DNA methylation biomarkers for the occurrence of lung adenocarcinoma from TCGA data mining

Abstract

The development of lung cancer is a combination of multifactor, multistage, and multiple genetic alterations processes. DNA methylation is an important factor. Currently, the study on the genome-scale epigenetic modification for studying the pathogenesis of lung cancer is still lacking. Here, we aimed to identify the epigenetic modifications of lung cancer, thus to provide scientific basis for the personalized medicine, and research of classification screening for lung adenocarcinoma patients. The DNA methylation data, and the corresponding clinical information of lung adenocarcinoma samples were extracted from the Cancer Genome Atlas (TCGA) database. We explored the association of DNA methylation and gene transcription expression of lung adenocarcinoma by identifying the differentially expressed genes, DNA methylated locis, functional gene clusters, and the relevant genes associated with the survival. We identified 17 differentially expressed genes which had differentially methylated locis, 4 functional gene clusters regulated by methylation, and 522 genes, which were relevant to the survival time of patients. Our study suggested that methylation controlled the gene expression in a variety of ways, which had high/low expression and hyper-/hypo-methylation. Genes of different methylation status showed the different survival curve. The genes and methylated locis identified in this study could be potential biomarkers and therapeutic targets for lung adenocarcinoma.

Associations of PGK1 promoter hypomethylation and PGK1‐mediated PDHK1 phosphorylation with cancer stage and prognosis: a TCGA pan‐cancer analysis

“…We downloaded clinical records, RNAseqV2 level 3 gene level data, and DNA methylation level 3 data for 11,908 cases across 34 cancer types from TCGA (http://xena.ucsc.edu/welcome-to-ucsc-xena/). Profiling data of the TCGA-retrieved cases were generated using the Illumina HiSeq 2000 RNA Sequencing and Illumina Infinium Human Methylation 450 platforms, as described by the TCGA network [16, 17]. Gene transcription estimates for each gene were presented as in RNA-Seq using the Expectation Maximization (RSEM) software.…”

Diagnostic and prognostic value of the BEX family in lung adenocarcinoma

“…However, few studies have investigated the association between the BEX family and lung cancer. A previous study reported that high expression levels of BEX2 and BEX4 were significantly associated with a favorable prognosis in patients with LUAD (21). Furthermore, overexpression of BEX4 may promote LUAD cell proliferation and growth in vitro (22).…”

The chromosome 19 microRNA cluster, regulated by promoter hypomethylation, is associated with tumour burden and poor prognosis in patients with hepatocellular carcinoma

“…In this study, we used HCC data from The Cancer Genome Atlas (TCGA; Zhu, Zhu, Wu, & Hu, 2018) to explore the differential expression level as well as the methylation level of the C19MC in HCC, together with evaluating the significant correlation between them. We further assessed the correlation between C19MC expression and clinical features.…”