Journal article
Integrative analysis to identify oncogenic gene expression changes associated with copy number variations of enhancer in ovarian cancer
Oncotarget, Vol.8(53), pp.91558-91567
2017
Abstract
Enhancers are short regulatory regions (50-1500 bp) of DNA that control the tissue-specific activation of gene expression by long distance interaction with targeting gene regions. Recently, genome-wide identification of enhancers in diverse tissues and cell lines was achieved using high-throughput sequencing. Enhancers have been associated with malfunctions in cancer development resulting from point mutations in regulatory regions. However, the potential impact of copy number variations (CNVs) on enhancer regions is unknown. To learn more about the relationship between enhancers and cancer, we integrated the CNVs data on enhancers and explored their targeting gene expression pattern in high-grade ovarian cancer. Using human enhancer-gene interaction data with 13,691 interaction pairs between 7,905 enhancers and 5,297 targeting genes, we found that the 2,910 copy number gain events of enhancer are significantly correlated with the up-regulation of targeting genes. We further identified that a number of highly mutated superenhancers, with concordant gene expression change on their targeting genes. We also identified 18 targeting genes by super-enhancers with prognostic significance for ovarian cancer, such as the tumour suppressor CDKN1B. We are the first to report that abundant copy number variations on enhancers could change the expression of their targeting genes which would be valuable for the design of enhancer-based cancer treatment strategy. © Li et al.
Details
- Title
- Integrative analysis to identify oncogenic gene expression changes associated with copy number variations of enhancer in ovarian cancer
- Authors
- Xiaoyan Li (Author) - Capital Medical University, ChinaYining Liu (Author) - Guangzhou Medical University, ChinaJiachun Lu (Author) - Guangzhou Medical University, ChinaMin Zhao (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
- Publication details
- Oncotarget, Vol.8(53), pp.91558-91567
- Publisher
- Impact Journals LLC
- Date published
- 2017
- DOI
- 10.18632/oncotarget.21227
- ISSN
- 1949-2553
- Copyright note
- Copyright © 2017 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- Organisation Unit
- School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; GeneCology Research Centre - Legacy; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99451086602621
- Output Type
- Journal article
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