J Gynecol Oncol.  2017 Nov;28(6):e83. 10.3802/jgo.2017.28.e83.

Identification of DNA methylation associated gene signatures in endometrial cancer via integrated analysis of DNA methylation and gene expression systematically

• Men C
• Chai H
• Song X
• Li Y
• Du H
• Ren Q

• KMID: 2413209
• DOI: http://doi.org/10.3802/jgo.2017.28.e83

Abstract

OBJECTIVE
Endometrial cancer (EC) is a common gynecologic cancer worldwide. However, the pathogenesis of EC has not been epigenetically elucidated. Here, this study aims to describe the DNA methylation profile and identify favorable gene signatures highly associated with aberrant DNA methylation changes in EC.
METHODS
The data regarding DNA methylation and gene expression were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially methylated CpG sites (DMCs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs) were identified, and the relationship between the 2 omics was further analyzed. In addition, weighted CpG site co-methylation network (WCCN) was constructed followed by an integrated analysis of DNA methylation and gene expression data.
RESULTS
Four hundred thirty-one tumor tissues and 46 tissues adjacent tumor of EC patients were analyzed. One thousand one hundred thirty-five DMCs (merging to 10 DMRs), and 1,488 DEGs were obtained between tumor and normal groups, respectively. One hundred forty-eight DMCs-DEGs correlated pairs and 13 regional DMCs-DEGs pairs were obtained. Interestingly, we found that some hub genes in 2 modules among 8 modules of WCCN analysis were down-regulated in tumor samples. Furthermore, protocadherins (PCDHs) clusters, DDP6, TNXB, and ZNF154 were identified as novel deregulated genes with altered methylation in EC.
CONCLUSION
Based on the analysis of DNA methylation in a systematic view, the potential long-range epigenetic silencing (LRES) composed of PCDHs was reported in ECs for the first time. PCDHs clusters, DDP6, and TNXB were firstly found to be associated with tumorigenesis, and may be novel candidate biomarkers for EC.

Keyword

Endometrial Neoplasms; DNA Methylation; Gene Expression

MeSH Terms

Cadherins/*genetics
Carcinoma, Endometrioid/*genetics
*DNA Methylation
Endometrial Neoplasms/*genetics
Female
Gene Expression Regulation, Neoplastic
Humans
Kruppel-Like Transcription Factors/*genetics
Neoplasms, Cystic, Mucinous, and Serous/*genetics
Tenascin/*genetics
Transcriptome
Cadherins
Kruppel-Like Transcription Factors
Tenascin