ceRNA network construction and comparison of gastric cancer with or without <i>Helicobacter pylori</i> infection

Liu, Yanyan; Zhu, Jingyu; Han, Shuyi; Xiao, Dongjie; Jia, Yanfei; Wang, Yunshan

doi:10.1002/jcp.27467

Cited by 41 publications

(35 citation statements)

References 57 publications

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“…For the first time, we found that these four novel lncRNAs play a vital role in LUAD. Studies have shown that highly expressed AP002478.1 has a poor prognosis in gastric cancer and hepatocellular carcinoma [35,36], and our study in LUAD also showed the same results, this suggests that AP002478.1 plays an important role as a carcinogenic factor in many kinds of cancers. LINC00518 was first discovered and developed as a non-invasive 2-gene molecule in the detection of cutaneous melanoma [37].…”

Section: Discussionsupporting

confidence: 83%

Comprehensive analysis of prognostic biomarkers in lung adenocarcinoma based on aberrant lncRNA–miRNA–mRNA networks and Cox regression models

Yao

Zhang

et al. 2020

Bioscience Reports

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Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide, and its underlying mechanism remains unclear. Accumulating evidence has highlighted that long non-coding RNA (lncRNA) acts as competitive endogenous RNA (ceRNA) and plays an important role in the occurrence and development of LUAD. Here, we comprehensively analyzed and provided an overview of the lncRNAs, miRNAs, and mRNAs associated with LUAD from The Cancer Genome Atlas (TCGA) database. Then, differentially expressed lncRNAs (DElncRNA), miRNAs (DEmiRNA), and mRNAs (DEmRNA) were used to construct a lncRNA–miRNA–mRNA regulatory network according to interaction information from miRcode, TargetScan, miRTarBase, and miRDB. Finally, the RNAs of the network were analyzed for survival and submitted for Cox regression analysis to construct prognostic indicators. A total of 1123 DElncRNAs, 95 DEmiRNAs, and 2296 DEmRNAs were identified (|log2FoldChange| (FC) > 2 and false discovery rate (FDR) or adjusted P value < 0.01). The ceRNA network was established based on this and included 102 lncRNAs, 19 miRNAs, and 33 mRNAs. The DEmRNAs in the ceRNA network were found to be enriched in various cancer-related biological processes and pathways. We detected 22 lncRNAs, 12 mRNAs, and 1 miRNA in the ceRNA network that were significantly associated with the overall survival of patients with LUAD (P < 0.05). We established three prognostic prediction models and calculated the area under the 1,3,5-year curve (AUC) values of lncRNA, mRNA, and miRNA, respectively. Among them, the prognostic index (PI) of lncRNA showed good predictive ability which was 0.737, 0.702 and 0.671 respectively, and eight lncRNAs can be used as candidate prognostic biomarkers for LUAD. In conclusion, our study provides a new perspective on the prognosis and diagnosis of LUAD on a genome-wide basis, and develops independent prognostic biomarkers for LUAD.

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Section: Discussionsupporting

confidence: 83%

Comprehensive analysis of prognostic biomarkers in lung adenocarcinoma based on aberrant lncRNA–miRNA–mRNA networks and Cox regression models

Yao

Zhang

et al. 2020

Bioscience Reports

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“…Next, the relationships between the lncRNAs and miRNAs were defined using the miRcode database (http://www.mircode.org). To further investigate the roles of DEmiRNAs in GBM, we used the following three databases to predict the target genes of the miRNAs:miRTarBase, TargetScan, and miRDB 12 . Then, to further ensure the reliability of the constructed ceRNA network, we compared the predicted target miRNAs and mRNAs with the dysregulated miRNAs and mRNAs in the TCGA or GEO GBM samples and retained only the data of the overlapping miRNAs and mRNAs and their interaction pairs for further analysis.…”

Section: Experimental Methods and Designmentioning

confidence: 99%

Construction of lncRNA‐associated ceRNA networks to identify prognostic lncRNA biomarkers for glioblastoma

