Background LncRNAs, range from 200 nt to >100 kilobases (kb), demonstrate a wide range of structural and functional roles through the regulation of a metastable epigenome and transcriptional network. Recently, accumulating evidence indicates aberrant expression of LncRNAs may play an important role in cancer biology.
Objective To study the profile of differentially expressed LncRNAs in esophageal cancer tissues and the adjacent normal tissues, and to find out the possible function of LncRNAs involved in the process of tumor development preliminarily.
Methods The total RNA were extracted from esophageal cancer tissues and the adjacent normal tissues and were quantified by the NanoDrop ND-1000 and standard denaturing agarose gel electrophoresis. Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar) including the global profiling of 33,045 human LncRNAs and 30,215 coding transcripts and then were scanned by the Agilent Scanner G2505B. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering or Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of those differentially expressed mRNAs played in biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.
Results With a criterion of Fold Change >= 2.0 and P-value <= 0.05, 1019 of differentially expressed LncRNAs were identified in esophageal cancer tissues, including 399 of overexpressed LncRNAs and 620 of downexpressed LncRNAs. The top 10 of aberrant LncRNAs were AK022914, chr10:127700955-127703336, LOC284233, RP11-38M15.6, RNU12, FAM25E, C21orf81, AK095500, AC009336.24, and RP11-397A15.4. Using GENCODE annotation of human genes, 11 of differentially expressed enhancer-like LncRNAs and their nearby coding genes were identified. In addition, there were 25 of differentially expressed lincRNAs and nearby coding gene pairs associated with esophageal cancer according to John Rinn reported lincRNAs profiling. The differentially expressed transcripts were further identified and the matched coding genes adjacent to differentially expressed LncRNAs (distance < 300kb) showed participating in the processes of cell cycle, cell differentiation, protease activities, and et al according to GO analysis and Pathway analysis.
Conclusions The results suggests a specific profile of differentially expressed LncRNAs in esophageal cancer, which function prediction implies the broad participation in the processes of oncogenesis.
Citation Format: Ran Liu, Miao Yang, Juan Liao, Yi Wang, Enchun Pan, Wei Guo, Lihong Yin, Yuepu Pu. A pilot study of long non-coding RNA expression profile in esophageal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1835. doi:10.1158/1538-7445.AM2013-1835
Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.