Comprehensive analysis of competitive endogenous RNAs network reveals potential prognostic lncRNAs in gastric cancer

• Main Authors: Dengzhong Sun, Yongzhi Miao, Wu Xu, Weijun Shi, Lili Wang, Tianwen Chen, Hexin Wen, Huazhang Wu, Mulin Liu
• Format: Article
• Language: English
• Published: Elsevier 2020-05-01
• Series: Heliyon
• Subjects: Bioinformatics; Cancer research; Biological sciences; CeRNA; Gastric cancer; LncRNA
• Online Access: http://www.sciencedirect.com/science/article/pii/S2405844020308239

Long non-coding RNAs (lncRNAs) are key regulators of a range of human diseases, including various cancers, with multiple previous studies having explored lncRNA dysregulation in the context of gastric cancer (GC). The present study sought to expand upon these previous results by downloading lncRNA, mRNA, and microRNA (miRNA) expression profiles derived from 180 GC tissues and 24 normal control tissues within the Cancer Genome Atlas (TCGA) database. These datasets were then interrogated to identify GC-related differentially expressed (DE) RNAs (|fold change| ≥ 2, FDR< 0.01), leading to the identification of 1946 DE lncRNAs, 123 DE miRNAs, and 3159 DE mRNAs. These results were then used to generate a putative GC-related competitive endogenous RNA (ceRNA) network composed of 131 lncRNAs, 9 miRNAs, and 78 mRNAs. Subsequent survival analyses based upon this network revealed 17 of these lncRNAs to be significantly associated with GC patient survival (P < 0.05). Further multivariable Cox regression and lasso analyses allowed for the construction of an 8-lncRNA risk score that was able to effectively predict GC patient survival with good discriminative ability. The Kaplan-Meier Plotter database further confirmed that network hub genes that were related to these 8 lncRNAs were associated with GC patient prognosis (P < 0.05). As the ceRNA network in the present study was constructed with a focus on both disease stage and differential gene expression, it represents a key resource that will offer valuable insights into the mechanistic roles of ceRNA pathways in GC development and progression.