Relationship of DNA Methylation and Gene Expression in Idiopathic Pulmonary Fibrosis

Abstract

Rationale: Idiopathic pulmonary fibrosis (IPF) is an untreatable and often fatal lung disease that is increasing in prevalence and is caused by complex interactions between genetic and environmental factors. Epigenetic mechanisms control gene expression and are likely to regulate the IPF transcriptome.Objectives: To identify methylation marks that modify gene expression in IPF lung. Methods:We assessed DNA methylation (comprehensive highthroughput arrays for relative methylation arrays [CHARM]) and gene expression (Agilent gene expression arrays) in 94 patients with IPF and 67 control subjects, and performed integrative genomic analyses to define methylation-gene expression relationships in IPF lung. We validated methylation changes by a targeted analysis (Epityper), and performed functional validation of one of the genes identified by our analysis.Measurements and Main Results: We identified 2,130 differentially methylated regions (DMRs; ,5% false discovery rate), of which 738 are associated with significant changes in gene expression and enriched for expected inverse relationship between methylation and expression (P , 2.2 3 10 216 ). We validated 13/15 DMRs by targeted analysis of methylation. Methylation-expression quantitative trait loci (methyl-eQTL) identified methylation marks that control cis and trans gene expression, with an enrichment for cis relationships (P , 2.2 3 10 216 ). We found five trans methyl-eQTLs where a methylation change at a single DMR is associated with transcriptional changes in a substantial number of genes; four of these DMRs are near transcription factors (castor zinc finger 1 [CASZ1], FOXC1, MXD4, and ZDHHC4). We studied the in vitro effects of change in CASZ1 expression and validated its role in regulation of target genes in the methyl-eQTL.Conclusions: These results suggest that DNA methylation may be involved in the pathogenesis of IPF.Keywords: DNA methylation; gene expression; pulmonary fibrosis; quantitative trait; mapping Idiopathic pulmonary fibrosis (IPF) appears to result from reprogramming of injured alveolar epithelial cells, which undergo early apoptosis, epithelial-mesenchymal transition, and produce mediators that lead to proliferation of resident fibroblasts and recruitment of fibrocytes. As the extracellular matrix (ECM) expands, myofibroblastic foci develop, resulting in further fibroproliferation in the ECM and the more extensive lung remodeling (1).

Mitochondria in the spotlight of aging and idiopathic pulmonary fibrosis

“…Epigenetic changes that are associated with age (33,34) seem to be highly conserved in mammals (35,36), especially the global change of DNA methylation patterns, also known as the "epigenetic clock." This particular loss of methylation and the subtle differences between changes in healthy aging and in age-related pathological processes (37) could be the key to identifying novel biomarkers in IPF, since it exhibits its own particular methylation profile (38).…”

Regulation of MUC5B Expression in Idiopathic Pulmonary Fibrosis

“…We intersected the 2,130 IPF-associated DMRs with recently identified loci from the two published genome-wide association studies in IPF [49,50] and identified methylation changes in genes within 5 of these loci [113]. Of special interest are genes that are differentially expressed in IPF lung and whose expression may be regulated by both genetic variants and DNA methylation.…”

“…Although many changes in the epigenome have unknown function, we are beginning to elucidate those associated with IPF. A recent study by Yang et al identified over 2,000 differentially methylated regions (DMRs) of which almost half were associated with changes in gene expression [113].…”

Idiopathic Pulmonary Fibrosis: Clinical Behavior, Pathogenic Mechanisms and Therapeutic Approach

“…In the latest report, Yang, et al, using comprehensive high-throughput arrays for relative methylation methodology, examined 4.6 million CpG sites distributed across the human genome, and simultaneously, the gene expression changes in lung tissues from 94 IPF patients and 67 control subjects 29 . They found that the IPF lungs have a large number of disease-associated methylation changes that also affect gene expression in the opposite direction.…”

“…After birth, many of these pathways are suppressed or restricted to tissue-specific stem cell maintenance, but may be re-expressed in response to tissue injury in a strictly regulated pattern favoring tissue regeneration, or deregulated contributing to adult diseases, including IPF. Thus, the analyses of transcriptional and epigenetic signatures have revealed that IPF lungs are significantly enriched with genes and networks associated with lung development, mainly WNT/β-catenin and sonic hedgehog (SHH) signaling pathways 29,40 . In IPF lungs, the WNT/β-catenin signaling pathway with its main canonical signal transducers, Gsk-3β and β-catenin, has been detected to be significantly activated mainly in hyperplastic type II epithelial cells, with nuclear translocation of β-catenin and over-expression of its response genes, like cyclin D1 and matrix metalloprotease-7 41,42 .…”