High-resolution transcriptomic and epigenetic profiling across disease stages identifies novel regulators of COPD phenotypes.

Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. For these to be developed, better understanding of molecular mechanisms driving disease onset is required. Considering the environmental cause of COPD, we hypothesized that the disease will be associated with altered epigenetic signalling in lung cells. Using whole-genome bisulfite sequencing, we generated genome-wide DNA methylation maps at single CpG resolution of parenchymal fibroblasts and alveolar type 2 (AT2) cells across COPD stages. We demonstrate that epigenetic landscape is severely changed in COPD, with epigenetics changes occurring predominantly in regulatory regions, including promoters and enhancers. RNA sequencing of matched samples showed dysregulation of pathways involved in proliferation, cell differentiation, extracellular matrix organisation, inflammation and viral immunity. Excitingly, we identify epigenetic changes and gene subsets dysregulated already in mild COPD, providing unique insight into early disease. Integration of profiling data identified epigenetically regulated pathways and candidate drivers of COPD phenotypes. We uncover a strong anticorrelation between gene expression and promoter methylation in AT2 cells, suggesting that aberrant transcriptional changes might be regulated by DNA methylation. Interferon (INF) signalling was the top upregulated pathway in AT2 cells with the strongest association to DNA methylation loss in the promoters of downstream genes. Using DNA methylation inhibitors and CRISPR-based epigenetic editing in lung cell lines we validated the link between methylation loss and activation of IFN-signalling.