Comprehensive analysis of competing endogenous RNA networks associated with cholangiocarcinoma

Abstract

Cholangiocarcinoma (CCA) is the second most common type of primary malignancy of the liver. Certain long non-coding RNAs (lncRNAs) have been demonstrated to have key roles in tumor pathogenesis by binding to microRNAs (miRNAs). However, the competing endogenous RNA (ceRNA) network of CCA remains to be fully determined. In the present study, the RNA expression profiles for CCA were downloaded from The Cancer Genome Atlas and further analyzed. A total of 318 differentially expressed (DE) lncRNAs, 87 DE miRNAs and 3,851 DE mRNAs were identified from 36 CCA samples and 9 adjacent non-tumor samples (for lncRNAs and miRNAs, fold change ≥2.5 and P<0.01; for mRNAs, fold change ≥2 and P<0.01). Further bioinformatics analyses were performed and the ceRNA network for CCA was constructed, which included 16 lncRNAs, 55 miRNAs and 373 mRNAs. Survival analysis of all genes in the network revealed that high expression of the mRNAs fucosyltransferase 4 (P<0.005) and huntingtin-interacting protein 1 related (P<0.001) has a positive impact on the overall survival of patients with CAA. Furthermore, the lncRNAs H19 and PVT1, and the miRNAs Homo sapiens (hsa)-miR-16-5p and hsa-miR-424-5p,

Multifaceted Aspects of Metabolic Plasticity in Human Cholangiocarcinoma: An Overview of Current Perspectives

“…[45] PPAR-α upregulation Tumor occurrence and progression in CCA patients with. [46,47] IDH1 and IDH2 mutations Increase of glucose uptake and glucose metabolism as well as upregulation of some metabolites in TCA cycle. Upregulation of PFKP.…”

“…The analysis performed has revealed that the genes identified were strongly linked to metabolism. Pathway analysis has found that carbon metabolism, bile secretion, fat digestion, and PPAR signaling pathway were processes significantly enriched and played a pivotal role in CCA patients [46] (Table 1).…”

Long noncoding RNA OSER1‑AS1 promotes the malignant properties of non‑small cell lung cancer by sponging microRNA‑433‑3p and thereby increasing Smad2 expression

“…OSER1-AS1 was found to be mostly located in the cytoplasm of NSCLC cells. Increasing evidence suggests that cytoplasmic lncRNAs can act as competitive endogenous RNAs (ceRNAs) and thereby competitively bind to the target sites of miRNAs, leading to the release of target mRNAs (38,39).…”

Identification of Prognostic Biomarkers and Correlation with Immune Infiltrates in Hepatocellular Carcinoma Based on a Competing Endogenous RNA Network

“…Currently, the ceRNA hypothesis of crosstalk between ncRNAs and mRNAs has received much attention and is considered a new measure of gene regulation at the posttranscriptional level, which provides new insight into revealing mechanisms of tumorigenesis and identifying potential diagnostic and prognostic biomarkers. A growing number of published studies have demonstrated that many predictive signatures are detected in various tumors based on ceRNA network analysis [29][30][31][32][33]. MiRNAs, included in ncRNAs, are identified to be evolutionarily conserved, with an average length of 22-nt, and may bind to the 3'untranslated region (3'UTR) of the targeted mRNAs according to the principle of complementary base pairing.…”