Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD)

Chronic lung diseases, including chronic obstructive pulmonary disease (COPD), affect over 500 million people and are a leading cause of death worldwide. A common feature of both chronic and acute lung diseases is altered respiratory barrier integrity and impaired lung regeneration. We hypothesized that alveolar type 2 (AT2) cells, as alveolar epithelial progenitors, will carry molecular alterations that compromise alveolar regeneration in COPD. Sorted AT2 cells from ex-smokers with and without COPD at different disease stages were subjected to RNA sequencing and whole-genome bisulfite sequencing to generate unbiased transcriptome and DNA methylation maps of alveolar progenitors in the lung. Our analysis revealed genome-wide epigenetic changes in AT2 cells during COPD that were associated with global gene expression changes. Integrative data analysis uncovered a strong anti-correlation between gene expression and promoter methylation, suggesting that dysregulation of COPD-associated pathways in AT2 cells may be regulated by DNA methylation. Interferon (IFN) signaling was the top-upregulated pathway associated with the concomitant loss of promoter DNA methylation. Epigenetic regulation of the IFN pathway was validated in both global and targeted DNA demethylation assays in A549 cells. Notably, targeted DNA demethylation of IRF9 triggered upregulation of IFN signaling, mimicking the effects observed in COPD AT2 cells in the profiling data. Our findings suggest that COPD-triggered epigenetic alterations in AT2 cells may impair internal regeneration programs in human lung parenchyma. ### Competing Interest Statement RZJ, MLP, VM, US, RT, SP and AB as employees of BioMed X Institute received research funding by Boehringer Ingelheim Pharma GmbH & Co KG. HS and DWy are employees of Boehringer Ingelheim Pharma GmbH & Co KG and receive compensation as such. TM received a research grant, non-financial support and has patent applications with Roche Diagnostics GmbH outside of the described work. CPH has stock ownership in GSK; received research funding from Siemens, Pfizer, MeVis and Boehringer Ingelheim; consultation fees from Schering-Plough, Pfizer, Basilea, Boehringer Ingelheim, Novartis, Roche, Astellas, Gilead, MSD, Lilly Intermune and Fresenius, and speaker fees from Gilead, Essex, Schering-Plough, AstraZeneca, Lilly, Roche, MSD, Pfizer, Bracco, MEDA Pharma, Intermune, Chiesi, Siemens, Covidien, Boehringer Ingelheim, Grifols, Novartis, Basilea and Bayer, outside the submitted work. HW received consultation fees from Intuitive and Roche.