Dataset Information

[Bioinformatics Analysis of DNA Methylation in the Promoters of LincRNA ?in Lung Adenocarcinoma].

ABSTRACT: BACKGROUND:Previous studies have found the lincRNAs play important roles in the occurrence and development of lung adenocarcinoma, but their regulated mechanims are still unclear. The aim of this study is to evaluate the relationship between DNA methylation and lincRNA expression, and the effect of prognosis in lung adenocarcinoma. METHODS:The whole genome Illumina Methylation 450 DNA methylatiuon data and RNAseq for lung adenocarcinoma were download from TCGA. DNA methylation around lincRNA and their relationship to gene expression were analyzed. Their contribution to lung adenocarcinoma were further analyzed by comparing DNA methylation and lincRNA expression in tumor and adjacent tissues. RESULTS:The methylation level in promoter region was lower than other positions in lincRNA, and was negatively correlated with gene expression. There were 427 lincRNA genes showed differential DNA methylation in their promoter regions in tumor and adjacent tissues. Among these, 15 lincRNA genes showed differential gene expression and negatively correlated with DNA methylation, including FENDRR (a tumor progression and metastasis gene) whose high methylation in its promoter showed poor survival in lung adenocarcinoma. CONCLUSIONS:The expression of lincRNA can be regulated by DNA methylation in their promoter regions, and the level of DNA methylation is related to patient prognosis in lung adenocarcinoma.

SUBMITTER: Zhang W

PROVIDER: S-EPMC6022035 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

[Bioinformatics Analysis of DNA Methylation in the Promoters of LincRNA  in Lung Adenocarcinoma].

Zhang Wen W Li Shaojun S Guo Nannan N Zhao Yingnan Y

Zhongguo fei ai za zhi = Chinese journal of lung cancer 20180601 6

<h4>Background</h4>Previous studies have found the lincRNAs play important roles in the occurrence and development of lung adenocarcinoma, but their regulated mechanims are still unclear. The aim of this study is to evaluate the relationship between DNA methylation and lincRNA expression, and the effect of prognosis in lung adenocarcinoma.<h4>Methods</h4>The whole genome Illumina Methylation 450 DNA methylatiuon data and RNAseq for lung adenocarcinoma were download from TCGA. DNA methylation aro ...[more]

PMID: 29945706

Similar Datasets

Project description:BackgroundAberrant DNA methylation is common in lung adenocarcinoma, but its timing in the phases of tumor development is largely unknown. Delineating when abnormal DNA methylation arises may provide insight into the natural history of lung adenocarcinoma and the role that DNA methylation alterations play in tumor formation.Methodology/principal findingsWe used MethyLight, a sensitive real-time PCR-based quantitative method, to analyze DNA methylation levels at 15 CpG islands that are frequently methylated in lung adenocarcinoma and that we had flagged as potential markers for non-invasive detection. We also used two repeat probes as indicators of global DNA hypomethylation. We examined DNA methylation in 249 tissue samples from 93 subjects, spanning the putative spectrum of peripheral lung adenocarcinoma development: histologically normal adjacent non-tumor lung, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS, formerly known as bronchioloalveolar carcinoma), and invasive lung adenocarcinoma. Comparison of DNA methylation levels between the lesion types suggests that DNA hypermethylation of distinct loci occurs at different time points during the development of lung adenocarcinoma. DNA methylation at CDKN2A ex2 and PTPRN2 is already significantly elevated in AAH, while CpG islands at 2C35, EYA4, HOXA1, HOXA11, NEUROD1, NEUROD2 and TMEFF2 are significantly hypermethylated in AIS. In contrast, hypermethylation at CDH13, CDX2, OPCML, RASSF1, SFRP1 and TWIST1 and global DNA hypomethylation appear to be present predominantly in invasive cancer.Conclusions/significanceThe gradual increase in DNA methylation seen for numerous loci in progressively more transformed lesions supports the model in which AAH and AIS are sequential stages in the development of lung adenocarcinoma. The demarcation of DNA methylation changes characteristic for AAH, AIS and adenocarcinoma begins to lay out a possible roadmap for aberrant DNA methylation events in tumor development. In addition, it identifies which DNA methylation changes might be used as molecular markers for the detection of preinvasive lesions.

Dataset Information

[Bioinformatics Analysis of DNA Methylation in the Promoters of LincRNA ?in Lung Adenocarcinoma].

Publications

[Bioinformatics Analysis of DNA Methylation in the Promoters of LincRNA  in Lung Adenocarcinoma].

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Dataset Information

[Bioinformatics Analysis of DNA Methylation in the Promoters of LincRNA ?in Lung Adenocarcinoma].

Publications

[Bioinformatics Analysis of DNA Methylation in the Promoters of LincRNA in Lung Adenocarcinoma].

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

[Bioinformatics Analysis of DNA Methylation in the Promoters of LincRNA  in Lung Adenocarcinoma].