Open Access

Identification of ceRNA network based on a RNA‑seq shows prognostic lncRNA biomarkers in human lung adenocarcinoma

  • Authors:
    • Xing Li
    • Bing Li
    • Pixin Ran
    • Lanying Wang
  • View Affiliations

  • Published online on: August 21, 2018     https://doi.org/10.3892/ol.2018.9336
  • Pages: 5697-5708
  • Copyright: © Li et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Previous studies have emphasized the significant functions of long non‑coding RNAs (lncRNAs) as competing endogenous RNAs (ceRNAs) in tumor biology. However, the functions of certain cancer lncRNAs in the lncRNA‑related ceRNA network in lung adenocarcinoma (LUAD) are unknown. A systematic and integrative survey of RNA‑seq data from The Cancer Genome Atlas (TCGA) was performed to identify candidate lncRNAs for the prognosis of LUAD. In total, 20,502 genes that contain 181 lncRNAs were evaluated in a cohort of 570 LUAD cases. Initially, 6,280 differentially expressed genes (fold‑change >2, P<0.05) were obtained using R package, which includes 75 lncRNAs. Next, by univariate regression and multivariate Cox proportional hazards analysis, 32 genes were associated with survival in LUAD. Using these 29 mRNAs and 3 lncRNAs, a prognosis index (PI) was calculated to accurately estimate the survival in LUAD: PI=∑exprisk gene x HRrisk gene. Furthermore, the 32‑gene signature was an independent prognostic indicator for LUAD (HR >1; P<0.05, by multivariate analysis). Weighted gene co‑expression network analysis (WGCNA) of three risk lncRNAs‑FAM138B, NHEG1 and TLX1NB‑was performed, based on the P‑values of the associated genes, and the top 27 miRNAs that bound to these lncRNAs were predicted by Miranda as target miRNAs. Next, these target miRNAs were transferred to the TarBase, miRTarBase, miRecards and starBase v2.0 databases to obtain their target genes. According to the previous miRNA‑mRNA and miRNA‑lncRNA data, three lncRNA‑miRNA‑mRNA ceRNA networks were established, based on the 29 prognostic mRNAs, forming a regulatory network in LUAD. The present study provided insight into the lncRNA‑related ceRNA network in LUAD and has identified potential diagnostic and prognostic biomarkers.
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November-2018
Volume 16 Issue 5

Print ISSN: 1792-1074
Online ISSN:1792-1082

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Copy and paste a formatted citation
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Spandidos Publications style
Li X, Li B, Ran P and Wang L: Identification of ceRNA network based on a RNA‑seq shows prognostic lncRNA biomarkers in human lung adenocarcinoma. Oncol Lett 16: 5697-5708, 2018
APA
Li, X., Li, B., Ran, P., & Wang, L. (2018). Identification of ceRNA network based on a RNA‑seq shows prognostic lncRNA biomarkers in human lung adenocarcinoma. Oncology Letters, 16, 5697-5708. https://doi.org/10.3892/ol.2018.9336
MLA
Li, X., Li, B., Ran, P., Wang, L."Identification of ceRNA network based on a RNA‑seq shows prognostic lncRNA biomarkers in human lung adenocarcinoma". Oncology Letters 16.5 (2018): 5697-5708.
Chicago
Li, X., Li, B., Ran, P., Wang, L."Identification of ceRNA network based on a RNA‑seq shows prognostic lncRNA biomarkers in human lung adenocarcinoma". Oncology Letters 16, no. 5 (2018): 5697-5708. https://doi.org/10.3892/ol.2018.9336