The human genome encodes thousands of long noncoding RNA (lncRNA) genes; the function of majority of them is poorly understood. Aberrant expression of a significant number of lncRNAs is observed in various diseases, including cancer. To gain insights into the role of lncRNAs in breast cancer progression, we performed genome-wide transcriptome analyses in an isogenic, triple negative breast cancer (TNBC/basal-like) progression cell lines using a 3D cell culture model. We identified significantly altered expression of 1853 lncRNAs, including ~500 natural antisense transcript (NATs) lncRNAs. A significant number of breast cancer-deregulated NATs displayed co-regulated expression with oncogenic and tumor suppressor protein-coding genes in cis. Further studies on one such NAT, PDCD4-AS1 lncRNA reveal that it positively regulates the expression and activity of the tumor suppressor PDCD4 in mammary epithelial cells. Both PDCD4-AS1 and PDCD4 show reduced expression in TNBC cell lines and in patients, and depletion of PDCD4-AS1 compromised the cellular levels and activity of PDCD4. Further, tumorigenic properties of PDCD4-AS1-depleted TNBC cells were rescued by exogenous expression of PDCD4, implying that PDCD4-AS1 acts upstream of PDCD4. Mechanistically, PDCD4-AS1 stabilizes PDCD4 RNA by forming RNA duplex and controls the interaction between PDCD4 RNA and RNA decay promoting factors such as HuR. Our studies demonstrate crucial roles played by NAT lncRNAs in regulating post-transcriptional gene expression of key oncogenic or tumor suppressor genes, thereby contributing to TNBC progression.

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A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability.

Hepatitis B virus (HBV) is one of the major risk factors of hepatocellular carcinoma (HCC). Increasing evidence indicates that microRNA (miRNA)–mRNA axis is involved in HCC. However, a comprehensive miRNA–mRNA regulatory network in HBV-related HCC is still absent. This study aims to identify potential miRNA–mRNA regulatory pathways contributing to pathogenesis of HBV-related HCC. Microarray GSE69580 was downloaded from Gene Expression Omnibus (GEO) database. GEO2R and ‘R-limma’ were used to conduct differential expression analysis. The common miRNAs appeared in the two analytic sets were screened as potential differentially expressed miRNAs (DE-miRNAs). The prognostic roles of screened DE-miRNAs in HCC were further evaluated using Kaplan–Meier plotter database. Target genes of DE-miRNAs were predicted by miRNet. Then, protein–protein interaction (PPI) networks were established for these targets via the STRING database, after which hub genes in the networks were identified by Cytoscape. Functional annotation and pathway enrichment analyses for the target genes were performed through DAVID database. Three enriched pathways related to HBV-related HCC were selected for further analysis and potential target genes commonly appeared in all three pathways were screened. Cytoscape was employed to construct miRNA-hub gene network. The expression and correlation of potential miRNAs and targets were further detected in clinical HBV-related HCC samples by qRT-PCR. 7 upregulated and 9 downregulated DE-miRNAs were accessed. 5 of 7 upregulated DE-miRNAs and 5 of 7 downregulated DE-miRNAs indicated significant prognostic roles in HCC. 2312 and 1175 target genes were predicted for the upregulated and downregulated DE-miRNAs, respectively. TP53 was identified as the hub gene in the PPI networks. Pathway enrichment analysis suggested that these predicted targets were linked to hepatitis B, pathways in cancer, microRNAs in cancer and viral carcinogenesis. Further analysis of these pathways screened 20 and 16 target genes for upregulated and downregulated DE-miRNAs, respectively. By detecting the expression of 36 target genes, six candidate target genes were identified. Finally, a potential miRNA–mRNA regulatory network was established based on the results of qRT-PCR and expression correlation analysis. In the study, potential miRNA–mRNA regulatory pathways were identified, exploring the underlying pathogenesis and effective therapy strategy of HBV-related HCC.

