Global Methylation Patterns in Idiopathic Pulmonary Fibrosis

Abstract

BackgroundIdiopathic Pulmonary Fibrosis (IPF) is characterized by profound changes in the lung phenotype including excessive extracellular matrix deposition, myofibroblast foci, alveolar epithelial cell hyperplasia and extensive remodeling. The role of epigenetic changes in determining the lung phenotype in IPF is unknown. In this study we determine whether IPF lungs exhibit an altered global methylation profile.Methodology/Principal FindingsImmunoprecipitated methylated DNA from 12 IPF lungs, 10 lung adenocarcinomas and 10 normal histology lungs was hybridized to Agilent human CpG Islands Microarrays and data analysis was performed using BRB-Array Tools and DAVID Bioinformatics Resources software packages. Array results were validated using the EpiTYPER MassARRAY platform for 3 CpG islands. 625 CpG islands were differentially methylated between IPF and control lungs with an estimated False Discovery Rate less than 5%. The genes associated with the differentially methylated CpG islands are involved in regulation of apoptosis, morphogenesis and cellular biosynthetic processes. The expression of three genes (STK17B, STK3 and HIST1H2AH) with hypomethylated promoters was increased in IPF lungs. Comparison of IPF methylation patterns to lung cancer or control samples, revealed that IPF lungs display an intermediate methylation profile, partly similar to lung cancer and partly similar to control with 402 differentially methylated CpG islands overlapping between IPF and cancer. Despite their similarity to cancer, IPF lungs did not exhibit hypomethylation of long interspersed nuclear element 1 (LINE-1) retrotransposon while lung cancer samples did, suggesting that the global hypomethylation observed in cancer was not typical of IPF.Conclusions/SignificanceOur results provide evidence that epigenetic changes in IPF are widespread and potentially important. The partial similarity to cancer may signify similar pathogenetic mechanisms while the differences constitute IPF or cancer specific changes. Elucidating the role of these specific changes will potentially allow better understanding of the pathogenesis of IPF.

Global DNA methylation and PTEN hypermethylation alterations in lung tissues from human silicosis

“…Genome-wide methylation arrays show that 402 differentially methylated CpG islands overlapped between IPF and lung cancer, three genes expression positive correlation with hypomethylated promoters (32). The Human Methylation 27 array find that multiple CpG sites across the genome are differentially methylated in IPF fibroblasts (33).…”

DNA methylation in the tumor microenvironment

“…Myofibroblasts are the primary contributors to fibrosis, which drives some invasive cancers, especially liver cancer (Pinzani et al, 2005;de Wever et al, 2008). Many studies have explored methylation changes in fibrotic diseases such as hepatic, pulmonary, and renal fibrosis (Mann et al, 2010;Rabinovich et al, 2012;Tampe et al, 2014). Gotze et al (2015) found global DNA hypomethylation in the early stage of hepatic stellate cell (HSC) activation, similar to the findings in CAFs.…”

DNA methylation in fibrosis

“…The IPF samples were then compared to samples from lung cancer patients; the lung cancer samples were found to have 2428 differentially methylated CpG islands when compared to healthy tissue samples. 65% of the differentially methylated CpG islands methylated in IPF samples were also seen in the lung cancer samples (Rabinovich et al, 2012).…”

“…how frequently methylated-CpG sequences occur within the gene, and also on the location of the methylation in relation to the promoter region of the gene (Bian et al, 2013;Hsieh, 1994) Epigenetic changes have been linked to many diseases including cardiovascular disease (Webster et al, 2013); as well as colon, lung, breast and thyroid cancer, where large hypomethylated blocks of the genomes have been found (Hansen et al, 2011) and promoter hypermethylation of classic tumour suppressor genes are found. More recently, methylation changes have been associated with fibrotic diseases such as hepatic, pulmonary, renal and cardiac fibrosis (Mann et al, 2010;Rabinovich et al, 2012;Tampe et al, 2014;Xu et al, 2015). Numerous genes have been found to be involved in this association and those referred to in this review are listed in Table 2.…”