Genomic Analysis of Tissue and Cellular Heterogeneity in IPF

Yale University, New Haven CT

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Abstract

? DESCRIPTION (provided by applicant): Idiopathic Pulmonary Fibrosis (IPF) is a chronic and progressive lung disease with significant morbidity and mortality. At present there is no effective treatment other than lung transplantation. The IPF lung displays distinct patterns of mRNA and microRNA expression patterns and global changes in DNA methylation. Recent observations, mainly in animal models of lung fibrosis, suggest a role for aberrations in multiple pathways such as coagulation, apoptosis, oxidative stress, shifts in epithelial cell phenotypes, endoplasmic reticulum stress, and developmental pathways. The hypothesis underlying this grant is that the unique histopathologic features of IPF-temporal heterogeneity, alveolar cell hyperplasia, abundance of myofibroblast foci and aberrant remodeling-represent a molecular disease mechanism specific to IPF. Therefore, understanding the molecular networks that underlie these characteristics will lead to better understanding of IPF and eventually more rational, disease mechanism based therapeutic interventions. For this purpose we have assembled a multi-disciplinary team of experts in lung fibrosis, genomics, computational biology, computer science, cell and molecular biology, statistics, high-throughput screening and bioinformatics. The study will undertake the following specific aims: 1) Identification of the unique genomic and transcriptomics characteristics of histologically defined lung microenvironments. This aim will include generation of mRNA, microRNA and epigenomic profiles of histologically distinct, differentially affected regions of the lung using microCT guidd microdissection, next generation sequencing and laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS). 2) Determination of the cellular contribution to the genomic and epigenomic changes in the IPF lung by a combination of LCM guided sampling of distinct cell populations in the IPF lung (myofibroblasts, hyperplastic epithelial cells), transcriptomic profiling of primary cells (alveolar type II and fibroblasts) isolated from patients with and without IPF at baseline and in response to fibrosis relevant perturbations. Cellular signatures will be validated, localized and quantified in IPF lungs by quantitative immunohistochemistry and in-situ hybridization. 3) Generate a dynamic regulatory model of IPF based on genomic data and perform preliminary experimental validation of model predictions. This aim includes generation of an integrated IPF genomic and epigenomic data compendium, application of novel analytic approaches to identify key regulators and performance of preliminary validation of predictions by testing effect of perturbations of potential The data and analyses will be incorporated into a simple, intuitive, web-based interface, IPFmap, that will allow investigators to interactively mine the data, use analytical tools, integrate their own data into these analyses, and provide seamless access to complementary databases enabling development of therapies.