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Identification of potential miRNA–mRNA regulatory network contributing to pathogenesis of HBV-related HCC

Background/Aims: Vascular smooth muscle cell (VSMC) hyperplasia plays important roles in the pathogenesis of many vascular diseases, such as atherosclerosis and restenosis. Many microRNAs (miRs) have recently been reported to regulate the proliferation and migration of VSMC. In the current study, we aimed to explore the function of miR-93 in VSMCs and its molecular mechanism. Methods: First, qRT-PCR and immunofluorescence assays were performed to determine miR-93 expression in rat VSMCs following carotid artery injury in vivo and platelet-derived growth factor-BB (PDGF-BB) stimulation in vitro. Next, the biological role of miR-93 in rat VSMC proliferation and migration was examined in vivo and vitro. EdU incorporation assay and MTT assay for measuring cell proliferation, Transwell cell invasion assay and Cell scratch wound assay for measuring cell migration. Then, the targets of miR-93 were identified. Finally, the expression levels of proteins in the Raf-ERK1/2 pathway were measured by western blot. Results: MiR-93 was upregulated in rat VSMCs following carotid artery injury in vivo. Similar results were observed in ex vivo cultured VSMCs after PDGF-BB treatment. MiR-93 inhibition suppressed neointimal formation after carotid artery injury. Moreover, our results demonstrated that a miR-93 inhibitor suppressed the PDGF-BB induced proliferation and migration of in VSMC. This inhibitor also decreased the expression levels of MMP2 and cyclin D1. Mechanistically, we discovered that mitofusin 2(Mfn2) is a direct target of miR-93. Furthermore, an analysis of the signaling events revealed that miR-93-mediated VSMC proliferation and migration occurred via the Raf-ERK1/2 pathway. Conclusions: Our findings suggest that miR-93 promotes VSMCs proliferation and migration by targeting Mfn2. MiR-93 may be a new target for treating in-stent restenosis.

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MiR-93 regulates vascular smooth muscle cell proliferation, and neointimal formation through targeting Mfn2.

Long non-coding RNA LINC00472 suppresses hepatocellular carcinoma cell proliferation, migration and invasion through miR-93-5p/PDCD4 pathway.

Programmed cell death 4 (PDCD4) is a tumor suppressor gene implicated in many cellular functions, including transcription, translation, apoptosis, and the modulation of different signal transduction pathways. The downstream mechanisms of PDCD4 have been well-discussed, but its upstream regulators have not been systematically summarized. Noncoding RNAs (ncRNAs) are gene transcripts with no protein-coding potential but play a pivotal role in the regulation of the pathogenesis of solid tumors, cardiac injury, and inflamed tissue. In recent studies, many ncRNAs, especially microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), were found to interact with PDCD4 to manipulate its expression through transcriptional regulation and function as oncogenes or tumor suppressors. For example, miR-21, as a classic oncogene, was identified as the key regulator of PDCD4 by targeting its 3'-untranslated region (UTR) to promote tumor proliferation, migration, and invasion in colon, breast, and bladder carcinoma. Therefore, we reviewed the recently emerging pleiotropic regulation of PDCD4 by ncRNAs in cancer and inflammatory disorders and aimed to shed light on the mechanisms of associated diseases, which could be conducive to the development of novel treatment strategies for PDCD4-induced diseases.

The Regulatory Role of Non-coding RNAs on Programmed Cell Death Four in Inflammation and Cancer.

Hepatocellular carcinoma (HCC) is the second leading cause of cancer mortality worldwide. Although advances have made in treatment of HCC, the overall survival rate remains low and the molecular pathogenesis of HCC is still poorly understood. The purpose of this study was to explore the molecular pathogenesis of HCC. A total of 89 patients were involved in the study. MicroRNA-93 (miR-93) was aberrantly up-regulated in HCC tissues as determined by qRT-PCR. The high level of miR-93 was closely associated with larger tumor size (p < 0.05) and poor overall survival (p < 0.05). In in vitro and in vivo assays, we demonstrated that high miR-93 levels enhanced cell growth of HCC. The luciferase activity assay showed that PDCD4 was a direct target of miR-93 and its expression was down-regulated by miR-93. Re-expression of PDCD4 inversely correlated with the level of miR-93 and attenuated the miR-93-induced promotion of cell growth in HCC. Taken together, our data indicate that miR-93 may function as an oncogenic factor in HCC, and promotes HCC cell proliferation by targeting PDCD4.

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S Han

Papers

The miR-93 promotes proliferation by directly targeting PDCD4 in hepatocellular carcinoma.