Epigenetic Alterations in IPF Fibroblastic Foci

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DESCRIPTION (provided by applicant): Idiopathic Pulmonary Fibrosis (IPF) is a deadly disease without a clearly-defined etiology. Because the incidence increases with age, it is plausible that environmental effects may be important. Recent data indicate re-expression of developmental gene signatures in IPF. Epigenetic regulation, including DNA methylation and histone modification, which often occurs during development and in response to aging and environmental stimuli, results in heritable changes in gene expression independent of any variation in the genes themselves. DNA methylation at gene promoter regions rich in cytosine-guanine (CpG islands) and histone modifications both play important roles in gene silencing; these paradigms are important in cellular differentiation during development, and are critical in silencing of tumor suppressors in many cancers. Epigenetic modifications are potentially reversible and therefore attractive targets for development of novel therapies. Although there is increasing evidence that epigenetic regulation may play an important role in fibrotic disease, few studies have explored epigenetic regulation in IPF. Our lab has established that Thy-1, which suppresses the fibrotic phenotype of fibroblasts, is absent in fibroblastic foci of IPF, that its absence can be caused by methylation at the Thy-1 promoter region and is reversible. Additional preliminary data from our lab demonstrates epigenetic silencing of other genes known to be downregulated in IPF. We hypothesize that epigenetic changes alter the gene expression profile in IPF, promoting fibrogenesis. This study will establish DNA methylation as an important factor in the pathogenesis of IPF, and provide support for further exploration of epigenetic alterations in this deadly disease, thus setting the stage for development of novel therapeutic approaches. This proposal will leverage the availability of well-characterized tissues available through the Lung Tissue Research Consortium (LTRC) to characterize global and gene-specific alterations in DNA methylation in IPF in comparison to chronic obstructive pulmonary disease (COPD), in order to establish epigenetic alterations as an important pathogenic mechanism in IPF. The aims of the study will be to: 1. Define the relationship of DNA methylation to gene expression in IPF in comparison to COPD and control lung tissue, by: a) microarray analysis of gene expression in IPF, COPD, and control tissues, b) methylation array analysis in these samples, and c) confirmation of selected genes by methylation-specific PCR; and 2. Measure regional alterations of global DNA methylation in IPF and COPD tissues, by: a) quantitative analysis and IHC for anti-methylcytosine, and b) analysis of DNA methyltranserases (DNMTs) and other regulators of DNA methylation at the local tissue level. These studies will define the extent to which epigenetic alterations, specifically changes in DNA methylation, occur in IPF. This important and previously unexplored paradigm is likely to yield significant additional insight into the pathogenesis of this devastating disease, as well as to define novel therapeutic targets for IPF and other fibrotic disorders. PUBLIC HEALTH RELEVANCE: Idiopathic Pulmonary Fibrosis (IPF) is a deadly incurable disease affecting over 100,000 Americans, the cause of which is unknown, and which produces progressive scarring in the lungs. There is a biological mechanism for controlling expression of genes during human development known as epigenetic regulation, which is increasingly found to be abnormal in cancer and other diseases. This project will take advantage of the well characterized IPF tissues available through the Lung Tissue Research Consortium (LTRC) in order to determine the extent to which epigenetic abnormalities are responsible for the uncontrolled scarring seen in IPF, thus leading the way to development of novel therapies for this devastating disease. (End of Abstract)