Abstract
Accumulating evidence highlights the important role of long non-coding RNAs (lncRNAs) in a large number of biological processes. However, the knowledge of genome scale expression of lncRNAs and their potential biological function in gastric cancer is still lacking. Using RNA-seq data from 420 gastric cancer patients in The Cancer Genome Atlas (TCGA), we identified 1,294 lncRNAs differentially expressed in gastric cancer compared with adjacent normal tissues. We also found 247 lncRNAs differentially expressed between intestinal subtype and diffuse subtype. Survival analysis revealed 33 lncRNAs independently associated with patient overall survival, of which 6 lncRNAs were validated in the internal validation set. There were 181 differentially expressed lncRNAs located in the recurrent somatic copy number alterations (SCNAs) regions and their correlations between copy number and RNA expression level were also analyzed. In addition, we inferred the function of lncRNAs by construction of a co-expression network for mRNAs and lncRNAs. Together, this study presented an integrative analysis of lncRNAs in gastric cancer and provided a valuable resource for further functional research of lncRNAs in gastric cancer.
Highlights
Gastric cancer is the fourth most common cancer and the second leading cause of cancerrelated death worldwide [1]
To systematically identify Long non-coding RNAs (lncRNAs) related to gastric cancer, RNA-seq data of 420 gastric cancers and 36 adjacent normal tissues were retrieved from The Cancer Genome Atlas (TCGA)
By the criteria of adjusted p-value < 0.05 and absolute fold change > 2, we identified 1,294 lncRNAs differentially expressed in gastric cancer compared with adjacent normal tissues, among which 846 were up-regulated and 448 were down-regulated (Fig 1A and S1 Table)
Summary
Gastric cancer is the fourth most common cancer and the second leading cause of cancerrelated death worldwide [1]. Without apparent protein coding potential, lncRNAs play critical regulatory roles in a large number of biological processes such as chromatin remodeling, transcription, post-transcriptional processing and intracellular trafficking [3, 4]. It was reported that lncRNAs played a role in carcinogenesis and could be diagnostic or prognostic biomarkers for gastric cancer. GAPLINC was firstly identified in gastric cancer and its upregulation was associated with shorter survival of gastric cancer patients [5]. Another lncRNA, GClnc, was up-regulated and associated with tumorigenesis, tumor size, metastasis, and poor prognosis in gastric cancer.
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