Epigenetic clustering of lung adenocarcinomas based on DNA methylation profiles in adjacent lung tissue: Its correlation with smoking history and chronic obstructive pulmonary disease

Abstract

The aim of this study was to clarify the significance of DNA methylation alterations during lung carcinogenesis. Infinium assay was performed using 139 paired samples of non-cancerous lung tissue (N) and tumorous tissue (T) from a learning cohort of patients with lung adenocarcinomas (LADCs). Fifty paired N and T samples from a validation cohort were also analyzed. DNA methylation alterations on 1,928 probes occurred in N samples relative to normal lung tissue from patients without primary lung tumors, and were inherited by, or strengthened in, T samples. Unsupervised hierarchical clustering using DNA methylation levels in N samples on all 26,447 probes subclustered patients into Cluster I (n = 32), Cluster II (n = 35) and Cluster III (n = 72). LADCs in Cluster I developed from the inflammatory background in chronic obstructive pulmonary disease (COPD) in heavy smokers and were locally invasive. Most patients in Cluster II were non-smokers and had a favorable outcome. LADCs in Cluster III developed in light smokers were most aggressive (frequently showing lymphatic and blood vessel invasion, lymph node metastasis and an advanced pathological stage), and had a poor outcome. DNA methylation levels of hallmark genes for each cluster, such as IRX2, HOXD8, SPARCL1, RGS5 and EI24, were again correlated with clinicopathological characteristics in the validation cohort. DNA methylation profiles reflecting carcinogenetic factors such as smoking and COPD appear to be established in non-cancerous lung tissue from patients with LADCs and may determine the aggressiveness of tumors developing in individual patients, and thus patient outcome.

DNA methylation and RNA expression profiles in lung adenocarcinomas of never-smokers

“…A smaller study focused on the methylation patterns of tumor suppressor genes reported that p16 was more commonly methylated in never smokers than current or former smokers [29]. A different study showed that heavy smokers, light smokers and never smokers separated into different groups based on an unsupervised hierarchical clustering analysis of DNA methylation levels [30]. Additionally, work from The Cancer Genome Atlas identified three sets of CpG island methylator phenotype (CIMP) samples: high, intermediate and low.…”

Modifications of H3K4 methylation levels are associated with DNA hypermethylation in acute myeloid leukemia

“…Loss of expression was particularly prevalent among samples for IRX2. Interestingly, IRX2 has been suggested to function in lineage-specific epithelial cell differentiation in the breast tissue and to act as a tumor suppressor or oncogene depending on the cellular and tissue context [54][55][56][57][58][59][60][61]. Therefore, we used infection with lentiviral expression constructs to restore IRX2 in HL60 and AML-193 cell lines to determine the gene's impact on differentiation block in AML.…”

An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers

“…11 In NSCLC, hypermethylation at CpG-dense sequences in gene promoters (CpG islands) is associated with cigarette smoking 12 , histological subtype 13, 14 , progression 15, 16 , clinically-relevant molecular subtypes 17, 18 , and patient prognosis 19, 20 . Here, from genome-wide screening of differential DNA methylation in adjacent tumor and non-tumor tissues from three cohorts, HOXA9 promoter methylation emerged as a candidate prognostic biomarker.…”