DeCyFir: Determining functional DNA cytosine modification in idiopathic pulmonary fibrosis pathology

Idiopathic pulmonary fibrosis (IPF) is a devastating condition characterised by progressive fibrosis, debilitating shortness of breath, and early mortality, with a median survival of only 3-5 years from diagnosis. There are limited treatment options to slow IPF progression and improve patient outcomes and new therapies are needed. The cause of IPF is unknown. Complex interactions between genetics and environmental exposures (virus, cigarette smoking, air pollution) cause repeated damage to the alveolar epithelium and drives fibrosis in the parenchyma. Pathology throughout the lung is heterogenous, and there is an unmet need to understand the molecular mechanisms driving and defining pathology and by extension reveal novel targets for therapeutic intervention. DNA methylation (DNAm) is a reversible epigenetic modification, with exploitable therapeutic potential, at the nexus of environmental exposures and genetics. Coupled with the potential for targeting site-specific DNAm, now is the optimum time to fully characterise the lung DNA methylome, providing a step change in our understanding and tangible targets for patient benefit. DNAm is the addition and removal of methyl groups to DNA cytosine residues, by DNA methyltransferases and Ten Eleven Translocation enzymes. DNAm consists of four DNA cytosine modifications, each with a distinct role in transcriptional regulation. Most studies profiling DNAm use technologies unable to distinguish cytosine modifications, limiting understanding and translatability of disease associated findings. DNAm is dysregulated in IPF. Global decreases in DNAm occur in IPF lung tissue linked to genes involved in lung development and fibrosis. Airway macrophages, immune regulatory cells, show differential DNAm associated with lipid/glucose metabolism and IPF severity. Fibroblasts, important for lung structural integrity, have IPF-associated DNAm changes correlated with fibroblast-myofibroblast transition and resistance to apoptosis. However, validation of links between DNAm and gene expression by direct manipulation and functional response assessment are required. Understanding the role of DNA cytosine modification to the generation of IPF pathology is not feasible in tissue with developed pathology. Instead, study of a potential driver and its alteration of DNA cytosine modification is required. Air pollution contributes to lung disease, causing 7 million deaths worldwide annually. Long-term air pollution exposure increases IPF risk, and subsequent air pollution exposure increases the risk of respiratory failure, hospitalisation and mortality. Air pollutants including vehicle exhaust alter DNAm, and our data show IPF fibroblast DNAm overlaps with air pollutant driven changes. We will test the hypothesis that: Dysfunctional DNA cytosine modification contributes to distinct IPF pathology and identifies novel therapeutic targets. Objective 1: Map individual DNA cytosine modifications associated with specific radiological fibrosis in IPF lungs, linking to gene expression. Objective 2: Define the functional impact of specific IPF pathology-associated DNA cytosine modifications on gene/protein expression and cellular function. Objective 3: Define the generation of DNA cytosine modification dysfunction in IPF using air pollution (engine exhaust) as a disease driver. DeCyFir will provide the first comprehensive profiling of DNA cytosine modification in the lung, including functional impacts on cellular biology. The focus on IPF will provide a step change in our understanding of DNA cytosine modification specific targets for translation to patients. This paradigm shift will put me in the ideal position to drive subsequent studies confirming specific targets in larger populations and conducting pre-clinical programs to assess functionality of targeting central mediators with inhibitors/repurposed therapies and modifying specific DNA cytosine modifications, springboarding and solidifying my reputation in the field.