogenesis.

MiR-520f promotes cell aggressiveness by regulating fibroblast growth factor 16 in hepatocellular carcinoma

Cancer metastasis is a multistep cellular process, which has be confirmed one of mainly causes of cancer associated-death in hepatocellular carcinoma (HCC). MicroRNAs (miRNAs) participate in tumorigenesis function as either tumor suppressor genes or oncogenes. In order to elaborate the critical miRNAs and their targets in HCC, we compared the differential expression of miRNA between HCC tissues and normal tissues. Microarray analysis revealed there were several significantly up-expression miRNAs in HCC, compared to normal solid tissue. Among them, the expression of miR-520f was the most over-expression in HCC cell lines than that in human normal liver cells LO2, as well as up-regulated in HCC than that in the corresponding normal tissues. Moreover, Kaplan Meier-plotter analyses revealed that higher miR-520f levels were negatively correlated with poor overall survival. By applying bioinformatics methods to identify the targeting genes of miRNA, we demonstrated that fibroblast growth factor 16 (FGF16) was the miR-520f-targeted gene. Meanwhile, FGF16 exhibited similar expression patterns to miR-520f in HCC. Forced miR-520f expression accelerated HCC cells proliferation and aggressiveness in vitro and in vivo, whereas down-regulation of miR-520f caused an opposite outcome. Moreover, over-expression of FGF16 was closely related to the metastatic potential of HCC cells. Herein, we also confirmed that ectopic expression of FGF16 in HCC cells promoted proliferation, colony formation, and increased migration, invasion of HCC cells in vitro. Collectively, our results indicated that over-expression of miR-520f and FGF16 was positively associated with aggressive phenotypes and poor survival of patients with HCC, and miR-520f promoted HCC aggressive phenotypes by regulating the expression of FGF16. MiR-520f may be employed as a prognostic factor and therapeutic target for HCC.