Variable DNA methylation of aging-related genes is associated with male COPD

Abstract

BackgroundChronic obstructive pulmonary disease (COPD) is a chronic lung inflammatory disease which has a close relationship with aging. Genome-wide analysis reveals that DNA methylation markers vary obviously with age. DNA methylation variations in peripheral blood have the potential to be biomarkers for COPD. However, the specific DNA methylation of aging-related genes in the peripheral blood of COPD patients remains largely unknown.MethodsFirstly, 9 aging-related differentially expressed genes (DEGs) in COPD patients were screened out from the 25 aging-related genes profile through a comprehensive screening strategy. Secondly, qPCR and multiple targeted bisulfite enrichment sequencing (MethTarget) were used to detect the mRNA level and DNA methylation level of the 9 differentially expressed genes in the peripheral blood of 60 control subjects and 45 COPD patients. The candidate functional CpG sites were selected on the basis of the regulation ability of the target gene expression. Thirdly, the correlation was evaluated between the DNA methylation level of the key CpG sites and the clinical parameters of COPD patients, including forced expiratory volume in one second (FEV1), forced expiratory volume in one second as percentage of predicted volume (FEV1%), forced expiratory volume/ forced vital capacity (FEV/FVC), modified British medical research council (mMRC) score, acute exacerbation frequency and the situation of frequent of acute aggravation (CAT) score. Lastly, differentially methylated CpG sites unrelated to smoking were also determined in COPD patients.ResultsOf the 9 differentially expressed aging-related genes, the mRNA expression of 8 genes were detected to be significantly down-regulated in COPD group, compared with control group. Meanwhile, the methylated level of all aging-related genes was changed in COPD group containing 219 COPD-related CpG sites in total. Notably, 27 CpG sites of FOXO3 gene showed a lower False Discovery Rate (FDR) and higher methylation difference values. Also, some variable DNA methylation is associated with the severity of COPD. Additionally, of the 219 COPD-related CpG sites, 147 CpG sites were not related to smoking.ConclusionThese results identified that the mRNA expression and DNA methylation level of aging-related genes were changed in male COPD patients, which provides a molecular link between aging and COPD. The identified CpG markers are associated with the severity of COPD and provide new insights into the prediction and identification of COPD.

Variable Expressed Methylation Sites of Aging-related Genes in Asthma

“…Aging-related CpG sites have insu cient DNAm or DNA hypermethylation in COPD and other aging-related diseases [40,41]. Our previous research identi ed the differential expression and DNAm level of aging-related genes in COPD patients [18]. As asthma and COPD have similar even overlapping clinical phenotypes in chronic in ammation and decreased lung function.…”

“…CpG islands located between 2K upstream of the gene transcription start site and 1K downstream of the rst exon were selected to measure methylation level. 18 CpG islands from the 9 screened aging-related genes were selected (2 from AREG, 2 from ATG3, 1 from E2F1, 3 from FOXO3, 1 from HDAC1, 3 from MMP2, 1 from NUF2, 3 from TGFB1 and 2 from TP53) according to our previous publications [18]. Then, bisul te modi cation of DNA sample, methylation library construction and MethTarget were performed [18].…”

“…18 CpG islands from the 9 screened aging-related genes were selected (2 from AREG, 2 from ATG3, 1 from E2F1, 3 from FOXO3, 1 from HDAC1, 3 from MMP2, 1 from NUF2, 3 from TGFB1 and 2 from TP53) according to our previous publications [18]. Then, bisul te modi cation of DNA sample, methylation library construction and MethTarget were performed [18]. 856 CpG sites from 9 distinguishingly expressed aging-related genes in the methylation assay were detected.…”

“…Our previous study screened and evaluated the differentially expression and methylation levels of 9 aging-related genes (AREG, ATG3, E2F1, FOXO3, HDAC1, MMP2, NUF2, TGFB1and TP53) in COPD patients [18]. It is found that DNAm regulates the expression of 9 aging-related genes in peripheral venous blood of COPD patients.…”

“…It is found that DNAm regulates the expression of 9 aging-related genes in peripheral venous blood of COPD patients. Besides, the methylation level of certain special CpG sites was closely related to the incidence and severity of COPD [18]. To further probe the potential involvement of these previous screened 9 aging-related genes in the parthenogenesis of asthma, we aim to probe the involvement of DNAm of aging-related genes in asthma patients.…”