Abstract
Esophageal squamous cell carcinoma (ESCC) is the leading cause of cancer-related death worldwide. Previous studies have suggested that DNA methylation involved in the development of ESCC. However, the precise mechanisms underlying the regulation and maintenance of the methylome as well as their relationship with ESCC remain poorly understood. Herein, we used methylated DNA immunoprecipitation sequencing (MeDIP-Seq) and RNA-Seq to investigate whole-genome DNA methylation patterns and the genome expression profiles in ESCC samples. The results of MeDIP-Seq analyses identified differentially methylated regions (DMRs) covering almost the entire genome with sufficient depth and high resolution. The gene ontology (GO) analysis showed that the DMRs related genes belonged to several different ontological domains, such as cell cycle, adhesion, proliferation and apoptosis. The RNA-Seq analysis identified a total of 6150 differentially expressed genes (3423 up-regulated and 2727 down-regulated). The significant GO terms showed that these genes belonged to several molecular functions and biological pathways. Moreover, the bisulfite-sequencing of genes MLH1, CDH5, TWIST1 and CDX1 confirmed the methylation status identified by MeDIP-Seq. And the mRNA expression levels of MLH1, TWIST1 and CDX1 were consistent with their DNA methylation profiles. The DMR region of MLH1 was found to correlate with survival. The identification of whole-genome DNA methylation patterns and gene expression profiles in ESCC provides new insight into the carcinogenesis of ESCC and represents a promising avenue through which to investigate novel therapeutic targets.
Highlights
Esophageal cancer, mainly including squamous cell carcinoma and adenocarcinoma, is the sixth leading cause of cancer-related death and the eighth most common cancer worldwide [1, 2]
Esophageal squamous cell carcinoma (ESCC), which mainly occurs in an area referred to the “esophageal cancer belt” that extends from northeast China to the Middle East [4], constitutes the vast majority of cases [5, 6]
In the ESCC group, 90.89 % of the reads could be mapped to human genome and 73.26% were uniquely mapped to human genome
Summary
Esophageal cancer, mainly including squamous cell carcinoma and adenocarcinoma, is the sixth leading cause of cancer-related death and the eighth most common cancer worldwide [1, 2]. It is considered as a serious malignancy with respect to its extremely aggressive histopathological features and poor survival rate [3]. Total number of mapped reads Mapping rate(%) ESCC NE. Total number of unique Unique mapping mapped reads rate (%). With the increasing understanding of genetic and epigenetic mechanisms of the carcinogenesis, many studies indicated that highly sensitive and specific molecular biomarkers would help to optimize the clinical management of esophageal carcinomas and improve patient outcomes
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