Identification of Differentially Expressed and Prognostic lncRNAs for the Construction of ceRNA Networks in Lung Adenocarcinoma

Abstract

Background. Long noncoding RNAs (lncRNAs) could function as competitive endogenous RNAs (ceRNAs) to competitively adsorb microRNAs (miRNAs), thereby regulating the expression of their target protein-coding mRNAs. In this study, we aim to identify more effective diagnostic and prognostic markers for lung adenocarcinoma (LUAD). Methods. We obtained differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) for LUAD by using The Cancer Genomes Atlas (TCGA) portal. Weighted gene coexpression network analysis (WGCNA) was performed to unveil core gene modules associated with LUAD. The Cox proportional hazards model was performed to determine the prognostic significance of DElncRNAs. The diagnostic and prognostic significance of DElncRNAs was further verified based on the receiver operating characteristic curve (ROC). Cytoscape was used to construct the ceRNA networks comprising the lncRNAs-miRNAs-mRNAs axis based on the correlation obtained from the miRcode, miRDB, and TargetScan. Results. Compared with normal lung tissues, 2355 DElncRNAs, 820 DEmiRNAs, and 17289 DEmRNAs were identified in LUAD tissues. We generated 8 WGCNA core modules in the lncRNAs coexpression network, 5 modules in the miRNAs, and 12 modules in the mRNAs coexpression network, respectively. One lncRNA module (blue) consisting of 441 lncRNAs, two miRNA modules (blue and turquoise) containing 563 miRNAs, and one mRNA module (turquoise), which consisted of 15162 mRNAs, were mostly significantly related to LUAD status. Furthermore, 67 DEmRNAs were found to be tumor-associated as well as the target genes of the DElncRNAs-DEmiRNAs axis. Survival analyses showed that 6 lncRNAs (LINC01447, WWC2-AS2, OGFRP1, LINC00942, LINC01168, and AC005863.1) were significantly correlated with the prognosis of LUAD patients. Ultimately, the potential ceRNA networks including 6 DElncRNAs, 4 DEmiRNAs, and 22 DEmRNAs were constructed. Conclusion. Our study indicated that 6 DElncRNAs had the possibilities as diagnostic and prognostic biomarkers for LUAD. The lncRNA-mediated ceRNA networks might provide novel insights into the molecular mechanisms of LUAD progression.

Prognostic markers of ferroptosis-related long non-coding RNA in lung adenocarcinomas

“…Liu et al demonstrated that downregulation of OGFRP1 inhibited the progression of NSCLC through miR-4640-5p/eIF5A axis (Liu X. et al, 2021). Furthermore, it has been reported that OGFRP1 is highly expressed in NSCLC tissues and significantly correlated with the prognosis of LUAD patients (Cui et al, 2021). As another core ferroptosis-related lncRNA noted in this study, APTR has been shown to reduce miR-132-3p and enhance YAP1 expression, which in turn promotes osteosarcoma progression (Guan et al, 2019).…”

“…The EMT process can thus be strongly induced in vivo by it (Song et al, 2018). Liu et al demonstrated that downregulation of OGFRP1 inhibited the progression of NSCLC through miR-4640-5p/eIF5A axis (Liu X. et al, 2021). Furthermore, it has been reported that OGFRP1 is highly expressed in NSCLC tissues and significantly correlated with the prognosis of LUAD patients (Cui et al, 2021).…”

A graphSAGE discovers synergistic combinations of Gefitinib, paclitaxel, and Icotinib for Lung adenocarcinoma management by targeting human genes and proteins: the RAIN protocol

“…Cui's published work in Hindawi Journal of Oncology identified WWC2-AS2 as one of the lncRNAs involved in the construction of a Predictive long non-coding RNA (lncRNA) pattern in lung adenocarcinoma. [133][134][135][136] Lung Adenocarcinoma treatment:…”