Liu

Wang

Yang

et al. 2020

J of Cellular Biochemistry

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Long noncoding RNAs (lncRNAs) serve as competitive endogenous RNAs (ceRNAs) that play significant regulatory roles in the pathogenesis of tumors. However, the role of lncRNAs, especially the lncRNA-related ceRNA regulatory network, in glioblastoma (GBM) has not been fully elucidated. The goal of the current study was to construct lncRNA-microRNA-mRNA-related ceRNA networks for further investigation of their mechanism of action in GBM. We downloaded data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases and identified differential lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) associated with GBM. A ceRNA network was constructed and analyzed to examine the relationship between lncRNAs and patients' overall survival. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGGs) were used to analyze the related mRNAs to indirectly explain the mechanism of action of lncRNAs. The potential effective drugs for the treatment of GBM were identified using the connectivity map (CMap). After integrated analysis, we obtained a total of 210 differentially expressed lncRNAs, 90 differentially expressed miRNAs, and 2508 differentially expressed mRNAs (DEmRNAs) from the TCGA and GEO databases. Using these differential genes, we constructed a lncRNA-associated ceRNA network. Six lncRNAs in the ceRNA network were associated with the overall survival of patients with GBM. Through KEGG analysis, it was found that the DEmRNAs involved in the network are related to cancer-associated pathways, for instance, mitogen-activated protein kinase and Ras signaling pathways. CMap analysis revealed four small-molecule compounds that could be used as drugs for the treatment of GBM. In this study, a multi-database joint analysis was used to construct a lncRNA-related ceRNA network to help identify the regulatory functions of lncRNAs in the pathogenesis of GBM.

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“…forming a lncRNA-miRNA-mRNA ceRNA network, which can regulate multiple signaling pathways, including the HIF-1α pathway (74,75). In addition, the HIF-1α-mediated hypoxia-induced upregulation of lncRNA-NEAT1 in hepatocellular carcinoma regulates the expression of the uridine-cytidine kinase 2 gene, which is associated with low survival rates of patients with liver cancer, by suppressing miR-199a-3p, and ultimately promotes tumor growth (76).…”

Section: Role Of Hif-1 In Non-coding Rna Associated With Cscsmentioning

confidence: 99%

Role of hypoxia inducible factor-1 in cancer stem cells (Review)

et al. 2020

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Cancer stem cells (CSCs) have been found to play a decisive role in cancer recurrence, metastasis, and chemo-, radio-and immuno-resistance. Understanding the mechanism of CSC self-renewal and proliferation may help overcome the limitations of clinical treatment. The microenvironment of tumor growth consists of a lack of oxygen, and hypoxia has been confirmed to induce cancer cell invasion, metastasis and epithelial-mesenchymal transition, and is usually associated with poor prognosis and low survival rates. Hypoxia inducible factor-1 (HIF-1) can be stably expressed under hypoxia and act as an important molecule to regulate the development of CSCs, but the specific mechanism remains unclear. The present review attempted to explain the role of HIF-1 in the generation and maintenance of CSCs from the perspective of epigenetics, metabolic reprogramming, tumor immunity, CSC markers, non-coding RNA and signaling pathways associated with HIF-1, in order to provide novel targets with HIF-1 as the core for clinical treatment, and extend the life of patients. Contents 1. Introduction 2. Structural characteristics of HIF-1 3. Role of epigenetic and post-translational modification of HIF-1 in CSCs 4. Role of HIF-1 in non-coding RNA associated with CSCs 5. Role of HIF-1 in CSC markers 6. Role of HIF-1 in tumor immunity of CSCs 7. Role of HIF-1 in metabolic reprogramming of CSCs 8. Role of HIF-1 in signaling pathways associated with CSCs 9. Potential targets for CSC therapy 10. Conclusions and perspectives

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ceRNA network construction and comparison of gastric cancer with or without Helicobacter pylori infection

Cited by 41 publications

References 57 publications

Comprehensive analysis of prognostic biomarkers in lung adenocarcinoma based on aberrant lncRNA–miRNA–mRNA networks and Cox regression models

Comprehensive analysis of prognostic biomarkers in lung adenocarcinoma based on aberrant lncRNA–miRNA–mRNA networks and Cox regression models

Construction of lncRNA‐associated ceRNA networks to identify prognostic lncRNA biomarkers for glioblastoma

Role of hypoxia inducible factor-1 in cancer stem cells (Review)

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