Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma
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...
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doaj-e97e7b11cbd04cb491369857e4e1baf62020-11-24T21:23:57ZengHindawi LimitedInternational Journal of Genomics2314-436X2314-43782013-01-01201310.1155/2013/480534480534Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell CarcinomaWei Cao0Wei Wu1Fachun Shi2Xiaobing Chen3Lihua Wu4Ke Yang5Fu Tian6Minghui Zhu7Guoyong Chen8WeiWei Wang9Fred G. Biddle10Jianqin Gu11Clinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaClinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaScience and Education Department, Health Bureau of Zhengzhou, ChinaClinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaClinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaClinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaClinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaClinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaClinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaClinical Research Center, People’s Hospital of Zhengzhou, 33 Yellow River Road, Zhengzhou, Henan 45003, ChinaDepartments of Medical Genetics and Biological Sciences, University of Calgary, Calgary, AB, T2N 4N1, CanadaScience and Education Department, Health Bureau of Zhengzhou, ChinaTumorigenesis 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.http://dx.doi.org/10.1155/2013/480534 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Wei Cao Wei Wu Fachun Shi Xiaobing Chen Lihua Wu Ke Yang Fu Tian Minghui Zhu Guoyong Chen WeiWei Wang Fred G. Biddle Jianqin Gu |
spellingShingle |
Wei Cao Wei Wu Fachun Shi Xiaobing Chen Lihua Wu Ke Yang Fu Tian Minghui Zhu Guoyong Chen WeiWei Wang Fred G. Biddle Jianqin Gu Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma International Journal of Genomics |
author_facet |
Wei Cao Wei Wu Fachun Shi Xiaobing Chen Lihua Wu Ke Yang Fu Tian Minghui Zhu Guoyong Chen WeiWei Wang Fred G. Biddle Jianqin Gu |
author_sort |
Wei Cao |
title |
Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma |
title_short |
Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma |
title_full |
Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma |
title_fullStr |
Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma |
title_full_unstemmed |
Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma |
title_sort |
integrated analysis of long noncoding rna and coding rna expression in esophageal squamous cell carcinoma |
publisher |
Hindawi Limited |
series |
International Journal of Genomics |
issn |
2314-436X 2314-4378 |
publishDate |
2013-01-01 |
description |
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. |
url |
http://dx.doi.org/10.1155/2013/480534 |
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