Oncotarget

Research Papers:

Identification of a RNA-Seq based prognostic signature with five lncRNAs for lung squamous cell carcinoma

Rui-Xue Tang, Wen-Jie Chen, Rong-Quan He, Jiang-Hui Zeng, Liang Liang, Shi-Kang Li, Jie Ma, Dian-Zhong Luo and Gang Chen _

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Oncotarget. 2017; 8:50761-50773. https://doi.org/10.18632/oncotarget.17098

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Abstract

Rui-Xue Tang1,*, Wen-Jie Chen2,*, Rong-Quan He3, Jiang-Hui Zeng1, Liang Liang4, Shi-Kang Li2, Jie Ma3, Dian-Zhong Luo1 and Gang Chen1

1Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China

2Department of Thoracic and Cardiovascular Diseases, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China

3Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China

4Department of General Surgery, First Affiliated Hospital of Guangxi Medical University (West Branch), Nanning, Guangxi Zhuang Autonomous Region, P. R. China

*These authors contributed equally to this work

Correspondence to:

Gang Chen, email: chen_gang_triones@163.com

Dian-Zhong Luo, email: 13878802796@163.com

Keywords: lncRNAs, LUSC, biomarker, prognosis index, overall survival

Received: December 01, 2016     Accepted: April 02, 2017     Published: April 13, 2017

ABSTRACT

Long non-coding RNAs (lncRNAs) expression profile signature for survival assessment in lung squamous cell carcinoma (LUSC) are largely inconsistent due to distinct detecting approaches and small sample size. Systematic and integrative investigation of RNA-Seq based data from The Cancer Genome Atlas (TCGA) herein was performed to determine candidate lncRNAs for prognosis evaluation of LUSC. A total of 60483 genes, including 7589 lncRNAs were assessed in a cohort including 478 LUSC cases with follow-up data. Firstly, 4225 differentially expressed lncRNAs were obtained via R packages. Next, univariate and multivariate Cox proportional hazards regression revealed that 41 lncRNAs were closely related to the survival of LUSC. Finally, lncRNA based prognosis index (PI) could predict overall survival of LUSC with high accuracy (AUC = 0.652, CI: 0.598, 0.705), PI = expCYP4F26PCYP4F26P+expRP11-108M12.3RP11-108M12.3+expRP11-38M8.1RP11-38M8.1+expRP11-54H7.4RP11-54H7.4+expZNF503-AS1ZNF503-AS1. Furthermore, it was confirmed that the five-lncRNA signature could act as an independent prognostic indicator for LUSC (HR = 2.068, p < 0.001 with univariate analysis, HR = 1.928, p = 0.038 with multivariate). Besides, we constructed a weighted gene co-expression network analysis (WGCNA) of key lncRNA RP11-54H7.4 according to the p-value of related genes’ weight. This study provides a RNA-Seq based prognostic signature with five lncRNAs for further clinical application to LUSC patients.


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