Abstract

Chronic lung diseases are one of the great challenges of modern medicine, with 540 million patients waiting for curative treatments. Chronic obstructive pulmonary disease (COPD) is a life-limiting and currently incurable disease where patients experience a progressive decline in lung function. Currently, the molecular mechanisms driving disease onset are poorly understood, and there are no effective treatments. Considering the environmental cause of COPD (cigarette smoke) and disease phenotypes, including defective cell renewal and differentiation, we hypothesised that COPD would be driven by altered epigenetic signaling in lung cells.

Using whole-genome bisulfite sequencing, we generated the first genome-wide DNA methylation maps at single CpG resolution of purified parenchymal fibroblasts, airway basal cells and alveolar progenitor cells (AT2) across COPD stages. We demonstrate that the epigenetic landscape is severely changed in COPD , with changes occurring predominantly in regulatory regions, including promoters and enhancers. RNA sequencing of matched samples showed dysregulation of key disease-relevant pathways involved in proliferation, cell differentiation, inflammation, extracellular matrix organisation and viral immunity. Excitingly, we identify epigenetic changes and gene subsets dysregulated already

in mild COPD , providing a unique insight into the early disease. Integration of profiling data identified epigenetically regulated pathways and candidate drivers of COPD phenotypes. We uncovered a strong anti-correlation between gene expression and promoter methylation, suggesting that disease programs in these progenitors might be regulated by DNA methylation. Interferon (INF) signalling was the top upregulated pathway in AT2 cells with the strongest association with DNA methylation loss in the promoter 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 the IFN -signalling pathway.

Our data demonstrate that epigenetic regulation in COPD is an exciting research field that should be explored in-depth, as it can provide important insights into COPD -driving cell populations and associated mechanisms.