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Competing Endogenous RNA Network Analysis Reveals Pivotal ceRNAs in Adrenocortical Carcinoma.

ABSTRACT: Objective: To construct ceRNA network and identify pivotal competing endogenous RNAs (ceRNAs) in adrenocortical carcinoma (ACC) using ceRNA network analysis. Methods: The RNA sequencing expression data of 77 ACCs in TCGA were obtained from GEPIA. Cancer specific ceRNAs, cancer specific microRNAs (miRNAs), and cancer specific messenger RNAs (mRNAs) were identified. The interaction of cancer specific miRNAs with cancer specific ceRNAs and cancer specific mRNAs were predicted. CeRNA network was constructed and visualized by Cytoscape 3.7.0 software. The genes in ceRNA network regulated GO terms and regulated pathways were performed by function analysis. Survival analysis of pivotal ceRNAs was performed for the pivotal lncRNAs. Result: Twenty-eight cancer specific ceRNAs, 149 cancer specific miRNAs, and 104 mRNAs were identified. CeRNA network was constructed including 10 ceRNAs, 35 miRNAs, and 34 mRNAs. The genes in ceRNA network regulated GO terms and were classified into three groups: cellular component (CC), molecular function (MF), and biological process (BP). The genes in ceRNA network regulated the following pathways: leukocyte transendothelial migration, and proteoglycans in cancer. Survival analysis showed that CTB-63M22.1 and RP1-241P17.4 were significantly associated with ACC patient disease free survival and overall survival. Conclusion: This study has constructed ceRNA networks in ACC. The study provides a set of pivotal ceRNAs for future investigation into the molecular mechanisms.

SUBMITTER: Liang W

PROVIDER: S-EPMC6529643 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Competing Endogenous RNA Network Analysis Reveals Pivotal ceRNAs in Adrenocortical Carcinoma.

Liang Weiwei W Sun Fangfang F

Frontiers in endocrinology 20190515

<b>Objective:</b> To construct ceRNA network and identify pivotal competing endogenous RNAs (ceRNAs) in adrenocortical carcinoma (ACC) using ceRNA network analysis. <b>Methods:</b> The RNA sequencing expression data of 77 ACCs in TCGA were obtained from GEPIA. Cancer specific ceRNAs, cancer specific microRNAs (miRNAs), and cancer specific messenger RNAs (mRNAs) were identified. The interaction of cancer specific miRNAs with cancer specific ceRNAs and cancer specific mRNAs were predicted. CeRNA n ...[more]

PMID: 31156552

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Project description:The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis. A support vector machine (SVM) classifier was built using 15 feature genes, and its classification effect was validated using two microarray data sets that were downloaded from the Gene Expression Omnibus (GEO) database. In addition, Gene Ontology function and Kyoto Encyclopedia Genes and Genomes pathway enrichment analyses were conducted for genes identified in the ceRNA network. A total of 506 samples, including 447 tumor samples and 59 normal samples, were obtained from The Cancer Genome Atlas (TCGA); 16 DE‑lncRNAs, 917 DEGs and 30 DE‑miRNAs were screened. The miRNA‑mRNA regulatory network comprised 353 nodes and 577 interactions. From these data, 15 feature genes with high predictive precision (>95%) were extracted from the network and were used to form an SVM classifier with an accuracy of 96.05% (486/506) for PTC samples downloaded from TCGA, and accuracies of 96.81 and 98.46% for GEO downloaded data sets. The ceRNA regulatory network comprised 596 lines (or interactions) and 365 nodes. Genes in the ceRNA network were significantly enriched in 'neuron development', 'differentiation', 'neuroactive ligand‑receptor interaction', 'metabolism of xenobiotics by cytochrome P450', 'drug metabolism' and 'cytokine‑cytokine receptor interaction' pathways. Hox transcript antisense RNA, miRNA‑206 and kallikrein‑related peptidase 10 were nodes in the ceRNA regulatory network of the selected feature gene, and they may serve import roles in the development of PTC.

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Competing Endogenous RNA Network Analysis Reveals Pivotal ceRNAs in Adrenocortical Carcinoma.

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Competing Endogenous RNA Network Analysis Reveals Pivotal ceRNAs in Adrenocortical Carcinoma.

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