Comprehensive analysis of microRNA-regulated protein interaction network reveals the tumor suppressive role of microRNA-149 in human hepatocellular carcinoma via targeting AKT-mTOR pathway

Abstract

BackgroundOur previous study identified AKT1, AKT2 and AKT3 as unfavorable prognostic factors for patients with hepatocellular carcinoma (HCC). However, limited data are available on their exact mechanisms in HCC. Since microRNAs (miRNAs) are implicated in various human cancers including HCC, we aimed to screen miRNAs targeting AKTs and investigate their underlying mechanisms in HCC by integrating bioinformatics prediction, network analysis, functional assay and clinical validation.MethodsFive online programs of miRNA target prediction and RNAhybrid which calculate the minimum free energy (MFE) of the duplex miRNA:mRNA were used to screen optimized miRNA-AKT interactions. Then, miRNA-regulated protein interaction network was constructed and 5 topological features (‘Degree’, ‘Node-betweenness’, ‘Edge-betweenness’, ‘Closeness’ and ‘Modularity’) were analyzed to link candidate miRNA-AKT interactions to oncogenesis and cancer hallmarks. Further systematic experiments were performed to validate the prediction results.ResultsSix optimized miRNA-AKT interactions (miR-149-AKT1, miR-302d-AKT1, miR-184-AKT2, miR-708-AKT2, miR-122-AKT3 and miR-124-AKT3) were obtained by combining the miRNA target prediction and MFE calculation. Then, 103 validated targets for the 6 candidate miRNAs were collected from miRTarBase. According to the enrichment analysis on GO items and KEGG pathways, these validated targets were significantly enriched in many known oncogenic pathways for HCC. In addition, miRNA-regulated protein interaction network were divided into 5 functional modules. Importantly, AKT1 and its interaction with mTOR respectively had the highest node-betweenness and edge-betweenness, implying their bottleneck roles in the network. Further experiments confirmed that miRNA-149 directly targeted AKT1 in HCC by a miRNA luciferase reporter approach. Then, re-expression of miR-149 significantly inhibited HCC cell proliferation and tumorigenicity by regulating AKT1/mTOR pathway. Notably, miR-149 down-regulation in clinical HCC tissues was correlated with tumor aggressiveness and poor prognosis of patients.ConclusionThis comprehensive analysis identified a list of miRNAs targeting AKTs and revealed their critical roles in HCC malignant progression. Especially, miR-149 may function as a tumor suppressive miRNA and play an important role in inhibiting the HCC tumorigenesis by modulating the AKT/mTOR pathway. Our clinical evidence also highlight the prognostic potential of miR-149 in HCC. The newly identified miR-149/AKT/mTOR axis might be a promising therapeutic target in the prevention and treatment of HCC.Electronic supplementary materialThe online version of this article (doi:10.1186/1476-4598-13-253) contains supplementary material, which is available to authorized users.

The clinicopathological significance of miR-149 and PARP-2 in hepatocellular carcinoma and their roles in chemo/radiotherapy

“…Treatment with CPNP-emiR-149 and CPNPshPARP-2 significantly inhibited Hep G2 cell proliferation. [12]. This study showed that miR-149 level was significantly lower in HCC tumor tissues than that in peritumoral tissues (P < 0.001).…”

“…The roles of PARP inhibitors in tumor therapy have been widely investigated. In general, PARP inhibitors can be used in cancer therapy as chemo/radiopotentiators or as stand-alone therapy for tumors deficient in certain types of DNA repair mechanisms [12]. However, current PARP inhibitors have no isoform specificity.…”

“…The accumulated evidence has suggested that miRNAs can function as oncogenes or tumor suppressor genes involved in the regulation of tumorigenesis, growth, apoptosis, metastasis, and prognosis of HCC [11]. A recent study demonstrated that miR-149 functions as a tumor suppressor gene in human HCC [12]. Moreover, miR-149 has been demonstrated to inhibit PARP-2 and promote mitochondrial biogenesis in skeletal muscle cells [13].…”

Increased miR‐124‐3p in microglial exosomes following traumatic brain injury inhibits neuronal inflammation and contributes to neurite outgrowthviatheir transfer into neurons

“…3B). mTOR signaling plays a significant role in regulating immunoinflammatory response, and its activity was suppressed by miR-124-3p in various diseases, such as Parkinson's disease and hepatocellular carcinoma (42,43). Therefore, we put emphasis on studying the roles of the mTOR signaling underlying the regulation of miR-124-3p in neuronal inflammation, to clarify the function and mechanism of microglial exosomes after TBI.…”

MicroRNA-149 Increases the Sensitivity of Colorectal Cancer Cells to 5-Fluorouracil by Targeting Forkhead Box Transcription Factor FOXM1

“…Second, miR-149 is reported to function as a tumor suppressor in human cancers. Zhang et al showed that miR-149 functions as a tumor suppressive miRNA and plays an important role in inhibiting the tumorigenesis of hepatocelluar carcinoma by modulating the AKT/mTOR pathway [16]. Wang et al showed that miR-149 inhibits proliferation and cell cycle progression through the target of ZBTB2 in gastric cancer [17].…”