TCGA dataset‑based construction and integrated analysis of aberrantly expressed long non‑coding RNA mediated competing endogenous RNA network in gastric cancer

Abstract

The aberrant expression of long non-coding RNAs (lncRNAs) has been confirmed to play a pivotal role in tumor initiation and development. LncRNAs can interact with microRNAs (miRNAs) as competing endogenous RNAs (ceRNAs) to regulate the expression of target genes in various cancers. In the present study, the authors investigated the functions of lncRNAs as ceRNAs in gastric cancer (GC) and their implications for the prognosis. The RNA sequencing profiles of 372 tumor samples and 32 adjacent non-tumor gastric samples were downloaded from The Cancer Genome Atlas (TCGA) database. The differential expression of RNAs was identified using the ʻedgeRʼ package in R language software. Survival analysis was estimated based on Kaplan-Meier curves. The Gene Ontology biological processes and the Kyoto Encyclopedia of Genes and Genomes pathways were analyzed for differentially expressed mRNAs. Finally, a total of 999 lncRNAs, 137 miRNAs and 1629 mRNAs were identified as differentially expressed (DE) in GC with log fold change (FC) thresholds >2 and adjusted P-values <0.01. A ceRNA network was constructed with 65 DElncRNAs, nine DEmiRNAs and 24 DEmRNAs. Of the 65 DElncRNAs in the ceRNA network, nine were identified to be significantly associated with overall survival (P<0.05). A total of four DElncRNAs from the ceRNA network were validated by reverse transcription-quantitative polymerase chain reaction and revealed to be associated with tumorigenesis and/or progression. In conclusion, the results of the present study provide information on the role of the ceRNA network in GC. These identified novel lncRNAs are potential candidate biomarkers and require further studies.

RETRACTED: MALAT1 promotes gastric adenocarcinoma through the MALAT1/miR-181a-5p/AKT3 axis

“…Studies have shown that lncRNA is essential in many biological processes including the regulation of the cell cycle and cell differentiation, the dose compensation effect and epigenetic regulation, making it a hot research subject in genetics [6]. In recent years, emerging evidence has shown that R e t r a c t e d lncRNA plays an important role in tumorigenesis and tumour development, including gastric adenocarcinoma [7][8][9][10].…”

Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for hepatocellular carcinoma

“…Fan et al reported that LINC00221 is upregulated in breast cancer compared to adjacent-normal breast tissues and is involved in the lncRNA–miRNA–mRNA ceRNA network of breast cancer [31]. He et al demonstrated that LINC00221 is dysregulated in gastric cancer and competes with six miRNAs (hsa‑miR‑96, hsa‑miR‑143, hsa‑miR‑204, hsa‑miR‑372, hsa‑miR‑373 and hsa‑miR‑519d) to mediate target mRNA expression in gastric cancer [32]. Zhang et al found that LINC00221 is associated with a poor prognosis in patients with gastric cancer, and an 11‑lncRNA signature consisting of LINC00221 can predict the survival rate for gastric cancer [33].…”

Construction of a Competitive Endogenous RNA Network and Identification of Potential Regulatory Axis in Gastric Cancer

“…Several studies have been carried out on the construction of ceRNA networks for gastric cancer which majorly focused on certain lncRNAs, and were not experimentally validated (8, 11, 13, 14). Our study emphasizes the establishment of a regulatory network rather than analyzing individual genes.…”