Longitudinal DNA Methylation Analysis Reveals Pathways Influencing Lung Function

Chronic Obstructive Pulmonary Disease (COPD) accounted for 6% of the world’s total deaths in 2019. Genetic variation influences COPD risk, but other molecular factors likely also influence COPD pathogenesis. Identifying epigenetic biomarkers for lung function may reveal molecular mechanisms and regulatory pathways related to COPD development and progression.
COPDGene is a large-scale multicenter longitudinal cohort with pulmonary function data at baseline, 5 and 10 year visits. The Illumina EPIC array was used to assay DNA methylation for 12002 COPDGene blood samples from 6500 subjects from enrollment (Phase1) and 5501 subjects from Phase2 (approximately 5 years later). Robust linear regression was performed across all samples to address the association between site specific CpG methylation and lung function. All models were adjusted for age, sex, race, height, current smoking status, pack-years of smoking, estimated cell type proportions, and the smoking-associated CpG site near AHRR (cg05575921). Probes associated with lung function at a genome-wide p-value threshold of 6.4×10-8 were considered significant. eFORGE2 and missmethyl were leveraged to perform the functional downstream and gene set enrichment analyses.
For FEV1/FVC, we identified significant associations for 107 CpGs (in 72 genes) in Phase1 and 485 CpGs (in 307 genes) in Phase2. Between the two phases, there were 27 overlapping CpG associations in 19 genes, including HDAC4 and MIR181A1HG. For FEV1, we identified 849 CpGs (in 503 genes) significantly differentially methylated at Phase 1, and 1130 CpGs (in 675 genes) in Phase 2. There were 337 overlapping CpG associations between both phases, including four microRNA encoding genes and six zinc finger protein genes. These overlapping methylation sites for FEV1 at both phases were enriched in regulatory H3 chromatin elements in lung tissue (FDR <0.05). We found pathway enrichment for multiple immune/inflammatory pathways across the lung function traits, including for Wnt signaling, cytokine production and NF-KappaB pathways.