Genomic Analysis of Tissue and Cellular Heterogeneity in IPF

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PROJECT SUMMARY AND SUPPLEMENT TO R01 Idiopathic Pulmonary Fibrosis (IPF) is a chronic progressive lung disease with significant morbidity and mortality. In the previous period of this grant, we performed bulk RNA-seq and microRNA profiling of microCT defined differentially affected lung regions. This work led to identification of numerous molecular targets and insights, development of computational methods, and development of a transcriptional model of fibrosis progression. Using the powerful high-resolution technologies of single cell profiling, we generated a ‘map’ of all human cells in patients with IPF, discovered novel, ectopic and aberrant cell populations, and replacement of the distal alveolar cellular content with cells that usually populate the airways. These exciting findings are foundations of this renewal application that focuses on identification of the signals that drive the changes we identified, their sequence and their spatial organization. The hypothesis underlying this application is that the unique histopathologic features of IPF reflect a disruption in the homeostatic cellular networks in alveolar niche, that activates an aberrant but coordinated repair process that leads to the proximalization of the distal lung. To address this hypothesis, we have assembled a multi-disciplinary team of experts in lung fibrosis, genomics, proteomics, computational biology, computer science, cell and molecular biology, statistics, imaging, bioengineering, pathology, and bioinformatics that will perform the following specific aims: Specific Aim 1: To identify the specific sequence of changes in cell compositions and phenotypes during the progression of fibrosis in the human IPF lung. Specific Aim 2: To identify the changes in spatial relations, interactions, and connections between cellular members of the fibrotic niche at different stages of fibrosis and progression of fibrosis. Specific Aim 3: Generation of a systems biology model of human pulmonary fibrosis with a specific focus on regulators of disease emergence and progression. At the completion of this project, we will have a cell level, comprehensive transcriptional regulatory, mechanistically relevant model of IPF based on the unique histological features of the disease. The model, the discovered key regulatory modules and the accompanying data sharing, and dissemination tools will be useful for understanding disease mechanisms and generation of novel, effective and precise therapeutic interventions.