Transcriptional profiling analysis and functional prediction of long noncoding RNAs in cancer

Abstract

// Jiao Yuan 1, 2, 3, * , Haiyan Yue 1, 2, 3, * , Meiying Zhang 4 , Jianjun Luo 1, 2 , Lihui Liu 1, 2, 3 , Wei Wu 1, 2, 3 , Tengfei Xiao 1, 2 , Xiaowei Chen 1, 2 , Xiaomin Chen 1, 2 , Dongdong Zhang 1, 2 , Rui Xing 5 , Xin Tong 6 , Nan Wu 5 , Jian Zhao 6, 7 , Youyong Lu 5 , Mingzhou Guo 4 , Runsheng Chen 1, 2 1 Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China 2 Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China 3 University of Chinese Academy of Sciences, Beijing 100049, China 4 Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China 5 Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China 6 PLA General Hospital Cancer Center Key Laboratory, Medical School of Chinese PLA, Beijing 100853, China 7 International Joint Cancer Institute, the Second Military Medical University, Shanghai 200433, China * These authors have contributed equally to this work Correspondence to: Runsheng Chen, e-mail: rschen@ibp.ac.cn Mingzhou Guo, e-mail: mzguo@hotmail.com Youyong Lu, e-mail: youyonglu@hsc.pku.edu.cn Jian Zhao, e-mail: zhaojian@smmu.edu.cn Keywords: IncRNA, expression, biomarker, gastric cancer, colon cancer Received: August 10, 2015      Accepted: January 01, 2016      Published: January 23, 2016 ABSTRACT Long noncoding RNAs (lncRNAs), which are noncoding RNAs (ncRNAs) with length more than 200 nucleotides (nt), have been demonstrated to be involved in various types of cancer. Consequently, it has been frequently discussed that lncRNAs with aberrant expression in cancer serve as potential diagnostic biomarkers and therapeutic targets. However, one major challenge of developing cancer biomarkers is tumor heterogeneity which means that tumor cells show different cellular morphology, metastatic potential as well as gene expression. In this study, a custom designed microarray platform covering both mRNAs and lncRNAs was applied to tumor tissues of gastric, colon, liver and lung. 316 and 157 differentially expressed (DE-) protein coding genes and lncRNAs common to these four types of cancer were identified respectively. Besides, the functional roles of common DE-lncRNAs were inferred based on their expression and genomic position correlation with mRNAs. Moreover, mRNAs and lncRNAs with tissue specificity were also identified, suggesting their particular roles with regard to specific biogenesis and functions of different organs. Based on the large-scale survey of mRNAs and lncRNAs in four types of cancer, this study may offer new biomarkers common or specific for various types of cancer.