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Development of a novel signature of long noncoding RNAs as a prognostic biomarker for esophageal cancer

By Yan Miao, Jing Sui, Ying Zhang, Lihong Yin

Posted 13 Oct 2018
bioRxiv DOI: 10.1101/441568

Objectives. This study aims to develop a lncRNA signature based on RNA-Seq data to predict overall survival in esophageal cancer patients. Methods. The lncRNA expression profiles and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database on August 30, 2017. Differentially expressed lncRNAs were screened out between tumor tissues and adjacent normal tissues. The univariate and multivariate Cox regression models were used to develop a prognostic signature for all esophageal cancer patients. The receiver operating curve (ROC) was used to test the sensitivity and specificity of lncRNA signature. Survivals were compared via log-rank test. GO and KEGG enrichment analyses were used to explore the potential functions of prognostic lncRNAs. Results. We identified two lncRNAs (RPL34-AS1 and GK3P) were significantly associated with the overall survival of the total 150 esophageal cancer patients. A novel two-lncRNA signature was constructed by Cox regression models. Signature low-risk cases showed better overall survival (median 625.560 days vs. 478.000 days, p = 0.002) than high-risk cases. Further analysis suggested that this two-lncRNA signature was independent of clinical characteristics. GO functional and KEGG pathway enrichment analyses revealed potential functional roles of the two prognostic lncRNAs in tumorigenesis. Conclusions. Our findings suggest that the two-lncRNA signature may be a useful prognostic biomarker for predicting overall survival in esophageal cancer patients.

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