Analysis of tissue-specific differentially methylated genes with differential gene expression in non-small cell lung cancers

Abstract

Adenocarcinoma (ADC) and squamous cell carcinomas (SCC) are two subtypes of non small cell lung carcinomas which are regarded as the leading cause of cancer related malignancy worldwide. The aim of this study was to detect the differentially methylated loci (DML) and differentially methylated genes (DMGs) of these two tumor sets, and then to illustrate the different expression levels of specific methylated genes. Using the TCGA database and Illumina HumanMethylation27 arrays, we first screened the DMGs and DML in tumor samples. Then, we explored the Biological Process terms of hypermethylated and hypom ethylated genes using Functional Gene Ontology (GO) catalogues. Hypermethylation intensively occurred in the CpG island, whereas hypomethylation was located in the non CpG island. Most SCC and ADC hypermethylated genes involved GO function of DNA dependent regulation of transcription, and hypome thylated genes mainly enriched in the term of immune responses. Additionally, the expression levels of spe cific differentially methylated genes are distinct between ADC and SCC. It was concluded that ADC and SCC have a different methylation status that might play an important role in carcinogenesis.

Integrated analysis of gene expression and DNA methylation datasets identified key genes and a 6-gene prognostic signature for primary lung adenocarcinoma

“…Moreover, those HR values were less than 1, and these two genes were hypermethylated, suggesting genes B3GALT2 and VSIG2 with hypermethylated-down-regulation were protective genes. In a former study, 1 down-regulated gene B3GALT2 was identified among 139 LUAD-specific hypermethylated genes ( Yin et al, 2014 ), which is in line with our results. B3GALT2 is applied to form a prognostic biomarker of carcinoma-associated fibroblasts in NSCLC ( Navab et al, 2011 ).…”

Comprehensive multimodal and multiomic profiling reveals epigenetic and transcriptional reprogramming in lung tumors

“…The reliability of this method was underscored by the substantial literature support for more than 77% of SPDEF’s regulatees, highlighting their close interaction with NSCLC ( Figure 6B ). These regulatees encompass a diverse range of biomolecules, including early-stage biomarkers (ATXN10 55 ), validated therapeutic targets (TCP1 56 ), small-nuclear RNAs with prognostic potentials (SNORA7B 57,58 ), and genes that control migration and invasion of NSCLC (SERINC2 59 and VANGL2 60 ). For instance, the long noncoding RNA (lncRNA) RP11-523H20.3 61 has been demonstrated to be related with the proliferation and metastasis of NSCLC.…”