DNA methylation perturbations may link altered development and aging in the lung

Abstract

Fetal perturbations in DNA methylation during lung development may reveal insights into the enduring impacts on adult lung health and disease during aging that have not been explored altogether before. We studied the association between genome-wide DNA-methylation and post-conception age in fetal-lung (n=78, 42 exposed to in-utero-smoke (IUS)) tissue and chronological age in adult-lung tissue (n=160, 114 with Chronic Obstructive Pulmonary Disease) using multi-variate linear regression models with covariate adjustment and tested for effect modification by phenotypes. Overlapping age-associations were evaluated for functional and tissue-specific enrichment using the Genotype-Tissue-Expression (GTEx) project. We identified 244 age-associated differentially methylated positions and 878 regions overlapping between fetal and adult-lung tissues. Hyper-methylated CpGs (96%) were enriched in transcription factor activity (FDR adjusted P=2x10^-33) and implicated in developmental processes including embryonic organ morphogenesis, neurogenesis and growth delay. Hypo-methylated CpGs (2%) were enriched in oxido-reductase activity and VEGFA-VEGFR2 Signaling. Twenty-one age-by-sex and eleven age-by-pack-years interactions were statistically significant (FDR<0.05) in adult-lung tissue. DNA methylation in transcription factors during development in fetal lung recapitulates in adult-lung tissue with aging. These findings reveal molecular mechanisms and pathways that may link disrupted development in early-life and age-associated lung diseases.

Keywords: DNA methylation; aging; development; lung; transcription factors.

Figure 1

Manhattan plot depicting significance on y-axis and distribution of CpGs across all chromosomes on x-axis for fetal lung dataset (top panel) and adult lung dataset associations with age (bottom panel). Top 20 CpGs in both datasets have been highlighted in green. The two red lines represent the CpG sites significant at an FDR<0.05 and at a Bonferroni threshold (0.05/number of tests) in fetal and adult lung datasets.

Figure 2

Network visualization, functional enrichment and region-gene associations in both fetal and adult lung tissue datasets. Network clusters of the molecular function gene ontology terms and annotated pathways including reactome and wikiPathways were created using the gene symbols mapped to the significant and age-associated differentially methylated positions (DMPs) overlapping between fetal and adult lung datasets. (A) Hyper-methylated CpGs were mainly enriched in transcription factor DNA binding whereas (B) hypo-methylated CpGs were enriched in oxidoreductase activity. Size corresponds to the overlap of genes between the enriched terms and color corresponds to significance. The analysis for hypo-methylated CpGs was limited by few numbers of genes represented by few CpGs (C) Functional enrichment of age-associated hyper-methylated DMPs in both fetal and adult lung tissue datasets amongst differentially expressed genes in 54 GTEx tissues (x-axis) and –log10(P-value) on the y-axis. Tissues with significant gene enrichment (FDR<0.05) are highlighted by red bars and tissues with the highest enrichment amongst the downregulated and upregulated genes are highlighted by arrows (D) Region-Gene associations using chromosomal coordinates for the differentially methylated regions in fetal lung dataset (E) Adult lung tissue dataset. TSS: transcription start site.