Identification of a competing endogenous RNA network associated with prognosis of pancreatic adenocarcinoma

• Published in: Cancer cell international Vol. 20; no. 1; pp. 231 - 14
• Main Authors: Weng, Wanqing, Zhang, Zhongjing, Huang, Weiguo, Xu, Xiangxiang, Wu, Boda, Ye, Tingbo, Shan, Yunfeng, Shi, Keqing, Lin, Zhuo
• Format: Journal Article
• Language: English
• Published: London BioMed Central 11.06.2020; BMC
• Subjects: Accuracy; Adenocarcinoma; Biomedical and Life Sciences; Biomedicine; Cancer Research; Cell Biology; Competing endogenous RNA network; Gene expression; Genes; Genomes; Genotypes; Homeostasis; Hypotheses; Medical prognosis; Metabolism; MicroRNAs; miRNA; mRNA; Non-coding RNA; Pancreas; Pancreatic adenocarcinoma; Pancreatic cancer; Prognosis; Time-dependent receiver operating characteristic; Pancreatic adenocarcinoma; Competing endogenous RNA network; Time-dependent receiver operating characteristic
• ISSN: 1475-2867; 1475-2867
• DOI: 10.1186/s12935-020-01243-6

Background Emerging evidence suggests that competing endogenous RNAs plays a crucial role in the development and progress of pancreatic adenocarcinoma (PAAD). The objective was to identify a new lncRNA-miRNA-mRNA network as prognostic markers, and develop and validate a multi-mRNAs-based classifier for predicting overall survival (OS) in PAAD. Methods Data on pancreatic RNA expression and clinical information of 445 PAAD patients and 328 normal subjects were downloaded from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Genotype-Tissue Expression (GTEx). The weighted correlation network analysis (WGCNA) was used to analyze long non-coding RNA (lncRNA) and mRNA, clustering genes with similar expression patterns. MiRcode was used to predict the sponge microRNAs (miRNAs) corresponding to lncRNAs. The downstream targeted mRNAs of miRNAs were identified by starBase, miRDB, miRTarBase and Targetscan. A multi-mRNAs-based classifier was develop using least absolute shrinkage and selection operator method (LASSO) COX regression model, which was tested in an independent validation cohort. Results A lncRNA-miRNA-mRNA co-expression network which consisted of 60 lncRNAs, 3 miRNAs and 3 mRNAs associated with the prognosis of patients with PAAD was established. In addition, we constructed a 14-mRNAs-based classifier based on a training cohort composed of 178 PAAD patients, of which the area under receiver operating characteristic (AUC) in predicting 1-year, 3-year, and 5-year OS was 0.719, 0.806 and 0.794, respectively. The classifier also shown good prediction function in independent verification cohorts, with the AUC of 0.604, 0.639 and 0.607, respectively. Conclusions A novel competitive endogenous RNA (ceRNA) network associated with progression of PAAD could be used as a reference for future molecular biology research.