Oncotarget

Research Papers:

The landscape of DNA methylation-mediated regulation of long non-coding RNAs in breast cancer

Chunlong Zhang, Xinyu Wang, Xuecang Li, Ning Zhao, Yihan Wang, Xiaole Han, Ce Ci, Jian Zhang, Meng Li and Yan Zhang _

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Oncotarget. 2017; 8:51134-51150. https://doi.org/10.18632/oncotarget.17705

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Abstract

Chunlong Zhang1,*, Xinyu Wang2,*, Xuecang Li1, Ning Zhao3, Yihan Wang2, Xiaole Han1, Ce Ci2, Jian Zhang1, Meng Li1 and Yan Zhang2

1Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China

2College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China

3School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150081, China

*These authors contributed equally to this work

Correspondence to:

Yan Zhang, email: tyozhang@ems.hrbmu.edu.cn

Keywords: lncRNA, DNA methylation, network, breast cancer, hallmark

Received: February 24, 2017     Accepted: April 24, 2017     Published: May 08, 2017

ABSTRACT

Although systematic studies have identified a host of long non-coding RNAs (lncRNAs) which are involved in breast cancer, the knowledge about the methyla-tion-mediated dysregulation of those lncRNAs remains limited. Here, we integrated multi-omics data to analyze the methylated alteration of lncRNAs in breast invasive carcinoma (BRCA). We found that lncRNAs showed diverse methylation patterns on promoter regions in BRCA. LncRNAs were divided into two categories and four subcategories based on their promoter methylation patterns and expression levels be-tween tumor and normal samples. Through cis-regulatory analysis and gene ontology network, abnormally methylated lncRNAs were identified to be associated with can-cer regulation, proliferation or expression of transcription factors. Competing endog-enous RNA network and functional enrichment analysis of abnormally methylated lncRNAs showed that lncRNAs with different methylation patterns were involved in several hallmarks and KEGG pathways of cancers significantly. Finally, survival analysis based on mRNA modules in networks revealed that lncRNAs silenced by high methylation were associated with prognosis significantly in BRCA. This study enhances the understanding of aberrantly methylated patterns of lncRNAs and pro-vides a novel insight for identifying cancer biomarkers and potential therapeutic tar-gets in breast cancer.


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