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International Journal of Genomics
Volume 2013, Article ID 480534, 10 pages
http://dx.doi.org/10.1155/2013/480534
Research Article

Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma

1Clinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, China
2Department of Pathology and Experimental Medicine, University of Calgary, Calgary, AB, Canada T2N 4N1
3Science and Education Department, Health Bureau of Zhengzhou, China
4Departments of Medical Genetics and Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 4N1

Received 28 May 2013; Accepted 26 August 2013

Academic Editor: Soraya E. Gutierrez

Copyright © 2013 Wei Cao et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Tumorigenesis is a complex dynamic biological process that includes multiple steps of genetic and epigenetic alterations, aberrant expression of noncoding RNA, and changes in the expression profiles of coding genes. We call the collection of those perturbations in genome space the “cancer initiatome.” Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome and they have key regulatory functions in chromatin remodeling and gene expression. Spatiotemporal variation in the expression of lncRNAs has been observed in development and disease states, including cancer. A few dysregulated lncRNAs have been studied in cancers, but the role of lncRNAs in the cancer initiatome remains largely unknown, especially in esophageal squamous cell carcinoma (ESCC). We conducted a genome-wide screen of the expression of lncRNAs and coding RNAs from ESCC and matched adjacent nonneoplastic normal tissues. We identified differentially expressed lncRNAs and coding RNAs in ESCC relative to their matched normal tissue counterparts and validated the result using polymerase chain reaction analysis. Furthermore, we identified differentially expressed lncRNAs that are co-located and co-expressed with differentially expressed coding RNAs in ESCC and the results point to a potential interaction between lncRNAs and neighboring coding genes that affect ether lipid metabolism, and the interaction may contribute to the development of ESCC. These data provide compelling evidence for a potential novel genomic biomarker of esophageal squamous cell cancer.