Identification of key genes by integrating DNA methylation and next-generation transcriptome sequencing for esophageal squamous cell carcinoma | Zendy

Yang Chen | Zendy; LianDi Liao | Zendy; ZhiYong Wu | Zendy; Qian Yang | Zendy; Jincheng Guo | Zendy; Jianzhong He | Zendy; Shaohong Wang | Zendy; XiuE Xu | Zendy; JianYi Wu | Zendy; Feng Pan | Zendy; DeChen Lin | Zendy; Li–Yan Xu | Zendy; EnMin Li | Zendy

Open Access

Identification of key genes by integrating DNA methylation and next-generation transcriptome sequencing for esophageal squamous cell carcinoma

Author(s) -

Yang Chen,

LianDi Liao,

ZhiYong Wu,

Qian Yang,

Jincheng Guo,

Jianzhong He,

Shaohong Wang,

XiuE Xu,

JianYi Wu,

Feng Pan,

DeChen Lin,

Li–Yan Xu,

EnMin Li

Publication year - 2020

Publication title -

aging

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.473

H-Index - 90

ISSN - 1945-4589

DOI - 10.18632/aging.102686

Subject(s) - dna methylation , epigenomics , biology , transcriptome , gene , methylation , histone , epigenetics , cancer research , microrna , gene expression , genetics , computational biology

Aberrant DNA methylation leads to abnormal gene expression, making it a significant regulator in the progression of cancer and leading to the requirement for integration of gene expression with DNA methylation. Here, we identified 120 genes demonstrating an inverse correlation between DNA methylation and mRNA expression in esophageal squamous cell carcinoma (ESCC). Sixteen key genes, such as SIX4, CRABP2, and EHD3, were obtained by filtering 10 datasets and verified in paired ESCC samples by qRT-PCR. 5-Aza-dC as a DNA methyltransferase (DNMT) inhibitor could recover their expression and inhibit clonal growth of cancer cells in seven ESCC cell lines. Furthermore, 11 of the 16 genes were correlated with OS (overall survival) and DFS (disease-free survival) in 125 ESCC patients. ChIP-Seq data and WGBS data showed that DNA methylation and H3K27ac histone modification of these key genes displayed inverse trends, suggesting that there was collaboration between DNA methylation and histone modification in ESCC. Our findings illustrate that the integrated multi-omics data (transcriptome and epigenomics) can accurately obtain potential prognostic biomarkers, which may provide important insight for the effective treatment of cancers.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.

Having issues? You can contact us here

Accelerating Research