High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD phenotypes in human lung fibroblasts

Abstract

Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering environmental causes of COPD and disease phenotypes, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung fibroblasts from ex-smokers and COPD patients. Epigenetic landscape is markedly changed in lung fibroblasts across COPD stages, with DNA methylation changes occurring predominantly in regulatory regions. RNA sequencing of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair and matrix organization. Notably, we identified epigenetic and transcriptional dysregulation already in mild COPD, providing unique insights into early disease. Integration of profiling data identified 110 candidate regulators of disease phenotypes. Using phenotypic screens, we linked the function of multiple candidates to repair processes in the lung. Our study provides first integrative high-resolution epigenetic and transcriptomic maps of human lung fibroblasts across COPD stages. We reveal novel signatures associated with COPD onset and progression and identify candidate regulators involved in the pathogenesis of chronic respiratory diseases.

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

“…Using high-resolution epigenetic profiling, we uncovered widespread alterations of DNA methylation landscape in AT2 cells in COPD that were associated with global gene expression changes. Consistent with our earlier methylation data from COPD lung fibroblasts (Schwartz et al 2023), epigenetic changes in AT2 were enriched at cis-regulatory regions, including enhancers and promoters, indicating that they may drive aberrant transcriptional programs in COPD. This was further supported by the strong anticorrelation between DNA methylation and gene expression, with more than 500 dysregulated genes showing corresponding DNA methylation changes in promoters.…”

“…However, they used low resolution microarray-based approaches, covering a representation of the genome only, and profiled complex samples with heterogenous cellular composition, making direct comparison to our data very difficult. Two studies investigated DNA methylation changes in isolated lung fibroblasts (Clifford et al 2018; Schwartz et al 2023), but the epigenetic dysregulation of AT2 cells across COPD stages remained uncharted.…”

“…Read alignment and methylation quantification were performed as described (Schwartz et al 2023). Briefly, the MethylCtools pipeline was modified for TWGBS data and used for whole genome bisulfite sequencing mapping (Hovestadt et al 2014).…”

“…Alterations in DNA methylation patterns have been implicated in aging, chronic inflammatory diseases, and cancer. In addition, cigarette smoke alters DNA methylation in several clinically relevant samples (Belinsky et al 2002; Chen et al 2013; Zeilinger et al 2013; Wan et al 2015) and has been associated with altered expression of genes important in COPD pathology (Liu et al 2010; Vucic et al 2014; Wan et al 2015; Yoo et al 2015; Morrow et al 2016; Song et al 2017; Sundar et al 2017; Clifford et al 2018; Casas-Recasens et al 2021; Schwartz et al 2023). However, previous studies mostly assessed DNA methylation using heterogeneous material with complex cellular composition (e.g., epithelium, blood, or lung tissue) and focused on selected parts of the genome only (mostly gene promoters).…”

Review of the British Thoracic Society Winter Meeting 23 November 2022 23–25 November 2022

“…Importantly, cryopreservation did not compromise tissue viability, cellular integrity or modify the transcriptional and epigenetic profiles of cells. Subsequent whole-genome bisulfite sequencing found genome-wide methylation alterations in lung fibroblasts of ex-smokers associated with COPD disease stage 57. This level of molecular resolution may reveal early disease trajectories and identify potential biomarkers for disease onset and progression.…”